From eb11c024c9afd32fc7b15da7b2762e8b33eda6db Mon Sep 17 00:00:00 2001
From: Maria Voigt <maria.voigt@idiv.de>
Date: Tue, 5 Sep 2017 10:46:08 +0200
Subject: [PATCH] fixing bug in prediction
---
src/prediction/abundance_prediction.R | 15 ++++++++++-----
1 file changed, 10 insertions(+), 5 deletions(-)
diff --git a/src/prediction/abundance_prediction.R b/src/prediction/abundance_prediction.R
index 1991647..a2fa220 100644
--- a/src/prediction/abundance_prediction.R
+++ b/src/prediction/abundance_prediction.R
@@ -57,10 +57,12 @@ option_list <- list (
default = TRUE,
help = "don't print all intermediate results"))
+
# verbose option a bit counterintuitive
# because I make action store_false, when I say -q that
# means that verbose == F, which is quiet
-
+print("pass checkpoint")
+option_list
options <- parse_args(OptionParser(option_list=option_list))
@@ -102,7 +104,7 @@ if(is_verbose){print(paste("indir", indir))}
outdir <- options$output_directory
if(is_verbose){print(paste("outdir", outdir))}
-indir_model <- option$input_model
+indir_model <- options$input_model
if(is_verbose){print(paste("indir_model", indir_model))}
@@ -113,7 +115,7 @@ print(paste("for year to predict" , year_to_predict))
exclude_year <- as.numeric(options$exclude_year)
if(is_verbose){print(paste("exclude year", exclude_year))}
-focal_change_predictor <- options$focal_change_predictor
+focal_change_predictor <- as.numeric(options$focal_change_predictor)
if(is_verbose){print(paste("focal_change_predictor", focal_change_predictor))}
if(is_verbose){print(paste(Sys.time(), "0. start run"))}
@@ -199,13 +201,14 @@ predictors_obs_path <- path.to.current(indir,
paste0("predictors_observation_scaled_",
name_suffix),
"rds")} else{
-predictors_obs_path <- path.to.current(indir, "predictors_observation_scaled_",
+predictors_obs_path <- path.to.current(indir_model, "predictors_observation_scaled_",
"rds")}
if(is_verbose){print(paste("this is predictors-obs path", predictors_obs_path))}
predictors_obs <- readRDS(predictors_obs_path)
+
# Scale the grid-predictors using mean and sd of predictors_obs
# predictors for scaling
@@ -242,10 +245,12 @@ saveRDS(predictors_grid, file.path(outdir, paste0("predictors_grid_scaled_", nam
#-------------------------------------#
if(!is.na(focal_change_predictor)){
# load 1999 value to add the values, but use the scaled table
- predictors_grid_1999_path <- path.to.current(indir,
+ predictors_grid_1999_path <- path.to.current(indir_model,
paste0("predictors_grid_scaled_",
1999),
"rds")
+
+ print(predictors_grid_1999_path)
predictors_grid_1999 <- readRDS( predictors_grid_1999_path)
change_predictors <- c("year", "peatswamp",
"lowland_forest",
--
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