Even simpler example files

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: tima
 Title: Taxonomically Informed Metabolite Annotation
-Version: 2.10.0
+Version: 2.10.1
 Authors@R: c(
     person("Adriano", "Rutz", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-0443-9902")),

R/get_example_files.R

@@ -7,28 +7,42 @@
 #' @include go_to_cache.R
 #' @include parse_yaml_paths.R
 #'
+#' @param example The example(s) you want to download
+#'
 #' @return Example files.
 #'
 #' @export
 #'
 #' @examples NULL
-get_example_files <- function() {
-  go_to_cache()
-  message("Features")
-  get_file(
-    url = tima::parse_yaml_paths()$urls$examples$features,
-    export = tima::parse_yaml_paths()$data$source$features
-  )
-  message("Metadata")
-  get_file(
-    url = tima::parse_yaml_paths()$urls$examples$metadata,
-    export = tima::parse_yaml_paths()$data$source$metadata
-  )
-  message("Sirius")
-  get_example_sirius()
-  message("Spectra")
-  get_file(
-    url = tima::parse_yaml_paths()$urls$examples$spectra,
-    export = tima::parse_yaml_paths()$data$source$spectra
+get_example_files <- function(example = c("features", "metadata", "sirius", "spectra")) {
+  stopifnot(
+    "Example files available are `features`, `metadata`, `sirius` and `spectra`." =
+      example %in% c("features", "metadata", "sirius", "spectra")
   )
+  go_to_cache()
+  if ("features" %in% example) {
+    message("Features")
+    get_file(
+      url = tima::parse_yaml_paths()$urls$examples$features,
+      export = tima::parse_yaml_paths()$data$source$features
+    )
+  }
+  if ("metadata" %in% example) {
+    message("Metadata")
+    get_file(
+      url = tima::parse_yaml_paths()$urls$examples$metadata,
+      export = tima::parse_yaml_paths()$data$source$metadata
+    )
+  }
+  if ("sirius" %in% example) {
+    message("Sirius")
+    get_example_sirius()
+  }
+  if ("spectra" %in% example) {
+    message("Spectra")
+    get_file(
+      url = tima::parse_yaml_paths()$urls$examples$spectra,
+      export = tima::parse_yaml_paths()$data$source$spectra
+    )
+  }
 }

codemeta.json

@@ -8,7 +8,7 @@
   "codeRepository": "https://github.com/taxonomicallyinformedannotation/tima",
   "issueTracker": "https://github.com/taxonomicallyinformedannotation/tima/issues",
   "license": "https://spdx.org/licenses/GPL-3.0",
-  "version": "2.10.0",
+  "version": "2.10.1",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
@@ -644,7 +644,7 @@
     "SystemRequirements": null
   },
   "keywords": ["metaboliteannotation", "chemotaxonomy", "scoringsystem", "naturalproducts", "computationalmetabolomics", "taxonomicdistance", "specializedmetabolome"],
-  "fileSize": "3169.746KB",
+  "fileSize": "3170.327KB",
   "citation": [
     {
       "@type": "ScholarlyArticle",

vignettes/articles/II-preparing.Rmd

@@ -175,13 +175,10 @@ The edges are created based on the `spectral entropy similarity` calculated betw
 targets::tar_make(names = matches("fea_edg_spe"))
 ```
 
-If needed, you can get an example of what your minimal feature table should look like by running (no parameters needed):
+If needed, you can get an example of what your minimal feature table should look like by running:
 
 ```{r get-features, results="hide", message=FALSE, warning=FALSE}
-tima::get_file(
-  url = tima::parse_yaml_paths()$urls$examples$features,
-  export = tima::parse_yaml_paths()$data$source$features
-)
+tima::get_example_files(example = "features")
 ```
 
 ```{r prepare-features, results="hide", message=FALSE, warning=FALSE, include = FALSE}