In wallace: A Modular Platform for Reproducible Modeling of Species Niches and Distributions

```{asis, echo = {{envs_userEnvs_knit}}, eval = {{envs_userEnvs_knit}}, include = {{envs_userEnvs_knit}}}

Obtain environmental data

Using user-specified variables.

```r}, include = {{envs_userEnvs_knit}}}
## Specify the directory with the environmental variables
dir_envs_{{spAbr}} <- ""
envs_path <- file.path(dir_envs_{{spAbr}}, {{userRasName_rmd}})
# Create environmental object 
envs_{{spAbr}} <- envs_userEnvs(
  rasPath = envs_path,
  rasName = {{userRasName_rmd}},
  doBrick = {{userBrick_rmd}})
occs_xy_{{spAbr}} <- occs_{{spAbr}}[c('longitude', 'latitude')]
occs_vals_{{spAbr}} <- as.data.frame(raster::extract(envs_{{spAbr}}, occs_xy_{{spAbr}}, cellnumbers = TRUE))
# Remove duplicated same cell values
occs_{{spAbr}} <- occs_{{spAbr}}[!duplicated(occs_vals_{{spAbr}}[, 1]), ]
occs_vals_{{spAbr}} <- occs_vals_{{spAbr}}[!duplicated(occs_vals_{{spAbr}}[, 1]), -1]
# remove occurrence records with NA environmental values
occs_{{spAbr}} <- occs_{{spAbr}}[!(rowSums(is.na(occs_vals_{{spAbr}})) >= 1), ]
# also remove variable value rows with NA environmental values
occs_vals_{{spAbr}} <- na.omit(occs_vals_{{spAbr}})
# add columns for env variable values for each occurrence record
occs_{{spAbr}} <- cbind(occs_{{spAbr}}, occs_vals_{{spAbr}})

wallace documentation built on Sept. 11, 2024, 9:16 p.m.