Merge pull request #22 from tece-lab/res

Res

R/default_params_doc.R

@@ -119,8 +119,6 @@
 #'   clade in the empirical data
 #' @param ylim4 maximum of the plot of the rank of the largest clade.
 #' @param title title of the plot.
-#' @param res Sets the maximum number of species for which a probability must
-#'   be computed, must be larger than the size of the largest clade.
 #' @param ddmodel Sets the model of diversity-dependence:
 #'   * `ddmodel = 0`: no diversity dependence
 #'   * `ddmodel = 1`: linear dependence in speciation rate
@@ -182,6 +180,10 @@
 #'   of a numeric which is used to detect whether multiple data set from the
 #'   same data source is being run. This is the case, for example, when fitting
 #'   a DAISIE model to a posterior distribution of data.
+#' @param res A numeric determining the resolution of the likelihood
+#'   calculations, it sets the limit for the maximum number of species for
+#'   which a probability must be computed, which must be larger than the size
+#'   of the largest clade.
 #'
 #' @return Nothing
 #' @keywords internal
@@ -212,7 +214,6 @@ default_params_doc <- function(model,
                                sumstats,
                                ylim4,
                                title,
-                               res,
                                ddmodel,
                                verbose,
                                island_ontogeny,
@@ -223,6 +224,7 @@ default_params_doc <- function(model,
                                x_I, # nolint
                                mainland_n,
                                low_rates,
-                               rep_index) {
+                               rep_index,
+                               res) {
   # Nothing
 }

R/run_daisie_ml.R

@@ -29,6 +29,7 @@ run_daisie_ml <- function(daisie_data,
                           results_dir = NULL,
                           low_rates = FALSE,
                           rep_index = "NULL",
+                          res = 100,
                           test = FALSE) {
   if (test) {
     seed <- array_index
@@ -81,8 +82,10 @@ run_daisie_ml <- function(daisie_data,
     idparsopt = idparsopt,
     parsfix = parsfix,
     idparsfix = idparsfix,
+    res = res,
     ddmodel = ddmodel,
     cond = cond,
+    methode = methode,
     optimmethod = optimmethod,
     CS_version = cs_version
   )

R/setup_model.R

@@ -27,7 +27,7 @@ setup_model <- function(model,
   } else {
     lac <- stats::runif(1, min = 0, max = 0.1)
     mu <- stats::runif(1, min = 0, max = 0.1)
-    k <- stats::runif(1, min = 100, max = 200)
+    k <- stats::runif(1, min = 250, max = 500)
     gam <- stats::runif(1, min = 1e-5, max = 0.1)
     laa <- stats::runif(1, min = 0, max = 0.1)
     sd <- stats::runif(1, min = 0.1, max = 1)

bash/submit_run_daisie_ml.sh

@@ -42,6 +42,18 @@
 # model. If left unspecified defaults to the lsodes method.
 # optimmethod - The optimization algorithm used to maximize the likelihood. If
 # left unspecified, the default subplex algorithm is used.
+# low_rates - A boolean determining whether to sample the initial parameter
+# estimates from the standard distribution (FALSE, default) or whether to sample
+# from a restricted distribution in which the upper bound of the initial
+# parameter estimates are lower
+# rep_index - A numeric or NULL which determines whether the data being read is
+# a single data set (i.e. a single replicate), set by NULL which is default, or
+# one of several data sets, in which case the data set to choice is set by
+# rep_index
+# res - A numeric determining the resolution of the likelihood calculations, it
+# sets the limit for the maximum number of species for which a probability
+# must be computed, which must be larger than the size of the largest clade
+
 ################################################################################
 ##### Before running make sure install_DAISIEutils.sh has been run ####
 # Example:
@@ -61,6 +73,7 @@ methode=${6-lsodes}
 optimmethod=${7-subplex}
 low_rates=${8-FALSE}
 rep_index=${9-NULL}
+res=${10-100}
 seed=${SLURM_ARRAY_TASK_ID}
 
 ml R
@@ -73,4 +86,5 @@ Rscript DAISIEutils/scripts/run_daisie_ml.R ${data} \
                                             ${methode} \
                                             ${optimmethod} \
                                             ${low_rates} \
-                                            ${rep_index}
+                                            ${rep_index} \
+                                            ${res}

bash/submit_run_daisie_ml_long.sh

@@ -42,8 +42,18 @@
 # model. If left unspecified defaults to the lsodes method.
 # optimmethod - The optimization algorithm used to maximize the likelihood. If
 # left unspecified, the default subplex algorithm is used.
-# low_rates - A logical, TRUE resulting in a model parametrisation with lower
-# rates.
+# low_rates - A boolean determining whether to sample the initial parameter
+# estimates from the standard distribution (FALSE, default) or whether to sample
+# from a restricted distribution in which the upper bound of the initial
+# parameter estimates are lower
+# rep_index - A numeric or NULL which determines whether the data being read is
+# a single data set (i.e. a single replicate), set by NULL which is default, or
+# one of several data sets, in which case the data set to choice is set by
+# rep_index
+# res - A numeric determining the resolution of the likelihood calculations, it
+# sets the limit for the maximum number of species for which a probability
+# must be computed, which must be larger than the size of the largest clade
+
 ################################################################################
 ##### Before running make sure install_DAISIEutils.sh has been run ####
 # Example:
@@ -61,6 +71,8 @@ results_dir=${5-NULL}
 methode=${6-lsodes}
 optimmethod=${7-subplex}
 low_rates=${8-FALSE}
+rep_index=${9-NULL}
+res=${10-100}
 seed=${SLURM_ARRAY_TASK_ID}
 
 ml R
@@ -72,4 +84,6 @@ Rscript DAISIEutils/scripts/run_daisie_ml.R ${data} \
                                             ${results_dir} \
                                             ${methode} \
                                             ${optimmethod} \
-                                            ${low_rates}
+                                            ${low_rates} \
+                                            ${rep_index} \
+                                            ${res}

scripts/run_daisie_ml.R

@@ -20,7 +20,8 @@ if (identical(args[6], "NULL")) {
     methode = args[7],
     optimmethod = args[8],
     low_rates = as.logical(args[9]),
-    rep_index = args[10]
+    rep_index = args[10],
+    res = as.numeric(args[11])
   )
 } else if (identical(args[6], "NA")){
   DAISIEutils::run_daisie_ml(
@@ -33,7 +34,8 @@ if (identical(args[6], "NULL")) {
     methode = args[7],
     optimmethod = args[8],
     low_rates = as.logical(args[9]),
-    rep_index = args[10]
+    rep_index = args[10],
+    res = as.numeric(args[11])
   )
 } else {
   DAISIEutils::run_daisie_ml(
@@ -46,6 +48,7 @@ if (identical(args[6], "NULL")) {
     methode = args[7],
     optimmethod = args[8],
     low_rates = as.logical(args[9]),
-    rep_index = args[10]
+    rep_index = args[10],
+    res = as.numeric(args[11])
   )
 }