diff --git a/.gitignore b/.gitignore index 64f7ac6..a79b0cf 100644 --- a/.gitignore +++ b/.gitignore @@ -49,3 +49,7 @@ inst/doc # prevent readme html from accidentally getting pushed README.html .Rproj.user + +# ignore test stuff +inst/extdata/out/w8* +inst/extdata/rh_dev diff --git a/DESCRIPTION b/DESCRIPTION index 413495c..efd4e1b 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,9 +1,9 @@ Package: RHESSysIOinR Type: Package Title: Tools for Running RHESSys from R -Version: 0.0.0.9001 +Version: 2.0.0 Date: 2016-09-11 -Author: Ryan R. Bart +Author: Ryan R. Bart, Will Burke Maintainer: Ryan R. Bart Description: This package contains functions for the setup of RHESSys files, calibration and simulation of RHESSys, and the analysis of RHESSys output. @@ -20,10 +20,15 @@ Imports: lhs, readr, tibble, - data.table -RoxygenNote: 7.1.0 -Suggests: testthat, + data.table, + sensitivity, + yaml +RoxygenNote: 7.1.1 +Suggests: + testthat (>= 3.0.0), knitr, - rmarkdown + rmarkdown, + gert VignetteBuilder: knitr Encoding: UTF-8 +Config/testthat/edition: 3 diff --git a/NAMESPACE b/NAMESPACE index 12b6221..bef5bfb 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -1,16 +1,25 @@ # Generated by roxygen2: do not edit by hand +export(IOin_clim) +export(IOin_def_pars_simple) +export(IOin_def_pars_sobol) +export(IOin_hdr) +export(IOin_output_filters) +export(IOin_output_vars) +export(IOin_rhessys_input) +export(IOin_std_pars) +export(IOin_tec_std) export(add_dates) +export(build_output_filter) export(build_redefine) export(cal.wyd) export(change_def_file) export(cleanup_rhessys) -export(clim_auto) export(compile_rhessys) export(evaluation) export(generate_input_files) export(generate_option_sets) -export(input_tec) +export(insert_in_worldfile) export(make_all_option_table) export(make_clim_base_file) export(make_dated_seq) @@ -19,15 +28,19 @@ export(make_option_set_combinations) export(make_rhessys_folders) export(make_tec_file) export(mkdate) +export(modify_output_filter) export(patch_fam_agg) export(process_input_preexisting_table) export(read_clim) +export(read_output_filter) export(read_world) export(readin_rhessys_output) export(readin_rhessys_output_cal) export(readin_rhessys_output_old) export(rhessys_command) export(run_rhessys) +export(run_rhessys_multi) +export(run_rhessys_single) export(select_output_variables) export(select_output_variables_R) export(select_output_variables_w_awk) @@ -35,8 +48,10 @@ export(select_parameter_sets) export(separate_canopy_output) export(tec_repeat) export(watbal_basin) +export(watbal_basin_of) export(watbal_patch) export(watbal_patch_mult) +export(write_output_filter) export(write_sample_clim) importFrom(data.table,"%between%") importFrom(data.table,"%like%") diff --git a/R/IOin_clim.R b/R/IOin_clim.R new file mode 100644 index 0000000..543f322 --- /dev/null +++ b/R/IOin_clim.R @@ -0,0 +1,76 @@ +#' IOin_clim +#' +#' Generate input for run_rhessys climate basestation input +#' @param base_station_id Base station ID. +#' @param x_coordinate X coordinate. +#' @param y_coordinate Y coordinate. +#' @param z_coordinate Z coordinate. +#' @param effective_lai Effective LAI. +#' @param screen_height Screen height. +#' @param annual_prefix Prefix for annual climate inputs. +#' @param num_non_critical_annual_sequences Number of non critical annual climate inputs. Defaults to 0. +#' @param monthly_prefix Prefix for monthly climate inputs. +#' @param num_non_critical_monthly_sequences Number of non critical annual climate inputs. Defaults to 0. +#' @param daily_prefix Prefix for daily climate inputs. +#' @param num_non_critical_daily_sequences Number of non critical annual climate inputs. Defaults to 0. +#' @param hourly_prefix Prefix for hourly climate inputs. +#' @param num_non_critical_hourly_sequences Number of non critical annual climate inputs. Defaults to 0. +#' +#' @author Will Burke +#' +#' @export + +IOin_clim = function(base_station_id, + x_coordinate, + y_coordinate, + z_coordinate, + effective_lai, + screen_height, + annual_prefix = "annual", + num_non_critical_annual_sequences = 0, + monthly_prefix = "monthly", + num_non_critical_monthly_sequences = 0, + daily_prefix = "daily", + num_non_critical_daily_sequences = 0, + hourly_prefix = "hourly", + num_non_critical_hourly_sequences = 0) { + + + + output_clim_base = data.frame( + "values" = c( + base_station_id, + x_coordinate, + y_coordinate, + z_coordinate, + effective_lai, + screen_height, + annual_prefix, + num_non_critical_annual_sequences, + monthly_prefix, + num_non_critical_monthly_sequences, + daily_prefix, + num_non_critical_daily_sequences, + hourly_prefix, + num_non_critical_hourly_sequences + ), + "vars" = c( + "base_station_id", + "x_coordinate", + "y_coordinate", + "z_coordinate", + "effective_lai", + "screen_height", + "annual_climate_prefix", + "number_non_critical_annual_sequences", + "monthly_climate_prefix", + "number_non_critical_monthly_sequences", + "daily_climate_prefix", + "number_non_critical_daily_sequences", + "hourly_climate_prefix", + "number_non_critical_hourly_sequences" + ) + ) + + return(output_clim_base) +} diff --git a/R/IOin_def_pars_simple.R b/R/IOin_def_pars_simple.R new file mode 100644 index 0000000..07465ad --- /dev/null +++ b/R/IOin_def_pars_simple.R @@ -0,0 +1,90 @@ +#' IOin_def_pars_simple +#' +#' The definition file parameters to modify. This input function generates an input parameter object, either for a single simulation, +#' or using simple random sampling over a set range (based on percent difference from input values). This later functionality can be put into +#' a seperate funciton later if desired. +#' @param ... Any number of lists, each containing 3 elements in format: list("", "", ) +#' @param n The number of parameter sets to generate. +#' @param pct_range The percent range of variation from input values over which sampling (if any), will happen. +#' @param rm_dup TRUE/FALSE should duplicate def file + variable entries be automatically removed? A warning will occur regardless. +#' +#' @author Will Burke +#' +#' @export + +# pars = list(list("defs/veg_p301_conifer.def", "epc.allocation_flag","dickenson"), +# list("defs/veg_p301_conifer.def", "epc.alloc_frootc_leafc", 1), +# list("defs/veg_p301_conifer.def", "epc.alloc_stemc_leafc", 0.6), +# list("defs/veg_p301_conifer.def", "epc.netpabs_shade", 0.2)) + +# --- IMPORTANT DATA ASSUMPTIONS --- +# We can discuss revising this, but this code (and potentially other I(WB) write) will assume that parameters +# for a single run will use the following data format (as the ultimate structure that gets passed to run_rhessys_core) +# +# +# < repeat above format for each unique def file variable> +# +# For a set of def file parameters, regardless of how they are generated, I propose using the same format except instead of a single value +# there would be a vector of values for each def file variable. Ex: +# +# +# < repeat above format for each unique def file variable> +# +# Def file variables not being varied, or which don't make sense to be +# (e.g. text fields like epc.allocation_flag) would need to be replicated so that each def variable list has a vector of target values +# that are the same length. These can then be iterated through or lapply'd across, potentially in parallel. +# +# How these data structures are achieved can vary by IOin function/type of parameter variation, since different methods will require +# different inputs (see the simplest option I could come up with below) + +IOin_def_pars_simple = function(..., n = 1, pct_range = 0.25, rm_dup = F) { + + pars = list(...) + + # if ... is already a list of lists, ie you're inputting the output of this function, unlist to keep foramt correct + if (length(pars) == 1 && all(lapply(pars[[1]], length) == 3)) { + pars = pars[[1]] + } + + # some checks here, should get done regardless but mostly important for multiple param sets + if (any(lapply(pars, length) != 3)) { + stop("Each input list must have 3 elements - 1) file path to def file 2) def file variable 3) value") + } + + # name some things to be helpful + name_pars = function(x) { + names(x) = c("Def_file", "Variable", "Value") + return(x) + } + pars = lapply(pars, name_pars) + + # check for duplicate def_file + variable entries, if rm_dup is T, keep only the first + file_var = paste0(sapply(pars, "[[",1), "--", sapply(pars, "[[",2)) + if (length(pars[duplicated(file_var)]) > 0) { + warning("There are duplicate def file + variable entries, these should be corrected before running RHESSys.") + if (rm_dup) { + pars[duplicated(file_var)] = NULL + cat("Duplicate def file + variable entries have been removed.\n") + } + } + + if (n > 1) { + # only vary the variables that are numbers + values = unlist(lapply(pars, "[[", 3)) + values = suppressWarnings(as.numeric(values)) + #if (any(is.na(values))) { + #cat() # idk guess doesn't matter + #} + + value_sets = lapply(values[!is.na(values)], function(x) runif(n = n, min = x - (pct_range * x), max = x + (pct_range * x))) + pars[!is.na(values)] = mapply(function(x, y) {x[[3]] = y; return(x)}, x = pars[!is.na(values)], y = value_sets, SIMPLIFY = F) + + if (any(is.na(values))) { + pars[is.na(values)] = lapply(pars[is.na(values)], function(x) {x[[3]] = rep.int(x[[3]], n); return(x)}) + } + + } + + return(pars) + +} diff --git a/R/IOin_def_pars_sobol.R b/R/IOin_def_pars_sobol.R new file mode 100644 index 0000000..e125fa8 --- /dev/null +++ b/R/IOin_def_pars_sobol.R @@ -0,0 +1,51 @@ +#' IOin_def_pars_sobol +#' +#' Geneartes multiple def file changes based on sobol sensativity. +#' @param ... Any number of lists, each containing 3 elements in format: list("", "", ) +#' @param nboot The number of bootstraps to run for sobol2007 +#' @param rm_dup TRUE/FALSE should duplicate def file + variable entries be automatically removed? A warning will occur regardless. + +#' @author Will Burke +#' +#' @export + + +IOin_def_pars_sobol = function(..., nboot = 100, rm_dup) { + + pars = list(...) + + # if ... is already a list of lists, ie you're inputting the output of this function, unlist to keep format correct + if (length(pars) == 1 && all(lapply(pars[[1]], length) == 3)) { + pars = pars[[1]] + } + # some checks here, should get done regardless but mostly important for multiple param sets + if (any(lapply(pars, length) != 3)) { + stop("Each input list must have 4 elements - Def_file, Variable, Prior_dist") + } + # name some things to be helpful + name_pars = function(x) { + names(x) = c("Def_file", "Variable","Prior_dist") + return(x) + } + pars = lapply(pars, name_pars) + + # check for duplicate def_file + variable entries, if rm_dup is T, keep only the first + file_var = paste0(sapply(pars, "[[",1), "--", sapply(pars, "[[",2)) + if (length(pars[duplicated(file_var)]) > 0) { + warning("There are duplicate def file + variable entries, these should be corrected before running RHESSys.") + if (rm_dup) { + pars[duplicated(file_var)] = NULL + cat("Duplicate def file + variable entries have been removed.\n") + } + } + + par_dists = sapply(pars, "[[", 3) + #colnames(par_dists) = sapply(pars, "[[", 2) + + sobol_out = sensitivity::sobol2007(model = NULL, X1 = par_dists, X2 = par_dists, nboot = nboot) + + pars_out = mapply(function(x, y) {x[[3]] = y; return(x)}, x = pars, y = as.data.frame(sobol_out$X), SIMPLIFY = F) + + return(pars_out) + +} diff --git a/R/IOin_hdr.R b/R/IOin_hdr.R new file mode 100644 index 0000000..a351329 --- /dev/null +++ b/R/IOin_hdr.R @@ -0,0 +1,53 @@ +#' IOin_hdr +#' +#' Creates a header file based on specified parameter definition files and climate basestations. +#' @param basin Path to basin parameter definition file. +#' @param hillslope Path to hillslope parameter definition file.(s) +#' @param zone Path to zone parameter definition file(s). +#' @param soil Path to soil parameter definition file(s). +#' @param landuse Path to landuse parameter definition file(s). +#' @param stratum Path to stratum parameter definition file(s). +#' @param fire Path to fire parameter definition file. +#' @param fire_grid_prefix Path and basename/prefix name of the fire grid files used for the RHESSys WMFire model. +#' @param spinup Path to spinup parameter definition file(s). +#' @param basestations Path to basin climate basestation file(s). +#' +#' @author Will Burke +#' +#' @export + +# LIST NAMING - MIRRORS INPUT ARS +# shorter, and still clear since the whole object is the header info, don't need to specify def +# ORDERING - keep in current order, same as args, should use names to reference though + + +IOin_hdr = function(basin, + hillslope, + zone, + soil, + landuse, + stratum, + fire = NULL, + fire_grid_prefix = NULL, + spinup = NULL, + basestations) { + + input_hdr_list <- list() + + # TODO check for each file, warn if missing - should work for everything expect clim which might be generated + # remember each input can be a character vector of length 1+ + + input_hdr_list$basin_def <- basin + input_hdr_list$hillslope_def <- hillslope + input_hdr_list$zone_def <- zone + input_hdr_list$soil_def <- soil + input_hdr_list$landuse_def <- landuse + input_hdr_list$stratum_def <- stratum + input_hdr_list$fire_def <- fire + input_hdr_list$fire_grid_prefix <- fire_grid_prefix + input_hdr_list$spinup <- spinup + input_hdr_list$base_stations <- basestations + + return(input_hdr_list) + +} diff --git a/R/IOin_output_filters.R b/R/IOin_output_filters.R new file mode 100644 index 0000000..1e93029 --- /dev/null +++ b/R/IOin_output_filters.R @@ -0,0 +1,36 @@ +#' IOin_output_filters +#' +#' Reads in and/or combines filters into a single R list filter object. Also checks that all filters are valid and contain the required fields +#' with valid options when possible to check. +#' @param ... Any number of valid filter objects (R lists), to be written to the same output filter file. +#' @param file_name The name of the output filter file created. if left NULL an autogenerated file name will be used. +#' @param filter_in Path to an existing yaml filter file. +#' +#' @author Will Burke +#' +#' @export + +IOin_output_filters = function(..., + file_name = NULL, + filter_in = NULL) { + + # ---------- Read in existing yaml filter ---------- + if (!is.null(filter_in)) { + filter = read_output_filter(filter_in = filter_in) + } else { + filter = NULL + } + + # ---------- Combine filters ---------- + list_in = c(unlist(list(...), recursive = F)) + if (length(list_in) > 0) { + testvalid = lapply(X = list_in, FUN = valid_filter) + filter = c(filter, list_in) + } + + if (!is.null(file_name)) { + filter$file_name = file_name + } + + return(filter) +} diff --git a/R/IOin_output_vars.R b/R/IOin_output_vars.R new file mode 100644 index 0000000..ca487f1 --- /dev/null +++ b/R/IOin_output_vars.R @@ -0,0 +1,26 @@ +#' IOin_output_vars +#' +#' @param ... Any number of two element character vectors or dataframes, each specifying the output file using "pd", "pdg", "cd", "cdg" +#' style format in the first item/column and the variable of interest in the second item/column. +#' +#' @author Will Burke +#' +#' @export + +# setting it up so you can either input a single df, seperate dfs that get combined, or individual vectors that get combined + +IOin_output_vars = function(...) { + + pars = list(...) + + if (length(pars) > 1 && is.data.frame(pars[[1]])) { + pars = do.call(rbind, pars) + } else if (length(pars) > 1) { + pars = as.data.frame(do.call(rbind, pars)) + } else { + pars = as.data.frame(pars) + } + + return(pars) + +} diff --git a/R/IOin_rhessys_input.R b/R/IOin_rhessys_input.R new file mode 100644 index 0000000..5499391 --- /dev/null +++ b/R/IOin_rhessys_input.R @@ -0,0 +1,86 @@ +#' IOin_rhessys_input +#' +#' Basic inputs to run RHESSys +#' +#' @param version Path to compiled RHESSys binary. +#' @param tec_file Path and name of input tec file. +#' @param world_file Path and name of input world file. +#' @param world_hdr_prefix Prefix for folder and temporary header files to be written. +#' @param flowtable Path and name of input tec file. +#' @param start Start date of simulation. +#' @param end End date of simulation. +#' @param output_folder Path to folder where simulation output will go. +#' @param output_prefix Prefix for output files. +#' @param commandline_options Commandline options to be passed to RHESSys, e.x. '-g' or '-p' +#' @param prefix_command A shell command to be run previous to the RHESSys command line call. +#' This can be used to source a shell script, which itself can run multiple commands if needed. +#' +#' @author Will Burke +#' +#' @export + +IOin_rhessys_input = function(version, + tec_file, + world_file, + world_hdr_prefix, + flowtable, + start, + end, + output_folder, + output_prefix, + commandline_options, + prefix_command = NULL) { + + rh_list = list() + + # ----- rhessys binary version ----- + # TODO this could be built on to automatically pull and compile rhessys + if (!file.exists(version)) { + warning("RHESSys binary version '",version,"' not found.") + } + rh_list$rhessys_version <- version + + # ----- tec file ----- + # TODO since tec_file can be built via inputs, could check for it existing, but no error. + # TODO Could potentially use this input tec file, if it exists, as a basis for a new tec file, so only modificaitons would need to be added + # in the IOin_tec_ function. That actually should probably stay/occur in that file. + # There is potential for conflict here though so a check should happen in the run_rhessys_core or scenario iteration functions + rh_list$tec_file <- tec_file + + # ----- world file ----- + if (!file.exists(world_file)) { + warning("RHESSys world file '",world_file ,"' not found.") + } + rh_list$world_file <- world_file + + # ----- world file header prefix ----- + # this is unclear what the purpose is - we could just delete this and do it all automatically using input name and scenario IDs we generate + rh_list$world_hdr_prefix <- world_hdr_prefix + + # ----- flowtable ----- + if (!file.exists(flowtable)) { + warning("RHESSys flowtable '",flowtable ,"' not found.") + } + rh_list$flow_file <- flowtable + + # ----- dates ----- + # TODO start and end dates, should have automatic coversion to rhessys format from R Date at least + + rh_list$start_date <- start + rh_list$end_date <- end + + # TODO check if exists, create if not + rh_list$output_folder <- output_folder + + rh_list$output_filename <- output_prefix + + # TODO compare against a vector of known commandline options, warn if not in that list + rh_list$command_options <- commandline_options + + # prefix command + rh_list$prefix_command = prefix_command + + return(rh_list) + + +} diff --git a/R/IOin_std_pars.R b/R/IOin_std_pars.R new file mode 100644 index 0000000..05a6c34 --- /dev/null +++ b/R/IOin_std_pars.R @@ -0,0 +1,77 @@ +#' IOin_std_pars +#' +#' Input standard soil parameters for RHESSys, see https://github.com/RHESSys/RHESSys/wiki/RHESSys-command-line-options +#' @param m Decay of hydraulic conductivity with depth. +#' @param k Hydraulic conductivity at the surface. +#' @param soil_dep Soil depth. +#' @param m_v Multiplier to scale the vertical decay of hydraulic conductivity with depth. +#' @param k_v Multiplier to scale the vertical hydraulic conductivity at the surface. +#' @param pa Multiplier to scale the pore size index, set in soil def file. +#' @param po Multiplier to scale the psi air entry, set in soil def file. +#' @param gw1 Multiplier on the sat_to_gw_coeff parameter set in the soil definition file +#' (representing the amount of water moving from the saturated store to the groundwater store). +#' @param gw2 Multiplier on the gw_loss_coeff parameter in the hillslope default file +#' (representing the amount of water moving from the groundwater store to the stream). +#' @param vgseng1 Multiples specific leaf areas. +#' @param vgseng2 Multiplies the ratio of shaded to sunlit leaf area. +#' @param vgseng3 Multiplier used only with the Dickenson algorithm of carbon allocation +#' (set with the epc.allocation_flag variable in the vegetation definition file). It changes +#' the allocation of net photosynthate sensitivity based on the current LAI. If not using the +#' Dickenson strategy of carbon allocation (i.e. using Waring or default Constant strategies), +#' set third value to 1.0. (i.e. -vgsen 1.0 2.0 1.0) +#' @param n The number of parameter sets to generate. +#' @param pct_range The percent range of variation from input values over which sampling (if any), will happen. +#' +#' @author Will Burke +#' +#' @export +#' + +# FORMAT - this is pretty constrained, so a named vector works well here + +# STANDARD PARS USAGE +# With the exception of gw and gw2, all of the command line parameters can be instead set via def file parameters. +# Because of this, the assumption moving forward will be that this function will not be used by default, and so the +# default values will all be set to 1, and if left as 1 (but still passed the run_rhessys_single/multi), will be ignored, since +# they would have no effect. Only non 1 parameters will be passed to the command line. + +IOin_std_pars = function(m = 1, + k = 1, + soil_dep = 1, + m_v = 1, + k_v = 1, + pa = 1, + po = 1, + gw1 = 1, + gw2 = 1, + vgseng1 = 1, + vgseng2 = 1, + vgseng3 = 1, + n = 1, + pct_range = 0.25) { + + + # TODO check here for real world ranges of the parameters, warn if out of bounds + # + std_pars = list( + m = m, + k = k, + soil_dep = soil_dep, + m_v = m_v, + k_v = k_v, + pa = pa, + po = po, + gw1 = gw1, + gw2 = gw2, + vgseng1 = vgseng1, + vgseng2 = vgseng2, + vgseng3 = vgseng3 + ) + + if (n > 1) { + std_pars = lapply(std_pars, function(x) runif(n = n, min = x - (pct_range * x), max = x + (pct_range * x))) + } + + return(std_pars) + +} diff --git a/R/IOin_tec_std.R b/R/IOin_tec_std.R new file mode 100644 index 0000000..7adab88 --- /dev/null +++ b/R/IOin_tec_std.R @@ -0,0 +1,81 @@ +#' IOin_tec_std +#' +#' Input function to construct a dataframe of standard tec events, including start, grow start, and output state +#' +#' @param start start date of run - used along with 'end' arg +#' @param end End date of run +#' @param output_state TRUE/FALSE if an output_current_state tec event should be scheduled at the end of the simulation +#' +#' @author Will Burke +#' +#' @export + +IOin_tec_std = function(start, end, output_state = TRUE) { + + + # check if inputs are dates or already in RHESSys date format + + + start_split = unlist(strsplit(as.character(start), split = " ")) + end_split = unlist(strsplit(as.character(end), split = " ")) + input_tec_data <- + data.frame( + year = integer(), + month = integer(), + day = integer(), + hour = integer(), + name = character() + ) + input_tec_data[1,] <- + data.frame( + as.numeric(start_split[1]), + as.numeric(start_split[2]), + as.numeric(start_split[3]), + as.numeric(start_split[4]), + "print_daily_on" + ) + input_tec_data[2,] <- + data.frame( + as.numeric(start_split[1]), + as.numeric(start_split[2]), + as.numeric(start_split[3]), + (as.numeric(start_split[4]) + 1), + "print_daily_growth_on" + ) + + if (output_state) { + input_tec_data[3,] <- + data.frame( + as.numeric(end_split[1]), + as.numeric(end_split[2]), + (as.numeric(end_split[3]) - 1), + 1, + "output_current_state" + ) + } + + + # if (!is.null(...)) { + # b = list(...) + # if (class(b[[1]])=="data.frame"){ + # return(b[[1]]) + # } else{ + # if(length(b[[1]])!=5){ + # c = unlist(b) + # b = split(c,rep(c(1:(length(c)/5)),each=5)) + # } + # a = data.frame(t(data.frame(b)),stringsAsFactors = FALSE) # list to df, transpose df autoconverts to mat, back to df + # a[,1] = as.integer(a[,1]) # this could be a sapply or something but whatever + # a[,2] = as.integer(a[,2]) + # a[,3] = as.integer(a[,3]) + # a[,4] = as.integer(a[,4]) + # rownames(a) = c() # gross rownames gone + # colnames(a) = c("year","month","day","hour","name") # not sure if needed, but nice anyways + # return(a) + # } + # } + + # COMBINE METHODS - INSERT TEC EVENTS INTO AUTO GENERATED ONES, IN CORRECT ORDER + + return(input_tec_data) +} diff --git a/R/build_output_filter.R b/R/build_output_filter.R new file mode 100644 index 0000000..5284d17 --- /dev/null +++ b/R/build_output_filter.R @@ -0,0 +1,56 @@ +#' build_output_filter +#' +#' Creates a single output filter in R list format. This can be combined with other filters +#' and/or written to file to be read by RHESSys when running. +#' @param timestep The timestep of the filter: 'daily', 'monthly', 'annual', 'hourly' +#' @param output_format The format for the RHESSys output files to be written: 'csv' or 'netcdf' +#' @param output_path The path where RHESSys output will be written. +#' @param output_filename The filename for RHESSys output +#' @param spatial_level The spatial level for output to be collected at/aggregated to: 'basin', 'hillslope', 'zone', 'patch', 'stratum' +#' @param spatial_ID IDs to subset the spatial units by. +#' @param variables The RHESSys internal variable names to output. If aggregating from a finer spatial level use syntax: '.' +#' +#' @author Will Burke +#' @export + + +# ---------- build_output_filter ---------- + +# Make a single output filter in R +# Filter is a data object with following format +# list object containing 1 list named 'filter' +# list 'filter' contains 3 items: +# 'timestep' - 'daily', 'monthly', 'annual', 'hourly' +# 'output' +# 'format' - 'csv' or 'netcdf' +# 'path' +# 'filename' +# '' - 'basin', 'hillslope', 'zone', 'patch', 'stratum' +# 'ids' - the basin or patch id or ids +# 'variables' - the rhessys internal variable names, +# if aggregating up to a larger spatial level, use . format. + +build_output_filter = function(timestep, + output_format, + output_path, + output_filename, + spatial_level, + spatial_ID, + variables) { + + filter_obj = list("filter" = list( + "timestep" = timestep, + "output" = list( + "format" = output_format, + "path" = output_path, + "filename" = output_filename + ), + list("ids" = as.numeric(spatial_ID), + "variables" = paste(variables, collapse = ", ")) + )) + names(filter_obj$filter)[3] = spatial_level + + # if you're allowed to have multiple spatial levels per filter, take the basin part out and append that + return(filter_obj) + +} diff --git a/R/change_def_file.R b/R/change_def_file.R index 2a712e4..f7679fc 100644 --- a/R/change_def_file.R +++ b/R/change_def_file.R @@ -1,6 +1,6 @@ #' Replaces parameters in a def file #' -#' This function imports a def file, replaces the values of selected parameters, and exports a def file. +#' This function reads a def file, replaces the values of selected parameters, and writes a new def file. #' @param def_file Path and name of def file #' @param par_sets Data frame with parameter names as colnames and a single row of parameter values #' @param file_name_ext Optional extension to add to file name @@ -44,7 +44,7 @@ change_def_file <- function(def_file, par_sets, file_name_ext = NULL){ def_table = rbind(def_table, par_sets_df[!in_def,]) } - def_table <- format(def_table, scientific=FALSE); + def_table <- format(def_table, scientific = FALSE); # ------------------------------ Output def file ------------------------------ path <- dirname(def_file) @@ -53,12 +53,18 @@ change_def_file <- function(def_file, par_sets, file_name_ext = NULL){ # Create new directory path_new <- file.path(path, name_no_ext) - if(dir.exists(path_new) == FALSE){dir.create(path_new)} + if (dir.exists(path_new) == FALSE) {dir.create(path_new)} + if (!is.null(file_name_ext)) { + file_name_ext = paste0("_",file_name_ext) + } # Write new file - file_name_out <- file.path(path_new, paste(name_no_ext,"_",file_name_ext,".def",sep="")) + file_name_out <- file.path(path_new, paste(name_no_ext,file_name_ext,".def",sep = "")) # if there are comments, this should remove extra NAs def_table[def_table == "NA"] = " " - write.table(def_table, file = file_name_out, row.names = FALSE, col.names = FALSE, quote=FALSE, sep=" ") + write.table(def_table, file = file_name_out, row.names = FALSE, col.names = FALSE, quote = FALSE, sep = " ") + + return(file_name_out) + } diff --git a/R/clim_auto.R b/R/clim_auto.R deleted file mode 100644 index 841ac68..0000000 --- a/R/clim_auto.R +++ /dev/null @@ -1,113 +0,0 @@ -#' clim_auto -#' -#' Generate input for run_rhessys basestation input -#' -#' @author Will Burke -#' -#' @export - -clim_auto = function(base_station_id, - x_coordinate, - y_coordinate, - z_coordinate, - effective_lai, - screen_height, - annual_prefix = "annual", - monthly_prefix = "monthly", - daily_prefix = "daily", - hourly_prefix = "hourly") { - - input_clim_base_list <- list( - list( - core = data.frame( - c1 = character(), - c2 = character(), - stringsAsFactors = FALSE - ), - annual = data.frame( - c1 = character(), - c2 = character(), - stringsAsFactors = FALSE - ), - monthly = data.frame( - c1 = character(), - c2 = character(), - stringsAsFactors = FALSE - ), - daily = data.frame( - c1 = character(), - c2 = character(), - stringsAsFactors = FALSE - ), - hourly = data.frame( - c1 = character(), - c2 = character(), - stringsAsFactors = FALSE - ) - ) - ) - - input_clim_base_list[[1]][[1]][1, ] <- - data.frame(c1 = base_station_id, - c2 = "base_station_id", - stringsAsFactors = FALSE) - input_clim_base_list[[1]][[1]][2, ] <- - data.frame(c1 = x_coordinate, - c2 = "x_coordinate", - stringsAsFactors = FALSE) - input_clim_base_list[[1]][[1]][3, ] <- - data.frame(c1 = y_coordinate, - c2 = "y_coordinate", - stringsAsFactors = FALSE) - input_clim_base_list[[1]][[1]][4, ] <- - data.frame(c1 = z_coordinate, - c2 = "z_coordinate", - stringsAsFactors = FALSE) - input_clim_base_list[[1]][[1]][5, ] <- - data.frame(c1 = effective_lai, - c2 = "effective_lai", - stringsAsFactors = FALSE) - input_clim_base_list[[1]][[1]][6, ] <- - data.frame(c1 = screen_height, - c2 = "screen_height", - stringsAsFactors = FALSE) - - input_clim_base_list[[1]][[2]][1, ] <- - data.frame(c1 = annual_prefix, - c2 = "annual_climate_prefix", - stringsAsFactors = FALSE) - input_clim_base_list[[1]][[2]][2, ] <- - data.frame(c1 = 0, - c2 = "number_non_critical_annual_sequences", - stringsAsFactors = FALSE) - - input_clim_base_list[[1]][[3]][1, ] <- - data.frame(c1 = monthly_prefix, - c2 = "monthly_climate_prefix", - stringsAsFactors = FALSE) - input_clim_base_list[[1]][[3]][2, ] <- - data.frame(c1 = 0, - c2 = "number_non_critical_monthly_sequences", - stringsAsFactors = FALSE) - - input_clim_base_list[[1]][[4]][1, ] <- - data.frame(c1 = daily_prefix, - c2 = "daily_climate_prefix", - stringsAsFactors = FALSE) - input_clim_base_list[[1]][[4]][2, ] <- - data.frame(c1 = 0, - c2 = "number_non_critical_daily_sequences", - stringsAsFactors = FALSE) - - input_clim_base_list[[1]][[5]][1, ] <- - data.frame(c1 = hourly_prefix, - c2 = "hourly_climate_prefix", - stringsAsFactors = FALSE) - input_clim_base_list[[1]][[5]][2, ] <- - data.frame(c1 = 0, - c2 = "number_non_critical_hourly_sequences", - stringsAsFactors = FALSE) - - return(input_clim_base_list) - -} diff --git a/R/compile_rhessys.R b/R/compile_rhessys.R index 59932dc..8270c19 100644 --- a/R/compile_rhessys.R +++ b/R/compile_rhessys.R @@ -4,13 +4,19 @@ #' @param location The file patch to where the rhessys makefile or folder is #' @param delete_obj TRUE/FALSE to delete objects (before and after) #' @param destination Optional input of where to move resulting RHESSys executable +#' @param make_args Arguments passed to the end of the make commandline call (examples: "wmfire='T'", "clean", or "clobber", ) #' @param CFLAGS Overwrite CFLAGS in the makefile #' @param ignore.stdout Passed through to system() #' @author Will Burke #' #' @export -compile_rhessys = function(location, delete_objs = TRUE, destination = NULL, make_args = NULL, CFLAGS = NULL, ignore.stdout = FALSE) { +compile_rhessys = function(location, + delete_objs = TRUE, + destination = NULL, + make_args = NULL, + CFLAGS = NULL, + ignore.stdout = FALSE) { # find the makefile - i think foolproof but who knows if (endsWith(location, "makefile") && file.exists(location)) { @@ -21,7 +27,6 @@ compile_rhessys = function(location, delete_objs = TRUE, destination = NULL, mak makeopts = list.files(location, pattern = "makefile$", recursive = TRUE) makeopts = grep(file.path("rhessys","makefile"), makeopts, value = TRUE) makeopts = file.path(location, makeopts) - if (length(makeopts) == 0) { stop(noquote(paste0("Could not find any valid makefiles at path: ",location))) } else if (length(makeopts) > 1) { @@ -31,72 +36,83 @@ compile_rhessys = function(location, delete_objs = TRUE, destination = NULL, mak } } + # read in the makefile cat("\n -------------------- Start compile_rhessys.R -------------------- \n\n") cat("Compiling RHESSys using makefile: ", makefile,"\n") - #print(paste0("Compiling RHESSys using makefile: ", makefile), quote = FALSE) read_make = readLines(makefile) make_info = c(read_make[startsWith(read_make, "VERSION")], read_make[startsWith(read_make, "CFLAGS")]) - #print(paste(make_info, collapse = " | "), quote = FALSE) cat(paste(make_info, collapse = " | "), "\n") - # delete objects + # delete objects if they exist if (delete_objs) { objs = file.path(dirname(makefile), "objects") - if (!file.exists(objs)) { stop("Couldn't find the objects folder")} - out = file.remove(file.path(objs, list.files(objs))) - if (length(out) > 0 && out) { - #print("Objects removed", quote = FALSE) - cat("RHESSys objects removed \n") + if (!file.exists(objs)) { + cat("Couldn't find the objects folder - may not exist yet\n") + } else { + out = file.remove(file.path(objs, list.files(objs))) + if (length(out) > 0 && out) { + cat("RHESSys objects removed before compilation\n") + } } } - # CFLAGS - write a new makefile and point to that one if (!is.null(CFLAGS)) { - new_makefile = read_make - new_makefile[startsWith(read_make, "CFLAGS")] = paste0(new_makefile[startsWith(read_make, "CFLAGS")], " ", trimws(CFLAGS)) - makefile = file.path(dirname(makefile), ".makefile_tmp") - writeLines(new_makefile, makefile) - #print(paste0("Wrote temporary makefile '", makefile,"' with additional CFLAGS: ", CFLAGS), quote = FALSE) - cat("Wrote temporary makefile '", makefile,"' with additional CFLAGS: ", CFLAGS,"\n\n") + # if the CFLAGS have an override, use that, otherwise make a temp makefile with changed cflags + if (any(startsWith(read_make, "override CFLAGS"))) { + if (!startsWith(CFLAGS,"CFLAGS=")) { + CFLAGS = paste0(" CFLAGS=", shQuote(trimws(CFLAGS), type = "sh")) + } + } else { + new_makefile = read_make + new_makefile[startsWith(read_make, "CFLAGS")] = paste0(new_makefile[startsWith(read_make, "CFLAGS")], " ", trimws(CFLAGS)) + makefile = file.path(dirname(makefile), ".makefile_tmp") + writeLines(new_makefile, makefile) + cat("Wrote temporary makefile '", makefile,"' with additional CFLAGS: ", CFLAGS,"\n\n") + } } - make_cmd = paste0("make -C ", dirname(makefile), " -f ", basename(makefile)) - if (!is.null(make_args)) { - make_cmd = paste(make_cmd, make_args) + make_args = paste0(" ", trimws(make_args)) } + make_cmd = paste0("make -C ", dirname(makefile), " -f ", basename(makefile), make_args, CFLAGS) + if (.Platform$OS.type == "windows") { - make_cmd2 = paste0("bash -c ", shQuote(make_cmd, type = "sh")) + make_cmd2 = paste0("wsl ", make_cmd) } else { - make_cmd2 = shQuote(make_cmd, type = "sh") + #make_cmd2 = shQuote(make_cmd, type = "sh") + make_cmd2 = make_cmd } cat("Running makefile... \n\n") - sysout = system(command = make_cmd2, ignore.stdout = ignore.stdout) - #print(paste("Command line echo:", make_cmd2), quote = FALSE) cat("\nCommand line echo:", make_cmd2,"\n") - # if (sysout != 0) { - # warning("Make probably failed, returned: ", sysout) - # } + if (sysout == 2) { + warning("Make probably failed, returned: ", sysout) + } if (!is.null(CFLAGS)) { - out_rm = file.remove(makefile) - #print(paste0("Removed temporary makefile: '", makefile, "'"), quote = FALSE) - cat("Removed temporary makefile: '", makefile, "'","\n", sep = "") + if (!any(startsWith(read_make, "override CFLAGS")) ) { + out_rm = file.remove(makefile) + cat("Removed temporary makefile: '", makefile, "'","\n", sep = "") + } } # move rhessys if (!is.null(destination)) { rhessys_write = file.path(dirname(makefile), paste0("rhessys", substr(make_info[1], 11, nchar(make_info[1])))) file.rename(rhessys_write, to = file.path(destination, basename(rhessys_write))) - #print(paste0("Moved ",basename(rhessys_write), " from ", dirname(makefile), " to ", destination), quote = FALSE) cat("Moved '",basename(rhessys_write), "' from '", dirname(makefile), "' to '", destination,"'\n", sep = "") } + # delete new objects + if (delete_objs) { + out = file.remove(file.path(objs, list.files(objs))) + if (length(out) > 0 && out) { cat("RHESSys objects removed after compilation\n") } + } + cat("\n -------------------- End compile_rhessys.R -------------------- \n") } diff --git a/R/input_tec.R b/R/input_tec.R deleted file mode 100644 index ae8d1ca..0000000 --- a/R/input_tec.R +++ /dev/null @@ -1,132 +0,0 @@ -#' input_tec -#' -#' Tiny wrapper to simplify input of tec events -#' -#' @param ... Vector(s) containing tec events in format c(,,,,). -#' Additional tec events can be added just as additional arguments. -#' @param start_end Vector of two charaters, indicating start and end dates, same as used to input start and end date for input_rhessys. -#' Used to auto generate tec events for printing (normal and grow), and output current state at end -#' @param start start date of run - used along with 'end' arg -#' @param end End date of run -#' @param output_state TRUE/FALSE if an output_current_state tec event should be scheduled at the end of the simulation -#' @author Will Burke -#' -#' @export - -input_tec = function(start_end = NULL, start = NULL, end = NULL, output_state = TRUE){ - - if (is.null(start_end) & is.null(start) & is.null(end)){ - return(NULL) - } - - if (!is.null(start_end)) { - date_split = strsplit(start_end,split = " ") - input_tec_data <- - data.frame( - year = integer(), - month = integer(), - day = integer(), - hour = integer(), - name = character(), - stringsAsFactors = FALSE - ) - input_tec_data[1, ] <- - data.frame( - as.numeric(date_split[[1]][1]), - as.numeric(date_split[[1]][2]), - as.numeric(date_split[[1]][3]), - as.numeric(date_split[[1]][4]), - "print_daily_on", - stringsAsFactors = FALSE - ) - input_tec_data[2, ] <- - data.frame( - as.numeric(date_split[[1]][1]), - as.numeric(date_split[[1]][2]), - as.numeric(date_split[[1]][3]), - (as.numeric(date_split[[1]][4]) + 1), - "print_daily_growth_on", - stringsAsFactors = FALSE - ) - if (output_state) { - input_tec_data[3, ] <- - data.frame( - as.numeric(date_split[[2]][1]), - as.numeric(date_split[[2]][2]), - as.numeric(date_split[[2]][3]), 1, - "output_current_state", - stringsAsFactors = FALSE - ) - } - - } - - if (!is.null(start) & !is.null(end) & is.null(start_end)) { - start_split = unlist(strsplit(as.character(start),split = " ")) - end_split = unlist(strsplit(as.character(end),split = " ")) - input_tec_data <- - data.frame( - year = integer(), - month = integer(), - day = integer(), - hour = integer(), - name = character(), - stringsAsFactors = FALSE - ) - input_tec_data[1, ] <- - data.frame( - as.numeric(start_split[1]), - as.numeric(start_split[2]), - as.numeric(start_split[3]), - as.numeric(start_split[4]), - "print_daily_on", - stringsAsFactors = FALSE - ) - input_tec_data[2, ] <- - data.frame( - as.numeric(start_split[1]), - as.numeric(start_split[2]), - as.numeric(start_split[3]), - (as.numeric(start_split[4]) + 1), - "print_daily_growth_on", - stringsAsFactors = FALSE - ) - - if (output_state) { - input_tec_data[3, ] <- - data.frame( - as.numeric(end_split[1]), - as.numeric(end_split[2]), - as.numeric(end_split[3]), - 1, - "output_current_state", - stringsAsFactors = FALSE - ) - } - } - - - # if (!is.null(...)) { - # b = list(...) - # if (class(b[[1]])=="data.frame"){ - # return(b[[1]]) - # } else{ - # if(length(b[[1]])!=5){ - # c = unlist(b) - # b = split(c,rep(c(1:(length(c)/5)),each=5)) - # } - # a = data.frame(t(data.frame(b)),stringsAsFactors = FALSE) # list to df, transpose df autoconverts to mat, back to df - # a[,1] = as.integer(a[,1]) # this could be a sapply or something but whatever - # a[,2] = as.integer(a[,2]) - # a[,3] = as.integer(a[,3]) - # a[,4] = as.integer(a[,4]) - # rownames(a) = c() # gross rownames gone - # colnames(a) = c("year","month","day","hour","name") # not sure if needed, but nice anyways - # return(a) - # } - # } - - # COMBINE METHODS - INSERT TEC EVENTS INTO AUTO GENERATED ONES, IN CORRECT ORDER - - return(input_tec_data) -} diff --git a/R/insert_in_worldfile.R b/R/insert_in_worldfile.R new file mode 100644 index 0000000..954d38c --- /dev/null +++ b/R/insert_in_worldfile.R @@ -0,0 +1,63 @@ +#' Insert in Worldfile +#' +#' Inserts new state variables and values into a worldfile at specified location(s). +#' @param world_in Path to input worldfile. Cannot create from scratch (use RHESSysPreprocessing) +#' @param world_out Path to output worldfile. If set to FALSE, no file will be written. +#' @param insert Character vector of length = 2, containing state variable and value to be inserted into a worldfile. +#' @param insert_loc Location, in the form of an existing state variable name, for a new state variable(s) to be inserted following. +#' @param return_data TRUE/FALSE should an R data object be returned. +#' @param overwrite TRUE/FALSE should output worldfile overwrite existing file. +#' +#' @author Will Burke +#' @export + +insert_in_worldfile = function(world_in, + world_out, + insert, + insert_loc, + return_data = FALSE, + overwrite = FALSE) { + + # ---------- Check Arguments ---------- + if (!file.exists(world_in)) { stop(noquote(paste0("No file found at: ", world_in))) } + if (file.exists(world_out) & overwrite) { + cat("File:", world_out, "will be overwritten.\n") + } else if (file.exists(world_out) & !overwrite) { + stop(noquote(paste0("Existing file found at: ", world_in, " & overwrite == FALSE"))) + } + if (!is.vector(insert) | length(insert) != 2) { + stop("Insert is not a length == 2 character vector") + } + + # ---------- Read World ---------- + # this is the slow version - if needed switch to faster not in function method + read_world = readLines(world_in, warn = FALSE, encoding = "UTF-8") + read_world = read_world[nchar(trimws(read_world)) > 0] + world = strsplit(trimws(read_world), "\\s+") + world = data.frame(matrix(unlist(world), nrow = length(world), byrow = T), stringsAsFactors = FALSE) + names(world) = c("values","vars") + + # Check insert_loc is valid + insert_loc_i = which(world$vars == insert_loc) + if (length(insert_loc_i) == 0) { + stop(noquote(paste0("Could not find state variable: ", insert_loc, " in worldfile: ", world_in))) + } + + # text string to insert - follows existing formatting + insert_txt = gsub(insert_loc,insert[1], read_world[insert_loc_i[1]]) + insert_txt = gsub(world$values[world$vars == insert_loc][1], insert[2], insert_txt) + write_world = read_world + + # short loop through replacement indexes + for (i in seq_along(insert_loc_i)) { + write_world = c(write_world[1:(insert_loc_i[i] + i - 1)], insert_txt, write_world[(insert_loc_i[i] + i):length(write_world)]) + } + + # Report changes + cat("Inserted line: ", trimws(insert_txt), "\nat ", length(insert_loc_i), " instances following state variable: ", insert_loc,"\n") + + # Write new worldfile + writeLines(text = write_world, world_out) + cat("Wrote new worldfile to: ", world_out) + +} diff --git a/R/make_clim_base_file.R b/R/make_clim_base_file.R index 76f3b9d..ffa5ae8 100644 --- a/R/make_clim_base_file.R +++ b/R/make_clim_base_file.R @@ -5,13 +5,12 @@ #' @param ??? ??? #' @param ??? ??? #' @param ??? ??? -#' -#' #' @export + make_clim_base_file <- function(input_clim_base, clim_base_path, input_dated_seq, - clim_dated_ext){ + clim_dated_ext) { # Create core part of climate base file clim_base_core <- do.call(dplyr::bind_rows, input_clim_base) diff --git a/R/make_hdr_file2.R b/R/make_hdr_file2.R new file mode 100644 index 0000000..bfd80a2 --- /dev/null +++ b/R/make_hdr_file2.R @@ -0,0 +1,64 @@ +#' Write Header File +#' +#' New version of header file creation function. +#' @inheritParams run_rhessys_single +#' @param def_pars_df Data frame of def file parameter changes +#' +#' @author Will Burke + +make_hdr_file2 = function(input_rhessys, + hdr_files, + def_files, + runID) { + + # Create hdr output folder + world_hdr_path <- file.path(dirname(input_rhessys$world_file), input_rhessys$world_hdr_prefix) + if (!dir.exists(world_hdr_path)) {dir.create(world_hdr_path)} + + # check the hdr items being used + hdr_def_opts = c("basin_def", "hillslope_def", "zone_def", "soil_def", "landuse_def", + "stratum_def", "fire_def", "fire_grid_prefix", "spinup_def", "base_stations") + if (any(!names(hdr_files[!is.null(hdr_files)]) %in% hdr_def_opts)) { + warning("header definition for ", + names(hdr_files[!is.null(hdr_files)])[!names(hdr_files[!is.null(hdr_files)]) %in% hdr_def_opts], + "is invalid and won't be added to header") + } + # ignore any that aren't valid, specifically to ignore patch header files which it seems should be soil defs + hdr_files = hdr_files[names(hdr_files[!is.null(hdr_files)]) %in% hdr_def_opts] + + # get needed info for hdr file format + hdr_values = lapply(hdr_files, function(x) c(length(x), x)) + hdr_vars = mapply(function(x, y) { + x[1] = paste0("num_", y) + x[2:length(x)] = y + return(x) + }, hdr_values, names(hdr_values), SIMPLIFY = F) + + # make combined df + hdr_df = data.frame(unlist(hdr_values), unlist(hdr_vars), row.names = NULL) + # fix the names up + hdr_df[,2] = gsub("def", "default_file", hdr_df[,2]) + hdr_df[,2] = gsub("base_stations", "base_stations_file", hdr_df[,2]) + hdr_df[,2][startsWith(hdr_df[,2], "num")] = paste0(hdr_df[,2][startsWith(hdr_df[,2], "num")],"s") + + # replace with modified defs where needed + if (!is.null(def_files)) { + rep_ind = lapply(def_files$old, function(x, y) {which(y == x)}, hdr_df[,1]) + hdr_df[unlist(rep_ind),1] = def_files$new + } + + if (!is.null(runID)) { + runID = paste0("_",runID) + } + world_hdr_name_out <- file.path(world_hdr_path, paste0(input_rhessys$world_hdr_prefix, runID, ".hdr")) + write.table(hdr_df, file = world_hdr_name_out, col.names = FALSE, row.names = FALSE, quote = FALSE, sep = "\t\t") + cat("===== Wrote hdr file '",world_hdr_name_out,"' =====\n", sep = "") + + # NOTE ON WRITE SPEEDS + # write times w data.table::fwrite is only ~100 microsec faster for the header + # for example so leaving all the writing as write.table for now + + return(world_hdr_name_out) + +} + diff --git a/R/make_tec_file.R b/R/make_tec_file.R index c8ec894..690f176 100644 --- a/R/make_tec_file.R +++ b/R/make_tec_file.R @@ -14,5 +14,3 @@ make_tec_file <- function(tec_file, tec_data){ write.table(tec_data, file = tec_file, col.names = FALSE, row.names=FALSE, quote = FALSE) } - - diff --git a/R/modify_output_filter.R b/R/modify_output_filter.R new file mode 100644 index 0000000..4088e16 --- /dev/null +++ b/R/modify_output_filter.R @@ -0,0 +1,60 @@ +#' modify_output_filter +#' +#' Modify a single existing output filter, either from file or based on an existing R object. Will error if given multiple filters. +#' This could be done via normal list modification in R as well. +#' @inheritParams read_output_filter +#' @inheritParams build_output_filter +#' @author Will Burke +#' +#' @export + +modify_output_filter = function(filter_in, + timestep = NULL, + output_format = NULL, + output_path = NULL, + output_filename = NULL, + spatial_level = NULL, + spatial_ID = NULL, + variables = NULL) { + + if (!is.list(filter_in)) { + filter = read_output_filter(filter_in = filter_in) + } + + if (length(filter) > 1) { + stop("Can only modify 1 filter at a time.") + } + + if (!is.null(timestep)) { filter[[1]]$timestep = timestep } + + if (!is.null(output_format)) { filter[[1]]$output$format = output_format } + + if (!is.null(output_path)) { filter[[1]]$output$path = output_path } + + if (!is.null(output_filename)) { filter[[1]]$output$filename = output_filename } + + if (!is.null(spatial_level)) { + if (is.null(variables)) { + warning("If spatial level is being changed, variables will almost certainly need to be changed.") + } + + filter[[1]][names(filter[[1]]) %in% c('basin', 'hillslope', 'zone', 'patch', 'stratum')] = NULL + + filter[[1]]$tmp = list("ids" = spatial_ID, "variables" = paste(variables, collapse = ", ")) + + names(filter[[1]])[names(filter[[1]]) == "tmp"] = spatial_level + + } + + if (!is.null(spatial_ID)) { + filter[[1]][[which(names(filter[[1]]) %in% c('basin', 'hillslope', 'zone', 'patch', 'stratum'))]]$ids = spatial_ID + } + + if (!is.null(variables)) { + filter[[1]][[which(names(filter[[1]]) %in% c('basin', 'hillslope', 'zone', 'patch', 'stratum'))]]$variables = paste(variables, collapse = ", ") + + } + + return(filter) + +} diff --git a/R/output_control.R b/R/output_control.R new file mode 100644 index 0000000..9486b51 --- /dev/null +++ b/R/output_control.R @@ -0,0 +1,63 @@ +#' output_control +#' +#' Passes output variables to appropriate output selection method. +#' @param output_method Output method (function) to use. "awk" will use awk, "r" will use new R based method, +#' any other non NULL input will use the older R based output selection. +#' @param output_variables Datafrane with two named columns: "variables" containing variables of interest +#' found in the header of standard rhessys output files, "out_file" points to the files containing the associated variables, +#' this can be either the path to that file, can use the abbreviation for the different output types +#' (patch daily = pd, patch daily grow = pdg etc.) and the files in output_folder will be parsed appropriately, +#' or can use the fully written out space.time suffix, e.g. "patch.daily" or "grow_patch.daily" +#' @param output_folder Folder where rhessys output is located +#' @param output_filename Base file name of standard rhessys output +#' @param runID Integer ID of the current run, used internally +#' @inheritParams select_output_variables_R + +# if output function has a new arg, add function to inheritsParams + +output_control = function(output_method, + output_variables, + return_data, + output_folder, + output_filename, + runID = 1) { + + if (!is.null(output_variables[1]) & !is.null(output_method)) { + + # make allsim folder in output location - won't overwrite, warning for if exists is supressed + dir.create(file.path(input_rhessys$output_folder, "allsim"), + showWarnings = FALSE) + + if (output_method == "awk") { + select_output_variables_w_awk( + output_variables = output_variables, + output_folder = output_folder, + run = runID, + output_initiation = 1 + ) + + } else if (output_method == "r") { + data_out = select_output_variables_R( + output_variables = output_variables, + output_folder = output_folder, + output_filename = output_filename, + run = runID, + return_data = return_data + ) + return(data_out) + + } else { + select_output_variables( + output_variables = output_variables, + output_folder = input_rhessys$output_folder, + run = runID, + output_initiation = output_initiation + ) + + } + + return() + + } + +} diff --git a/R/read_output_filter.R b/R/read_output_filter.R new file mode 100644 index 0000000..1c176f7 --- /dev/null +++ b/R/read_output_filter.R @@ -0,0 +1,46 @@ +#' read_output_filter +#' +#' Reads a yaml format RHESSys output filter and creates a R list. Handles tabs in input file, +#' @param filter_in Path to the yaml filter file +#' @author Will Burke +#' @export + +read_output_filter = function(filter_in) { + + # ----- handle tabs instead of spaces ----- + read_try = try(yaml::yaml.load_file(filter_in), silent = T) + if (class(read_try) == "try-error" && grepl("cannot open the connection", attr(read_try, 'condition'))) { + stop("Could not load '", filter_in, "', no such file at the specified path.") + } + if (class(read_try) == "try-error" && grepl("Scanner error", attr(read_try, 'condition'))) { + filter_tabs = readLines(filter_in) + filter_clean = gsub(pattern = "\\t", replacement = " ", x = filter_tabs) + + # ----- handle multiple filters mapped as 'filter' ----- + read_try2 = try(yaml::yaml.load(filter_clean), silent = T) + if (class(read_try2) == "try-error" && grepl("Duplicate map key: 'filter'", attr(read_try2, 'condition'))) { + filter_loc = grep("filter", filter_clean) + replacement = paste0('filter',seq_along(filter_loc)) + filter_clean[filter_loc] = mapply(gsub, pattern = 'filter', replacement, filter_clean[filter_loc]) + # if it fails here, there's something else wrong, not just the filter missing unique IDs + read_try2 = yaml::yaml.load(filter_clean) + } + read_try = read_try2 + } + + # ----- handle multiple filters mapped as 'filter' ----- + if (class(read_try) == "try-error" && grepl("Duplicate map key: 'filter'", attr(read_try, 'condition'))) { + filter_clean = readLines(filter_in) + filter_loc = grep("filter", filter_clean) + replacement = paste0('filter', seq_along(filter_loc)) + filter_clean[filter_loc] = mapply(gsub, pattern = 'filter', replacement, filter_clean[filter_loc]) + # if it fails here, there's something else wrong, not just the filter missing unique IDs + read_try = yaml::yaml.load(filter_clean) + } + + filter = read_try + names(filter) = rep("filter", length(filter)) + + + return(filter) +} diff --git a/R/rhessys_command.R b/R/rhessys_command.R index 9538c40..e3963ac 100644 --- a/R/rhessys_command.R +++ b/R/rhessys_command.R @@ -1,24 +1,23 @@ #' Executes single RHESSys run on command line #' -#' \code{rhessys_command} calls rhessys on the command line. -#' -#' Requires that supporting files be developed prior to running RHESSys. These -#' include ... -#' -#' @param rhessys_version path and file of compiled version of RHESSys. -#' @param world_file path and file of world_file. World_file is produced using -#' grass-to-world -#' @param world_hdr_file ??? -#' @param tec_file ??? -#' @param flow_file ??? -#' @param start_date ??? -#' @param end_date ??? -#' @param output_file ??? -#' @param input_parameters ??? -#' @param command_options ??? -#' +#' \code{rhessys_command} Assembles command line RHESSys call, and runs it. See the RHESSys wiki: +#' https://github.com/RHESSys/RHESSys/wiki/RHESSys-command-line-options +#' @param rhessys_version Path and file name of compiled version of RHESSys. +#' @param world_file Oath and file name of RHESSys world_file. +#' @param world_hdr_file Path and file name of RHESSys header file +#' @param tec_file Path and file name of RHESSys temporal event control (tec) file +#' @param flow_file Path and file name of RHESSys flow table file +#' @param start_date Start date character vector in format , delimited by spaces. Ex. '1990 12 30 01' +#' @param end_date End date character vector, same format as start_date +#' @param output_file Path and base file name of RHESSys output +#' @param input_parameters Soil parameters passed to RHESSys command line. +#' @param output_filter Path to a yaml formatted output filter. +#' @param command_options RHESSys command line options, ex. '-g' or '-p'. +#' @param prefix_command A shell command to be run previous to the RHESSys command line call. +#' This can be used to source a shell script, which itself can run multiple commands if needed. #' #' @export + rhessys_command <- function(rhessys_version, world_file, world_hdr_file, @@ -26,34 +25,54 @@ rhessys_command <- function(rhessys_version, flow_file, start_date, end_date, - output_file, + output_file = NULL, input_parameters, - command_options){ + output_filter = NULL, + command_options, + prefix_command = NULL) { - # tmp <- sprintf("%s -w %s -whdr %s -t %s -r %s -st %s -ed %s -pre %s %s %s", - # rhessys_version, - # world_file, - # world_hdr_file, - # tec_file, - # flow_file, - # start_date, - # end_date, - # output_file, - # input_parameters, - # command_options) + tmp = paste0( + rhessys_version, + " -w ", world_file, + " -whdr ", world_hdr_file, + " -t ", tec_file, + " -r ", flow_file, + " -st ", start_date, + " -ed ", end_date + ) - # handles NULLS better - tmp = paste0(rhessys_version, " -w ", world_file, " -whdr ",world_hdr_file, " -t ", tec_file, " -r ", flow_file, - " -st ", start_date, " -ed ", end_date, " -pre ", output_file, " ", input_parameters, " ", command_options) + if (!is.null(output_file)) { + tmp = paste0(tmp, " -pre ", output_file) + } + if (!is.null(output_filter)) { + tmp = paste0(tmp, " -of ", output_filter) + } + if (!is.null(input_parameters)) { + tmp = paste0(tmp, " ", input_parameters) + } - # check OS and run via system correctly - windows requires the linux subsystem i think + if (length(command_options) > 0) { + tmp = paste0(tmp, " ", command_options) + } - if(.Platform$OS.type=="windows"){ - tmp = noquote(paste("bash -c \"",tmp,"\"",sep="")) + # add prefix command optionally + if (!is.null(prefix_command)) { + tmp = paste0(prefix_command, "; ", tmp) } - print(paste("Command line echo:",tmp),quote = FALSE) + # check OS and run via system correctly - windows requires the linux subsystem + # TODO add check for WSL installation + if (.Platform$OS.type == "windows") { + tmp = noquote(paste("bash -c \"", tmp, "\"", sep = "")) + } + + cat("Command line echo:", tmp, "\n") + #print(paste("Command line echo:", tmp), quote = FALSE) + + cat("\n----------------------------------------\n") + cat("===== Beginning RHESSys Simulation =====\n") + cat("----------------------------------------\n\n") system(tmp) diff --git a/R/run_rhessys.R b/R/run_rhessys.R index d665106..1e1ed59 100644 --- a/R/run_rhessys.R +++ b/R/run_rhessys.R @@ -33,7 +33,7 @@ run_rhessys <- function(parameter_method, input_tec_data, output_variables = NULL, output_initiation = 1, - return_data = FALSE){ + return_data = FALSE) { # ------------------------------ Input checks ------------------------------ if (!parameter_method %in% c("all_combinations","lhc","monte_carlo","exact_values")) {stop("Invalid parameter_method.")} diff --git a/R/run_rhessys_multi.R b/R/run_rhessys_multi.R new file mode 100644 index 0000000..ff4ae9d --- /dev/null +++ b/R/run_rhessys_multi.R @@ -0,0 +1,113 @@ +#' Run multiple RHESSys simulations +#' +#' Runs RHESSys simulations. +#' @inheritParams run_rhessys_single +#' @param parallel Defaults to TRUE. Should the parallel package be used to parallelize the rhessys runs. +#' @param n_cores The number of cores to use in a parallelized cluster. +#' @author Will Burke +#' +#' @export +#' + + +run_rhessys_multi = function(input_rhessys, + hdr_files, + tec_data, + def_pars = NULL, + output_filter = NULL, + runID = NULL, + parallel = TRUE, + n_cores = 2) { + + # TODO add logic on how to combine scenarios/iterations/param sets ACROSS data objects + # TODO add option to only aggregate to a table and output as R object, add opposite - to use input R object + # to run scenarios + + # list of data frames, each containing nrows where n is number of sims for each data object + dfs = NULL + + # ---------- def pars ---------- + if (!is.null(def_pars)) { + # transform into dataframe, both for convenience and storing, tho will need to go back to list form + def_pars_df = as.data.frame(lapply(def_pars, "[[", 3)) + def_names = sapply(def_pars, function(x) paste(x[[1]], x[[2]], sep = "::")) + names(def_pars_df) = def_names + + dfs <- c(dfs, list(def_pars_df)) + + } + + # ---------- tec events ---------- + # add here when tec event scenarios/iterations get added + + # ---------- clim sequences ---------- + + # ---------- combine scenarios ---------- + # get all combinations - expand grid but with dfs, taken from reshape::expand.grid.df + indexes <- lapply(dfs, function(x) 1:nrow(x)) + grid <- do.call(expand.grid, indexes) + df <- do.call(data.frame, mapply(function(df, index) df[index, , drop = FALSE], dfs, grid)) + colnames(df) <- unlist(lapply(dfs, colnames)) + rownames(df) <- 1:nrow(df) + + # ---------- dumb for loop ---------- + if (!parallel) { + for (i in 1:nrow(df)) { + + if (!is.null(def_pars)) { + def_pars_values = as.list(df[i, names(df) %in% def_names]) + def_pars_i = mapply(function(x, y) {x[[3]] = y; return(x)}, def_pars, def_pars_values, SIMPLIFY = F) + } else { + def_pars_i = NULL + } + + run_rhessys_single( + input_rhessys = input_rhessys, + hdr_files = hdr_files, + tec_data = tec_data, + def_pars = def_pars_i, + output_filter = output_filter, + runID = i + ) + } + } + + + # ---------- parallelized ---------- + if (parallel) { + + run_parallel = function(i, + input_rhessys, + hdr_files , + tec_data, + df, + def_pars, + output_filter) { + + library(RHESSysIOinR) + + if (!is.null(def_pars)) { + def_pars_i = mapply(function(x, y) {x[[3]] = y; return(x)}, def_pars, df[i, ], SIMPLIFY = F) + } else { + def_pars_i = NULL + } + + run_rhessys_single( + input_rhessys = input_rhessys, + hdr_files = hdr_files, + tec_data = tec_data, + def_pars = def_pars_i, + output_filter = output_filter, + runID = i + ) + + } + + cl = parallel::makeCluster(n_cores) + parallel::clusterExport(cl, c("df", "input_rhessys", "hdr_files", "tec_data", "def_pars")) + parallel::parLapply(cl = cl, X = 1:nrow(df), fun = run_parallel, input_rhessys, hdr_files, tec_data, df, def_pars) + parallel::stopCluster(cl) + } + + +} diff --git a/R/run_rhessys_single.R b/R/run_rhessys_single.R new file mode 100644 index 0000000..88108cf --- /dev/null +++ b/R/run_rhessys_single.R @@ -0,0 +1,193 @@ +#' Run RHESSys simulation +#' +#' Writes files and assembles inputs to run a single instance of RHESSys. +#' @param input_rhessys List containing the following named elements: "rhessys_version" (path to rhessys binary), +#' "tec_file"(name for tec file to be built), "world_file"(path to existing worldfile), "world_hdr_prefix"(prefix for headers to create), +#' "flow_file"(path to existing flowtable), "start_date"(format c('yyyy mm dd hr')), "end_date"(format c('yyyy mm dd hr')), +#' "output_folder"(path to output folder), "output_filename"(prefix for output files to create), "command_options"(additional commandline options) +#' @param hdr_files List of named elements, named for each def file type (basin_def, hillslope_def, zone_def, soil_def, landuse_def, patch_def, +#' stratum_def) as well as an element named "base_stations". Each element should contain the path to the corresponding def file. +#' @param std_pars List of standard (command line) parameters. +#' @param tec_data Input tec events, see input_tec function +#' @param def_pars To overwrite def file parameters. Format is a list of lists, with each sub-list having the format: +#' list(, , ). Defaults to NULL +#' @param clim_base Data for input climate basestation to be written. Defaults to NULL, which assumes you havean existing basestation pointed +#' to in input_rhessys. +#' @param output_filter An output filter, either an R list with 1 to n number of filters read in/modified/generated via IOin_output_filter.R +#' (or associated functions - build_output_filter.R, read_output_filter.R, modify_output_filter.R), or a file path pointing to an +#' existing output filter. +#' @param output_method "awk" will use awk, any other non NULL input will use R based output selection +#' @param output_variables List of output variables to subset via the indicated method, Defaults to NULL +#' @param return_data TRUE/FALSE if the function should return a data.table of the selected output - for now only works if doing 1 run +#' @param runID The unique ID used to track input and output files if running multiple scenarios, and thus multiple instances of run_rhessys_core. +#' @export + +run_rhessys_single <- function(input_rhessys, + hdr_files, + tec_data, + std_pars = NULL, + def_pars = NULL, + clim_base = NULL, + output_filter = NULL, + output_method = NULL, + output_variables = NULL, + return_data = FALSE, + runID = NULL) { + + cat("\n--------------------------------------------\n") + cat("===== Beginning RHESSysIO file writing =====\n") + cat("--------------------------------------------\n\n") + # ------------------------------ Input checks ------------------------------ + req_rhessys_input = c( "rhessys_version", "tec_file", "world_file", "world_hdr_prefix", "flow_file", + "start_date", "end_date") + if (any(!req_rhessys_input %in% names(input_rhessys))) { + stop(paste0("Missing rhessys_input(s):", names(input_rhessys)[!req_rhessys_input %in% names(input_rhessys)])) + } + # Following inputs must exist to run + if (!file.exists(input_rhessys$rhessys_version)) { stop(paste("RHESSys version", input_rhessys$rhessys_version, "does not exist."))} + if (!file.exists(input_rhessys$world_file)) { stop(paste("World file", input_rhessys$world_file, "does not exist."))} + if (!file.exists(input_rhessys$flow_file)) { stop(paste("Flow table", input_rhessys$flow_file, "does not exist."))} + # auto generate output folder + if (!is.null(input_rhessys$output_folder) && !dir.exists(input_rhessys$output_folder)) { + dir.create(input_rhessys$output_folder) + cat("Created output folder: ", input_rhessys$output_folder) + } + + # output filters don't work with the output subsetting + if (!is.null(output_filter) & !is.null(output_method)) { + stop("Cannot use both output filters and a output subsetting method.") + } + + # ------------------------------ Def file parameters ------------------------------ + # check the def files all exist - except for the fire grid prefix, and clim if clim is also given as input + not_check = 'fire_grid_prefix' + if (!is.null(clim_base)) {not_check = c(not_check, 'base_stations')} + + if (any(!file.exists(unlist(hdr_files[!names(hdr_files) %in% not_check])))) { + stop("Def file(s) '", unlist(hdr_files[!names(hdr_files) %in% not_check])[!file.exists(unlist(hdr_files[!names(hdr_files) %in% not_check]))],"' is/are not exist at specified path." ) + } + # TODO if keeping the fire grid header method - add check for those files if header is included + + # if there are def file pars to change + if (!is.null(def_pars)) { + if (!is.data.frame(def_pars)) { + def_pars_df = data.frame(matrix(unlist(def_pars), nrow = length(def_pars), byrow = T)) + } else { + def_pars_df = def_pars + } + + # check the def files to change are in the list of existing ones - warning only since maybe this is intentional? + if (any(!unique(def_pars_df$X1) %in% unlist(hdr_files))) { + warning("Def file '",unique(def_pars_df$X1)[!unique(def_pars_df$X1) %in% unlist(hdr_files)],"' is not included in header def files." ) + } + + def_files = data.frame(old = unique(def_pars_df$X1), new = NA) + for (f in unique(def_pars_df$X1)) { + # subset def file pars and put in format expected by the change_def_file function + def_par_subset = data.frame(t(def_pars_df[def_pars_df$X1 == f,3])) + names(def_par_subset) = def_pars_df[def_pars_df$X1 == f,2] + new_file = change_def_file(def_file = f, par_sets = def_par_subset, file_name_ext = runID) + def_files[def_files[,1] == f, 2] = new_file + } + cat("===== Wrote def files =====\n") + } else { + def_files = NULL + } + + # ------------------------------ Standard parameters ------------------------------ + if (!is.null(std_pars)) { + # value of 1 == null as far as RHESSys is concerned, setting all NULLs to 1 to be safe, then ignoring if all inputs are 1s + # std_pars = lapply(std_pars, function(X) {if (!is.null(X) && X == 1) X = NULL; return(X)}) + std_pars = lapply(std_pars, function(X) {if (is.null(X)) X = 1; return(X)}) + + if (std_pars[["m"]] != 1 | std_pars[["k"]] != 1) { + std_pars_out = paste("-s", std_pars$m, std_pars$k) + if (std_pars[["soil_dep"]] != 1) { + std_pars_out = paste(std_pars_out, std_pars$soil_dep) + } + } else { + std_pars_out = NULL + } + if (std_pars[["m_v"]] != 1 | std_pars[["k_v"]] != 1) { + std_pars_out = paste(std_pars_out, "-sv", std_pars$m_v, std_pars$k_v) + } + if (std_pars[["pa"]] != 1 | std_pars[["po"]] != 1) { + std_pars_out = paste(std_pars_out, "-svalt", std_pars$pa, std_pars$po) + } + if (std_pars[["gw1"]] != 1 | std_pars[["gw2"]] != 1) { + std_pars_out = paste(std_pars_out, "-gw", std_pars$gw1, std_pars$gw2) + } + if (std_pars[["vgseng1"]] != 1 | std_pars[["vgseng2"]] != 1 | std_pars[["vgseng3"]] != 1) { + std_pars_out = paste(std_pars_out, "-vgsen", std_pars$vgseng1, std_pars$vgseng2, std_pars$vgseng3) + } + } else { + std_pars_out = NULL + } + + # ------------------------------ Climate ------------------------------ + # TODO add climate and dated seqeunce functionality in here + if (!is.null(clim_base)) { + # Output standard clim file + cat("===== Wrote clim base station file =====\n") + write.table(clim_base, file = hdr_files$base_stations, row.names = FALSE, col.names = FALSE, quote = FALSE, sep = " ") + + } + + # ------------------------------ Header file ------------------------------ + # TODO add check for single path to existing hdr file + world_hdr_name_out = make_hdr_file2(input_rhessys, hdr_files, def_files, runID) + + # ------------------------------ Temporal event control (tec) file ------------------------------ + if (!is.null(tec_data)) { + write.table(tec_data, file = input_rhessys$tec_file, col.names = FALSE, row.names = FALSE, quote = FALSE) + cat("===== Wrote tec file =====\n") + } + + # ------------------------------ Output Filters ------------------------------ + if (!is.null(output_filter)) { + filter_path = write_output_filter(output_filter, runID) + output_path = NULL + + } else { + output_path = file.path(input_rhessys$output_folder, input_rhessys$output_filename) + if (!is.null(runID)) { + output_path = paste0(output_path, "_run", runID) + } + filter_path = NULL + } + + + cat("\n-------------------------------------------\n") + cat("===== Finished RHESSysIO file writing =====\n") + cat("-------------------------------------------\n\n") + + + # ------------------------------ Call RHESSys ------------------------------ + rhessys_command(rhessys_version = input_rhessys$rhessys_version, + world_file = input_rhessys$world_file, + world_hdr_file = world_hdr_name_out, + tec_file = input_rhessys$tec_file, + flow_file = input_rhessys$flow_file, + start_date = input_rhessys$start_date, + end_date = input_rhessys$end_date, + output_file = output_path, + input_parameters = std_pars_out, + output_filter = filter_path, + command_options = input_rhessys$command_options, + prefix_command = input_rhessys$prefix_command) + + if (!is.null(runID)) { + cat("\n===== Wrote output to: '",output_path ,"' =====\n", sep = "") + } + + # ------------------------------ Process Output ------------------------------ + data_out = output_control(output_method, + output_variables, + return_data) + + if (return_data) { + return(data_out) + } + return() + +} diff --git a/R/select_output_variables_R.R b/R/select_output_variables_R.R index 390d871..f1b321c 100644 --- a/R/select_output_variables_R.R +++ b/R/select_output_variables_R.R @@ -2,17 +2,30 @@ #' #' Somewhat optimized R-based read and subsetting of RHESSys output #' -#' @param output_variables Datafrane with named columns: "variables" containing variables matching variables of interest +#' @param output_variables Datafrane with named columns: "variables" containing variables of interest #' found in the header of rhessys output files, "out_file" points to the files containing the associated variables, -#' this can be either the path to that file, can use the abbreviation for the different output types (patch daily = pd, patch daily grow = pdg etc.) -#' and the files in output_folder will be parsed appropriately, or can use the fully written out space.time suffix, e.g. "patch.daily" or "grow_patch.daily" +#' this can be either the path to that file, can use the abbreviation for the different output types +#' (patch daily = pd, patch daily grow = pdg etc.) and the files in output_folder will be parsed appropriately, +#' or can use the fully written out space.time suffix, e.g. "patch.daily" or "grow_patch.daily" #' @param output_folder Folder where rhessys output is located (e.g. 'out') +#' @param output_filename Base file name of standard rhessys output #' @param run Simulation number. Used to reset files in allsim at beginning of simulation +#' @param max_run Max number of runs to collect output for - at run == max run, output will be pivoted from long to wide, +#' and date and spatial info will be added. #' @param return_data TRUE/FALSE if the function should return a data.table of the selected output - for now only works if doing 1 run #' @param out Output location, if not will use default "allsim" within output folder +#' @param no_write TRUE/FALSE to only return data within R, and not write any data. Only works is return_data == TRUE #' @export -select_output_variables_R <- function(output_variables, output_folder, output_filename, run, max_run = NULL, return_data = FALSE, out = NULL, no_write = FALSE) { +select_output_variables_R <- + function(output_variables, + output_folder, + output_filename, + run, + max_run = NULL, + return_data = FALSE, + out = NULL, + no_write = FALSE) { # could get rid of this but its the main difference from the other select functions so it's probably worthwhile if (is.null(max_run) && run == 1) { @@ -23,7 +36,6 @@ select_output_variables_R <- function(output_variables, output_folder, output_fi dir.create(file.path(output_folder, "allsim")) } - sufs = c("grow_basin.hourly", "basin.hourly", "grow_hillslope.hourly", "hillslope.hourly", "grow_zone.hourly", "zone.hourly", "grow_patch.hourly", "patch.hourly", "grow_stratum.hourly", "stratum.hourly", "grow_basin.daily", @@ -44,50 +56,58 @@ select_output_variables_R <- function(output_variables, output_folder, output_fi "cy", "fh", "fd", "fm", "fy") if (all(output_variables$out_file %in% sufs)) { - files_in = file.path(output_folder, paste0(output_filename, "_", output_variables$out_file)) - if (any(!file.exists(files_in))) stop(paste0("Cannot find ", files_in[!file.exists(files_in)])) + files_in = file.path(output_folder, + paste0(output_filename, "_", output_variables$out_file)) + if (any(!file.exists(files_in))) + stop(paste0("Cannot find ", files_in[!file.exists(files_in)])) + } else if (all(output_variables$out_file %in% abrevs)) { files_in = file.path(output_folder, paste0(output_filename, "_", sufs[match(output_variables$out_file, abrevs)])) - if (any(!file.exists(files_in))) stop(paste0("Cannot find ", files_in[!file.exists(files_in)])) - } else { # probs should add a check for if file exists etc. - need to double check on time penalty though + if (any(!file.exists(files_in))) + stop(paste0("Cannot find ", files_in[!file.exists(files_in)])) + + } else { + # probs should add a check for if file exists etc. - need to double check on time penalty though files_in = output_variables$out_file - if (any(!file.exists(files_in))) stop(paste0("Cannot find ", files_in[!file.exists(files_in)])) + if (any(!file.exists(files_in))) + stop(paste0("Cannot find ", files_in[!file.exists(files_in)])) } - files_out = file.path(output_folder,"allsim", output_variables$variable) + files_out = file.path(output_folder, "allsim", output_variables$variable) - if (run == 1){ + if (run == 1) { z = suppressWarnings(file.remove(files_out)) cat("\nWriting selection(s) to file(s):\n") - cat(noquote(paste0("> ", files_out," \n"))) - #system(sprintf("echo > %s/allsim/%s", output_folder, output_variables$variable[dd])) # I think this is just to print what is being output? + cat(noquote(paste0("> ", files_out, " \n"))) } + # read files files_read = unique(files_in) file_index = match(files_in, files_read) read_data = lapply(files_read, data.table::fread) - # no error checking rn, should add something - data_subset = lapply(seq_along(file_index), function(X) data.table:::subset.data.table(read_data[[file_index[X]]], select = output_variables$variable[X])) + # subset the output vars - no error checking rn, should add something + data_subset = lapply(seq_along(file_index), function(X) + data.table:::subset.data.table(read_data[[file_index[X]]], select = output_variables$variable[X])) + if (no_write && !return_data) { + warning("'no_write' argument requires 'return_data == TRUE', no data written or returned") + return() + } if (return_data && no_write) { return(data_subset) } if (run == 1) { - data_subset = lapply(seq_along(files_out), function(X) {colnames(data_subset[[X]]) = paste0(output_variables$variable[X],"_",run); data_subset[[X]]}) - z = lapply(seq_along(files_out), function(X) data.table::fwrite(data_subset[[X]], files_out[X])) + data_subset = lapply(seq_along(files_out), function(X) { + colnames(data_subset[[X]]) = paste0(output_variables$variable[X], "_", run) + data_subset[[X]] + }) + z = lapply(seq_along(files_out), function(X) + data.table::fwrite(data_subset[[X]], files_out[X])) } else { - - # OLD - # read_append = lapply(files_out, data.table::fread) - # data_append = function(X) { - # data.table::fwrite(read_append[[X]][, data.table::set(x = read_append[[X]], j = paste0(output_variables$variable[X],"_",run), value = data_subset[[X]])], files_out[X]) - # } - # z = lapply(seq_along(files_out), data_append) - - # FASTER - appends in a single col, optionally collects and renames at end (see below) + # appends in a single col, optionally collects and renames at end (see below) data_append = function(X) { data.table::fwrite(data_subset[[X]], files_out[X], append = TRUE) return() @@ -106,7 +126,17 @@ select_output_variables_R <- function(output_variables, output_folder, output_fi # get matching columns out_vars = colnames(read_data[[file_index[i]]])[colnames(read_data[[file_index[i]]]) %in% - c("day", "month", "year", "basinID", "hillID", "zoneID", "patchID", "stratumID", "area")] + c( + "day", + "month", + "year", + "basinID", + "hillID", + "zoneID", + "patchID", + "stratumID", + "area" + )] # get date from normal output of respective spatial level, cbind date w output date_subset = data.table:::subset.data.table(read_data[[file_index[i]]], select = out_vars) @@ -125,6 +155,7 @@ select_output_variables_R <- function(output_variables, output_folder, output_fi if (return_data && run == 1) { return(data_subset) } + return() } diff --git a/R/utils.R b/R/utils.R new file mode 100644 index 0000000..3ea85db --- /dev/null +++ b/R/utils.R @@ -0,0 +1,22 @@ +# file to contain small utility functions that don't need to be exposed to users (not exported) +# +# ---------- Function to test if filter is valid ---------- +valid_filter = function(f) { + # assumes f is the already indexed into object, so names(f) is 'timestamp', 'output', etc., not 'filter' + if (any(!c('timestep', 'output') %in% names(f))) { + stop("Filter object is missing: ", c('timestep', 'output')[!c('timestep', 'output') %in% names(f)]) + } + if (any(!c('format', 'path', 'filename') %in% names(f$output))) { + stop("Filter object is missing output sub item: ", c('format', 'path', 'filename')[!c('format', 'path', 'filename') %in% names(f$output)]) + } + + if (all(!c('basin', 'hillslope', 'zone', 'patch', 'stratum') %in% names(f) )) { + stop("Filter object is missing the spatial level. Can be: 'basin', 'hillslope', 'zone', 'patch', 'stratum'.") + } + spatial = which(names(f) %in% c('basin', 'hillslope', 'zone', 'patch', 'stratum')) + if (any(!c('ids', 'variables') %in% names(f[[spatial]]))) { + stop("Filter object is missing spatial level sub item: ", c('ids', 'variables')[!c('ids', 'variables') %in% names(f[[spatial]])]) + } + return(TRUE) + +} diff --git a/R/watbal_basin.R b/R/watbal_basin.R index b84e33b..2e82cbd 100644 --- a/R/watbal_basin.R +++ b/R/watbal_basin.R @@ -31,7 +31,6 @@ watbal_basin = function(bd) { # fluxes minus stores bd$watbal = with(bd, watbal_flux + sddiff - snodiff - detdiff - litdiff - candiff - gwdiff) - bd$watbal[1] = 0.0 # max(bd$watbal) # summary(bd$watbal) diff --git a/R/watbal_basin_of.R b/R/watbal_basin_of.R new file mode 100644 index 0000000..1173535 --- /dev/null +++ b/R/watbal_basin_of.R @@ -0,0 +1,47 @@ +#' watbal_basin_of.R +#' +#' Water balance for basin daily RHESSys output, as generated by outputfilters. To run, if your basin output is called "bd" type "bd=watbal(bd)". +#' This will add a number of fields to your basin output file, the last of which will be called "watbal". +#' This is your water balance error. You should see a minor numerical error here even if your water balances +#' (on the order of 10^-6). If your watbal values are negative then water inputs are less than water outputs, and vice versa. +#' @param bd The basin daily outputs from rhessys, most easily retrieved via `readin_rhessys_output()` +#' @export + +watbal_basin_of = function(bd) { + + # some error checks here + req_cols = c("total_water_in", "evaporation", "evaporation_surf", "exfiltration_sat_zone", + "exfiltration_unsat_zone", "transpiration_sat_zone", "transpiration_unsat_zone", "streamflow", "gw.Qout", "trans", "evap", "sat_deficit", "rz_storage", "unsat_storage", + "detention_store", "litter.rain_stored", "gw.storage","rain_stored", "snow_stored","snowpack.water_equivalent_depth") + + bd$evap = with(bd, evaporation+evaporation_surf+exfiltration_sat_zone+exfiltration_unsat_zone) + bd$trans = with(bd, transpiration_unsat_zone+transpiration_sat_zone ) + bd$streamflow = with(bd, streamflow+gw.Qout) + bd$canopy_store = with(bd, snow_stored+rain_stored ) + if (!is.data.frame(bd) || any(!req_cols %in% colnames(bd))) { + cat("Input is either not a data frame or is missing the correct columns") + return(NA) + } + + # main fluxes + bd$watbal_flux = with(bd, total_water_in - streamflow - trans - evap) + + # changes in stores + bd$sd = with(bd, sat_deficit - rz_storage - unsat_storage) + bd$sddiff = c(0, diff(bd$sd)) + bd$snodiff = c(0, diff(bd$snowpack.water_equivalent_depth)) + bd$detdiff = c(0, diff(bd$detention_store)) + bd$litdiff = c(0, diff(bd$litter.rain_stored)) + bd$candiff = c(0, diff(bd$canopy_store)) + bd$gwdiff = c(0, diff(bd$gw.storage)) + + # fluxes minus stores + bd$watbal = with(bd, watbal_flux + sddiff - snodiff - detdiff - litdiff - candiff - gwdiff) + bd$watbal[1] = 0.0 + # max(bd$watbal) + # summary(bd$watbal) + # hist(bd$watbal) + + return(bd) + +} diff --git a/R/write_output_filter.R b/R/write_output_filter.R new file mode 100644 index 0000000..199daeb --- /dev/null +++ b/R/write_output_filter.R @@ -0,0 +1,58 @@ +#' write_output_filter +#' +#' Writes an output filter file based on an input R list containing the needed elements. +#' @inheritParams run_rhessys_single +#' +#' @author Will Burke +#' @export + +write_output_filter = function(output_filter, runID = NULL) { + + # if it's just a path to an existing filter for a single run + if (is.character(output_filter) && is.null(runID)) { + return(output_filter) + + } else if (is.character(output_filter) && !is.null(runID)) { + # if it's a path but there's multi runs - need to read in so output name can be iterated + file_name = output_filter + output_filter = read_output_filter(output_filter) + + } + # if it's an r list object + # if there's a file name, remove it + file_name = NULL + if ("file_name" %in% names(output_filter)) { + file_name = output_filter[[which(names(output_filter) == "file_name")]] + output_filter = output_filter[-which(names(output_filter) == "file_name")] + } + # test the filters are valid + testvalid = lapply(X = output_filter, FUN = valid_filter) + # check for and remove duplicates + if (any(duplicated(output_filter))) { + output_filter = output_filter[!duplicated(output_filter)] + } + # check if a file name was given, otherwise autogen - can add unique id if we want + if (is.null(file_name)) { + file_name = "output_filter" + } + # add run ID to output if needed + if (!is.null(runID)) { + output_filter = lapply(output_filter, FUN = function(X, runID) {X$output$filename = paste0(X$output$filename, "_", runID); return(X)}, runID = runID) + file_name = paste0(file_name, "_", runID) + } + # write the output filter + #yaml::write_yaml(x = output_filter, file = file_name) + + # workaround beacuse brians code assumes integers + yaml_out = yaml::as.yaml(x = output_filter) + yaml_out = gsub("\\.0", "", yaml_out) + + file = file(file_name, "w") + cat(yaml_out, file = file, sep = "") + close(file) + + cat("===== Wrote output filter file =====\n") + + return(file_name) + +} diff --git a/RHESSysIOinR.Rproj b/RHESSysIOinR.Rproj index 488ba32..f0d6187 100644 --- a/RHESSysIOinR.Rproj +++ b/RHESSysIOinR.Rproj @@ -1,21 +1,21 @@ -Version: 1.0 - -RestoreWorkspace: Default -SaveWorkspace: Default -AlwaysSaveHistory: Default - -EnableCodeIndexing: Yes -UseSpacesForTab: Yes -NumSpacesForTab: 2 -Encoding: UTF-8 - -RnwWeave: Sweave -LaTeX: pdfLaTeX - -AutoAppendNewline: Yes -StripTrailingWhitespace: Yes - -BuildType: Package -PackageUseDevtools: Yes -PackageInstallArgs: --no-multiarch --with-keep.source -PackageRoxygenize: rd,collate,namespace,vignette +Version: 1.0 + +RestoreWorkspace: Default +SaveWorkspace: Default +AlwaysSaveHistory: Default + +EnableCodeIndexing: Yes +UseSpacesForTab: Yes +NumSpacesForTab: 2 +Encoding: UTF-8 + +RnwWeave: Sweave +LaTeX: pdfLaTeX + +AutoAppendNewline: Yes +StripTrailingWhitespace: Yes + +BuildType: Package +PackageUseDevtools: Yes +PackageInstallArgs: --no-multiarch --with-keep.source +PackageRoxygenize: rd,collate,namespace,vignette diff --git a/inst/extdata/clim/w8_base b/inst/extdata/clim/w8_base new file mode 100644 index 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a/inst/extdata/defs/soil_sandyloam.def b/inst/extdata/defs/soil_sandyloam.def new file mode 100644 index 0000000..3b68155 --- /dev/null +++ b/inst/extdata/defs/soil_sandyloam.def @@ -0,0 +1,32 @@ + + + +3.000000 patch_default_ID +2.000000 theta_psi_curve +3.000000 Ksat_0 +0.120000 m +0.454380 porosity_0 +4000.000000 porosity_decay +0.000000 P3 +0.195750 pore_size_index +0.798750 psi_air_entry +0.010000 psi_max +200.000000 soil_depth +0.400000 m_z +0.000000 detention_store_size +1.000000 deltaZ +10.000000 active_zone_z +-10.000000 maximum_snow_energy_deficit +0.000000 snow_water_capacity +10000.000000 snow_light_ext_coef +0.050000 snow_melt_Tcoef +0.000000 max_heat_capacity +0.000000 min_heat_capacity +0.280000 albedo +0.000000 NO3_adsorption_rate +0.120000 N_decay +0.700000 sand +0.100000 clay +0.200000 silt +0.0 sat_to_gw_coeff +0.5 nitrif_parm_smax \ No newline at end of file diff --git a/inst/extdata/defs/veg_douglasfir.def b/inst/extdata/defs/veg_douglasfir.def new file mode 100644 index 0000000..3242864 --- /dev/null +++ b/inst/extdata/defs/veg_douglasfir.def @@ -0,0 +1,139 @@ +7.000000 stratum_default_ID +TREE epc.veg.type +0.800000 K_absorptance +0.100000 K_reflectance +0.100000 K_transmittance +1.000000 PAR_absorptance +0.000000 PAR_reflectance +0.000000 PAR_transmittance +0.683700 epc.ext_coef +0.000215 specific_rain_capacity +0.000240 specific_snow_capacity +0.002000 wind_attenuation_coef +-999.900000 ustar_overu +1.500000 mrc.q10 +0.210000 mrc.per_N +0.200000 epc.gr_perc +1.000000 lai_stomatal_fraction +0.386300 epc.flnr +0.030000 epc.ppfd_coef +15.000000 epc.topt +40.000000 epc.tmax +0.200000 epc.tcoef +-0.650000 epc.psi_open +-4.599000 epc.psi_close +0.000000 epc.vpd_open +6419.200000 epc.vpd_close +0.004924 epc.gl_smax +0.000060 epc.gl_c +0.000000 gsurf_slope +1000000.000000 gsurf_intercept +static epc.phenology_flag +EVERGREEN epc.phenology.type +12.000000 epc.max_lai +8.708000 epc.proj_sla +2.600000 epc.lai_ratio +1.400000 epc.proj_swa +0.239700 epc.leaf_turnover +91.000000 epc.day_leafon +260.000000 epc.day_leafoff +30.000000 epc.ndays_expand +30.000000 epc.ndays_litfall +64.245000 epc.leaf_cn +70.000000 epc.leaflitr_cn +0.000000 min_heat_capacity +0.000000 max_heat_capacity +combined epc.allocation_flag +0.368750 epc.storage_transfer_prop +0.270000 epc.froot_turnover +0.093426 epc.livewood_turnover +0.010000 epc.kfrag_base +0.005000 epc.max_daily_mortality +0.005000 epc.min_daily_mortality +0.000000 epc.daily_mortality_threshold +139.700000 epc.froot_cn +200.000000 epc.livewood_cn +0.310000 epc.leaflitr_flab +0.450000 epc.leaflitr_fcel +0.240000 epc.leaflitr_flig +0.230000 epc.frootlitr_flab +0.410000 epc.frootlitr_fcel +0.360000 epc.frootlitr_flig +0.520000 epc.deadwood_fcel +0.480000 epc.deadwood_flig +0.672900 epc.alloc_frootc_leafc +0.300000 epc.alloc_crootc_stemc +1.620000 epc.alloc_stemc_leafc +0.658720 epc.alloc_frootc_crootc +0.073000 epc.alloc_livewoodc_woodc +0.050000 epc.maxlgf +0.500000 epc.alloc_prop_day_growth +0.000000 epc.daily_fire_turnover +0.570000 epc.height_to_stem_exp +0.198800 epc.height_to_stem_coef +0.010165 epc.branch_turnover +0 epc.Tacclim +0.7 epc.root_growth_direction +24.015000 epc.root_distrib_parm +0.126700 epc.waring_pa +0.572500 epc.waring_pb +0.001622 epc.cpool_mort_fract +0.003219 epc.min_percent_leafg +0.245520 epc.max_storage_percent +0.013388 epc.min_leaf_carbon +0.008178 epc.resprout_leaf_carbon +0.295300 epc.netpabs_age_mult +0.425010 epc.netpabs +9999.000000 epc.netpabs_sunlit +9999.000000 epc.netpabs_shade +0.043800 epc.flnr_age_mult +9999.000000 epc.flnr_sunlit +9999.000000 epc.flnr_shade +9999.000000 epc.gl_smax_sunlit +9999.000000 epc.gl_smax_shade +0 epc.dyn_alloc_prop_day_growth +100 epc.max_years_resprout +0.000000 epc.litter_gsurf_slope +100000000.000000 epc.litter_gsurf_intercept +1.000000 epc.coef_CO2 +2.000000 epc.max_root_depth #was8.721000 +0.600000 epc.crown_ratio +1.500000 epc.max_stem_density +0.030000 epc.resprout_stem_density +1.000000 understory_mort +1.000000 consumption +-10.000000 overstory_mort_k1 +1.000000 overstory_mort_k2 +-2.000000 epc.gs_tmin +5.000000 epc.gs_tmax +900.000000 epc.gs_vpd_min +4100.000000 epc.gs_vpd_max +36000.000000 epc.gs_dayl_min +39600.000000 epc.gs_dayl_max +-15.000000 epc.gs_psi_min +-14.000000 epc.gs_psi_max +6.000000 epc.gs_ravg_days +0.500000 epc.gsi_thresh +1.000000 epc.gs_npp_on +187.000000 epc.gs_npp_slp +197.000000 epc.gs_npp_intercpt +0.250000 epc.dickenson_pa +3.220000 epc.Tacclim_intercpt +0.046000 epc.Tacclim_slp +30 epc.Tacclim_days +0.000583 epc.litter_moist_coef +50.000000 epc.litter_density +0 epc.nfix +1 epc.edible +0 epc.psi_curve +-1.000000 epc.psi_threshold +0.200000 epc.psi_slp +1.000000 epc.psi_intercpt +0.000600 epc.gxylem_min_gs +0.004000 epc.gxylem_max +-9999.000000 epc.LWP_gxylem_min +0.000400 epc.gxylem_recovery_rate +4.080000 epc.gxylem_csat +-3.470000 epc.gxylem_bsat +0 epc.alternative_ra_surface +1 epc.zero_turnover_sprouts diff --git a/inst/extdata/defs/zone.def b/inst/extdata/defs/zone.def new file mode 100644 index 0000000..6c4951e --- /dev/null +++ b/inst/extdata/defs/zone.def @@ -0,0 +1,17 @@ + +1.000000 zone_default_ID +0.000029 atm_trans_lapse_rate +0.001500 dewpoint_lapse_rate +10.000000 max_effective_lai +0.006400 lapse_rate +0.025400 pptmin +0.750000 sea_level_clear_sky_trans +0.400000 temcf +0.003000 trans_coeff1 +2.200000 trans_coeff2 +1.000000 wind +1.000000 max_snow_temp +0.000000 min_rain_temp +0.031600 n_deposition +180.000000 wind_direction +-0.005053 lapse_rate_precip_default \ No newline at end of file diff --git a/inst/extdata/flowtables/w8TC.flow b/inst/extdata/flowtables/w8TC.flow new file mode 100644 index 0000000..73e2a5e --- /dev/null +++ b/inst/extdata/flowtables/w8TC.flow @@ -0,0 +1,1975 @@ +1 +74 247 +2362 2362 74 32 48 1175 900 900 0 199.0297 2 + 2437 2437 74 0.1531057 + 2438 2438 74 0.8468943 +2438 2438 74 33 48.5 1168 1800 1800 0 515.059 6 + 2437 2437 74 0.1545977 + 2513 2513 74 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/dev/null +++ b/inst/extdata/tecfiles/tec.test @@ -0,0 +1,2 @@ +1989 10 1 1 print_daily_on +1989 10 1 2 print_daily_growth_on diff --git a/inst/extdata/tecfiles/test_output_filter.yml b/inst/extdata/tecfiles/test_output_filter.yml new file mode 100644 index 0000000..0e380d1 --- /dev/null +++ b/inst/extdata/tecfiles/test_output_filter.yml @@ -0,0 +1,9 @@ +filter: + timestep: daily + output: + format: csv + path: ./out + filename: basin_daily + basin: + ids: 1 + variables: patch.total_water_in, patch.streamflow diff --git a/inst/extdata/tecfiles/w8TC.tec b/inst/extdata/tecfiles/w8TC.tec new file mode 100644 index 0000000..9a3bcda --- /dev/null +++ b/inst/extdata/tecfiles/w8TC.tec @@ -0,0 +1,3 @@ +1998 10 1 1 print_daily_on +1998 10 1 2 print_daily_growth_on +2000 10 0 1 output_current_state diff --git a/inst/extdata/worldfiles/w8TC.hdr b/inst/extdata/worldfiles/w8TC.hdr new file mode 100644 index 0000000..ac3a0d8 --- /dev/null +++ b/inst/extdata/worldfiles/w8TC.hdr @@ -0,0 +1,15 @@ + +1 +defs/basin.def +1 +defs/hill.def +1 +defs/zone.def zone_default_filename +1 +defs/soil_sandyloam.def +1 +defs/lu_undev.def +1 +defs/veg_douglasfir.def veg_default_filename +1 +clim/w8_base diff --git a/inst/extdata/worldfiles/w8TC.world b/inst/extdata/worldfiles/w8TC.world new file mode 100644 index 0000000..581c14e --- /dev/null +++ b/inst/extdata/worldfiles/w8TC.world @@ -0,0 +1,26449 @@ + +1 world_ID +1 num_basins + 1 basin_ID + 0.00000000 x + 0.00000000 y + 1067.13684211 z + 1 basin_parm_ID + 47.05000000 latitude + 0 basin_n_basestations + 1 num_hillslopes + 74 hillslope_ID + 0.00000000 x + 0.00000000 y + 1067.13684211 z + 1 hill_parm_ID + 0.00000000 gw.storage + 0.00000000 gw.NO3 + 0 hillslope_n_basestations + 247 num_zones + 2362 zone_ID + 0.00000000 x + 0.00000000 y + 1175.00000000 z + 1 zone_parm_ID + 900.00000000 area + 14.51357651 slope + 236.82148743 aspect + 1.00000000 precip_lapse_rate + 0.18899960 e_horizon + 0.18899960 w_horizon + 1 zone_n_basestations + 101 zone_basestation_ID + 1 num_patches + 2362 patch_ID + 0.00000000 x + 0.00000000 y + 1175.00000000 z + 3 soil_parm_ID + 1 landuse_parm_ID + 900.00000000 area + 14.51357651 slope + 7.00000000 lna + 1.00000000 Ksat_vertical + 0.00000000 mpar + 0.54070120 rz_storage + 1.97346326 unsat_storage + 3.95176867 sat_deficit + 0.00000000 snowpack.water_equivalent_depth + 0.00000000 snowpack.water_depth + 0.00000000 snowpack.T + 0.00000000 snowpack.surface_age + 0.00100000 snowpack.energy_deficit + 1.00000000 litter.cover_fraction + 0.00098831 litter.rain_stored + 0.03206641 litter_cs.litr1c + 0.00099888 litter_ns.litr1n + 0.19713304 litter_cs.litr2c + 0.75813213 litter_cs.litr3c + 0.69585706 litter_cs.litr4c + 0.05080418 soil_cs.soil1c + 0.00007218 soil_ns.sminn + 0.00212758 soil_ns.nitrate + 0.42765037 soil_cs.soil2c + 5.88077408 soil_cs.soil3c + 34.56363238 soil_cs.soil4c + 0 patch_n_basestations + 1 num_canopy_strata + 23621 canopy_strata_ID + 7 veg_parm_ID + 1.00000000 cover_fraction + 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0.01832676 ns.leafn + 0.00000000 ns.dead_leafn + 0.00485333 ns.leafn_store + 0.00000000 ns.leafn_transfer + 0.00279744 ns.live_stemn + 0.00032995 ns.livestemn_store + 0.00000000 ns.livestemn_transfer + 0.16073437 ns.dead_stemn + 0.00226482 ns.deadstemn_store + 0.00000000 ns.deadstemn_transfer + 0.00044073 ns.live_crootn + 0.00003526 ns.livecrootn_store + 0.00000000 ns.livecrootn_transfer + 0.03363417 ns.dead_crootn + 0.00024205 ns.deadcrootn_store + 0.00000000 ns.deadcrootn_transfer + 0.00652529 ns.frootn + 0.00063975 ns.frootn_store + 0.00000000 ns.frootn_transfer + -0.13375705 ns.cwdn + 0.00011320 ns.retransn + 489.00000000 cs.age + 0 epv.wstress_days + 0.00000000 epv.max_fparabs + 0.37292257 epv.min_vwc + 0 canopy_strata_n_basestations \ No newline at end of file diff --git a/inst/extdata/worldfiles/w8TC.world.Y2000M9D30H1.state b/inst/extdata/worldfiles/w8TC.world.Y2000M9D30H1.state new file mode 100644 index 0000000..9c559ac --- /dev/null +++ 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ns.retransn + 490.00000000 cs.age + 0 epv.wstress_days + 0.00000000 epv.max_fparabs + 0.00000000 epv.min_vwc + 0 canopy_strata_n_basestations + 4118 zone_ID + 0.00000000 x + 0.00000000 y + 981.00000000 z + 1 zone_parm_ID + 900.00000000 area + 12.26014709 slope + 265.60128784 aspect + 1.00000000 precip_lapse_rate + 0.18519787 e_horizon + 0.18519787 w_horizon + 1 zone_n_basestations + 101 zone_basestation_ID + 1 num_patches + 4118 patch_ID + 0.00000000 x + 0.00000000 y + 981.00000000 z + 3 soil_parm_ID + 1 landuse_parm_ID + 900.00000000 area + 12.26014709 slope + 7.00000000 lna + 1.00000000 Ksat_vertical + 0.00000000 mpar + 0.36089743 rz_storage + 0.00000000 unsat_storage + 0.81975266 sat_deficit + 0.00000000 snowpack.water_equivalent_depth + 0.00000000 snowpack.water_depth + 0.00000000 snowpack.T + 0.00000000 snowpack.surface_age + 0.00100000 snowpack.energy_deficit + 1.00000000 litter.cover_fraction + 0.00000000 litter.rain_stored + 0.01442785 litter_cs.litr1c + 0.00045414 litter_ns.litr1n + 0.17730891 litter_cs.litr2c + 0.63393172 litter_cs.litr3c + 0.66521909 litter_cs.litr4c + 0.04485138 soil_cs.soil1c + 0.00002840 soil_ns.sminn + 0.00123794 soil_ns.nitrate + 0.34485097 soil_cs.soil2c + 5.01992999 soil_cs.soil3c + 29.33684769 soil_cs.soil4c + 0 patch_n_basestations + 1 num_canopy_strata + 41181 canopy_strata_ID + 7 veg_parm_ID + 1.00000000 cover_fraction + 0.00000000 gap_fraction + 2.00000000 rootzone.depth + 0.00000000 snow_stored + 0.02000000 cs.stem_density + 0.00000000 rain_stored + 23.83289158 cs.cpool + 0.33601842 cs.leafc_age1 + 0.89653866 cs.leafc_age2 + 1.04485167 cs.leafc + 0.00000000 cs.dead_leafc + 0.35839493 cs.leafc_store + 0.00000000 cs.leafc_transfer + 0.52195955 cs.live_stemc + 0.05439177 cs.livestemc_store + 0.00000000 cs.livestemc_transfer + 57.66818069 cs.dead_stemc + 0.69070098 cs.deadstemc_store + 0.00000000 cs.deadstemc_transfer + 0.07731804 cs.live_crootc + 0.00732498 cs.livecrootc_store + 0.00000000 cs.livecrootc_transfer + 11.78148058 cs.dead_crootc + 0.09301720 cs.deadcrootc_store + 0.00000000 cs.deadcrootc_transfer + 0.69498892 cs.frootc + 0.10292360 cs.frootc_store + 0.00000000 cs.frootc_transfer + 1.04629701 cs.cwdc + 1.19962369 epv.prev_leafcalloc + 0.41792842 ns.npool + 0.01626355 ns.leafn + 0.00000000 ns.dead_leafn + 0.00557857 ns.leafn_store + 0.00000000 ns.leafn_transfer + 0.00260980 ns.live_stemn + 0.00027196 ns.livestemn_store + 0.00000000 ns.livestemn_transfer + 0.15585995 ns.dead_stemn + 0.00186676 ns.deadstemn_store + 0.00000000 ns.deadstemn_transfer + 0.00038659 ns.live_crootn + 0.00003662 ns.livecrootn_store + 0.00000000 ns.livecrootn_transfer + 0.03184184 ns.dead_crootn + 0.00025140 ns.deadcrootn_store + 0.00000000 ns.deadcrootn_transfer + 0.00497486 ns.frootn + 0.00073675 ns.frootn_store + 0.00000000 ns.frootn_transfer + -0.12400005 ns.cwdn + 0.00004285 ns.retransn + 490.00000000 cs.age + 0 epv.wstress_days + 0.00000000 epv.max_fparabs + 0.00000000 epv.min_vwc + 0 canopy_strata_n_basestations + 4193 zone_ID + 0.00000000 x + 0.00000000 y + 976.00000000 z + 1 zone_parm_ID + 900.00000000 area + 10.53989124 slope + 235.95405579 aspect + 1.00000000 precip_lapse_rate + 0.18421960 e_horizon + 0.18421960 w_horizon + 1 zone_n_basestations + 101 zone_basestation_ID + 1 num_patches + 4193 patch_ID + 0.00000000 x + 0.00000000 y + 976.00000000 z + 3 soil_parm_ID + 1 landuse_parm_ID + 900.00000000 area + 10.53989124 slope + 7.00000000 lna + 1.00000000 Ksat_vertical + 0.00000000 mpar + 0.18751504 rz_storage + 0.00000000 unsat_storage + 0.57813156 sat_deficit + 0.00000000 snowpack.water_equivalent_depth + 0.00000000 snowpack.water_depth + 0.00000000 snowpack.T + 0.00000000 snowpack.surface_age + 0.00100000 snowpack.energy_deficit + 1.00000000 litter.cover_fraction + 0.00000000 litter.rain_stored + 0.03303834 litter_cs.litr1c + 0.00104685 litter_ns.litr1n + 0.23658347 litter_cs.litr2c + 0.67041201 litter_cs.litr3c + 0.83611892 litter_cs.litr4c + 0.03562221 soil_cs.soil1c + 0.00014970 soil_ns.sminn + 0.00077108 soil_ns.nitrate + 0.35774926 soil_cs.soil2c + 5.03253629 soil_cs.soil3c + 29.00916787 soil_cs.soil4c + 0 patch_n_basestations + 1 num_canopy_strata + 41931 canopy_strata_ID + 7 veg_parm_ID + 1.00000000 cover_fraction + 0.00000000 gap_fraction + 2.00000000 rootzone.depth + 0.00000000 snow_stored + 0.02000000 cs.stem_density + 0.00000000 rain_stored + 23.31077991 cs.cpool + 0.33558276 cs.leafc_age1 + 0.89327452 cs.leafc_age2 + 1.04206499 cs.leafc + 0.00000000 cs.dead_leafc + 0.27044204 cs.leafc_store + 0.00000000 cs.leafc_transfer + 0.50313085 cs.live_stemc + 0.04107293 cs.livestemc_store + 0.00000000 cs.livestemc_transfer + 56.92799567 cs.dead_stemc + 0.52156992 cs.deadstemc_store + 0.00000000 cs.deadstemc_transfer + 0.07524430 cs.live_crootc + 0.00555144 cs.livecrootc_store + 0.00000000 cs.livecrootc_transfer + 11.47942985 cs.dead_crootc + 0.07049571 cs.deadcrootc_store + 0.00000000 cs.deadcrootc_transfer + 0.66718677 cs.frootc + 0.07784467 cs.frootc_store + 0.00000000 cs.frootc_transfer + 1.14546672 cs.cwdc + 1.19239444 epv.prev_leafcalloc + 0.41660719 ns.npool + 0.01622017 ns.leafn + 0.00000000 ns.dead_leafn + 0.00420954 ns.leafn_store + 0.00000000 ns.leafn_transfer + 0.00251566 ns.live_stemn + 0.00020536 ns.livestemn_store + 0.00000000 ns.livestemn_transfer + 0.15385945 ns.dead_stemn + 0.00140965 ns.deadstemn_store + 0.00000000 ns.deadstemn_transfer + 0.00037622 ns.live_crootn + 0.00002776 ns.livecrootn_store + 0.00000000 ns.livecrootn_transfer + 0.03102549 ns.dead_crootn + 0.00019053 ns.deadcrootn_store + 0.00000000 ns.deadcrootn_transfer + 0.00477585 ns.frootn + 0.00055723 ns.frootn_store + 0.00000000 ns.frootn_transfer + -0.11540238 ns.cwdn + 0.00000000 ns.retransn + 490.00000000 cs.age + 0 epv.wstress_days + 0.00000000 epv.max_fparabs + 0.00000000 epv.min_vwc + 0 canopy_strata_n_basestations + 4192 zone_ID + 0.00000000 x + 0.00000000 y + 974.00000000 z + 1 zone_parm_ID + 1800.00000000 area + 9.73792410 slope + 270.30439758 aspect + 1.00000000 precip_lapse_rate + 0.18375768 e_horizon + 0.18375768 w_horizon + 1 zone_n_basestations + 101 zone_basestation_ID + 1 num_patches + 4192 patch_ID + 0.00000000 x + 0.00000000 y + 974.00000000 z + 3 soil_parm_ID + 1 landuse_parm_ID + 1800.00000000 area + 9.73792410 slope + 7.00000000 lna + 1.00000000 Ksat_vertical + 0.00000000 mpar + 0.21685555 rz_storage + 0.00000000 unsat_storage + 0.68284092 sat_deficit + 0.00000000 snowpack.water_equivalent_depth + 0.00000000 snowpack.water_depth + 0.00000000 snowpack.T + 0.00000000 snowpack.surface_age + 0.00100000 snowpack.energy_deficit + 1.00000000 litter.cover_fraction + 0.00000000 litter.rain_stored + 0.01694040 litter_cs.litr1c + 0.00053538 litter_ns.litr1n + 0.18567799 litter_cs.litr2c + 0.64309791 litter_cs.litr3c + 0.70364080 litter_cs.litr4c + 0.04259066 soil_cs.soil1c + 0.00002829 soil_ns.sminn + 0.00111138 soil_ns.nitrate + 0.35118576 soil_cs.soil2c + 5.00721195 soil_cs.soil3c + 28.83857811 soil_cs.soil4c + 0 patch_n_basestations + 1 num_canopy_strata + 41921 canopy_strata_ID + 7 veg_parm_ID + 1.00000000 cover_fraction + 0.00000000 gap_fraction + 2.00000000 rootzone.depth + 0.00000000 snow_stored + 0.02000000 cs.stem_density + 0.00000000 rain_stored + 23.41198784 cs.cpool + 0.33306460 cs.leafc_age1 + 0.89195507 cs.leafc_age2 + 1.03846354 cs.leafc + 0.00000000 cs.dead_leafc + 0.34330045 cs.leafc_store + 0.00000000 cs.leafc_transfer + 0.51261206 cs.live_stemc + 0.05168244 cs.livestemc_store + 0.00000000 cs.livestemc_transfer + 56.81176537 cs.dead_stemc + 0.65629621 cs.deadstemc_store + 0.00000000 cs.deadstemc_transfer + 0.07570559 cs.live_crootc + 0.00700493 cs.livecrootc_store + 0.00000000 cs.livecrootc_transfer + 11.48626868 cs.dead_crootc + 0.08895297 cs.deadcrootc_store + 0.00000000 cs.deadcrootc_transfer + 0.67216131 cs.frootc + 0.09860933 cs.frootc_store + 0.00000000 cs.frootc_transfer + 1.06738832 cs.cwdc + 1.19015617 epv.prev_leafcalloc + 0.41599684 ns.npool + 0.01616412 ns.leafn + 0.00000000 ns.dead_leafn + 0.00534361 ns.leafn_store + 0.00000000 ns.leafn_transfer + 0.00256306 ns.live_stemn + 0.00025841 ns.livestemn_store + 0.00000000 ns.livestemn_transfer + 0.15354531 ns.dead_stemn + 0.00177377 ns.deadstemn_store + 0.00000000 ns.deadstemn_transfer + 0.00037853 ns.live_crootn + 0.00003502 ns.livecrootn_store + 0.00000000 ns.livecrootn_transfer + 0.03104397 ns.dead_crootn + 0.00024041 ns.deadcrootn_store + 0.00000000 ns.deadcrootn_transfer + 0.00481146 ns.frootn + 0.00070586 ns.frootn_store + 0.00000000 ns.frootn_transfer + -0.11750278 ns.cwdn + 0.00003495 ns.retransn + 490.00000000 cs.age + 0 epv.wstress_days + 0.00000000 epv.max_fparabs + 0.00000000 epv.min_vwc + 0 canopy_strata_n_basestations + 4267 zone_ID + 0.00000000 x + 0.00000000 y + 971.00000000 z + 1 zone_parm_ID + 1800.00000000 area + 7.16259575 slope + 258.99311066 aspect + 1.00000000 precip_lapse_rate + 0.18672893 e_horizon + 0.18672893 w_horizon + 1 zone_n_basestations + 101 zone_basestation_ID + 1 num_patches + 4267 patch_ID + 0.00000000 x + 0.00000000 y + 971.00000000 z + 3 soil_parm_ID + 1 landuse_parm_ID + 1800.00000000 area + 7.16259575 slope + 7.00000000 lna + 1.00000000 Ksat_vertical + 0.00000000 mpar + 0.38646132 rz_storage + 0.00000000 unsat_storage + 0.86547644 sat_deficit + 0.00000000 snowpack.water_equivalent_depth + 0.00000000 snowpack.water_depth + 0.00000000 snowpack.T + 0.00000000 snowpack.surface_age + 0.00100000 snowpack.energy_deficit + 1.00000000 litter.cover_fraction + 0.00000000 litter.rain_stored + 0.01256443 litter_cs.litr1c + 0.00039212 litter_ns.litr1n + 0.17211274 litter_cs.litr2c + 0.63556492 litter_cs.litr3c + 0.64306388 litter_cs.litr4c + 0.04748473 soil_cs.soil1c + 0.00002858 soil_ns.sminn + 0.00211456 soil_ns.nitrate + 0.34558557 soil_cs.soil2c + 5.11765093 soil_cs.soil3c + 30.07635524 soil_cs.soil4c + 0 patch_n_basestations + 1 num_canopy_strata + 42671 canopy_strata_ID + 7 veg_parm_ID + 1.00000000 cover_fraction + 0.00000000 gap_fraction + 2.00000000 rootzone.depth + 0.00000000 snow_stored + 0.02000000 cs.stem_density + 0.00000000 rain_stored + 24.59178831 cs.cpool + 0.33978933 cs.leafc_age1 + 0.90403616 cs.leafc_age2 + 1.05440388 cs.leafc + 0.00000000 cs.dead_leafc + 0.36406744 cs.leafc_store + 0.00000000 cs.leafc_transfer + 0.52038691 cs.live_stemc + 0.05667149 cs.livestemc_store + 0.00000000 cs.livestemc_transfer + 58.59329626 cs.dead_stemc + 0.71965026 cs.deadstemc_store + 0.00000000 cs.deadstemc_transfer + 0.07935544 cs.live_crootc + 0.00751846 cs.livecrootc_store + 0.00000000 cs.livecrootc_transfer + 12.16043757 cs.dead_crootc + 0.09547419 cs.deadcrootc_store + 0.00000000 cs.deadcrootc_transfer + 0.74587821 cs.frootc + 0.10475504 cs.frootc_store + 0.00000000 cs.frootc_transfer + 1.03569114 cs.cwdc + 1.21370834 epv.prev_leafcalloc + 0.42025750 ns.npool + 0.01641223 ns.leafn + 0.00000000 ns.dead_leafn + 0.00566686 ns.leafn_store + 0.00000000 ns.leafn_transfer + 0.00260194 ns.live_stemn + 0.00028336 ns.livestemn_store + 0.00000000 ns.livestemn_transfer + 0.15836026 ns.dead_stemn + 0.00194500 ns.deadstemn_store + 0.00000000 ns.deadstemn_transfer + 0.00039678 ns.live_crootn + 0.00003759 ns.livecrootn_store + 0.00000000 ns.livecrootn_transfer + 0.03286605 ns.dead_crootn + 0.00025804 ns.deadcrootn_store + 0.00000000 ns.deadcrootn_transfer + 0.00533914 ns.frootn + 0.00074986 ns.frootn_store + 0.00000000 ns.frootn_transfer + -0.13072515 ns.cwdn + 0.00001119 ns.retransn + 490.00000000 cs.age + 0 epv.wstress_days + 0.00000000 epv.max_fparabs + 0.00000000 epv.min_vwc + 0 canopy_strata_n_basestations + 4340 zone_ID + 0.00000000 x + 0.00000000 y + 966.00000000 z + 1 zone_parm_ID + 900.00000000 area + 9.01550961 slope + 256.32870483 aspect + 1.00000000 precip_lapse_rate + 0.18738711 e_horizon + 0.18738711 w_horizon + 1 zone_n_basestations + 101 zone_basestation_ID + 1 num_patches + 4340 patch_ID + 0.00000000 x + 0.00000000 y + 966.00000000 z + 3 soil_parm_ID + 1 landuse_parm_ID + 900.00000000 area + 9.01550961 slope + 7.00000000 lna + 1.00000000 Ksat_vertical + 0.00000000 mpar + 0.37665025 rz_storage + 0.00000000 unsat_storage + 0.89102230 sat_deficit + 0.00000000 snowpack.water_equivalent_depth + 0.00000000 snowpack.water_depth + 0.00000000 snowpack.T + 0.00000000 snowpack.surface_age + 0.00100000 snowpack.energy_deficit + 1.00000000 litter.cover_fraction + 0.00000000 litter.rain_stored + 0.01292840 litter_cs.litr1c + 0.00040220 litter_ns.litr1n + 0.16685536 litter_cs.litr2c + 0.63125081 litter_cs.litr3c + 0.61216850 litter_cs.litr4c + 0.04789783 soil_cs.soil1c + 0.00004938 soil_ns.sminn + 0.00363080 soil_ns.nitrate + 0.34174128 soil_cs.soil2c + 5.25580982 soil_cs.soil3c + 30.91546136 soil_cs.soil4c + 0 patch_n_basestations + 1 num_canopy_strata + 43401 canopy_strata_ID + 7 veg_parm_ID + 1.00000000 cover_fraction + 0.00000000 gap_fraction + 2.00000000 rootzone.depth + 0.00000000 snow_stored + 0.02000000 cs.stem_density + 0.00000000 rain_stored + 24.65899603 cs.cpool + 0.34043325 cs.leafc_age1 + 0.90920013 cs.leafc_age2 + 1.05932424 cs.leafc + 0.00000000 cs.dead_leafc + 0.37796831 cs.leafc_store + 0.00000000 cs.leafc_transfer + 0.52222509 cs.live_stemc + 0.05972700 cs.livestemc_store + 0.00000000 cs.livestemc_transfer + 59.02264206 cs.dead_stemc + 0.75845107 cs.deadstemc_store + 0.00000000 cs.deadstemc_transfer + 0.08059053 cs.live_crootc + 0.00785380 cs.livecrootc_store + 0.00000000 cs.livecrootc_transfer + 12.36186121 cs.dead_crootc + 0.09973248 cs.deadcrootc_store + 0.00000000 cs.deadcrootc_transfer + 0.76806921 cs.frootc + 0.10887220 cs.frootc_store + 0.00000000 cs.frootc_transfer + 1.01402349 cs.cwdc + 1.22088667 epv.prev_leafcalloc + 0.41823820 ns.npool + 0.01648882 ns.leafn + 0.00000000 ns.dead_leafn + 0.00588323 ns.leafn_store + 0.00000000 ns.leafn_transfer + 0.00261113 ns.live_stemn + 0.00029863 ns.livestemn_store + 0.00000000 ns.livestemn_transfer + 0.15952065 ns.dead_stemn + 0.00204987 ns.deadstemn_store + 0.00000000 ns.deadstemn_transfer + 0.00040295 ns.live_crootn + 0.00003927 ns.livecrootn_store + 0.00000000 ns.livecrootn_transfer + 0.03341043 ns.dead_crootn + 0.00026955 ns.deadcrootn_store + 0.00000000 ns.deadcrootn_transfer + 0.00549799 ns.frootn + 0.00077933 ns.frootn_store + 0.00000000 ns.frootn_transfer + -0.13477773 ns.cwdn + 0.00001149 ns.retransn + 490.00000000 cs.age + 0 epv.wstress_days + 0.00000000 epv.max_fparabs + 0.00000000 epv.min_vwc + 0 canopy_strata_n_basestations \ No newline at end of file diff --git a/inst/extdata/worldfiles/w8TC/w8TC.hdr b/inst/extdata/worldfiles/w8TC/w8TC.hdr new file mode 100644 index 0000000..dfe81a2 --- /dev/null +++ b/inst/extdata/worldfiles/w8TC/w8TC.hdr @@ -0,0 +1,14 @@ +1 num_basin_default_files +defs/basin.def basin_default_file +1 num_hillslope_default_files +defs/hill.def hillslope_default_file +1 num_zone_default_files +defs/zone.def zone_default_file +1 num_soil_default_files +defs/soil_sandyloam.def soil_default_file +1 num_landuse_default_files +defs/lu_undev.def landuse_default_file +1 num_stratum_default_files +defs/veg_douglasfir.def stratum_default_file +1 num_base_stations_files +clim/w8_base base_stations_file diff --git a/man/IOin_clim.Rd b/man/IOin_clim.Rd new file mode 100644 index 0000000..23f7409 --- /dev/null +++ b/man/IOin_clim.Rd @@ -0,0 +1,58 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/IOin_clim.R +\name{IOin_clim} +\alias{IOin_clim} +\title{IOin_clim} +\usage{ +IOin_clim( + base_station_id, + x_coordinate, + y_coordinate, + z_coordinate, + effective_lai, + screen_height, + annual_prefix = "annual", + num_non_critical_annual_sequences = 0, + monthly_prefix = "monthly", + num_non_critical_monthly_sequences = 0, + daily_prefix = "daily", + num_non_critical_daily_sequences = 0, + hourly_prefix = "hourly", + num_non_critical_hourly_sequences = 0 +) +} +\arguments{ +\item{base_station_id}{Base station ID.} + +\item{x_coordinate}{X coordinate.} + +\item{y_coordinate}{Y coordinate.} + +\item{z_coordinate}{Z coordinate.} + +\item{effective_lai}{Effective LAI.} + +\item{screen_height}{Screen height.} + +\item{annual_prefix}{Prefix for annual climate inputs.} + +\item{num_non_critical_annual_sequences}{Number of non critical annual climate inputs. Defaults to 0.} + +\item{monthly_prefix}{Prefix for monthly climate inputs.} + +\item{num_non_critical_monthly_sequences}{Number of non critical annual climate inputs. Defaults to 0.} + +\item{daily_prefix}{Prefix for daily climate inputs.} + +\item{num_non_critical_daily_sequences}{Number of non critical annual climate inputs. Defaults to 0.} + +\item{hourly_prefix}{Prefix for hourly climate inputs.} + +\item{num_non_critical_hourly_sequences}{Number of non critical annual climate inputs. Defaults to 0.} +} +\description{ +Generate input for run_rhessys climate basestation input +} +\author{ +Will Burke +} diff --git a/man/IOin_def_pars_simple.Rd b/man/IOin_def_pars_simple.Rd new file mode 100644 index 0000000..eea9589 --- /dev/null +++ b/man/IOin_def_pars_simple.Rd @@ -0,0 +1,25 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/IOin_def_pars_simple.R +\name{IOin_def_pars_simple} +\alias{IOin_def_pars_simple} +\title{IOin_def_pars_simple} +\usage{ +IOin_def_pars_simple(..., n = 1, pct_range = 0.25, rm_dup = F) +} +\arguments{ +\item{...}{Any number of lists, each containing 3 elements in format: list("", "", )} + +\item{n}{The number of parameter sets to generate.} + +\item{pct_range}{The percent range of variation from input values over which sampling (if any), will happen.} + +\item{rm_dup}{TRUE/FALSE should duplicate def file + variable entries be automatically removed? A warning will occur regardless.} +} +\description{ +The definition file parameters to modify. This input function generates an input parameter object, either for a single simulation, +or using simple random sampling over a set range (based on percent difference from input values). This later functionality can be put into +a seperate funciton later if desired. +} +\author{ +Will Burke +} diff --git a/man/IOin_def_pars_sobol.Rd b/man/IOin_def_pars_sobol.Rd new file mode 100644 index 0000000..511ba3e --- /dev/null +++ b/man/IOin_def_pars_sobol.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/IOin_def_pars_sobol.R +\name{IOin_def_pars_sobol} +\alias{IOin_def_pars_sobol} +\title{IOin_def_pars_sobol} +\usage{ +IOin_def_pars_sobol(..., nboot = 100, rm_dup) +} +\arguments{ +\item{...}{Any number of lists, each containing 3 elements in format: list("", "", )} + +\item{nboot}{The number of bootstraps to run for sobol2007} + +\item{rm_dup}{TRUE/FALSE should duplicate def file + variable entries be automatically removed? A warning will occur regardless.} +} +\description{ +Geneartes multiple def file changes based on sobol sensativity. +} +\author{ +Will Burke +} diff --git a/man/IOin_hdr.Rd b/man/IOin_hdr.Rd new file mode 100644 index 0000000..87f07d8 --- /dev/null +++ b/man/IOin_hdr.Rd @@ -0,0 +1,46 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/IOin_hdr.R +\name{IOin_hdr} +\alias{IOin_hdr} +\title{IOin_hdr} +\usage{ +IOin_hdr( + basin, + hillslope, + zone, + soil, + landuse, + stratum, + fire = NULL, + fire_grid_prefix = NULL, + spinup = NULL, + basestations +) +} +\arguments{ +\item{basin}{Path to basin parameter definition file.} + +\item{hillslope}{Path to hillslope parameter definition file.(s)} + +\item{zone}{Path to zone parameter definition file(s).} + +\item{soil}{Path to soil parameter definition file(s).} + +\item{landuse}{Path to landuse parameter definition file(s).} + +\item{stratum}{Path to stratum parameter definition file(s).} + +\item{fire}{Path to fire parameter definition file.} + +\item{fire_grid_prefix}{Path and basename/prefix name of the fire grid files used for the RHESSys WMFire model.} + +\item{spinup}{Path to spinup parameter definition file(s).} + +\item{basestations}{Path to basin climate basestation file(s).} +} +\description{ +Creates a header file based on specified parameter definition files and climate basestations. +} +\author{ +Will Burke +} diff --git a/man/IOin_output_filters.Rd b/man/IOin_output_filters.Rd new file mode 100644 index 0000000..e32d3f2 --- /dev/null +++ b/man/IOin_output_filters.Rd @@ -0,0 +1,22 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/IOin_output_filters.R +\name{IOin_output_filters} +\alias{IOin_output_filters} +\title{IOin_output_filters} +\usage{ +IOin_output_filters(..., file_name = NULL, filter_in = NULL) +} +\arguments{ +\item{...}{Any number of valid filter objects (R lists), to be written to the same output filter file.} + +\item{file_name}{The name of the output filter file created. if left NULL an autogenerated file name will be used.} + +\item{filter_in}{Path to an existing yaml filter file.} +} +\description{ +Reads in and/or combines filters into a single R list filter object. Also checks that all filters are valid and contain the required fields +with valid options when possible to check. +} +\author{ +Will Burke +} diff --git a/man/IOin_output_vars.Rd b/man/IOin_output_vars.Rd new file mode 100644 index 0000000..3183151 --- /dev/null +++ b/man/IOin_output_vars.Rd @@ -0,0 +1,18 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/IOin_output_vars.R +\name{IOin_output_vars} +\alias{IOin_output_vars} +\title{IOin_output_vars} +\usage{ +IOin_output_vars(...) +} +\arguments{ +\item{...}{Any number of two element character vectors or dataframes, each specifying the output file using "pd", "pdg", "cd", "cdg" +style format in the first item/column and the variable of interest in the second item/column.} +} +\description{ +IOin_output_vars +} +\author{ +Will Burke +} diff --git a/man/IOin_rhessys_input.Rd b/man/IOin_rhessys_input.Rd new file mode 100644 index 0000000..56a0c11 --- /dev/null +++ b/man/IOin_rhessys_input.Rd @@ -0,0 +1,50 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/IOin_rhessys_input.R +\name{IOin_rhessys_input} +\alias{IOin_rhessys_input} +\title{IOin_rhessys_input} +\usage{ +IOin_rhessys_input( + version, + tec_file, + world_file, + world_hdr_prefix, + flowtable, + start, + end, + output_folder, + output_prefix, + commandline_options, + prefix_command = NULL +) +} +\arguments{ +\item{version}{Path to compiled RHESSys binary.} + +\item{tec_file}{Path and name of input tec file.} + +\item{world_file}{Path and name of input world file.} + +\item{world_hdr_prefix}{Prefix for folder and temporary header files to be written.} + +\item{flowtable}{Path and name of input tec file.} + +\item{start}{Start date of simulation.} + +\item{end}{End date of simulation.} + +\item{output_folder}{Path to folder where simulation output will go.} + +\item{output_prefix}{Prefix for output files.} + +\item{commandline_options}{Commandline options to be passed to RHESSys, e.x. '-g' or '-p'} + +\item{prefix_command}{A shell command to be run previous to the RHESSys command line call. +This can be used to source a shell script, which itself can run multiple commands if needed.} +} +\description{ +Basic inputs to run RHESSys +} +\author{ +Will Burke +} diff --git a/man/IOin_std_pars.Rd b/man/IOin_std_pars.Rd new file mode 100644 index 0000000..f3d3f61 --- /dev/null +++ b/man/IOin_std_pars.Rd @@ -0,0 +1,64 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/IOin_std_pars.R +\name{IOin_std_pars} +\alias{IOin_std_pars} +\title{IOin_std_pars} +\usage{ +IOin_std_pars( + m = 1, + k = 1, + soil_dep = 1, + m_v = 1, + k_v = 1, + pa = 1, + po = 1, + gw1 = 1, + gw2 = 1, + vgseng1 = 1, + vgseng2 = 1, + vgseng3 = 1, + n = 1, + pct_range = 0.25 +) +} +\arguments{ +\item{m}{Decay of hydraulic conductivity with depth.} + +\item{k}{Hydraulic conductivity at the surface.} + +\item{soil_dep}{Soil depth.} + +\item{m_v}{Multiplier to scale the vertical decay of hydraulic conductivity with depth.} + +\item{k_v}{Multiplier to scale the vertical hydraulic conductivity at the surface.} + +\item{pa}{Multiplier to scale the pore size index, set in soil def file.} + +\item{po}{Multiplier to scale the psi air entry, set in soil def file.} + +\item{gw1}{Multiplier on the sat_to_gw_coeff parameter set in the soil definition file +(representing the amount of water moving from the saturated store to the groundwater store).} + +\item{gw2}{Multiplier on the gw_loss_coeff parameter in the hillslope default file +(representing the amount of water moving from the groundwater store to the stream).} + +\item{vgseng1}{Multiples specific leaf areas.} + +\item{vgseng2}{Multiplies the ratio of shaded to sunlit leaf area.} + +\item{vgseng3}{Multiplier used only with the Dickenson algorithm of carbon allocation +(set with the epc.allocation_flag variable in the vegetation definition file). It changes +the allocation of net photosynthate sensitivity based on the current LAI. If not using the +Dickenson strategy of carbon allocation (i.e. using Waring or default Constant strategies), +set third value to 1.0. (i.e. -vgsen 1.0 2.0 1.0)} + +\item{n}{The number of parameter sets to generate.} + +\item{pct_range}{The percent range of variation from input values over which sampling (if any), will happen.} +} +\description{ +Input standard soil parameters for RHESSys, see https://github.com/RHESSys/RHESSys/wiki/RHESSys-command-line-options +} +\author{ +Will Burke +} diff --git a/man/IOin_tec_std.Rd b/man/IOin_tec_std.Rd new file mode 100644 index 0000000..449a9ee --- /dev/null +++ b/man/IOin_tec_std.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/IOin_tec_std.R +\name{IOin_tec_std} +\alias{IOin_tec_std} +\title{IOin_tec_std} +\usage{ +IOin_tec_std(start, end, output_state = TRUE) +} +\arguments{ +\item{start}{start date of run - used along with 'end' arg} + +\item{end}{End date of run} + +\item{output_state}{TRUE/FALSE if an output_current_state tec event should be scheduled at the end of the simulation} +} +\description{ +Input function to construct a dataframe of standard tec events, including start, grow start, and output state +} +\author{ +Will Burke +} diff --git a/man/build_output_filter.Rd b/man/build_output_filter.Rd new file mode 100644 index 0000000..03fe14b --- /dev/null +++ b/man/build_output_filter.Rd @@ -0,0 +1,38 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/build_output_filter.R +\name{build_output_filter} +\alias{build_output_filter} +\title{build_output_filter} +\usage{ +build_output_filter( + timestep, + output_format, + output_path, + output_filename, + spatial_level, + spatial_ID, + variables +) +} +\arguments{ +\item{timestep}{The timestep of the filter: 'daily', 'monthly', 'annual', 'hourly'} + +\item{output_format}{The format for the RHESSys output files to be written: 'csv' or 'netcdf'} + +\item{output_path}{The path where RHESSys output will be written.} + +\item{output_filename}{The filename for RHESSys output} + +\item{spatial_level}{The spatial level for output to be collected at/aggregated to: 'basin', 'hillslope', 'zone', 'patch', 'stratum'} + +\item{spatial_ID}{IDs to subset the spatial units by.} + +\item{variables}{The RHESSys internal variable names to output. If aggregating from a finer spatial level use syntax: '.'} +} +\description{ +Creates a single output filter in R list format. This can be combined with other filters +and/or written to file to be read by RHESSys when running. +} +\author{ +Will Burke +} diff --git a/man/change_def_file.Rd b/man/change_def_file.Rd index f7e1845..dfb6e65 100644 --- a/man/change_def_file.Rd +++ b/man/change_def_file.Rd @@ -14,5 +14,5 @@ change_def_file(def_file, par_sets, file_name_ext = NULL) \item{file_name_ext}{Optional extension to add to file name} } \description{ -This function imports a def file, replaces the values of selected parameters, and exports a def file. +This function reads a def file, replaces the values of selected parameters, and writes a new def file. } diff --git a/man/clim_auto.Rd b/man/clim_auto.Rd deleted file mode 100644 index 845062c..0000000 --- a/man/clim_auto.Rd +++ /dev/null @@ -1,25 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/clim_auto.R -\name{clim_auto} -\alias{clim_auto} -\title{clim_auto} -\usage{ -clim_auto( - base_station_id, - x_coordinate, - y_coordinate, - z_coordinate, - effective_lai, - screen_height, - annual_prefix = "annual", - monthly_prefix = "monthly", - daily_prefix = "daily", - hourly_prefix = "hourly" -) -} -\description{ -Generate input for run_rhessys basestation input -} -\author{ -Will Burke -} diff --git a/man/compile_rhessys.Rd b/man/compile_rhessys.Rd index 8259b42..a4b2e50 100644 --- a/man/compile_rhessys.Rd +++ b/man/compile_rhessys.Rd @@ -18,6 +18,8 @@ compile_rhessys( \item{destination}{Optional input of where to move resulting RHESSys executable} +\item{make_args}{Arguments passed to the end of the make commandline call (examples: "wmfire='T'", "clean", or "clobber", )} + \item{CFLAGS}{Overwrite CFLAGS in the makefile} \item{ignore.stdout}{Passed through to system()} diff --git a/man/input_tec.Rd b/man/input_tec.Rd deleted file mode 100644 index d81293d..0000000 --- a/man/input_tec.Rd +++ /dev/null @@ -1,27 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/input_tec.R -\name{input_tec} -\alias{input_tec} -\title{input_tec} -\usage{ -input_tec(start_end = NULL, start = NULL, end = NULL, output_state = TRUE) -} -\arguments{ -\item{start_end}{Vector of two charaters, indicating start and end dates, same as used to input start and end date for input_rhessys. -Used to auto generate tec events for printing (normal and grow), and output current state at end} - -\item{start}{start date of run - used along with 'end' arg} - -\item{end}{End date of run} - -\item{output_state}{TRUE/FALSE if an output_current_state tec event should be scheduled at the end of the simulation} - -\item{...}{Vector(s) containing tec events in format c(,,,,). -Additional tec events can be added just as additional arguments.} -} -\description{ -Tiny wrapper to simplify input of tec events -} -\author{ -Will Burke -} diff --git a/man/insert_in_worldfile.Rd b/man/insert_in_worldfile.Rd new file mode 100644 index 0000000..f463c2c --- /dev/null +++ b/man/insert_in_worldfile.Rd @@ -0,0 +1,34 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/insert_in_worldfile.R +\name{insert_in_worldfile} +\alias{insert_in_worldfile} +\title{Insert in Worldfile} +\usage{ +insert_in_worldfile( + world_in, + world_out, + insert, + insert_loc, + return_data = FALSE, + overwrite = FALSE +) +} +\arguments{ +\item{world_in}{Path to input worldfile. Cannot create from scratch (use RHESSysPreprocessing)} + +\item{world_out}{Path to output worldfile. If set to FALSE, no file will be written.} + +\item{insert}{Character vector of length = 2, containing state variable and value to be inserted into a worldfile.} + +\item{insert_loc}{Location, in the form of an existing state variable name, for a new state variable(s) to be inserted following.} + +\item{return_data}{TRUE/FALSE should an R data object be returned.} + +\item{overwrite}{TRUE/FALSE should output worldfile overwrite existing file.} +} +\description{ +Inserts new state variables and values into a worldfile at specified location(s). +} +\author{ +Will Burke +} diff --git a/man/make_hdr_file2.Rd b/man/make_hdr_file2.Rd new file mode 100644 index 0000000..35643b4 --- /dev/null +++ b/man/make_hdr_file2.Rd @@ -0,0 +1,27 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/make_hdr_file2.R +\name{make_hdr_file2} +\alias{make_hdr_file2} +\title{Write Header File} +\usage{ +make_hdr_file2(input_rhessys, hdr_files, def_files, runID) +} +\arguments{ +\item{input_rhessys}{List containing the following named elements: "rhessys_version" (path to rhessys binary), +"tec_file"(name for tec file to be built), "world_file"(path to existing worldfile), "world_hdr_prefix"(prefix for headers to create), +"flow_file"(path to existing flowtable), "start_date"(format c('yyyy mm dd hr')), "end_date"(format c('yyyy mm dd hr')), +"output_folder"(path to output folder), "output_filename"(prefix for output files to create), "command_options"(additional commandline options)} + +\item{hdr_files}{List of named elements, named for each def file type (basin_def, hillslope_def, zone_def, soil_def, landuse_def, patch_def, +stratum_def) as well as an element named "base_stations". Each element should contain the path to the corresponding def file.} + +\item{runID}{The unique ID used to track input and output files if running multiple scenarios, and thus multiple instances of run_rhessys_core.} + +\item{def_pars_df}{Data frame of def file parameter changes} +} +\description{ +New version of header file creation function. +} +\author{ +Will Burke +} diff --git a/man/modify_output_filter.Rd b/man/modify_output_filter.Rd new file mode 100644 index 0000000..00a14a4 --- /dev/null +++ b/man/modify_output_filter.Rd @@ -0,0 +1,41 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/modify_output_filter.R +\name{modify_output_filter} +\alias{modify_output_filter} +\title{modify_output_filter} +\usage{ +modify_output_filter( + filter_in, + timestep = NULL, + output_format = NULL, + output_path = NULL, + output_filename = NULL, + spatial_level = NULL, + spatial_ID = NULL, + variables = NULL +) +} +\arguments{ +\item{filter_in}{Path to the yaml filter file} + +\item{timestep}{The timestep of the filter: 'daily', 'monthly', 'annual', 'hourly'} + +\item{output_format}{The format for the RHESSys output files to be written: 'csv' or 'netcdf'} + +\item{output_path}{The path where RHESSys output will be written.} + +\item{output_filename}{The filename for RHESSys output} + +\item{spatial_level}{The spatial level for output to be collected at/aggregated to: 'basin', 'hillslope', 'zone', 'patch', 'stratum'} + +\item{spatial_ID}{IDs to subset the spatial units by.} + +\item{variables}{The RHESSys internal variable names to output. If aggregating from a finer spatial level use syntax: '.'} +} +\description{ +Modify a single existing output filter, either from file or based on an existing R object. Will error if given multiple filters. +This could be done via normal list modification in R as well. +} +\author{ +Will Burke +} diff --git a/man/output_control.Rd b/man/output_control.Rd new file mode 100644 index 0000000..f22b595 --- /dev/null +++ b/man/output_control.Rd @@ -0,0 +1,36 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/output_control.R +\name{output_control} +\alias{output_control} +\title{output_control} +\usage{ +output_control( + output_method, + output_variables, + return_data, + output_folder, + output_filename, + runID = 1 +) +} +\arguments{ +\item{output_method}{Output method (function) to use. "awk" will use awk, "r" will use new R based method, +any other non NULL input will use the older R based output selection.} + +\item{output_variables}{Datafrane with two named columns: "variables" containing variables of interest +found in the header of standard rhessys output files, "out_file" points to the files containing the associated variables, +this can be either the path to that file, can use the abbreviation for the different output types +(patch daily = pd, patch daily grow = pdg etc.) and the files in output_folder will be parsed appropriately, +or can use the fully written out space.time suffix, e.g. "patch.daily" or "grow_patch.daily"} + +\item{return_data}{TRUE/FALSE if the function should return a data.table of the selected output - for now only works if doing 1 run} + +\item{output_folder}{Folder where rhessys output is located} + +\item{output_filename}{Base file name of standard rhessys output} + +\item{runID}{Integer ID of the current run, used internally} +} +\description{ +Passes output variables to appropriate output selection method. +} diff --git a/man/read_output_filter.Rd b/man/read_output_filter.Rd new file mode 100644 index 0000000..70c7150 --- /dev/null +++ b/man/read_output_filter.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/read_output_filter.R +\name{read_output_filter} +\alias{read_output_filter} +\title{read_output_filter} +\usage{ +read_output_filter(filter_in) +} +\arguments{ +\item{filter_in}{Path to the yaml filter file} +} +\description{ +Reads a yaml format RHESSys output filter and creates a R list. Handles tabs in input file, +} +\author{ +Will Burke +} diff --git a/man/rhessys_command.Rd b/man/rhessys_command.Rd index faae3ba..a86961b 100644 --- a/man/rhessys_command.Rd +++ b/man/rhessys_command.Rd @@ -12,37 +12,40 @@ rhessys_command( flow_file, start_date, end_date, - output_file, + output_file = NULL, input_parameters, - command_options + output_filter = NULL, + command_options, + prefix_command = NULL ) } \arguments{ -\item{rhessys_version}{path and file of compiled version of RHESSys.} +\item{rhessys_version}{Path and file name of compiled version of RHESSys.} -\item{world_file}{path and file of world_file. World_file is produced using -grass-to-world} +\item{world_file}{Oath and file name of RHESSys world_file.} -\item{world_hdr_file}{???} +\item{world_hdr_file}{Path and file name of RHESSys header file} -\item{tec_file}{???} +\item{tec_file}{Path and file name of RHESSys temporal event control (tec) file} -\item{flow_file}{???} +\item{flow_file}{Path and file name of RHESSys flow table file} -\item{start_date}{???} +\item{start_date}{Start date character vector in format , delimited by spaces. Ex. '1990 12 30 01'} -\item{end_date}{???} +\item{end_date}{End date character vector, same format as start_date} -\item{output_file}{???} +\item{output_file}{Path and base file name of RHESSys output} -\item{input_parameters}{???} +\item{input_parameters}{Soil parameters passed to RHESSys command line.} -\item{command_options}{???} +\item{output_filter}{Path to a yaml formatted output filter.} + +\item{command_options}{RHESSys command line options, ex. '-g' or '-p'.} + +\item{prefix_command}{A shell command to be run previous to the RHESSys command line call. +This can be used to source a shell script, which itself can run multiple commands if needed.} } \description{ -\code{rhessys_command} calls rhessys on the command line. -} -\details{ -Requires that supporting files be developed prior to running RHESSys. These -include ... +\code{rhessys_command} Assembles command line RHESSys call, and runs it. See the RHESSys wiki: +https://github.com/RHESSys/RHESSys/wiki/RHESSys-command-line-options } diff --git a/man/run_rhessys_multi.Rd b/man/run_rhessys_multi.Rd new file mode 100644 index 0000000..13f453f --- /dev/null +++ b/man/run_rhessys_multi.Rd @@ -0,0 +1,47 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/run_rhessys_multi.R +\name{run_rhessys_multi} +\alias{run_rhessys_multi} +\title{Run multiple RHESSys simulations} +\usage{ +run_rhessys_multi( + input_rhessys, + hdr_files, + tec_data, + def_pars = NULL, + output_filter = NULL, + runID = NULL, + parallel = TRUE, + n_cores = 2 +) +} +\arguments{ +\item{input_rhessys}{List containing the following named elements: "rhessys_version" (path to rhessys binary), +"tec_file"(name for tec file to be built), "world_file"(path to existing worldfile), "world_hdr_prefix"(prefix for headers to create), +"flow_file"(path to existing flowtable), "start_date"(format c('yyyy mm dd hr')), "end_date"(format c('yyyy mm dd hr')), +"output_folder"(path to output folder), "output_filename"(prefix for output files to create), "command_options"(additional commandline options)} + +\item{hdr_files}{List of named elements, named for each def file type (basin_def, hillslope_def, zone_def, soil_def, landuse_def, patch_def, +stratum_def) as well as an element named "base_stations". Each element should contain the path to the corresponding def file.} + +\item{tec_data}{Input tec events, see input_tec function} + +\item{def_pars}{To overwrite def file parameters. Format is a list of lists, with each sub-list having the format: +list(, , ). Defaults to NULL} + +\item{output_filter}{An output filter, either an R list with 1 to n number of filters read in/modified/generated via IOin_output_filter.R +(or associated functions - build_output_filter.R, read_output_filter.R, modify_output_filter.R), or a file path pointing to an +existing output filter.} + +\item{runID}{The unique ID used to track input and output files if running multiple scenarios, and thus multiple instances of run_rhessys_core.} + +\item{parallel}{Defaults to TRUE. Should the parallel package be used to parallelize the rhessys runs.} + +\item{n_cores}{The number of cores to use in a parallelized cluster.} +} +\description{ +Runs RHESSys simulations. +} +\author{ +Will Burke +} diff --git a/man/run_rhessys_single.Rd b/man/run_rhessys_single.Rd new file mode 100644 index 0000000..49b37ac --- /dev/null +++ b/man/run_rhessys_single.Rd @@ -0,0 +1,54 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/run_rhessys_single.R +\name{run_rhessys_single} +\alias{run_rhessys_single} +\title{Run RHESSys simulation} +\usage{ +run_rhessys_single( + input_rhessys, + hdr_files, + tec_data, + std_pars = NULL, + def_pars = NULL, + clim_base = NULL, + output_filter = NULL, + output_method = NULL, + output_variables = NULL, + return_data = FALSE, + runID = NULL +) +} +\arguments{ +\item{input_rhessys}{List containing the following named elements: "rhessys_version" (path to rhessys binary), +"tec_file"(name for tec file to be built), "world_file"(path to existing worldfile), "world_hdr_prefix"(prefix for headers to create), +"flow_file"(path to existing flowtable), "start_date"(format c('yyyy mm dd hr')), "end_date"(format c('yyyy mm dd hr')), +"output_folder"(path to output folder), "output_filename"(prefix for output files to create), "command_options"(additional commandline options)} + +\item{hdr_files}{List of named elements, named for each def file type (basin_def, hillslope_def, zone_def, soil_def, landuse_def, patch_def, +stratum_def) as well as an element named "base_stations". Each element should contain the path to the corresponding def file.} + +\item{tec_data}{Input tec events, see input_tec function} + +\item{std_pars}{List of standard (command line) parameters.} + +\item{def_pars}{To overwrite def file parameters. Format is a list of lists, with each sub-list having the format: +list(, , ). Defaults to NULL} + +\item{clim_base}{Data for input climate basestation to be written. Defaults to NULL, which assumes you havean existing basestation pointed +to in input_rhessys.} + +\item{output_filter}{An output filter, either an R list with 1 to n number of filters read in/modified/generated via IOin_output_filter.R +(or associated functions - build_output_filter.R, read_output_filter.R, modify_output_filter.R), or a file path pointing to an +existing output filter.} + +\item{output_method}{"awk" will use awk, any other non NULL input will use R based output selection} + +\item{output_variables}{List of output variables to subset via the indicated method, Defaults to NULL} + +\item{return_data}{TRUE/FALSE if the function should return a data.table of the selected output - for now only works if doing 1 run} + +\item{runID}{The unique ID used to track input and output files if running multiple scenarios, and thus multiple instances of run_rhessys_core.} +} +\description{ +Writes files and assembles inputs to run a single instance of RHESSys. +} diff --git a/man/select_output_variables_R.Rd b/man/select_output_variables_R.Rd index 689a598..d210fd3 100644 --- a/man/select_output_variables_R.Rd +++ b/man/select_output_variables_R.Rd @@ -16,18 +16,26 @@ select_output_variables_R( ) } \arguments{ -\item{output_variables}{Datafrane with named columns: "variables" containing variables matching variables of interest +\item{output_variables}{Datafrane with named columns: "variables" containing variables of interest found in the header of rhessys output files, "out_file" points to the files containing the associated variables, -this can be either the path to that file, can use the abbreviation for the different output types (patch daily = pd, patch daily grow = pdg etc.) -and the files in output_folder will be parsed appropriately, or can use the fully written out space.time suffix, e.g. "patch.daily" or "grow_patch.daily"} +this can be either the path to that file, can use the abbreviation for the different output types +(patch daily = pd, patch daily grow = pdg etc.) and the files in output_folder will be parsed appropriately, +or can use the fully written out space.time suffix, e.g. "patch.daily" or "grow_patch.daily"} \item{output_folder}{Folder where rhessys output is located (e.g. 'out')} +\item{output_filename}{Base file name of standard rhessys output} + \item{run}{Simulation number. Used to reset files in allsim at beginning of simulation} +\item{max_run}{Max number of runs to collect output for - at run == max run, output will be pivoted from long to wide, +and date and spatial info will be added.} + \item{return_data}{TRUE/FALSE if the function should return a data.table of the selected output - for now only works if doing 1 run} \item{out}{Output location, if not will use default "allsim" within output folder} + +\item{no_write}{TRUE/FALSE to only return data within R, and not write any data. Only works is return_data == TRUE} } \description{ Somewhat optimized R-based read and subsetting of RHESSys output diff --git a/man/watbal_basin_of.Rd b/man/watbal_basin_of.Rd new file mode 100644 index 0000000..d58c748 --- /dev/null +++ b/man/watbal_basin_of.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/watbal_basin_of.R +\name{watbal_basin_of} +\alias{watbal_basin_of} +\title{watbal_basin_of.R} +\usage{ +watbal_basin_of(bd) +} +\arguments{ +\item{bd}{The basin daily outputs from rhessys, most easily retrieved via `readin_rhessys_output()`} +} +\description{ +Water balance for basin daily RHESSys output, as generated by outputfilters. To run, if your basin output is called "bd" type "bd=watbal(bd)". +This will add a number of fields to your basin output file, the last of which will be called "watbal". +This is your water balance error. You should see a minor numerical error here even if your water balances +(on the order of 10^-6). If your watbal values are negative then water inputs are less than water outputs, and vice versa. +} diff --git a/man/write_output_filter.Rd b/man/write_output_filter.Rd new file mode 100644 index 0000000..3910887 --- /dev/null +++ b/man/write_output_filter.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/write_output_filter.R +\name{write_output_filter} +\alias{write_output_filter} +\title{write_output_filter} +\usage{ +write_output_filter(output_filter, runID = NULL) +} +\arguments{ +\item{output_filter}{An output filter, either an R list with 1 to n number of filters read in/modified/generated via IOin_output_filter.R +(or associated functions - build_output_filter.R, read_output_filter.R, modify_output_filter.R), or a file path pointing to an +existing output filter.} + +\item{runID}{The unique ID used to track input and output files if running multiple scenarios, and thus multiple instances of run_rhessys_core.} +} +\description{ +Writes an output filter file based on an input R list containing the needed elements. +} +\author{ +Will Burke +} diff --git a/tests/testthat.R b/tests/testthat.R new file mode 100644 index 0000000..11458cc --- /dev/null +++ b/tests/testthat.R @@ -0,0 +1,4 @@ +library(testthat) +library(RHESSysIOinR) + +test_check("RHESSysIOinR") diff --git a/tests/testthat/test-single_run.R b/tests/testthat/test-single_run.R new file mode 100644 index 0000000..546f76d --- /dev/null +++ b/tests/testthat/test-single_run.R @@ -0,0 +1,116 @@ +# this is to test input generation and running of a single rhessys simulation +library(RHESSysIOinR) +library(testthat) + +# TODO create reference objects to compare to? +# TODO find most efficient way to download and install rhessys - I think using same command line from vignette: +# TODO figure out a way to standardize which version of rhessys to test with + +# custom expects +expect_file_exists = function(path) { + # 1. Capture object and label + act <- quasi_label(rlang::enquo(path), arg = "path") + # 2. Call expect() + expect( + file.exists(act$val), + sprintf("%s file does not exist.", act$lab) + ) + # 3. Invisibly return the value + invisible(act$val) +} + +expect_file_sizeKB_gt = function(path, size_KB) { + # 1. Capture object and label + act <- quasi_label(rlang::enquo(path), arg = "path") + # 2. Call expect() + expect( + (file.size(act$val) / 1024) > size_KB, + sprintf("%s file is not greater than %f KB.", act$lab, size_KB) + ) + # 3. Invisibly return the value + invisible(act$val) +} + + +# PATHS - just setting wd to extdata at start and not doing any system.file() idk if its a problem +#withr::local_dir(new = system.file("extdata", package = "RHESSysIOinR")) +setwd("~/Repos/RHESSysIOinR/inst/extdata/") +setwd(system.file("extdata/", package = "RHESSysIOinR")) + +# no support for shallow clone depth so a little slow checking the commits +gert::git_clone(url = "https://github.com/RHESSys/RHESSys", + path = "./rh_dev", + branch = "develop") + +# this has a bonus effect of testing the compile_rhessys function: +compile_rhessys(location = "rh_dev/") + +# find the rhessys bin +rh_ver = dir(path = "rh_dev/rhessys/", pattern = "^rhessys\\d+",recursive = F) + +test_that("compile_rhessys works + rhessys compiles via R system", { + expect_gt(length(rh_ver), 0) +}) + +rh_path = file.path("rh_dev/rhessys/", rh_ver) + + +# with new testthat 3 use withr:: -- https://testthat.r-lib.org/articles/test-fixtures.html +# for file cleanup use local_file() +# for working dir change local_dir() + +input_rhessys = IOin_rhessys_input( + version = rh_path, + tec_file = "tecfiles/w8TC.tec", + world_file = "worldfiles/w8TC.world", + world_hdr_prefix = "w8TC", + flowtable = "flowtables/w8TC.flow", + start = "1998 10 1 1", + end = "2000 10 1 1", + output_folder = "out/", + output_prefix = "w8TC", + commandline_options = c("-g -b") +) + +input_tec_data = IOin_tec_std(start = "1998 10 1 1", + end = "2000 10 1 1", + output_state = TRUE) + +input_hdr = IOin_hdr( + basin = "defs/basin.def", + hillslope = "defs/hill.def", + zone = "defs/zone.def", + soil = "defs/soil_sandyloam.def", + landuse = "defs/lu_undev.def", + stratum = "defs/veg_douglasfir.def", + basestations = "clim/w8_base" +) + +# test_that("Input core RHESSys info can be generated", { +# +# }) +# +# test_that("Input tec file can be generated", { +# +# }) +# +# test_that("Input header file can be generated", { +# +# }) + +run_rhessys_single(input_rhessys = input_rhessys, + hdr_files = input_hdr, + tec_data = input_tec_data) + +test_that("Simplest RHSSys run options run successfully (core rhessys info, tec data, hdr data)", { + # check there is output file and they aren't empty + expect_file_exists(path = "out/w8TC_basin.daily") + expect_file_sizeKB_gt(path = "out/w8TC_basin.daily", size_KB = 5) + expect_file_exists(path = "out/w8TC_grow_basin.daily") + expect_file_sizeKB_gt(path = "out/w8TC_grow_basin.daily", size_KB = 5) +}) + +# should add cleanup here if more tests are going to be run that depend on the file system state - otherwise doesn't really matter + + + diff --git a/vignettes/IOin_examples.Rmd b/vignettes/IOin_examples.Rmd new file mode 100644 index 0000000..0378413 --- /dev/null +++ b/vignettes/IOin_examples.Rmd @@ -0,0 +1,271 @@ +--- +title: "IOin_examples" +author: "Will Burke" +date: "9/7/2020" +output: html_document +--- + +## RHESSysIOinR Input Functions + +This vignette shows example uses of the IOin_X functions, which together construct input data objects used to run one or many RHESSys simulations. + +#### New/renamed input functions: + +- IOin_rhessys_input +- IOin_tec_std +- IOin_cmd_pars +- IOin_hdr +- IOin_clim +- IOin_def_pars_simple + +### Setup + +Using rhessys/Testing as example input data. If you don't already have develop branch of RHESsys cloned, get that now too. + +```{r, setup, include=FALSE} +# to clone and checkout develop branch, a bit slow for some reason +# gert::git_clone(url = "https://github.com/RHESSys/RHESSys", +# path = "~/Repos/rhessys-devtest", +# branch = "develop") + +knitr::opts_knit$set(root.dir = "~/Repos/rhessys-devtest/Testing/") +knitr::opts_chunk$set(echo = TRUE) +``` + +### Compile RHESSys + +If needed + +```{r, echo=FALSE, results='hide'} +library(RHESSysIOinR) +# Should work for both Mac and WSL (Windows) +#compile_rhessys(location = "../") +``` + +### IOin_rhessys_input + +This is the basic RHESSys information needed to run RHESSys from the command line. + +```{r } +input_rhessys = IOin_rhessys_input( + version = "../rhessys/rhessys7.3", + tec_file = "tecfiles/w8TC.tec", + world_file = "worldfiles/w8TC.world", + world_hdr_prefix = "w8TC", + flowtable = "flowtables/w8TC.flow", + start = "1988 10 1 1", + end = "2000 10 1 1", + output_folder = "out/", + output_prefix = "w8TC", + commandline_options = c("-g -b") +) +``` + +### IOin_tec_std + +This creates a tec file, automatically adding entries for print_daily_on and print_daily_growth_on based on the start date, and adding output_current_state at the end date. output_current_state can be toggled off by setting output_state=FALSE. + +```{r} +input_tec_data = IOin_tec_std(start = "1988 10 1 1", + end = "2000 10 1 1", + output_state = TRUE) +``` + +### IOin_hdr + +This creates a header file in a folder using the world_hdr_prefix from IOin_rhessys_input and using the def files specified in the function below. + +```{r} +input_hdr = IOin_hdr( + basin = "defs/basin.def", + hillslope = "defs/hill.def", + zone = "defs/zone.def", + soil = "defs/soil_sandyloam.def", + landuse = "defs/lu_undev.def", + stratum = "defs/veg_douglasfir.def", + basestations = "clim/w8_base" +) +``` + +### Run RHESSys + +Together, these inputs (IOin_X) can be used to run RHESSys for a single simulation with very simple options. Future additions will allow for pointing to already generated header and tec files. + +```{r, echo=FALSE, results='hide'} +run_rhessys_single( + input_rhessys = input_rhessys, + hdr_files = input_hdr, + tec_data = input_tec_data +) +``` + +### IOin_std_pars + +Command line parameteres (standard paramters) are multipliers on some commonly varied exisitng paramter values (found in def files). Because it has become easier to modify the def file values directly, we are encoureging users to move away from this method of parameter variation, but this function is nonetheless how you would input/modify command line parameters. + +```{r, echo=FALSE, results='hide'} +input_std_pars = IOin_std_pars( + m = 0.355794, + k = 651.390265, + m_v = 0.355794, + k_v = 651.390265, + pa = 1.083102, + po = 1.193924, + gw1 = 0.116316, + gw2 = 0.916922 +) + +run_rhessys_single( + input_rhessys = input_rhessys, + hdr_files = input_hdr, + tec_data = input_tec_data, + std_pars = input_std_pars +) +``` + +### IOin_def_pars + +This function modifies def file parameters. This is done by creating modifed def files with the altered paramters, and pointing to that new def file in the header file. This allows for many parameter sets to be generated through many def files and associated header files. + +```{r, echo=FALSE, results='hide'} +input_def_pars = IOin_def_pars_simple( + list("defs/soil_sandyloam.def", "m", (0.12 * 0.355794)), + list("defs/soil_sandyloam.def", "Ksat_0", (3 * 651.390265)), + list("defs/soil_sandyloam.def", "m_z", (0.4 * 0.355794)), + list("defs/soil_sandyloam.def", "pore_size_index", (0.195750 * 1.193924)), + list("defs/soil_sandyloam.def", "psi_air_entry", (0.798750 * 1.083102)), + list("defs/soil_sandyloam.def", "sat_to_gw_coeff",(0 * 0.116316)), + list("defs/hill.def", "gw_loss_coeff", (0 * 0.916922)) +) + +run_rhessys_single( + input_rhessys = input_rhessys, + hdr_files = input_hdr, + tec_data = input_tec_data, + def_pars = input_def_pars +) +``` + +### IOin_clim + +This is just to generate a basestation on the fly, but can be useful when running across multiple climate series, and to ensure the paths in the base station file are correct. Future additions will support more complex modification of climate sequences and more. + +```{r, echo=FALSE, results='hide'} +input_clim = IOin_clim( + base_station_id = 101, + x_coordinate = 100.0, + y_coordinate = 100.0, + z_coordinate = 975, + effective_lai = 3.5, + screen_height = 160, + daily_prefix = "clim/w8_daily" +) +# if set to existing file name, existing base station will be overwritten. +input_hdr$base_stations = "clim/w8_base_test" + +run_rhessys_single( + input_rhessys = input_rhessys, + hdr_files = input_hdr, + tec_data = input_tec_data, + clim_base = input_clim +) + +``` + +## Output + +### Output Filters + +Output filters require a output filter file in yaml format, containing any number of filters. `run_rhessys_single()` can write a filter file based on an input R data object (list). The functions below allow for reading of existing output filters, modification, and creation of new output filters. + +```{r, echo=FALSE, results='hide'} +# read an existing filter file +filter1 = read_output_filter(filter_in = "tecfiles/testing_filter.yml") +# equivalent +# filter = IOin_output_filters(filter_in = "tecfiles/testing_filter.yml") + +# create a new filter R object +filter2 = build_output_filter( + timestep = "daily", + output_format = "csv", + output_path = "../Testing/out", + output_filename = "basin_daily", + spatial_level = "basin", + spatial_ID = as.integer("1"), + variables = c("patch.total_water_in", "patch.streamflow", "patch.evaporation") +) + +# modify an existing filter, either from file or R object, and return R obj +# all options left null (the default) will use the existing value. +filter3 = modify_output_filter( + filter_in = "tecfiles/testing_filter.yml", + variables = c("patch.total_water_in", "patch.streamflow", "patch.evaporation") +) + +# combine output filters and create object ready to input to run_rhessys_single/multi +filter4 = IOin_output_filters(filter, filter_in = "tecfiles/testing_filter2.yml", file_name = "test_output_filters") + +# for just a single filter with named filter file +input_filter = IOin_output_filters(filter2, file_name = "tecfiles/test_output_filter.yml") + +# adjust core rhessys inputs - can't have -b -p etc output along with output filters +input_rhessys$command_options = NULL + + +run_rhessys_single( + input_rhessys = input_rhessys, + hdr_files = input_hdr, + tec_data = input_tec_data, + def_pars = input_def_pars, + output_filter = input_filter +) + + +``` + +### Output Subsetting + +This is being deprecated and though it should still function, will not be supported as new features get added. + +```{r eval=FALSE} + # to use native R-based subsetting + output_method = "r" + my_vars = data.frame(c("pd", "Qout"), + c("pd", "psn"), + c("pdg", "lai"), + c("pdg", "plantc"), + c("cd", "height")) + output_vars = IOin_output_vars(my_vars) +``` + +## Running Multiple Scenarios + +The above input functions all generate RHESSys inputs for a single RHESSys run. With additional options, or different IOin_X functions, multiple RHESSys scenarios can be generated, and run via `run_rhessys_multi()`. + +The method for generating those multiple scenarios is flexible,, as long as the output data format adheres to what is expected input for `run_rhessys_multi()`. See the code/documentation/comments on `IOin_def_pars_simple()` for more info on the data format. + +### IOin_def_pars_sobol + +This is still work in progress, but shows how sobol paramter sampling can be used to generate RHESSys inputs. + +```{r, echo=FALSE, results='hide'} + +# this gives the most flexibility to how users want to generate a distribution +n = 10 +pars = list( + list("defs/veg_douglasfir.def", "epc.waring_pa", runif(n, 0.1, 0.4)), + list("defs/veg_douglasfir.def", "epc.proj_sla", runif(n, 2, 6)), + list("defs/soil_sandyloam.def", "pore_size_index", runif(n, 0.2, 0.5)), + list("defs/soil_sandyloam.def", "psi_air_entry", runif(n, 0.5, 8)) +) + +input_def_pars_sobol = IOin_def_pars_sobol(pars, nboot = 100) + +run_rhessys_multi( + input_rhessys = input_rhessys, + hdr_files = input_hdr, + tec_data = input_tec_data, + def_pars = input_def_pars_sobol +) + +``` diff --git a/vignettes/RHESSysIOinR_utilities_examples.Rmd b/vignettes/RHESSysIOinR_utilities_examples.Rmd new file mode 100644 index 0000000..96b739d --- /dev/null +++ b/vignettes/RHESSysIOinR_utilities_examples.Rmd @@ -0,0 +1,36 @@ +--- +title: "RHESSysIOinR Utilities Examples" +author: "Will Burke" +date: "11/10/2020" +output: html_document +--- + +```{r setup, include=FALSE} +knitr::opts_chunk$set(echo = TRUE) +``` + +## RHESSysIOinR Utilities + +The following are various utility functions included with RHESSysIOinR + +* `build_redefine()`: generates redefine worldfiles +* `cal.wyd()`: calculates wateryear day +* `change_def_file()`: create new def file based on existing file and input pars +* `clim_auto()`: helper to simplify climate input for `run_rhessys()` +* `evaluation()`: used to evaluate model output +* `input_tec()`: helper to simplify input of tec events +* `mkdate()`: generates wy, yd, and wyd based on day, month, year +* `read_clim()`: reads rhessys formatted climate data into R +* `readin_rhessys_output()`: reads rhessys output into R, includes some subsetting and simply aggregation +* `readin_rhessys_output_old()`: legacy method to read in rhessys output +* `tec_repeat()`: generates repeating tec events for input into `run_rhessys()`, can also copy+rename a redefine file as needed +* `watbal_basin()`: Calculate water balance for a the basin +* `watbal_patch()`: Calculate water balance for a single patch +* `watbal_patch_multi()`: Calculate water balance for a multiple patches +* `write_sample_clim()`: generate new climate based on existing climate + +## update_world + +```{r } + +``` diff --git a/vignettes/RHESSysIOinR_vignette.R b/vignettes/RHESSysIOinR_vignette.R deleted file mode 100644 index 0497c85..0000000 --- a/vignettes/RHESSysIOinR_vignette.R +++ /dev/null @@ -1,7 +0,0 @@ -## ---- fig.show='hold'--------------------------------------------------------- -plot(1:10) -plot(10:1) - -## ---- echo=FALSE, results='asis'---------------------------------------------- -knitr::kable(head(mtcars, 10)) - diff --git a/vignettes/RHESSysIOinR_vignette.Rmd b/vignettes/RHESSysIOinR_vignette.Rmd deleted file mode 100644 index aace6af..0000000 --- a/vignettes/RHESSysIOinR_vignette.Rmd +++ /dev/null @@ -1,58 +0,0 @@ ---- -title: "Vignette Title" -author: "Vignette Author" -date: "`r Sys.Date()`" -output: rmarkdown::html_vignette -vignette: > - %\VignetteIndexEntry{Vignette Title} - %\VignetteEngine{knitr::rmarkdown} - %\VignetteEncoding{UTF-8} ---- - -Vignettes are long form documentation commonly included in packages. Because they are part of the distribution of the package, they need to be as compact as possible. The `html_vignette` output type provides a custom style sheet (and tweaks some options) to ensure that the resulting html is as small as possible. The `html_vignette` format: - -- Never uses retina figures -- Has a smaller default figure size -- Uses a custom CSS stylesheet instead of the default Twitter Bootstrap style - -## Vignette Info - -Note the various macros within the `vignette` section of the metadata block above. These are required in order to instruct R how to build the vignette. Note that you should change the `title` field and the `\VignetteIndexEntry` to match the title of your vignette. - -## Styles - -The `html_vignette` template includes a basic CSS theme. To override this theme you can specify your own CSS in the document metadata as follows: - - output: - rmarkdown::html_vignette: - css: mystyles.css - -## Figures - -The figure sizes have been customised so that you can easily put two images side-by-side. - -```{r, fig.show='hold'} -plot(1:10) -plot(10:1) -``` - -You can enable figure captions by `fig_caption: yes` in YAML: - - output: - rmarkdown::html_vignette: - fig_caption: yes - -Then you can use the chunk option `fig.cap = "Your figure caption."` in **knitr**. - -## More Examples - -You can write math expressions, e.g. $Y = X\beta + \epsilon$, footnotes^[A footnote here.], and tables, e.g. using `knitr::kable()`. - -```{r, echo=FALSE, results='asis'} -knitr::kable(head(mtcars, 10)) -``` - -Also a quote using `>`: - -> "He who gives up [code] safety for [code] speed deserves neither." -([via](https://twitter.com/hadleywickham/status/504368538874703872)) diff --git a/vignettes/sample_inputs_simple.R b/vignettes/sample_inputs_simple.R deleted file mode 100644 index 3dcb2d5..0000000 --- a/vignettes/sample_inputs_simple.R +++ /dev/null @@ -1,130 +0,0 @@ -# RHESSys run script for multiscale testing - -library(RHESSysIOinR) - -# ----- Project/Run Name ----- -name = "p301_clip_multi" - -n_sim = 1 - -# ----- Climate Data ----- -clim_data = "p301_input/clim/Grove_lowprov_clim" -start_end = read_clim(clim_data, dates = TRUE) - -# ----- Parameter Method ----- -parameter_method = "exact_values" - -# ----- Input RHESSys ----- -input_rhessys <- list() -input_rhessys$rhessys_version <- "bin/Salsa/rhessys7.0" -input_rhessys$tec_file <- "p301_input/tecfiles/p301_clip.tec" -input_rhessys$world_file <- "p301_input/worldfiles/p301_clip.world" -input_rhessys$world_hdr_prefix <- "p301_clip" -input_rhessys$flow_file <- "p301_input/flowtables/p301_clip.flow" -input_rhessys$start_date <- start_end[1] -input_rhessys$end_date <- start_end[2] -input_rhessys$output_folder <- "output/" -input_rhessys$output_filename <- "p301_clip_multi" -input_rhessys$command_options <- c("-b -h -z -g -p -c") - -# ----- Input Headers ----- -input_hdr_list <- list() -input_hdr_list$basin_def <- c("p301_input/defs/basin_p301.def") -input_hdr_list$hillslope_def <- c("p301_input/defs/hill_p301.def") -input_hdr_list$zone_def <- c("p301_input/defs/zone_p301.def") -input_hdr_list$soil_def <- c("p301_input/defs/soil_sandyloam.def") -input_hdr_list$landuse_def <- c("p301_input/defs/lu_p301.def") -input_hdr_list$stratum_def <- c("p301_input/defs/veg_p301_conifer.def", - "p301_input/defs/veg_p301_grass.def", - "p301_input/defs/veg_p301_shrub.def", - "p301_input/defs/veg_p301_noveg.def") -input_hdr_list$base_stations <- c("p301_input/clim/Grove_lowprov_clim.base") - -# ----- Parameters ----- -input_preexisting_table <- NULL - -# ----- Def File Parameters ----- -input_def_list = NULL -# input_def_list <- list( -# list(input_hdr_list$stratum_def[2], "epc.leaf_turnover", c(0.1, 1, 4)), -# ) - -# ----- Standard (soil/subsurface) Parameters----- -# input_standard_par_list <- NULL -input_standard_par_list <- list( - m = c(2), - k = c(2), - m_v = c(2), - k_v = c(2), - pa = c(1), - po = c(1), - gw1 = c(0.2), - gw2 = c(0.2) -) - -# input_standard_par_list <- list( -# m = c(2, 2, n_sim), -# k = c(2, 2, n_sim), -# m_v = c(2, 2, n_sim), -# k_v = c(2, 2, n_sim), -# pa = c(1, 1, n_sim), -# po = c(1, 1, n_sim), -# gw1 = c(0.2, 0.2, n_sim), -# gw2 = c(0.2, 0.2, n_sim) -# ) -# ----- Make Climate Basestation ----- -#input_clim_base_list <- NULL - -input_clim_base_list = clim_auto(base_station_id = 101, - x_coordinate = 100.0, - y_coordinate = 100.0, - z_coordinate = 1748, - effective_lai = 3.5, - screen_height = 2, - daily_prefix = "p301_input/clim/Grove_lowprov_clim") - - -# ----- Make Dated Sequence ----- -# Make a list of dated sequence data.frames (file name, year, month, day, hour, value) -input_dated_seq_list <- NULL -# input_dated_seq_list <- list() -# input_dated_seq_list[[1]] <- data.frame(name = "lowProv",type = "pspread",year = 1941,month = 10,day = 1,hour = 1,value = 0.1,stringsAsFactors = FALSE) -# input_dated_seq_list[[2]] <- data.frame(name = "lowProv",type = "pspread",year = 1941,month = 10,day = 1,hour = 1,value = 0.2,stringsAsFactors = FALSE) - -# ----- Make Tec File ----- -#input_tec_data <- NULL -input_tec_data = input_tec(start_end = start_end) -# input_tec_data <- data.frame(year=integer(),month=integer(),day=integer(),hour=integer(),name=character(),stringsAsFactors=FALSE) -# input_tec_data[1,] <- data.frame(1941, 10, 1, 1, "print_daily_on", stringsAsFactors=FALSE) -# input_tec_data[2,] <- data.frame(1941, 10, 1, 2, "print_daily_growth_on", stringsAsFactors=FALSE) -# input_tec_data[3,] <- data.frame(1947, 10, 1, 1, "output_current_state", stringsAsFactors=FALSE) - -# ----- Output ----- -output_method = NULL -# ----- Output - Awks ----- -# Data frame containing variable of interest, location/name of awk file (relative to output file location), -# and the location/name of rhessys output file with variable of interest. -output_variables = NULL -# output_variables <- data.frame(variable=character(),awk_path=character(),out_file=character(),stringsAsFactors=FALSE) -# output_variables[1,] <- data.frame("lai", "awks/output_var_bd_lai.awk","patch_sim_basin.daily",stringsAsFactors=FALSE) -# ----- Output - R ----- -# Output variables for R version -# output_variables <- data.frame(out_type=character(), variable=character(), stringsAsFactors=FALSE) -# output_variables[1,] <- data.frame("bd", "lai", stringsAsFactors=FALSE) - -# ----- Run RHESSys ----- - -run_rhessys(parameter_method = parameter_method, - output_method = output_method, - input_rhessys = input_rhessys, - input_hdr_list = input_hdr_list, - input_preexisting_table = input_preexisting_table, - input_def_list = input_def_list, - input_standard_par_list = input_standard_par_list, - input_clim_base_list = input_clim_base_list, - input_dated_seq_list = input_dated_seq_list, - input_tec_data = input_tec_data, - output_variables = output_variables) - - -