From 318efecb9718b1ae20ccd799f92fee397f1027af Mon Sep 17 00:00:00 2001
From: Maria Voigt <maria.voigt@idiv.de>
Date: Fri, 7 Apr 2017 11:38:31 +0200
Subject: [PATCH] changing the script so dopar over years
---
.../abundance_prediction_bootstrap_per_boot.R | 61 ++++++++-----------
1 file changed, 25 insertions(+), 36 deletions(-)
diff --git a/src/prediction/abundance_prediction_bootstrap_per_boot.R b/src/prediction/abundance_prediction_bootstrap_per_boot.R
index f66f966..718e801 100644
--- a/src/prediction/abundance_prediction_bootstrap_per_boot.R
+++ b/src/prediction/abundance_prediction_bootstrap_per_boot.R
@@ -134,31 +134,35 @@ all_boots <- readRDS(all_boots_path) %>%
# HERE it already starts to be year specific
years_to_predict <- 1999:2015
+#preds 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" )
+
+quadratic_terms_names <- c("rain_dry")
+
-pred_per_boot <- foreach(year_to_predict = years_to_predict, .combine = rbind) %do% {
+pred_per_boot <- foreach(year_to_predict = years_to_predict, .combine = cbind) %dopar% {
suppressPackageStartupMessages(library(stringr))
+suppressMessages(library(doParallel))
+
predictors_grid_path <- path.to.current(indir, paste0("predictors_grid_scaled_",
year_to_predict),
"rds")
-if(is_verbose){print(paste("this is predictors_grid_path", predictors_grid_path))}
-predictors_grid <- readRDS(predictors_grid_path)
- # 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" )
+predictors_grid <- readRDS(predictors_grid_path)
-quadratic_terms_names <- c("rain_dry")
intercept <- rep(1, nrow(predictors_grid))
+
predictor_estimates <- cbind( intercept,
predictors_grid[ , predictor_names],
- predictors_grid[ ,quadratic_terms_names] * predictors_grid[ ,quadratic_terms_names])
-
+ predictors_grid[ ,quadratic_terms_names] * predictors_grid[ ,quadratic_terms_names])
+
names(predictor_estimates) <- c("intercept", predictor_names,
paste0("I(", quadratic_terms_names, "^2)"))
@@ -174,49 +178,30 @@ names(predictor_estimates) <- c("intercept", predictor_names,
if(is_verbose){print(paste("1. start pred_per_cell", Sys.time()))}
-
- #pred_per_cell <- foreach(cell = 1:nrow(predictor_estimates), .combine = c) %dopar% {
- pred_per_cell <- foreach(cell = 1:10, .combine = c) %dopar% {
+ pred_per_cell <- foreach(cell = 1:nrow(predictor_estimates), .combine = c) %do% {
t_predictor_estimates <- t( predictor_estimates[cell, ])
pred_estimates_wcoeffs <- data.frame(mapply(`*`, all_boots[nr_boot, ], t_predictor_estimates, SIMPLIFY = F))
pred_estimate_cell <- apply(pred_estimates_wcoeffs, 1, sum)
pred_estimate_cell <- exp(pred_estimate_cell)
return(pred_estimate_cell)
}
- return(pred_per_boot)
+ return(pred_per_cell)
}
-
if(is_verbose){print(paste(Sys.time(), "2. finished dopar loop"))}
pred_per_boot <- as.data.frame(pred_per_boot)
-sum_years <- as.data.frame(cbind(years_to_predict, pred_per_boot$V1))
-names(sum_years) <- c("year", "sum")
-min_years <- as.data.frame(cbind(years_to_predict, pred_per_boot$V2))
-names(min_years) <- c("year", "min")
-max_years <- as.data.frame(cbind(years_to_predict, pred_per_boot$V3))
-names(max_years) <- c("year", "max")
+names(pred_per_boot) <- paste0("year_", c(1999:2015))
-saveRDS(sum_years,
+saveRDS(pred_per_boot,
file = file.path(outdir,
- paste0("bootstrapped_abundance_sum_boot_",
+ paste0("bootstrapped_pred_per_pixel_",
nr_boot, "_",
Sys.Date(), ".rds")))
-saveRDS(min_years,
- file = file.path(outdir,
- paste0("bootstrapped_abundance_min_boot_",
- nr_boot, "_",
- Sys.Date(), ".rds")))
-
-saveRDS(max_years,
- file = file.path(outdir,
- paste0("bootstrapped_abundance_max_boot_",
- nr_boot, "_",
- Sys.Date(), ".rds")))
@@ -224,3 +209,7 @@ print(paste("Finish model_prediction script for boot", nr_boot,
Sys.time()))
+if (options$worker > 1) {
+ stopCluster(cl)
+ }
+
--
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