Check error message parsing on osx

R/filter_collinear.R

@@ -15,9 +15,9 @@
 #'
 #' @param x A [`terra::SpatRaster`] object, a data.frame (with only numeric
 #' variables)
-#' @param cutoff A numeric value used as a threshold to remove variables. 
+#' @param cutoff A numeric value used as a threshold to remove variables.
 #' For, "cor_caret" and "vif_cor",
-#' it is the pair-wise absolute correlation cutoff, which defaults to 0.7. For 
+#' it is the pair-wise absolute correlation cutoff, which defaults to 0.7. For
 #' "vif_step", it is the variable inflation factor, which defaults to 10
 #' @param verbose A boolean whether additional information should be provided
 #' on the screen
@@ -27,20 +27,20 @@
 #' (note that the function will return an error if the correlation among any of
 #' those variables is higher than the cutoff).
 #' @param method character. One of "cor_caret", "vif_cor" or "vif_step".
-#' @param cor_type character. For methods that use correlation, which type 
+#' @param cor_type character. For methods that use correlation, which type
 #' of correlation: "pearson", "kendall", or "spearman". Defaults to "pearson"
 #' @param max_cells positive integer. The maximum number of cells to be used. If this is smaller than ncell(x), a regular sample of x is used
 #' @param ... additional arguments specific to a given object type
 #' @returns A vector of names of columns that are below the correlation threshold
 #' (when \code{names = TRUE}), otherwise a vector of indices. Note that the indices
 #' are only for numeric variables (i.e. if factors are present, the indices do
 #' not take them into account).
-#' @author for `cor_caret`: Original R code by Dong Li, modified by Max Kuhn 
+#' @author for `cor_caret`: Original R code by Dong Li, modified by Max Kuhn
 #' and Andrea Manica; for `vif_step` and `vif_cor`, original algorithm by Babak
 #' Naimi, rewritten by Andrea Manica for `tidysdm`
-#' @references Naimi, B., Hamm, N.A.S., Groen, T.A., Skidmore, A.K., and 
-#' Toxopeus, A.G. 2014. Where is positional uncertainty a problem for species 
-#' distribution modelling?, Ecography 37 (2): 191-203. 
+#' @references Naimi, B., Hamm, N.A.S., Groen, T.A., Skidmore, A.K., and
+#' Toxopeus, A.G. 2014. Where is positional uncertainty a problem for species
+#' distribution modelling?, Ecography 37 (2): 191-203.
 #' @export
 
 filter_collinear <- function(x,
@@ -94,7 +94,7 @@ filter_collinear.SpatRaster <-
                                   exhaustive = exhaustive)
       } else {
         x_matrix <- stats::na.omit(terra::as.matrix(x))
-        
+
       }
       # now dispatch to the matrix method
       filter_collinear(
@@ -145,8 +145,8 @@ filter_collinear.data.frame <-
      max_cells = max_cells
    )
 }
-    
-    
+
+
 #' @rdname filter_collinear
 #' @export
 filter_collinear.matrix <- function(x,
@@ -161,12 +161,12 @@ filter_collinear.matrix <- function(x,
   if (ncol(x) <2) {
     stop("at least 2 numeric variables are needed")
   }
-  
+
   # check that to_keep is valid
   if (!is.null(to_keep)){
     if (!any(to_keep %in% colnames(x))) {
       stop("to_keep includes variables that are not present in x")
-    }    
+    }
   }
 
   # sample rows if needed
@@ -189,15 +189,15 @@ filter_collinear.matrix <- function(x,
       cutoff = cutoff,
       verbose = verbose,
       to_keep = to_keep
-    )    
+    )
   } else if (method == "vif_cor") {
     vars_kept <- filter_vif_cor(
       x,
       cutoff = cutoff,
       verbose = verbose,
       to_keep = to_keep,
       cor_type = cor_type
-    )    
+    )
   } else {
     stop (
       "the selected method is not valid: only options 'cor_caret', 'vif_step' and 'vif_cor' are accepted."
@@ -216,9 +216,3 @@ filter_collinear.matrix <- function(x,
 }
 
 
-
-################################################################################
-## legacy functions to be eventually removed
-################################################################################
-
-

tests/testthat/test_filter_collinear.R

@@ -34,14 +34,14 @@ test_that("filter collinear variables with cor_caret", {
   # error for defautl object
   expect_error(
     filter_collinear("blah"),
-    "no method available for this object type"
+    "^no method available for this object type"
   )
-  
+
   # sample from data.frame
   set.seed(123)
   expect_true(!identical(filter_collinear(lacerta_thin, max_cells = 100), vars_to_keep))
-  
-  
+
+
   # test method on SpatRaster
   climate_present <- terra::readRDS(system.file("extdata/lacerta_climate_present_10m.rds",
                                       package = "tidysdm"
@@ -61,8 +61,8 @@ test_that("filter collinear variables with vif_step", {
   # we should remove two variables
   expect_true(all(!c("bio01", "bio18") %in% vars_to_keep))
   # now keep them in
-  expect_true(all(c("bio01", "bio18") %in% 
-                    filter_collinear(lacerta_thin, method="vif_step", 
+  expect_true(all(c("bio01", "bio18") %in%
+                    filter_collinear(lacerta_thin, method="vif_step",
                                      to_keep = c("bio01", "bio18"))))
 })
 
@@ -75,7 +75,7 @@ test_that("filter collinear variables with vif_cor", {
   # we should remove two variables
   expect_true(all(!c("bio01", "bio18") %in% vars_to_keep))
   # now keep them in
-  expect_true(all(c("bio01", "bio18") %in% 
-                    filter_collinear(lacerta_thin, method="vif_cor", 
+  expect_true(all(c("bio01", "bio18") %in%
+                    filter_collinear(lacerta_thin, method="vif_cor",
                                      to_keep = c("bio01", "bio18"))))
 })