debug strategies for workign on new platform

buildZoopModel.R

@@ -31,7 +31,12 @@ version = "vtest.percentile.method.pcal"
 fp_md = "../calanus_data/Data/Databases/zooplankton_covar_data"
 species = "ctyp"
 biomod_dataset = "ECOMON"
-fp_covars = "Env_Covars"
+hostname = system("hostname", intern = TRUE)
+fp_covars = if (grepl("ecocast", hostname, fixed = TRUE)){
+  "/mnt/s1/projects/ecocast/projectdata/calanus4whales/Env_Covars"
+} else {
+  "Env_Covars"
+}
 env_covars = c("wind", "int_chl", "sst", "sst_grad", "jday", "uv_grad", "bat", "slope", "bots", "bott")
 years = 2003:2017
 fp_out = "../Models.Test"

test.R

@@ -20,13 +20,19 @@ if (!dir.exists(fp_config)) {
 # Whether to overwrite yaml file, if one already exists
 overwrite <- FALSE
 
+hostname = system("hostname", intern = TRUE)
+
 # Example parameters for test run
 params <- list(
   version = "vtest.percentile.method.ctyp",
   fp_md = "../calanus_data/Data/Databases/zooplankton_covar_data",
   species = "ctyp",
   biomod_dataset = "ECOMON",
-  fp_covars = "Env_Covars",
+  fp_covars = if (grepl("ecocast", hostname, fixed = TRUE)){
+      "/mnt/s1/projects/ecocast/projectdata/calanus4whales/Env_Covars"
+    } else {
+      "Env_Covars"
+    },
   env_covars = c("int_chl", "sst", "bat"),
   years = 2003:2006,
   fp_out = "../Models.Test",
@@ -49,6 +55,21 @@ if (!dir.exists(dir_version) | overwrite) {
 # Read in parameters (a bit redundant, but makes it traceable, ideally YAML is written in separate file)
 config <- yaml::read_yaml(filename)
 
+if (FALSE){
+  version = config$version
+   fp_md = config$fp_md
+   species = config$species
+   biomod_dataset = config$biomod_dataset
+   fp_covars = config$fp_covars
+   env_covars = config$env_covars
+   years = config$years
+   fp_out = config$fp_out
+   threshold = config$threshold
+   format_data = config$format_data
+   overwrite_proj = TRUE
+   fp_zpd = NULL
+}
+
 threshold <- buildZoopModel(version = config$version, 
              fp_md = config$fp_md, 
              species = config$species,