Merge branch 'develop'

.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

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 <ryanrbart@ucsb.edu>
 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

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)
@@ -19,24 +28,30 @@ 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)
 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%")

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)
+}

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("<def file>", "<parameter name>", <value>)
+#' @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)
+# <list, length = num of unique def file params to change>
+#   <list, length = 3, elements in order: def file path, variable name, value to be set to>
+#   < 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:
+# <list, length = num of unique def file params to change>
+#   <list, length = 3, elements in order: def file path, variable name, VECTOR of values to be set to>
+#   < 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)
+
+}

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("<def file>", "<parameter name>", <value>)
+#' @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)
+
+}

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)
+
+}