changes: unwrapping examples for exported functions when possible, wi…

…th minor correction when needed.

R/all_out_var.R

@@ -72,7 +72,7 @@ all_out_var <- function(stics_version = "latest") {
 #'
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' # Find by variable name (fuzzy search):
 #' SticsRFiles::get_var_info("lai")
 #'
@@ -138,16 +138,15 @@ get_var_info <- function(var = NULL,
 #' @param version `r lifecycle::badge("deprecated")` `version` is no
 #'   longer supported, use `stics_version` instead.
 #'
-#' @return A boolean vector: `TRUE` if the variable exist, `FALSE` if it doesn't
+#' @return A boolean vector: `TRUE` if the variable exist, `FALSE` otherwise
 #'
 #' @seealso `get_var_info()` for interactive use.
 #'
 #' @export
 #'
 #' @examples
-#' \dontrun{
-#' is_stics_var(c("lai(n)", "masec(n)", "truc"))
-#' }
+#' is_stics_var(c("lai(n)", "masec(n)", "unknown"))
+#'
 is_stics_var <- function(var,
                          stics_version = "latest",
                          version = lifecycle::deprecated()) {

R/convert_xml2txt.R

@@ -22,7 +22,7 @@
 #' @return None
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' xml_path <- "/path/to/corn_plt.xml"
 #' javastics_path <- "/path/to/JavaSTICS/folder"
 #' convert_xml2txt(xml_file = xml_path, java_dir = javastics_path)

R/download_usm_xl.R

@@ -27,7 +27,7 @@
 #' @return A vector of copied files path.
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' download_usm_xl()
 #' download_usm_xl(out_dir = "/path/to/destination/dir")
 #' }
@@ -155,7 +155,7 @@ download_usm_xl <- function(file = NULL,
 #' @return A vector of copied files path.
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' download_usm_csv(out_dir = "/path/to/destination/dir")
 #' }
 #'

R/extract.R

@@ -10,11 +10,10 @@
 #' @export
 #'
 #' @examples
-#' \dontrun{
-#' library(SticsRFiles)
-#' sim <- SticsRFiles::get_sim(workspace = "inst/extdata/stics_example_1")
-#' sim[[1]] # returns a `cropr_simulation` list
-#' }
+#' path <- file.path(get_examples_path("sti"), "workspace1")
+#' sim <- SticsRFiles::get_sim(workspace = path)
+#' # sim returns a `cropr_simulation` list
+#'
 `[.cropr_simulation` <- function(x, ...) {
   l <- unclass(x)[...]
   attr_names <- names(attributes(x))

R/force_param_values.R

@@ -26,11 +26,11 @@
 #' @return A logical status TRUE if successful, FALSE otherwise
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' example_txt_dir <- get_examples_path(file_type = "txt")
 #' force_param_values(example_txt_dir,
 #'   setNames(object = c(220, 330), c("stlevamf", "stamflax")),
-#'   javastics = "/path/to/JavaSTICS/folder"
+#'   javastics = tempdir()
 #' )
 #' }
 #'

R/gen_obs.R

@@ -34,12 +34,9 @@
 #' files (FALSE), TRUE when no errors.
 #'
 #' @examples
-#' \dontrun{
-#'
 #' xl_path <- download_usm_xl(file = "inputs_stics_example.xlsx")
 #' obs_df <- read_params_table(file = xl_path, sheet_name = "Obs")
 #' gen_obs(df = obs_df, out_dir = "/path/to/dest/dir")
-#' }
 #'
 #' @export
 #'

R/gen_sta_xml.R

@@ -39,12 +39,9 @@
 #' @return an invisible xml_document object or a list of
 #'
 #' @examples
-#' \dontrun{
-#'
 #' xl_path <- download_usm_xl(file = "inputs_stics_example.xlsx")
 #' sta_param_df <- read_params_table(file = xl_path, sheet_name = "Station")
-#' gen_sta_xml(out_dir = "/path/to/dest/dir", param_df = sta_param_df)
-#' }
+#' gen_sta_xml(out_dir = tempdir(), param_df = sta_param_df)
 #'
 #' @export
 #'

R/gen_tec_xml.R

@@ -50,12 +50,9 @@
 #' @return an invisible xml_document object or a list of
 #'
 #' @examples
-#' \dontrun{
-#'
 #' xl_path <- download_usm_xl(file = "inputs_stics_example.xlsx")
 #' tec_param_df <- read_params_table(file = xl_path, sheet_name = "Tec")
-#' gen_tec_xml(out_dir = "/path/to/dest/dir", param_df = tec_param_df)
-#' }
+#' gen_tec_xml(out_dir = tempdir(), param_df = tec_param_df)
 #'
 #' @export
 #'

R/gen_usms_xml.R

@@ -51,12 +51,9 @@
 #' @return an invisible xml_document object
 #'
 #' @examples
-#' \dontrun{
-#'
 #' xl_path <- download_usm_xl(file = "inputs_stics_example.xlsx")
 #' usms_param_df <- read_params_table(file = xl_path, sheet_name = "USMs")
 #' gen_usms_xml(usms_out_file = "usms.xml", usms_param = usms_param_df)
-#' }
 #'
 #' @export
 #'

R/gen_usms_xml2txt.R

@@ -45,7 +45,7 @@
 #' have been successfully copied in usms directories
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' javastics <- "/path/to/JavaSTICS/folder"
 #' workspace <- "/path/to/workspace"
 #'

R/gen_varmod.R

@@ -25,13 +25,11 @@
 #' @return None
 #'
 #' @examples
-#' \dontrun{
 #' gen_varmod(".", c("lai(n)", "hauteur"))
-#' gen_varmod("/path/to/stics/workspace", c("lai(n)", "hauteur"))
 #' # Add a variable to the others:
 #' gen_varmod(".", "masec(n)", append = TRUE)
 #' # NB: var.mod will have "lai(n)","hauteur" and "masec(n)"
-#' }
+#'
 #'
 #' @export
 #'

R/get_climate_txt.R

@@ -23,9 +23,9 @@
 #'
 #'
 #' @examples
-#' library(SticsRFiles)
 #' path <- get_examples_path(file_type = "txt")
 #' Meteo <- get_climate_txt(path)
+#'
 #' @export
 #'
 get_climate_txt <- function(workspace = getwd(),

R/get_obs.R

@@ -58,15 +58,16 @@
 #'
 #'
 #' @examples
-#' \dontrun{
+#'
 #' path <- file.path(get_examples_path(file_type = "obs"), "mixed")
 #'
 #' # Get observations for all usms, but only banana has observations:
 #' Meas <- get_obs(path)
+#'
 #' # Get observations only for banana:
 #' Meas_banana <- get_obs(path, "banana")
 #'
-#'
+#' \donttest{
 #' # Get observations with real plant names when plant
 #' # folder is not in the workspace:
 #' get_obs(path, "banana", javastics = "/path/to/JavaSTICS/folder")

R/get_param_info.R

@@ -35,9 +35,9 @@
 #' @export
 #'
 #' @examples
-#'
+#' \donttest{
 #' get_param_info(param = "albedo")
-#' \dontrun{
+
 #' get_param_info(param = "albedo", file = "/path/to/file.xml")
 #'
 #' get_param_info(param = "albedo", formalism = "special")

R/get_param_txt.R

@@ -40,14 +40,12 @@
 #'
 #'
 #' @examples
-#' # Read the interrow distance parameter:
-#' \dontrun{
-#' library(SticsRFiles)
 #' path <- get_examples_path(file_type = "txt")
-#' get_param_txt(path, param = "interrang")
 #'
-#' # Getting varietal values:
+#' # Getting the interrow distance parameter value
+#' get_param_txt(path, param = "interrang")
 #'
+#' # Getting varietal parameters values
 #' # Get the leaf lifespan of the variety used in the usm:
 #' get_param_txt(workspace = path, param = "durvieF")
 #' # Get the leaf lifespan of another variety available in the plant file:
@@ -57,7 +55,7 @@
 #' get_param_txt(workspace = path, param = "durvieF", variety = varieties)
 #' # Or get it from the output of the function returning all parameters:
 #' get_param_txt(workspace = path)$plant$plant1$durvieF
-#' }
+#'
 #'
 #' @export
 get_param_txt <- function(workspace = getwd(),

R/get_plants_nb.R

@@ -16,8 +16,6 @@
 #' @return A named numeric vector of plants number per usm
 #'
 #' @examples
-#' \dontrun{
-#'
 #' # Xml case
 #' xml_usms <- file.path(get_examples_path(file_type = "xml"), "usms.xml")
 #' get_plants_nb(xml_usms)
@@ -27,7 +25,6 @@
 #' # Txt case
 #' txt_usm <- file.path(get_examples_path(file_type = "txt"), "new_travail.usm")
 #' get_plants_nb(txt_usm)
-#' }
 #'
 #' @export
 #'

R/get_report_results.R

@@ -21,7 +21,6 @@
 #' @export
 #'
 #' @examples
-#' \dontrun{
 #' path <- get_examples_path(file_type = "sti")
 #' get_report_results(workspace = path)
 #'
@@ -34,7 +33,7 @@
 #' get_report_results(workspace = path)
 #'
 #' get_report_results(workspace = path, file_name = "mod_rapportA.sti")
-#' }
+#'
 #'
 get_report_results <- function(workspace,
                                file_name = "mod_rapport.sti",

R/get_sim.R

@@ -85,10 +85,8 @@ get_daily_results <- function(...) {
 #' See Details section for more information about the "Plant" column.
 #'
 #' @examples
-#' \dontrun{
 #' path <- get_examples_path(file_type = "sti")
-#' get_sim(path, "banana")
-#' }
+#' sim_data <- get_sim(path, "banana")
 #'
 #' @export
 #'

R/get_stics_versions_compat.R

@@ -11,9 +11,6 @@
 #' an existing version selected using version_index.
 #'
 #' @examples
-#' #
-#' \dontrun{
-#'
 #' # Getting the complete versions list
 #' get_stics_versions_compat()
 #'
@@ -23,8 +20,6 @@
 #' # Getting the previous version of the latest one
 #' get_stics_versions_compat(-1)
 #'
-#' #
-#' }
 #'
 #' @export
 #'

R/get_usms_files.R

@@ -27,7 +27,7 @@
 #' and `get_usms_list()` to get the list of usms.
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #'
 #' get_usms_files(
 #'   workspace = "/path/to/workspace",

R/set_param_txt.R

@@ -48,8 +48,6 @@
 #' @export
 #'
 #' @examples
-#' \dontrun{
-#'
 #' # Getting example data path
 #' path <- get_examples_path(file_type = "txt")
 #'
@@ -72,7 +70,7 @@
 #' # in the soil file, we use set_soil_txt():
 #' set_soil_txt(file = file.path(path, "param.sol"),
 #'              param = "cailloux", layer = 2, value = 1)
-#' }
+#'
 #'
 set_param_txt <- function(workspace = getwd(),
                           param,

R/set_param_xml.R

@@ -33,7 +33,7 @@
 #' value= list(c(1,2), c(2.3,4.5))
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #'
 #' # Soil file
 #'

R/stics_examples_utils.R

@@ -13,14 +13,12 @@
 #' @export
 #'
 #' @examples
-#' \dontrun{
-#'
 #' get_examples_path(file_type = "csv")
 #'
 #' get_examples_path(file_type = c("csv", "sti"))
 #'
 #' get_examples_path(file_type = "csv", stics_version = "V8.5")
-#' }
+#'
 get_examples_path <- function(file_type, stics_version = "latest",
                               version_name = lifecycle::deprecated()) {
   if (lifecycle::is_present(version_name)) {

R/upgrade_param_newform_xml.R

@@ -21,7 +21,7 @@
 #' @details See SticsRFiles::get_stics_versions_compat() for listing versions
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' upgrade_param_newform_xml(
 #'   file = "/path/to/param_newform.xml",
 #'   out_dir = "/path/to/directory",

R/upgrade_plt_xml.R

@@ -20,10 +20,10 @@
 #'
 #' @export
 #'
-#' @details See SticsRFiles::get_stics_versions_compat() for listing versions
+#' @details See get_stics_versions_compat() for listing versions
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' upgrade_plt_xml(
 #'   file = "/path/to/_plt.xml",
 #'   param_gen_file = "/path/to/param_gen.xml",

R/upgrade_sta_xml.R

@@ -21,7 +21,7 @@
 #' @details See SticsRFiles::get_stics_versions_compat() for listing versions
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' upgrade_sta_xml(
 #'   file = "/path/to/_sta.xml",
 #'   out_dir = "/path/to/directory",

R/upgrade_usms_xml.R

@@ -18,10 +18,10 @@
 #'
 #' @export
 #'
-#' @details See SticsRFiles::get_stics_versions_compat() for listing versions
+#' @details See get_stics_versions_compat() for listing versions
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' upgrade_usms_xml(
 #'   file = "/path/to/usms.xml",
 #'   out_dir = "/path/to/directory",