From 537a87ae0b39bb253e36d2c5e30616625c12852a Mon Sep 17 00:00:00 2001
From: Maria Voigt <maria.voigt@idiv.de>
Date: Mon, 29 May 2017 14:04:33 +0200
Subject: [PATCH] fix bugs in random crossvalidation
---
src/model_fitting/abundance_model.R | 15 +++++++++------
1 file changed, 9 insertions(+), 6 deletions(-)
diff --git a/src/model_fitting/abundance_model.R b/src/model_fitting/abundance_model.R
index 88b1e45..6d7eb95 100644
--- a/src/model_fitting/abundance_model.R
+++ b/src/model_fitting/abundance_model.R
@@ -52,7 +52,7 @@ option_list <- list (
dest = "exclude_grid_rand_perc",
type = "integer",
default = NA,
- help = "percemt cells to be excluded",
+ help = "percent cells to be excluded",
metavar = "10"),
make_option(c("-q", "--quiet"), dest = "verbose_script",
action = "store_false",
@@ -115,6 +115,9 @@ if(is_verbose){print(paste("exclude grid", exclude_grid))}
exclude_grid_rand <- options$exclude_grid_rand
if(is_verbose){print(paste("exclude grid random", exclude_grid_rand))}
+exclude_grid_rand_perc <- options$exclude_grid_rand_perc
+if(is_verbose){print(paste("exclude_grid_rand_perc", exclude_grid_rand_perc))}
+
#---------#
# Globals #
#---------#
@@ -364,7 +367,7 @@ m_terms <- c("1",
"I(rain_dry^2)")
-save.image(file.path(outdir, "image_before_model.RData"))
+save.image(file.path(outdir, paste0("image_before_model_", exclude_grid_rand, ".RData")))
# save model_terms here
model_terms <- names(glm.nb(as.formula(paste("nr_nests~", paste(m_terms,
@@ -513,13 +516,13 @@ results_res <- foreach(i = 1:nrow(all_model_terms),
}
if (!is.na(exclude_grid_rand)){
- predictors_excluded_grid_pred <- predictors_excluded_grid_rand
- predictors_excluded_grid_pred$offset_term <- 0
- prediction_transect_excluded_grid <- predict.glm(res,
+ predictors_excluded_grid_rand_pred <- predictors_excluded_grid_rand
+ predictors_excluded_grid_rand_pred$offset_term <- 0
+ prediction_transect_excluded_grid_rand<- predict.glm(res,
newdata = predictors_excluded_grid_rand,
type = "response")
cross_lm_random = lm(log(predictors_excluded_grid_rand$ou_dens+ 1) ~
- log(prediction_transect_excluded_random + 1))
+ log(prediction_transect_excluded_grid_rand+ 1))
result[ , "R2_cross"] <- summary(cross_lm_random)$r.squared
result[ , "nr_excluded"] <- nr_excluded
--
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