Fixing moses analyses to work with spatvector

Our do.call rbind magic stopped working, turns out with terra all you need to do is call vect() on a list and it does the trick quite handily!
danlwarren · Jan 16, 2024 · 74b2078 · 74b2078
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commit 74b2078
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Showing 4 changed files with 5 additions and 5 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: ENMTools
 Type: Package
 Title: Analysis of Niche Evolution using Niche and Distribution Models
-Version: 1.1.1
+Version: 1.1.2
 Date: 2024-01-10
 Encoding: UTF-8
 Authors@R: c(person(given = "Dan", family = "Warren", role = c("aut", "cre"), email = "dan.l.warren@gmail.com", comment = c(ORCID = "0000-0002-8747-2451")),

diff --git a/R/check.species.R b/R/check.species.R
@@ -92,7 +92,7 @@ check.species <- function(this.species, env = NA, trim.dupes = FALSE){
 }
 
 
-format.latlon <- function(latlon){
+reformat.latlon <- function(latlon){
 
   # Basically this bit just tries to auto-identify the lat and lon columns, then returns a
   # reformatted data frame with col names "x" and "y"

diff --git a/R/moses.list.R b/R/moses.list.R
@@ -34,8 +34,8 @@ moses.list <- function(species.list, env, f = NULL, eval = FALSE, nback = 1000,
   names(separate.glms) <- lapply(species.list, function(x) x$species.name)
   separate.aic <- sum(unlist(lapply(separate.glms, function(x) x$model$aic)))
 
-  combined.species <- enmtools.species(presence.points = as.data.frame(do.call("rbind", lapply(species.list, function(x) rbind(x$presence.points)))),
-                                       background.points = as.data.frame(do.call("rbind", lapply(species.list, function(x) rbind(x$background.points)))),
+  combined.species <- enmtools.species(presence.points = terra::vect(lapply(species.list, function(x) rbind(x$presence.points))),
+                                       background.points = terra::vect(lapply(species.list, function(x) rbind(x$background.points))),
                                        species.name = "combined")
   combined.glm <- enmtools.glm(combined.species, env, f, eval, verbose = verbose, step = step, ...)
   combined.aic <- combined.glm$model$aic

diff --git a/R/utils.R b/R/utils.R
@@ -36,7 +36,7 @@ check.points <- function(pts, name = "input") {
     warning(sprintf('%s are not the expected SpatVector class (instead, it is of class %s). ENMTools will attempt to coerce using terra::vect(as.matrix(...), crs = "EPSG:4326"), but we cannot guaranteed the correctness of the result. Please consider using SpatVector format directly in the future, to minimize unexpected results.',
             name,
             cls))
-    pts <- format.latlon(pts)
+    pts <- reformat.latlon(pts)
     pts <- terra::vect(as.matrix(pts), crs = "EPSG:4326")
   }
   pts