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Merge pull request #25 from tece-lab/develop
Adding 2-type and relaxed-rate functionality
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -50,5 +50,3 @@ Imports: | |
| DAISIE (>= 4.2.1), | ||
| ggplot2, | ||
| cowplot | ||
| Remotes: | ||
| rsetienne/DAISIE | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,134 @@ | ||
| #' Run 2 type DAISIE analysis | ||
| #' | ||
| #' @inheritParams default_params_doc | ||
| #' | ||
| #' @return Nothing. Writes [`DAISIE`] analysis results to a `.rds` file. This | ||
| #' file is stored in `file_path`. The directory in of `file_path` is created | ||
| #' if it doesn't exist. | ||
| #' @export | ||
| #' | ||
| #' @examples | ||
| #' \dontrun{ | ||
| #' data(Galapagos_datalist, package = "DAISIE") | ||
| #' run_daisie_2type_ml( | ||
| #' daisie_data = Galapagos_datalist, | ||
| #' data_name = "Galapagos_datalist", | ||
| #' model = "cr_dd", | ||
| #' array_index = 1, | ||
| #' cond = 1 | ||
| #' ) | ||
| #' } | ||
| #' @author Pedro Santos Neves, Joshua W. Lambert, Luis Valente | ||
| run_daisie_2type_ml <- function(daisie_data, | ||
| data_name, | ||
| model, | ||
| array_index, | ||
| cond, | ||
| methode = "lsodes", | ||
| optimmethod = "subplex", | ||
| results_dir = NULL, | ||
| low_rates = FALSE, | ||
| rep_index = "NULL", | ||
| res = 100, | ||
| prop_type2_pool, | ||
| test = FALSE) { | ||
| if (test) { | ||
| seed <- array_index | ||
| } else { | ||
| seed <- as.integer(Sys.time()) %% 10000L * array_index | ||
| } | ||
|
|
||
| set.seed( | ||
| seed, | ||
| kind = "Mersenne-Twister", | ||
| normal.kind = "Inversion", | ||
| sample.kind = "Rejection" | ||
| ) | ||
|
|
||
| print_metadata( | ||
| data_name = data_name, | ||
| model = model, | ||
| array_index = array_index, | ||
| seed = seed, | ||
| methode = methode, | ||
| optimmethod = optimmethod | ||
| ) | ||
|
|
||
| output_folder_path <- create_output_folder( | ||
| data_name = data_name, | ||
| results_dir = results_dir | ||
| ) | ||
|
|
||
| testit::assert(is.numeric(array_index) && is.finite(array_index)) | ||
| testit::assert(is.numeric(cond) && is.finite(cond)) | ||
|
|
||
| model_arguments <- setup_2type_model( | ||
| model = model, | ||
| prop_type2_pool = prop_type2_pool, | ||
| low_rates = low_rates | ||
| ) | ||
|
|
||
| initparsopt <- model_arguments$initparsopt | ||
| idparsnoshift <- model_arguments$idparsnoshift | ||
| idparsopt <- model_arguments$idparsopt | ||
| parsfix <- model_arguments$parsfix | ||
| idparsfix <- model_arguments$idparsfix | ||
| ddmodel <- model_arguments$ddmodel | ||
| cs_version <- model_arguments$cs_version | ||
|
|
||
| ##### ML Optimization #### | ||
| lik_res <- DAISIE::DAISIE_ML( | ||
| datalist = daisie_data, | ||
| initparsopt = initparsopt, | ||
| idparsnoshift = idparsnoshift, | ||
| idparsopt = idparsopt, | ||
| parsfix = parsfix, | ||
| idparsfix = idparsfix, | ||
| res = res, | ||
| ddmodel = ddmodel, | ||
| cond = cond, | ||
| methode = methode, | ||
| optimmethod = optimmethod, | ||
| CS_version = cs_version | ||
| ) | ||
|
|
||
| bic <- calc_bic(results = lik_res, daisie_data = daisie_data) | ||
| lik_res <- cbind(lik_res, bic) | ||
|
|
||
| if (identical(rep_index, "NULL")) { | ||
| output_path <- file.path( | ||
| output_folder_path, | ||
| paste0( | ||
| data_name, | ||
| "_", | ||
| model, | ||
| "_", | ||
| array_index, | ||
| ".rds" | ||
| ) | ||
| ) | ||
| } else { | ||
| output_path <- file.path( | ||
| output_folder_path, | ||
| paste0( | ||
| data_name, | ||
| "_", | ||
| model, | ||
| "_", | ||
| array_index, | ||
| "_", | ||
| rep_index, | ||
| ".rds" | ||
| ) | ||
| ) | ||
| } | ||
|
|
||
| if (is.na(output_path)) { | ||
| return(lik_res) | ||
| } else { | ||
| saveRDS( | ||
| lik_res, | ||
| file = output_path | ||
| ) | ||
| } | ||
| } |
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