From 2f676f2723389feda85ba208cd17d7ff35e75fe4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?K=C3=B6nig?= <ye87zine@usr.idiv.de>
Date: Thu, 9 Jan 2025 11:08:45 +0100
Subject: [PATCH] some tweaks in presence and absence preparation
---
R/03_01_presence_preparation.R | 3 ++-
R/03_02_absence_preparation.R | 16 +++++++---------
2 files changed, 9 insertions(+), 10 deletions(-)
diff --git a/R/03_01_presence_preparation.R b/R/03_01_presence_preparation.R
index 6344de7..9fb6ee3 100644
--- a/R/03_01_presence_preparation.R
+++ b/R/03_01_presence_preparation.R
@@ -74,5 +74,6 @@ occs_final = st_transform(occs_final, proj_string)
env_data = extract(raster_data, vect(occs_final), ID = F)
# Save occurrences
-occs_final = bind_cols(occs_final, env_data)
+occs_final = bind_cols(occs_final, env_data) %>%
+ drop_na()
save(occs_final, file = "data/r_objects/occs_final.RData")
diff --git a/R/03_02_absence_preparation.R b/R/03_02_absence_preparation.R
index 6104ae6..951dded 100644
--- a/R/03_02_absence_preparation.R
+++ b/R/03_02_absence_preparation.R
@@ -103,12 +103,15 @@ model_data = furrr::future_walk(
abs_prob = spatial_kde * env_kde
while(nrow(abs_spec) < nrow(occs_spec)){
sample_points_raw = st_sample(sampling_region, nrow(occs_spec))
- p = extract(abs_prob, vect(sample_points_raw))$z
+ p = na.omit(extract(abs_prob, vect(sample_points_raw))$z)
x = runif(length(p))
sample_points = sample_points_raw[x<p]
+ if(length(sample_points) == 0){
+ next
+ }
+
samples_required = nrow(occs_spec) - nrow(abs_spec)
-
if(length(sample_points) > samples_required){
sample_points = sample(sample_points, samples_required)
}
@@ -145,11 +148,6 @@ model_data = furrr::future_walk(
#
# ggsave(paste0(species, ".pdf"), path = "plots/pa_sampling", device = "pdf", scale = 2)
- # Split into train and test datasets
- train_index = caret::createDataPartition(pa_spec$present, p = 0.7, list = FALSE)
- pa_spec$train = 0
- pa_spec$train[train_index] = 1
-
# Define cross-validation folds
folds = tryCatch({
spatial_folds = suppressMessages(
@@ -174,9 +172,9 @@ model_data = furrr::future_walk(
save(pa_spec, file = paste0("data/r_objects/pa_sampling/", species, ".RData"))
})
-# Combine presence absence data
+# Combine presence-absence data
files = list.files("data/r_objects/pa_sampling/", full.names = T)
model_data = lapply(files, function(f){load(f); return(pa_spec)}) %>%
bind_rows()
-save(model_data, file = "data/r_objects/model_data.RData")
\ No newline at end of file
+save(model_data, file = "data/r_objects/pa_sampling/model_data.RData")
--
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