From fb0d1b6970fe837920193980ba8a851cbb23b0d0 Mon Sep 17 00:00:00 2001
From: Maria Voigt <maria.voigt@idiv.de>
Date: Wed, 7 Jun 2017 18:25:51 +0200
Subject: [PATCH] two changes, deleting redundant predictor names and
introducing focal change
way to keep changing predictors constant to see their contribution to decline
---
src/prediction/abundance_prediction.R | 36 ++++++++++++++++++++-------
1 file changed, 27 insertions(+), 9 deletions(-)
diff --git a/src/prediction/abundance_prediction.R b/src/prediction/abundance_prediction.R
index 3aaac2e..cb644ec 100644
--- a/src/prediction/abundance_prediction.R
+++ b/src/prediction/abundance_prediction.R
@@ -44,6 +44,11 @@ option_list <- list (
type = "integer",
help = "year of the survey years (1994:2015) to predict abundance to",
metavar = "2015"),
+ make_option("--focal-change-predictor",
+ dest = "focal_change_predictor",
+ type = "character",
+ help = "predictor that is allowed to vary in stability analysis",
+ metavar = "year"),
make_option(c("-q", "--quiet"), dest = "verbose_script",
action = "store_false",
default = TRUE,
@@ -160,6 +165,8 @@ predictor_names_coeffs <- predictor_names_coeffs[predictor_names_coeffs != "(Int
# don't include interaction or quadratic term
predictor_names <- predictor_names_coeffs[!grepl("I(*)", predictor_names_coeffs)]
+
+
#----------------------------#
# Load and prepare estimates #
#----------------------------#
@@ -213,15 +220,26 @@ predictors_grid <- scale.predictors.grid(predictor_names_for_scaling,
saveRDS(predictors_grid, file.path(outdir, paste0("predictors_grid_scaled_", name_suffix,
year_to_predict, "_", Sys.Date(), ".rds")))
-
-
-# predictors used in model
-predictor_names <- c("year", "temp_mean", "rain_var", "rain_dry", "dom_T_OC",
- "peatswamp", "lowland_forest",
- "lower_montane_forest", "deforestation_hansen",
- "human_pop_dens", "ou_killing_prediction",
- "perc_muslim" )
-
+#-------------------------------------#
+# Prepare analysis of decline drivers #
+#-------------------------------------#
+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),
+ "rds")
+ predictors_grid_1999 <- readRDS( predictors_grid_1999_path)
+ change_predictors <- c("year", "peatswamp",
+ "lowland_forest",
+ "lower_montane_forest",
+ "deforestation_hansen")
+ change_predictors <- change_predictors[!change_predictors %in% focal_change_predictor]
+ for (change_predictor in change_predictors){
+ # go through all predictors and set their value to the 1999 value
+ predictors_grid[ , change_predictor] <- predictors_grid_1999[ , change_predictor]
+ }
+}
#--------------------------#
# PREDICTION FOR each year #
--
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