Merge branch 'main' into add/xml-upgrades/v11

CITATION.cff

@@ -8,7 +8,7 @@ message: 'To cite package "SticsRFiles" in publications use:'
 type: software
 license: LGPL-3.0-or-later
 title: 'SticsRFiles: Read and Modify ''STICS'' Input/Output Files'
-version: 1.3.0
+version: 1.4.0
 abstract: Manipulating input and output files of the 'STICS' crop model. Files are
   either 'JavaSTICS' XML files or text files used by the model 'fortran' executable.
   Most basic functionalities are reading or writing parameter names and values in
@@ -35,7 +35,7 @@ authors:
 repository: https://CRAN.R-project.org/package=SticsRFiles
 repository-code: https://github.com/SticsRPacks/SticsRFiles
 url: https://doi.org/10.5281/zenodo.4443206
-date-released: '2024-04-10'
+date-released: '2024-07-16'
 contact:
 - family-names: Lecharpentier
   given-names: Patrice
@@ -68,7 +68,7 @@ references:
   title: crayon
   abstract: 'crayon: Colored Terminal Output'
   notes: Imports
-  url: https://github.com/r-lib/crayon#readme
+  url: https://r-lib.github.io/crayon/
   repository: https://CRAN.R-project.org/package=crayon
   authors:
   - family-names: Csárdi

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: SticsRFiles
 Title: Read and Modify 'STICS' Input/Output Files
-Version: 1.3.0
-Date: 2024-04-10
+Version: 1.4.0
+Date: 2024-07-16
 Authors@R: c(
     person("Patrice", "Lecharpentier", , "patrice.lecharpentier@inrae.fr", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-4044-4322")),
@@ -83,6 +83,7 @@ Collate:
     'check_output_files.R'
     'check_param_names.R'
     'col_names_to_var.R'
+    'compute_date_from_day.R'
     'compute_day_number.R'
     'convert_xml2txt.R'
     'convert_xml2txt_int.R'
@@ -114,6 +115,8 @@ Collate:
     'gen_usms_xml2txt.R'
     'gen_varmod.R'
     'get_climate_txt.R'
+    'get_cultivars_list.R'
+    'get_cultivars_param.R'
     'get_file.R'
     'get_file_int.R'
     'get_formalisms_xml.R'

NAMESPACE

@@ -1,6 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
 S3method("[",cropr_simulation)
+export(compute_date_from_day)
 export(compute_day_from_date)
 export(convert_xml2txt)
 export(download_data)
@@ -16,6 +17,8 @@ export(gen_usms_xml)
 export(gen_usms_xml2txt)
 export(gen_varmod)
 export(get_climate_txt)
+export(get_cultivars_list)
+export(get_cultivars_param)
 export(get_examples_path)
 export(get_general_txt)
 export(get_ini_txt)

NEWS.md

@@ -1,3 +1,21 @@
+# SticsRFiles 1.4.0 _2024-07-16_
+
+* FUNCTIONS
+  * New functions for computing dates from days numbers with reference to
+   starting year
+  * compute_day_from_date now uses a start year instead of a date, and date may
+  of type character
+  * get_param_txt, set_param_txt, get_param_xml, set_param_xml now use values
+  ids for getting or setting specific parameter vector values 
+  specific values
+  * New functions for getting cultivars list and extracting cultivars parameters
+  as a data.frame
+
+* FIXES
+  * management of STICS version consistency with text files content using
+  get_param_txt or set_param_txt
+
+
 # SticsRFiles 1.3.0 _2024-04-10_
 
 * FUNCTIONS

R/compute_date_from_day.R

@@ -0,0 +1,25 @@
+#' Convert day number into date
+#'
+#' Computes the date corresponding to a given day number (or vector of)
+#' with reference to a start year. Typically, the start year should
+#' be the year of a STICS simulation start, but not necessarily.
+#' @param day day number(s) to be converted
+#' @param start_year year to be used as time reference (simulation start year).
+#'
+#' @return Date vector
+#' @author Timothee Flutre
+#' @examples
+#'
+#' compute_date_from_day(day = 290, start_year = 1994)
+#'
+#' compute_date_from_day(day = 700, start_year = 1994)
+#'
+#' @export
+#'
+compute_date_from_day <- function(day, start_year){
+  stopifnot(all(is.numeric(day)),
+            length(start_year) == 1,
+            is.numeric(start_year))
+
+  return(as.Date(day - 1, origin = paste0(start_year, "-01-01")))
+}

R/get_cultivars_list.R

@@ -0,0 +1,38 @@
+#' @title Get the cultivar names for an xml plant file (*_plt.xml)
+#'
+#' @description Extracts the cultivar names from a plant file
+#'
+#' @param file The path of a plant file.
+#'
+#' @return A vector of cultivar names
+#'
+#' @examples
+#' path <- get_examples_path(file_type = "xml")
+#'
+#' # Read from a plant file (all cultivars available in a plant file)
+#' cv_list <- get_cultivars_list(file = file.path(path, "file_plt.xml"))
+#'
+#' @export
+#'
+get_cultivars_list <- function(file) {
+
+  xml_doc <- xmldocument(file)
+
+  stopifnot(is_stics_plt(xml_doc))
+
+  xml_name <- "variete"
+
+  cv_list <- unique(
+      unlist(
+          lapply(
+              XML::getNodeSet(doc = xml_doc@content,
+                              path = paste0("//", xml_name)),
+              function(x) {
+                XML::xmlGetAttr(x, "nom")
+              }
+          )
+      )
+  )
+
+  return(cv_list)
+}

R/get_cultivars_param.R

@@ -0,0 +1,28 @@
+#' @title Get the values of cultivar-specific parameters from an xml
+#' plant file (*_plt.xml)
+#'
+#' @description Extracts the values of cultivar-specific parameters from a
+#' plant file
+#'
+#' @param file The path of a plant file.
+#'
+#' @return A data.frame with one row per cultivar and one column per parameter
+#'
+#' @examples
+#' path <- get_examples_path(file_type = "xml")
+#'
+#' # Read from a plant file (all cultivars available in a plant file)
+#' cv_param_df <- get_cultivars_param(file = file.path(path, "file_plt.xml"))
+#'
+#' @export
+#'
+get_cultivars_param <- function(file) {
+
+  cv_list <- get_cultivars_list(file)
+
+  out <- get_param_xml(file, select = "variete", select_value = cv_list)
+  out <- as.data.frame(do.call(cbind, out[[1]]))
+  rownames(out) <- cv_list
+
+  return(out)
+}

R/get_param_txt.R

@@ -367,7 +367,7 @@ get_ini_txt <- function(file = "ficini.txt",
 
   if (stics_version_num < 10) {
 
-    if (length(params) > 28)
+    if (length(params) > 48)
       stop("The used STICS version ",
            stics_version_num,
            " does not correspond to the file content (STICS version >= 10)")
@@ -399,7 +399,7 @@ get_ini_txt <- function(file = "ficini.txt",
     ini$NH4init <- params[[28]]
   } else {
 
-    if (length(params) < 49)
+    if (length(params) < 48)
       stop("The used STICS version ",
            stics_version_num,
            " does not correspond to the file content (STICS version < 10)")

R/get_param_xml.R

@@ -15,6 +15,8 @@
 #' (optional, default to no selection)
 #' @param select_value Vector of values used for select (see examples).
 #' Optional, should be provided only if select is provided.
+#' @param value_id Vector of ids of the parameters values to be retrieved
+#' from the parameter values vector
 #' @param value `r lifecycle::badge("deprecated")` `value` is no
 #'   longer supported, use `select_value` instead.
 #' @param ... Pass further arguments to `get_param_value()`
@@ -48,6 +50,7 @@ get_param_xml <- function(file,
                           param = NULL,
                           select = NULL,
                           select_value = NULL,
+                          value_id = NULL,
                           xml_file = lifecycle::deprecated(),
                           param_name = lifecycle::deprecated(),
                           value = lifecycle::deprecated(),
@@ -97,6 +100,7 @@ get_param_xml <- function(file,
     param_name = param_name,
     parent_name = select,
     parent_sel_attr = value,
+    ids = value_id,
     ...
   )
   xml_names <- lapply(xml_file, basename) %>% unlist()

R/set_param_xml.R

@@ -12,6 +12,8 @@
 #' (optional, default to no selection)
 #' @param select_value Vector of values used for select (see examples).
 #' Optional, should be provided only if select is provided.
+#' @param value_id Vector of ids of the parameters values to be retrieved
+#' from the parameter values vector
 #' @param overwrite Logical TRUE for overwriting the output file,
 #' FALSE otherwise (default)
 #' @param xml_file `r lifecycle::badge("deprecated")` `xml_file` is no
@@ -71,22 +73,39 @@
 #' set_param_xml(sol_path, c("epc", "HCCF"),
 #'   select = "sol",
 #'   select_value = c("solcanne", "solbanane"),
-#'   param_value = list(c(20:24, 10:14), c(50:54, 40:44)), overwrite = TRUE
+#'   values = list(c(20:24, 10:14), c(50:54, 40:44)),
+#'   overwrite = TRUE
 #' )
+#'
 #' # Getting changed values
 #' # get_param_xml(sol_path, c("epc", "HCCF"),
 #' # select = "sol",
 #' # select_value = c("solcanne", "solbanane")
 #' # )
 #'
+#' # For specific values of vector parameters
+#' set_param_xml(sol_path, "HCCF",
+#'   select = "sol",
+#'   select_value = "solcanne",
+#'   values = c(46.8, 48.5, 50.1),
+#'   value_id = c(1,3,5),
+#'   overwrite = TRUE
+#'  )
+#'
+#' # Getting changed values
+#' # get_param_xml(sol_path, "HCCF",
+#' # select = "sol",
+#' # select_value = "solcanne",
+#' # value_id = c(1,3,5)
+#' # )
 #'
 #' # Crop management file
 #'
 #' tec_path <- file.path(ex_path, "file_tec.xml")
 #'
 #' # Modifying irrigations parameters
 #' set_param_xml(tec_path, c("julapI_or_sum_upvt", "amount"),
-#'   param_value = list(200:215, 20:35), overwrite = TRUE
+#'   values = list(200:215, 20:35), overwrite = TRUE
 #' )
 #' # Getting changed values
 #' # get_param_xml(tec_path, c("julapI_or_sum_upvt", "amount"))
@@ -99,6 +118,7 @@ set_param_xml <- function(file,
                           save_as = NULL,
                           select = NULL,
                           select_value = NULL,
+                          value_id = NULL,
                           overwrite = FALSE,
                           xml_file = lifecycle::deprecated(),
                           out_path = lifecycle::deprecated(),
@@ -188,6 +208,7 @@ set_param_xml <- function(file,
                   param_value = param_value,
                   parent_name = select,
                   parent_sel_attr = value,
+                  ids = value_id,
                   ...
   )
 

README.Rmd

@@ -26,7 +26,7 @@ knitr::opts_chunk$set(
 
 <!-- badges: end -->
 
-The goal of SticsRFiles is to perform manipulations of the [STICS](https://eng-stics.paca.hub.inrae.fr/)  model files either on XML files (used by the JavaSTICS GUI) or on text files used by the model fortran executable.
+The goal of SticsRFiles is to perform manipulations of the [STICS](https://stics.inrae.fr/eng/)  model files either on XML files (used by the JavaSTICS GUI) or on text files used by the model fortran executable.
 
 The basic functionalities allows to read parameters names and values through XML queries and replace parameters values in files. A starting guide is available on the [Get started page](https://sticsrpacks.github.io/SticsRFiles/articles/SticsRFiles.html).
 

README.md

@@ -17,9 +17,9 @@ coverage](https://codecov.io/gh/SticsRPacks/SticsRFiles/branch/master/graph/badg
 <!-- badges: end -->
 
 The goal of SticsRFiles is to perform manipulations of the
-[STICS](https://eng-stics.paca.hub.inrae.fr/) model files either on XML
-files (used by the JavaSTICS GUI) or on text files used by the model
-fortran executable.
+[STICS](https://stics.inrae.fr/eng/) model files either on XML files
+(used by the JavaSTICS GUI) or on text files used by the model fortran
+executable.
 
 The basic functionalities allows to read parameters names and values
 through XML queries and replace parameters values in files. A starting

_pkgdown.yml

@@ -67,6 +67,8 @@ reference:
       - get_usms_files
       - get_usms_list
       - get_soils_list
+      - get_cultivars_list
+      - get_cultivars_param
 
   - title: "Generate Stics Input files (Text format)"
     desc: Input parameters files, outputs definition files or observations files
@@ -117,3 +119,4 @@ reference:
       - is_windows
       - "`[.cropr_simulation`"
       - compute_day_from_date
+      - compute_date_from_day