Replace function with data object

Fix #134

.Rbuildignore

@@ -10,3 +10,4 @@
 ^appveyor\.yml$
 ^\.github$
 ^codecov\.yml$
+^data-raw$

NAMESPACE

@@ -11,7 +11,6 @@ export(get_table_pathways)
 export(indicator_introduction_year)
 export(indicator_native_range_year)
 export(indicator_total_year)
-export(pathways_cbd)
 export(update_download_list)
 export(verify_taxa)
 export(visualize_pathways_level1)

R/data-pathways_cbd.R

@@ -0,0 +1,10 @@
+#' Pathways of introduction as defined by the Convention on Biological Diversity
+#'
+#' This data frame contains all pathways of introdution at level 1
+#' (`pathway_level1`) and level 2 (`pathway_level2`) as defined by the
+#' Convention on Biological Diversity (CBD). Added pathway `unknown` at level 1
+#' and level 2 for classifying taxa without pathway (at level 1 or level 2)
+#' information.
+#' 
+#' @family pathways data
+"pathways_cbd"

R/visualize_pathways_level1.R

@@ -326,7 +326,7 @@ visualize_pathways_level1 <- function(df,
     ))
   # Import all CBD pathways level 1
   pathways_level1_all <-
-    pathways_cbd() %>%
+    pathways_cbd %>%
     dplyr::distinct(.data$pathway_level1)
   # Select pathways
   if (!is.null(pathways)) {

R/visualize_pathways_level2.R

@@ -7,7 +7,7 @@
 #' @param df df.
 #' @param chosen_pathway_level1 character. A pathway level 1. If CBD standard is
 #'   followed (see argument `cbd_standard`), one of the level 1 pathways from
-#'   `pathways_cbd()`.
+#'   `pathways_cbd`.
 #' @param category `NULL` (default) or character. One of the kingdoms as given
 #'   in GBIF or `Chordata` (the phylum) or `Not Chordata` (all other phyla of
 #'   `Animalia`):
@@ -51,7 +51,7 @@
 #' @param first_observed character. Name of the column of `df` containing
 #'   information about year of introduction. Default: `"first_observed"`.
 #' @param cbd_standard logical. If `TRUE` the values of pathway level 2 are
-#'   checked based on CBD standard as returned by `pathways_cbd()`. Error is
+#'   checked based on CBD standard in `pathways_cbd`. Error is
 #'   returned if unmatched values are found. If `FALSE`, a warning is returned.
 #'   Default: `TRUE`.
 #' @param title `NULL` or character. Title of the graph. Default: `NULL`.
@@ -398,7 +398,7 @@ visualize_pathways_level2 <- function(df,
     ))
   # Import all CBD pathways level 2 within chosen pathway level 1
   pathways_level2_all <-
-    pathways_cbd() %>%
+    pathways_cbd %>%
     dplyr::filter(.data$pathway_level1 == chosen_pathway_level1) %>%
     dplyr::distinct(.data$pathway_level2)
   # Select pathways

R/visualize_pathways_year_level1.R

@@ -44,7 +44,7 @@
 #' @param first_observed character. Name of the column of `df` containing
 #'  information about year of introduction. Default: `"first_observed"`.
 #' @param cbd_standard logical. If `TRUE` the values of pathway level 1 are
-#'   checked based on CBD standard as returned by `pathways_cbd()`. Error is
+#'   checked based on CBD standard in `pathways_cbd`. Error is
 #'   returned if unmatched values are found. If `FALSE`, a warning is returned.
 #'   Default: `TRUE.`
 #' @param title `NULL` or character. Title of the graph. Default: `NULL`.
@@ -342,7 +342,7 @@ visualize_pathways_year_level1 <- function(
     ))
   # Import all CBD pathways level 1
   pathways_level1_all <-
-    pathways_cbd() %>%
+    pathways_cbd %>%
     dplyr::distinct(.data$pathway_level1)
   # Select pathways
   if (!is.null(pathways)) {

R/visualize_pathways_year_level2.R

@@ -48,7 +48,7 @@
 #' @param first_observed character. Name of the column of `df` containing
 #'   information about year of introduction. Default: `"first_observed"`.
 #' @param cbd_standard logical. If `TRUE` the values of pathway level 1 are
-#'   checked based on CBD standard as returned by `pathways_cbd()`. Error is
+#'   checked based on CBD standard in `pathways_cbd()`. Error is
 #'   returned if unmatched values are found. If `FALSE`, a warning is returned.
 #'   Default: `TRUE`.
 #' @param title `NULL` or character. Title of the graph. Default: `NULL`.
@@ -405,7 +405,7 @@ visualize_pathways_year_level2 <- function(
     ))
   # Import all CBD pathways level 2 within chosen pathway level 1
   pathways_level2_all <-
-    pathways_cbd() %>%
+    pathways_cbd %>%
     dplyr::filter(.data$pathway_level1 == chosen_pathway_level1) %>%
     dplyr::distinct(.data$pathway_level2)
   # Select pathways

R/pathways_cbd.R → data-raw/pathways_cbd.R

@@ -1,17 +1,6 @@
-#' Pathways of introduction as defined by CBD
-#'
-#' Function to get all CBD pathays of introdution at level 1 (`pathway_level1`)
-#' and level 2 (`pathway_level2`). Added pathway `unknown` at level 1 and level
-#' 2 for classifying taxa without pathway (at level 1 or level 2) information.
-#'
-#' @return A tibble data.frame with 2 columns: `pathway_level1` and
-#'   `pathway_level2`.
-#' @export
-#' @usage pathways_cbd()
+# Code to prepare `pathwayscbd` dataset
 
-pathways_cbd <- function() pathwayscbd
-
-pathwayscbd <- dplyr::tibble(
+pathways_cbd <- dplyr::tibble(
   pathway_level1 = c(
     rep("release", 9),
     rep("escape", 13),
@@ -75,3 +64,5 @@ pathwayscbd <- dplyr::tibble(
     "unknown"
   )
 )
+
+# Then run `usethis::use_data(pathways_cbd, overwrite = TRUE)`

tests/testthat/test-visualize_pathways_level1.R

@@ -8,7 +8,7 @@ input_test_df <- read.delim(
 )
 
 valid_pathways <-
-  pathways_cbd() %>%
+  pathways_cbd %>%
   dplyr::distinct(pathway_level1) %>%
   dplyr::pull()
 

tests/testthat/test-visualize_pathways_level2.R

@@ -9,7 +9,7 @@ input_test_df <- read.delim(
 
 
 valid_pathways_escape <-
-  pathways_cbd() %>%
+  pathways_cbd %>%
   filter(pathway_level1 == "escape") %>%
   distinct(pathway_level2) %>%
   pull()

tests/testthat/test-visualize_pathways_year_level1.R

@@ -15,7 +15,7 @@ n_first_observed_na <-
   nrow(input_test_df_with_nas) - nrow(input_test_df)
 
 valid_pathways <-
-  pathways_cbd() %>%
+  pathways_cbd %>%
   dplyr::distinct(pathway_level1) %>%
   dplyr::pull()
 

tests/testthat/test-visualize_pathways_year_level2.R

@@ -31,7 +31,7 @@ input_test_df_other_colnames <-
   )
 
 valid_pathways_escape <-
-  pathways_cbd() %>%
+  pathways_cbd %>%
   dplyr::filter(pathway_level1 == "escape") %>%
   dplyr::distinct(pathway_level2) %>%
   dplyr::pull()