From fd5a8f8043be14bc2a26d438ef21fdcf85ebb144 Mon Sep 17 00:00:00 2001
From: Maria Voigt <maria.voigt@idiv.de>
Date: Fri, 16 Jun 2017 18:05:38 +0200
Subject: [PATCH] including alternative to have focal predictors and name
suffixes
---
src/prediction/abundance_prediction.R | 25 +++++++++++++++----------
1 file changed, 15 insertions(+), 10 deletions(-)
diff --git a/src/prediction/abundance_prediction.R b/src/prediction/abundance_prediction.R
index cb644ec..b5d3525 100644
--- a/src/prediction/abundance_prediction.R
+++ b/src/prediction/abundance_prediction.R
@@ -106,6 +106,9 @@ 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
+if(is_verbose){print(paste("focal_change_predictor", focal_change_predictor))}
+
if(is_verbose){print(paste(Sys.time(), "0. start run"))}
#------------------------#
# command line arguments #
@@ -116,10 +119,12 @@ indir_fun <- "~/orangutan_density_distribution/src/functions/"
crs_aea <- "+proj=aea +lat_1=7 +lat_2=-32 +lat_0=-15 +lon_0=125 +x_0=0
+y_0=0 +ellps=WGS84 +datum=WGS84 +units=m +no_defs" # final projection
-if (is.na(exclude_year)){
- name_suffix <- ""} else {
+if (!is.na(exclude_year)){
name_suffix <- paste0(exclude_year, "_")
- }
+}else{
+ if (!is.na(focal_change_predictor)){
+ name_suffix <- paste0(focal_change_predictor, "_") }else{
+ name_suffix <- ""}}
#----------------#
# Load functions #
@@ -181,10 +186,15 @@ if(is_verbose){print(paste("this is predictors path", predictors_path))}
predictors <- readRDS(predictors_path)
# import here the already z-transformed or not
+
+if (!is.na(exclude_year)){
predictors_obs_path <- path.to.current(indir,
paste0("predictors_observation_scaled_",
name_suffix),
- "rds")
+ "rds")} else{
+predictors_obs_path <- path.to.current(indir, "predictors_observation_scaled_",
+ "rds")}
+
if(is_verbose){print(paste("this is predictors-obs path", predictors_obs_path))}
predictors_obs <- readRDS(predictors_obs_path)
@@ -227,7 +237,7 @@ 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,
paste0("predictors_grid_scaled_",
- name_suffix, 1999),
+ 1999),
"rds")
predictors_grid_1999 <- readRDS( predictors_grid_1999_path)
change_predictors <- c("year", "peatswamp",
@@ -298,11 +308,6 @@ print(paste(Sys.time(),
sum(pred_per_cell$abundance_pred > 10)))
-if (is.na(exclude_year)){
- name_suffix <- ""} else {
- name_suffix <- paste0(exclude_year, "_")
- }
-
saveRDS(pred_per_cell,
file = file.path(outdir,
--
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