Adding in remaining maxent related functions and test scripts

R/env_stack_transform.R

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+#' @title Coverts a list of 'SpatRaster' stacks where the elements are environmental
+#' variables and the layers are depths to a list of SpatRaster stacks where the elements
+#' are depths and the layers are environmental variables
+#'
+#' @description A user will likely already have environmental data organized into a list
+#' of 'spatRaster' stacks where each element is a different environmental variable and each
+#' layer corresponds to a depth slice for background sampling and extracting. However, the
+#' maxent_3D function requires the data be input as a list of 'spatRaster' stacks where
+#' each element corresponds to a depth slice and each layer is an environmental variable
+#' for the purpose of projecting the model back into geographic space, and this function
+#' has been developed for ease of conversion.
+#'
+#' @param envs_all a list of 'spatRaster' stacks where each element is a different
+#' environmental variable and each layer is a depth slice.
+#'
+#' @param envs_names A 'character' vector of the names of the environmental variables
+#' to be applied to the layers of the resulting list of 'spatRaster' stacks
+#'
+#' @details The extents of each environmental variable layer should match on a depth slice
+#' by depth slice basis.
+#'
+#' @return A list of 'spatRaster' stacks where each list element is a depth slice and
+#' each layer is an environmental variable.
+#'
+#' @examples
+#' library(terra)
+#'
+#' # creating a list of spatRaster stacks where each element is an environmental variable
+#' and each layer is a depth
+#'
+#' env1_d1 <- rast(ncol = 50, nrow = 50)
+#' values(env1_d1) <- sample(c(1:100), size = 2500, replace = T)
+#' env2_d1 <- rast(ncol = 50, nrow = 50)
+#' values(env2_d1) <- sample(c(1:100), size = 2500, replace = T)
+#' env1_d2 <- rast(ncol = 50, nrow = 50)
+#' values(env1_d2) <- sample(c(1:100), size = 2500, replace = T)
+#' env2_d2 <- rast(ncol = 50, nrow = 50)
+#' values(env2_d2) <- sample(c(1:100), size = 2500, replace = T)
+#'
+#' env1 <- c(env1_d1, env1_d2)
+#' env2 <- c(env2_d1, env2_d2)
+#' envs <- list(env1, env2)
+#' envnames <- c("env1", "env2")
+#'
+#' # Here's the function
+#' result <- env_stack_transform(envs_all = envs, envs_names = envnames)
+#'
+#' @import terra
+#'
+#' @keywords transform list SpatRaster stack
+#'
+#' @export
+
+
+env_stack_transform <- function(envs_all, envs_names) {
+  env_call <- vector(length = length(envs_all))
+  for (i in 1:length(envs_all)) {
+    place <- paste0("envs_all[[", i, "]][[i]]")
+    env_call[i] <- place
+  }
+
+  stack_list_all <- vector("list", length = dim(envs_all[[1]])[3])
+  for (i in 1:dim(envs_all[[1]])[3]) {
+    j_list <- vector("list", length = length(env_call))
+    for (j in 1:length(env_call)) {
+      j_list[[j]] <- eval(parse(text = env_call[j]))
+    }
+    st <- rast(j_list)
+    names(st) <- envs_names
+    stack_list_all[[i]] <- st
+  }
+  return(stack_list_all)
+}