From df109efb66e23c488e9d48c08f41a230b4378b17 Mon Sep 17 00:00:00 2001
From: Maria Voigt <maria.voigt@idiv.de>
Date: Wed, 30 Aug 2017 12:03:48 +0200
Subject: [PATCH] adding a path to the model files in case I don't run the
postprocessing
---
src/prediction/abundance_prediction.R | 9 ++++++++-
1 file changed, 8 insertions(+), 1 deletion(-)
diff --git a/src/prediction/abundance_prediction.R b/src/prediction/abundance_prediction.R
index b5d3525..1991647 100644
--- a/src/prediction/abundance_prediction.R
+++ b/src/prediction/abundance_prediction.R
@@ -34,6 +34,9 @@ option_list <- list (
make_option(c("-i", "--input-directory"), dest = "input_directory",
type = "character", help = "directory with input files",
metavar = "/path/to/input-dir"),
+ make_option(c("--input-model"), dest = "input_model",
+ type = "character", help = "directory with model input files",
+ metavar = "/path/to/input-dir"),
make_option(c("-o", "--output-directory"), dest = "output_directory",
type = "character", help = "directory with output files",
metavar = "/path/to/output-dir"),
@@ -99,6 +102,10 @@ if(is_verbose){print(paste("indir", indir))}
outdir <- options$output_directory
if(is_verbose){print(paste("outdir", outdir))}
+indir_model <- option$input_model
+if(is_verbose){print(paste("indir_model", indir_model))}
+
+
year_to_predict <- as.numeric(options$year_to_predict )
print(paste("for year to predict" , year_to_predict))
@@ -138,7 +145,7 @@ source(file.path(indir_fun, "project_functions/scale.predictors.R"))
# Prepare coefficients #
#----------------------#
# Load coefficients and weights
-abundMod_results_path <- path.to.current(indir, "abundMod_results", "rds" )
+abundMod_results_path <- path.to.current(indir_model, "abundMod_results", "rds" )
if(is_verbose){print(paste("this is abundMod_results_path:", abundMod_results_path))}
abundMod_results <- readRDS(abundMod_results_path)
# exclude the first column, which contains models, exclude the coefficient of the
--
GitLab