Merge pull request #24 from tece-lab/upbound

Added upper bound parameter integration to DAISIE scripts

DESCRIPTION

@@ -50,5 +50,3 @@ Imports:
     DAISIE (>= 4.2.1),
     ggplot2,
     cowplot
-Remotes: 
-    rsetienne/DAISIE@relaxed

R/default_params_doc.R

@@ -202,6 +202,10 @@
 #'   of the largest clade.
 #' @param prop_type2_pool A numeric determining the proportion of the mainland
 #'   species pool that is composed on type 2 species.
+#' @param par_upper_bound A numeric defining the upper limit of the integration
+#'   of a parameter when fitting the relaxed-rate DAISIE model. If the DAISIE
+#'   model being applied is not the relaxed-rate model, this parameter can be
+#'   ignored and left as its default as it does not influence the model.
 #'
 #' @return Nothing
 #' @keywords internal
@@ -244,6 +248,7 @@ default_params_doc <- function(model,
                                low_rates,
                                rep_index,
                                res,
-                               prop_type2_pool) {
+                               prop_type2_pool,
+                               par_upper_bound) {
   # Nothing
 }

R/run_daisie_ml.R

@@ -30,6 +30,7 @@ run_daisie_ml <- function(daisie_data,
                           low_rates = FALSE,
                           rep_index = "NULL",
                           res = 100,
+                          par_upper_bound = Inf,
                           test = FALSE) {
   if (test) {
     seed <- array_index
@@ -63,7 +64,8 @@ run_daisie_ml <- function(daisie_data,
 
   model_arguments <- setup_model(
     model = model,
-    low_rates = low_rates
+    low_rates = low_rates,
+    par_upper_bound = par_upper_bound
   )
 
   initparsopt <- model_arguments$initparsopt

R/setup_model.R

@@ -12,7 +12,8 @@
 #'   model = model
 #' )
 setup_model <- function(model,
-                        low_rates = FALSE) {
+                        low_rates = FALSE,
+                        par_upper_bound = Inf) {
   expected_models <- get_available_models()
   testit::assert(model %in% expected_models)
 
@@ -75,31 +76,36 @@ setup_model <- function(model,
     if (grepl("rr_lac", model)) {
       cs_version <- DAISIE::create_CS_version(
         model = 2,
-        relaxed_par = "cladogenesis"
+        relaxed_par = "cladogenesis",
+        par_upper_bound = par_upper_bound
       )
     }
     if (grepl("rr_mu", model)) {
       cs_version <- DAISIE::create_CS_version(
         model = 2,
-        relaxed_par = "extinction"
+        relaxed_par = "extinction",
+        par_upper_bound = par_upper_bound
       )
     }
     if (grepl("rr_k", model)) {
       cs_version <- DAISIE::create_CS_version(
         model = 2,
-        relaxed_par = "carrying_capacity"
+        relaxed_par = "carrying_capacity",
+        par_upper_bound = par_upper_bound
       )
     }
     if (grepl("rr_gam", model)) {
       cs_version <- DAISIE::create_CS_version(
         model = 2,
-        relaxed_par = "immigration"
+        relaxed_par = "immigration",
+        par_upper_bound = par_upper_bound
       )
     }
     if (grepl("rr_laa", model)) {
       cs_version <- DAISIE::create_CS_version(
         model = 2,
-        relaxed_par = "anagenesis"
+        relaxed_par = "anagenesis",
+        par_upper_bound = par_upper_bound
       )
     }
   }

bash/submit_run_daisie_ml.sh

@@ -53,6 +53,10 @@
 # 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
+# par_upper_bound - A numeric defining the upper limit of the integration
+# of a parameter when fitting the relaxed-rate DAISIE model. If the DAISIE
+# model being applied is not the relaxed-rate model, this parameter can be
+# ignored and left as its default as it does not influence the model
 
 ################################################################################
 ##### Before running make sure install_DAISIEutils.sh has been run ####
@@ -74,6 +78,7 @@ optimmethod=${7-subplex}
 low_rates=${8-FALSE}
 rep_index=${9-NULL}
 res=${10-100}
+par_upper_bound=${11-Inf}
 seed=${SLURM_ARRAY_TASK_ID}
 
 ml R
@@ -87,4 +92,5 @@ Rscript DAISIEutils/scripts/run_daisie_ml.R ${data} \
                                             ${optimmethod} \
                                             ${low_rates} \
                                             ${rep_index} \
-                                            ${res}
+                                            ${res} \
+                                            ${par_upper_bound}

bash/submit_run_daisie_ml_long.sh

@@ -53,6 +53,10 @@
 # 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
+# par_upper_bound - A numeric defining the upper limit of the integration
+# of a parameter when fitting the relaxed-rate DAISIE model. If the DAISIE
+# model being applied is not the relaxed-rate model, this parameter can be
+# ignored and left as its default as it does not influence the model
 
 ################################################################################
 ##### Before running make sure install_DAISIEutils.sh has been run ####
@@ -73,6 +77,7 @@ optimmethod=${7-subplex}
 low_rates=${8-FALSE}
 rep_index=${9-NULL}
 res=${10-100}
+par_upper_bound=${11-Inf}
 seed=${SLURM_ARRAY_TASK_ID}
 
 ml R
@@ -86,4 +91,5 @@ Rscript DAISIEutils/scripts/run_daisie_ml.R ${data} \
                                             ${optimmethod} \
                                             ${low_rates} \
                                             ${rep_index} \
-                                            ${res}
+                                            ${res} \
+                                            ${par_upper_bound}

scripts/run_daisie_ml.R

@@ -21,7 +21,8 @@ if (identical(args[6], "NULL")) {
     optimmethod = args[8],
     low_rates = as.logical(args[9]),
     rep_index = args[10],
-    res = as.numeric(args[11])
+    res = as.numeric(args[11]),
+    par_upper_bound = as.numeric(args[12])
   )
 } else if (identical(args[6], "NA")){
   DAISIEutils::run_daisie_ml(
@@ -35,7 +36,8 @@ if (identical(args[6], "NULL")) {
     optimmethod = args[8],
     low_rates = as.logical(args[9]),
     rep_index = args[10],
-    res = as.numeric(args[11])
+    res = as.numeric(args[11]),
+    par_upper_bound = as.numeric(args[12])
   )
 } else {
   DAISIEutils::run_daisie_ml(
@@ -49,6 +51,7 @@ if (identical(args[6], "NULL")) {
     optimmethod = args[8],
     low_rates = as.logical(args[9]),
     rep_index = args[10],
-    res = as.numeric(args[11])
+    res = as.numeric(args[11]),
+    par_upper_bound = as.numeric(args[12])
   )
 }