Final fixes for CRAN

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: pastclim
 Type: Package
 Title: Manipulate Time Series of Palaeoclimate Reconstructions 
-Version: 1.2.0
+Version: 1.2.1
 Authors@R: c(
        person("Michela", "Leonardi", role = "aut"),
        person(c("Emily","Y."), "Hallet", role = "ctb"),
@@ -11,8 +11,9 @@ Authors@R: c(
          email = "[email protected]")
      )
 Maintainer: Andrea Manica <[email protected]>
-Description: This R package is designed to provide an easy way to extract and manipulate palaeoclimate
-  reconstructions for ecological and anthropological analyses.
+Description: Methods to easily extract and manipulate palaeoclimate
+  reconstructions for ecological and anthropological analyses, as described
+  in Leonardi et al. (2022) <doi:10.1101/2022.05.18.492456>.
 License: CC BY 4.0
 Language: en-GB
 URL: https://github.com/EvolEcolGroup/pastclim,

NAMESPACE

@@ -23,6 +23,7 @@ export(region_slice)
 export(sample_region_series)
 export(sample_region_slice)
 export(set_data_path)
+export(set_data_path_for_CRAN)
 export(slice_region_series)
 export(time_bp)
 export(time_series_for_locations)

R/get_data_path.R

@@ -25,8 +25,8 @@ get_data_path <- function(silent=FALSE) {
       "pastclim_data.txt"
     ))) {
       if (!silent) {
-        message("A default data_path was not set for pastclim\n",
-                "Use `set_data_path()` to set it")
+        message("A default data_path was not set for pastclim;\n",
+                "use `set_data_path()` to set it.")
       }
       return(NULL)
     }
@@ -35,8 +35,8 @@ get_data_path <- function(silent=FALSE) {
       "pastclim_data.txt"
     ))[1, 1]
     if (!dir.exists(path_to_nc)){
-      error("the path ",path_to_nc," from the config file does not exist!\n",
-            "you can reset the path with `set_data_path`")
+      stop("The path ",path_to_nc," from the config file does not exist!\n",
+            "You can reset the path with `set_data_path`.")
     }
     return(path_to_nc)
   }

R/set_data_path.R

@@ -43,7 +43,7 @@ set_data_path <- function(path_to_nc = NULL, ask = TRUE, write_config = TRUE,
                               "You will have to reset the path when R is restarted.\n")
     }
     message_to_user<-paste0(message_to_user,"Proceed?")
-    user_choice <- menu(c("Yes","No"), title = message_to_user)
+    user_choice <- utils::menu(c("Yes","No"), title = message_to_user)
   } else { # else, if we don't ask, answer yes
     user_choice <- 1 
   }
@@ -103,3 +103,24 @@ copy_example_data <- function() {
   return(TRUE)
 }
 
+#' Set the data path for examples on CRAN
+#'
+#' Users should NOT need this function. It is used to set up a
+#' data path in the temporary directory for examples and tests
+#' to run on CRAN.
+#' 
+#' @returns None
+#' @export
+
+
+set_data_path_for_CRAN <- function() {
+  # set up data path for this test
+  data_path <- file.path(tempdir(),"pastclim_data")
+  # clear it if it exists
+  unlink(data_path, recursive = TRUE)
+  # set data path
+  set_data_path(path_to_nc = data_path,
+                ask = FALSE,
+                write_config = FALSE,
+                copy_example = TRUE)
+}

R/var_labels.R

@@ -17,6 +17,10 @@
 #' @examples
 #' var_labels("bio01", dataset = "Example")
 #' 
+#' # set the data_path for this example to run on CRAN
+#' # users don't need to run this line
+#' set_data_path_for_CRAN()
+#' 
 #' # for a SpatRaster
 #' climate_20k <- region_slice(
 #' time_bp = -20000,

vignettes/a0_pastclim_overview.Rmd

@@ -94,37 +94,32 @@ library(pastclim)
 set_data_path()
 ```
 
-```{r echo=FALSE}
-data_path <- file.path(tempdir(),"pastclim_data")
-unlink(data_path, recursive = TRUE) # it should not exist, but remove it just in case
-# set data path
-set_data_path(path_to_nc = data_path,
-              ask = FALSE,
-              write_config = FALSE,
-              copy_example = TRUE)
+```{r echo=FALSE, results='hide'}
+library(pastclim)
+set_data_path_for_CRAN()
 ```
 
-
 ```
-The data_path will be set to /home/am315/.local/share/R/pastclim.
-A copy of the Example dataset will be copied there.
-This path will be saved by pastclim for future use.
-Proceed? 
-
-1: Yes
-2: No
+#> The data_path will be set to /home/andrea/.local/share/R/pastclim.
+#> A copy of the Example dataset will be copied there.
+#> This path will be saved by pastclim for future use.
+#> Proceed? 
+#> 
+#> 1: Yes
+#> 2: No
 ```
 
+Press 1 if you are happy with the offered choices, and `pastclim`
+will remember your data path in future sessions. Note that your
+data path will look different than in this example, as it depends
+on your user name and operating system.
 
 If you prefer using a custom path (e.g. in "~/my_reconstructions"), it can be set with:
 
 ```{r eval=FALSE}
 set_data_path(path_to_nc = "~/my_reconstructions")
 ```
 
-`pastclim` will remember this new path in the future, even after closing and restarting
-R.
-
 The package includes a small dataset, *Example*, that we will use in this vignette but is not suitable for running analyses;
 the real datasets are large (from 100s of Mb to a few Gb), and you will need to specify
 what you want to download (see below).

vignettes/a1_available_datasets.Rmd

@@ -21,6 +21,20 @@ A number of datasets are available in pastclim. It is possible to use custom dat
 
 ```{r}
 library(pastclim)
+```
+
+```{r echo=FALSE, results='hide'}
+data_path <- file.path(tempdir(),"pastclim_data")
+# clear it in case it exists already
+unlink(data_path, recursive = TRUE) 
+# set data path
+set_data_path(path_to_nc = data_path,
+              ask = FALSE,
+              write_config = FALSE,
+              copy_example = TRUE)
+```
+
+```{r}
 get_available_datasets()
 ```
 

vignettes/a2_custom_datasets.Rmd

@@ -65,9 +65,23 @@ ncdf4::nc_close(nc_in)
 
 ```
 
-We can now read in our custom netcdf file.
+We can now read in our custom netcdf file with `pastclim`.
 ```{r}
 library(pastclim)
+```
+
+```{r echo=FALSE, results='hide'}
+data_path <- file.path(tempdir(),"pastclim_data")
+# clear it in case it exists already
+unlink(data_path, recursive = TRUE) 
+# set data path
+set_data_path(path_to_nc = data_path,
+              ask = FALSE,
+              write_config = FALSE,
+              copy_example = TRUE)
+```
+
+```{r}
 custom_series <- region_series(bio_variables = "bio01",
                                 dataset = "custom",
                                 path_to_nc = nc_name
@@ -92,7 +106,7 @@ it allows for smaller files).
 
 # Making the data available to others
 
-Once you have created suitably fomatted netcdf files that can be used as custom datasets in 
+Once you have created suitably formatted netcdf files that can be used as custom datasets in 
 `pastclim`, you can add those data officially to the package, and thus make them available
 to others. Here are the necessary steps:
 
@@ -142,6 +156,6 @@ the *nc* dataset.
 3) Once you have added lines detailing the variables in your dataset, run the script "./inst/rawdata_scripts/create_files_by_dataset.R" to store
 that information into the appropriate dataset in `pastclim`.
 
-4) Provide information on the new dataset in the file "./R/dataset_docs", using `roxygen2` notation. Make sure that you provide an appropriate reference for the original data, as it is important that users can refer back to the original source.
+4) Provide information on the new dataset in the file "./R/dataset_docs", using `roxygen2` syntax. Make sure that you provide an appropriate reference for the original data, as it is important that users can refer back to the original source.
 
 4) Make a Pull Request on GitHub.