{ "_id": "6ad26cb07af56c173f120867", "Package": "SticsRFiles", "Title": "Read and Modify STICS Input/Output Files", "Version": "1.7.3", "Date": "2026-10-12", "Authors@R": "c(\nperson(\"Patrice\", \"Lecharpentier\", , \"patrice.lecharpentier@inrae.fr\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-4044-4322\")),\nperson(\"Remi\", \"Vezy\", , \"remi.vezy@cirad.fr\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-0808-1461\")),\nperson(\"Samuel\", \"Buis\", , \"samuel.buis@inrae.fr\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-8676-5447\")),\nperson(\"Michel\", \"Giner\", , \"michel.giner@cirad.fr\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-9310-2377\")),\nperson(\"Timothee\", \"Flutre\", , \"timothee.flutre@inrae.fr\", role = \"aut\",\ncomment = c(ORCID = \"0000-0003-4489-4782\")),\nperson(\"Valentine\", \"Rahier\", , \"valentine.rahier@inrae.fr\", role = \"aut\"),\nperson(\"Thomas\", \"Robine\", role = \"ctb\"),\nperson(\"Amine\", \"Barkaoui\", role = \"ctb\"),\nperson(\"Patrick\", \"Chabrier\", role = \"ctb\"),\nperson(\"Julie\", \"Constantin\", role = \"rev\"),\nperson(\"Dominique\", \"Ripoche\", role = \"rev\"),\nperson(\"Marie\", \"Launay\", role = \"rev\"),\nperson(\"Alain\", \"Mollier\", role = \"rev\"),\nperson(\"Christine\", \"Le Bas\", role = \"rev\"),\nperson(\"Joel\", \"Leonard\", role = \"rev\")\n)", "Description": "Manipulating input and output files of the 'STICS' crop\nmodel (Beaudouin et al. (2022)\n). The package is based on the\nmodel software, which is accessible, as well as resources, on\nits web site . Files are either\n'JavaSTICS' XML files or text files used by the model 'fortran'\nexecutable. Most basic functionalities are reading or writing\nparameter names and values in both XML or text input files, and\ngetting data from output files. Advanced functionalities\ninclude XML files generation from XML templates and/or\nspreadsheets, or text files generation from XML files by using\n'xslt' transformation.", "License": "LGPL (>= 3)", "URL": "https://github.com/SticsRPacks/SticsRFiles,\nhttps://doi.org/10.5281/zenodo.4443206", "BugReports": "https://github.com/SticsRPacks/SticsRFiles/issues", "VignetteBuilder": "knitr", "ByteCompile": "true", "Config/roxygen2/version": "8.1.0", "Encoding": "UTF-8", "Language": "en-US", "Roxygen": "list(markdown = TRUE)", "Collate": "'add_node_to_doc.R' 'add_stics_nodes.R' 'all_in_par.R'\n'all_out_var.R' 'approx_vapour_pressure.R'\n'attributes_list2matrix.R' 'check_choice_param.R'\n'check_java_path.R' 'check_java_workspace.R'\n'check_output_files.R' 'check_param_names.R'\n'check_upgrade_versions.R' 'col_names_to_var.R'\n'compute_date_from_day.R' 'compute_day_number.R'\n'convert_xml2txt.R' 'convert_xml2txt_int.R' 'download_data.R'\n'download_usm_xl.R' 'exist_param_xml.R'\n'exists_javastics_pref.R' 'exists_param.R'\n'expand_stics_names.R' 'extract.R' 'extract_workspace.R'\n'global.R' 'file_document.R' 'find_names.R'\n'force_param_values.R' 'gen_climate.R'\n'gen_general_param_xml.R' 'gen_ini_doc.R' 'gen_ini_xml.R'\n'gen_new_travail.R' 'gen_obs.R' 'gen_paramsti.R'\n'gen_sol_xsl_file.R' 'gen_sols_xml.R' 'gen_sta_doc.R'\n'gen_sta_xml.R' 'gen_tec_doc.R' 'gen_tec_xml.R'\n'gen_usms_sols_doc.R' 'gen_usms_xml.R' 'gen_usms_xml2txt.R'\n'gen_varmod.R' 'get_climate_txt.R' 'get_cores_nb.R'\n'get_cultivars_list.R' 'get_cultivars_param.R'\n'get_dev_stages.R' 'get_file.R' 'get_file_int.R'\n'get_files_list.R' 'get_formalisms_xml.R'\n'get_java_workspace.R' 'get_lai_forcing.R'\n'get_name_value_file_value.R' 'get_obs.R' 'get_obs_sd.R'\n'get_option_choice_param_values.R' 'get_options_choices.R'\n'get_options_names.R' 'get_param_bounds.R'\n'get_param_bounds_xml.R' 'get_param_formalisms.R'\n'get_param_info_xml.R' 'get_param_names.R'\n'get_param_names_xml.R' 'get_param_number.R' 'get_param_txt.R'\n'get_param_type.R' 'get_param_value.R' 'get_param_xml.R'\n'get_params_dict.R' 'get_params_from_doc.R'\n'get_params_from_doc_attr.R' 'get_params_from_doc_node.R'\n'get_params_from_table.R' 'get_plant_name.R' 'get_plants_nb.R'\n'get_report_results.R' 'get_sim.R' 'get_soils_list.R'\n'get_stics_versions_compat.R' 'get_used_param.R'\n'get_usms_list.R' 'get_values_by_param.R' 'get_varmod.R'\n'get_xml_base_doc.R' 'get_xml_base_node.R'\n'get_xml_doc_example.R' 'get_xml_files_param_df.R'\n'get_xml_stics_version.R' 'init_javastics_pref.R'\n'is_os_name.R' 'is_stics_doc.R' 'is_stics_xml.R'\n'javastics_cmd_util.R' 'javastics_path.R'\n'manage_stics_versions.R' 'merge_nodesets.R'\n'read_params_table.R' 'remove_node_from_doc.R'\n'remove_parent_from_doc.R' 'replace_string_in_file.R'\n'replace_txt_param_value.R' 'rewrite_xml_files.R'\n'set_codeoptim.R' 'set_file_executable.R'\n'set_java_workspace.R' 'set_param_txt.R' 'set_param_value.R'\n'set_param_xml.R' 'set_sols_param_xml.R' 'set_usms_param_xml.R'\n'setup_parallelism.R' 'static_help.R' 'stics_environment.R'\n'stics_files_utils.R' 'upgrade_v10_v11.R' 'upgrade_v9_v10.R'\n'upgrade_xml_files.R' 'var_to_col_names.R' 'xml_document.R'\n'xml_files_functions.R' 'zzz.R'", "Config/pak/sysreqs": "libicu-dev libxml2-dev libxslt-dev libssl-dev", "Repository": "https://sticsrpacks.r-universe.dev", "Date/Publication": "2026-10-16 13:44:24 UTC", "RemoteUrl": "https://github.com/SticsRPacks/SticsRFiles", "RemoteRef": "HEAD", "RemoteSha": "678a2703a357910b0358297b1075301f00af4e84", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-16 17:50:57 UTC", "User": "root" }, "Author": "Patrice Lecharpentier [aut, cre] (ORCID:\n),\nRemi Vezy [aut] (ORCID: ),\nSamuel Buis [aut] (ORCID: ),\nMichel Giner [aut] (ORCID: ),\nTimothee Flutre [aut] (ORCID: ),\nValentine Rahier [aut],\nThomas Robine [ctb],\nAmine Barkaoui [ctb],\nPatrick Chabrier [ctb],\nJulie Constantin [rev],\nDominique Ripoche [rev],\nMarie Launay [rev],\nAlain Mollier [rev],\nChristine Le Bas [rev],\nJoel Leonard [rev]", "Maintainer": "Patrice Lecharpentier ", "_user": "sticsrpacks", "_type": "src", "_file": "SticsRFiles_1.7.3.tar.gz", "_fileid": "https://r2.ropensci.org/827511ad3acf8ff15ce7bf86e477f710c34e00183a1704c7b0aaf6dd210effc4", "_filesize": 1975838, "_sha256": "827511ad3acf8ff15ce7bf86e477f710c34e00183a1704c7b0aaf6dd210effc4", "_expires": "2027-01-24T18:27:58.000Z", "_created": "2026-10-16T17:50:57.000Z", "_published": "2026-10-16T18:28:00.322Z", "_buildurl": "https://github.com/r-universe/sticsrpacks/actions/runs/38942361914", "_status": "success", "_host": "GitHub-Actions", "_jobs": [ { "job": 117114648078, "time": 230, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12064206875" }, { "job": 117114648329, "time": 236, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12063703720" }, { "job": 117114648046, "time": 199, "config": "macos-oldrel-arm64", "r": 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"Merge pull request #319 from SticsRPacks/plecharpent/fix-gen-txt-missing-files\n\nPlecharpent/fix gen txt missing files", "time": 1792158264 }, "_maintainer": { "name": "Patrice Lecharpentier", "email": "patrice.lecharpentier@inrae.fr", "login": "plecharpent", "description": "", "uuid": 3098097, "orcid": "0000-0002-4044-4322" }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0.0", "role": "Depends" }, { "package": "cli", "role": "Imports" }, { "package": "crayon", "role": "Imports" }, { "package": "curl", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "doParallel", "role": "Imports" }, { "package": "dplyr", "version": ">= 1.0.0", "role": "Imports" }, { "package": "foreach", "role": "Imports" }, { "package": "httr", "role": "Imports" }, { "package": "lifecycle", "role": "Imports" }, { "package": "lubridate", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "parallel", 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"count": 103, "uuid": 6650744 }, { "user": "ginerm", "count": 95, "uuid": 47385647 }, { "user": "vrahier", "count": 33, "uuid": 32514202 }, { "user": "timflutre", "count": 29, "uuid": 607508 }, { "user": "thomasrobine", "count": 9, "uuid": 45353523 }, { "user": "cyrillemidingoyi", "count": 6, "uuid": 34443570 }, { "user": "aminebarkaoui", "count": 1, "uuid": 66622330 }, { "user": "cyrilgandon", "count": 1, "uuid": 2806672 }, { "user": "chabrier", "count": 1, "uuid": 2590591 } ], "_userbio": { "uuid": 46886130, "type": "organization", "name": "SticsRPacks", "followers": 11 }, "_downloads": { "count": 598, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/SticsRFiles" }, "_devurl": "https://github.com/sticsrpacks/sticsrfiles", "_searchresults": 92, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/SticsRFiles.html" ], "_homeurl": "https://github.com/sticsrpacks/sticsrfiles", "_realowner": "sticsrpacks", "_cranurl": true, "_releases": [ { "version": "1.1.3", "date": "2023-07-11" }, { "version": "1.2.0", "date": "2024-02-23" }, { "version": "1.3.0", "date": "2024-04-11" }, { "version": "1.4.0", "date": "2024-07-17" }, { "version": "1.5.0", "date": "2024-11-14" }, { "version": "1.6.0", "date": "2025-06-03" }, { "version": "1.7.0", "date": "2026-09-15" }, { "version": "1.7.2", "date": "2026-10-07" } ], "_exports": [ "approx_vapour_pressure", "compute_date_from_day", "compute_day_from_date", "convert_xml2txt", "download_data", "download_usm_csv", "download_usm_xl", "extract_workspace", "force_param_values", "gen_general_param_xml", "gen_ini_xml", "gen_obs", "gen_obs_sd", "gen_sols_xml", "gen_sta_xml", "gen_tec_xml", "gen_usms_xml", "gen_usms_xml2txt", "gen_varmod", "get_climate_txt", "get_cultivars_list", "get_cultivars_param", "get_dev_stages", "get_examples_path", "get_files_list", "get_general_txt", "get_ini_txt", "get_lai_forcing", "get_obs", "get_obs_sd", "get_param_info", "get_param_txt", "get_param_xml", "get_plant_txt", "get_plants_nb", "get_report_results", "get_sim", "get_soil_txt", "get_soils_list", "get_station_txt", "get_stics_versions_compat", "get_tec_txt", "get_tmp_txt", "get_usm_txt", "get_usms_list", "get_var_info", "get_varmod", "get_xml_files_param_df", "is_mac", "is_stics_param", "is_stics_var", "is_unix", "is_windows", "read_params_table", "set_general_txt", "set_ini_txt", "set_param_txt", "set_param_xml", "set_plant_txt", "set_soil_txt", "set_station_txt", "set_tec_txt", "set_tmp_txt", "set_usm_txt", "upgrade_ini_xml", "upgrade_param_gen_xml", "upgrade_param_newform_xml", "upgrade_plt_xml", "upgrade_sols_xml", "upgrade_sta_xml", "upgrade_tec_xml", "upgrade_usms_xml", "upgrade_workspace_xml" ], "_help": [ { "page": "sub-.cropr_simulation", "title": "'[' method for 'cropr_simulation'", "topics": [ "[.cropr_simulation" ] }, { "page": "approx_vapour_pressure", "title": "Approximate vapour pressure", "topics": [ "approx_vapour_pressure" ] }, { "page": "compute_date_from_day", "title": "Convert day number into date", "topics": [ "compute_date_from_day" ] }, { "page": "compute_day_from_date", "title": "Convert date into day number", "topics": [ "compute_day_from_date" ] }, { "page": "convert_xml2txt", "title": "Transforming a STICS xml file into a text file", "topics": [ "convert_xml2txt" ] }, { "page": "download_data", "title": "Download example USMs", "topics": [ "download_data" ] }, { "page": "download_usm_csv", "title": "Downloading a CSV usms data file example into a directory", "topics": [ "download_usm_csv" ] }, { "page": "download_usm_xl", "title": "Downloading an Excel usms data file example into a directory", "topics": [ "download_usm_xl" ] }, { "page": "extract_workspace", "title": "Extract an XML JavaSTICS workspace from a source workspace", "topics": [ "extract_workspace" ] }, { "page": "force_param_values", "title": "Generates files to force parameters values in STICS simulations", "topics": [ "force_param_values" ] }, { "page": "gen_general_param_xml", "title": "Generate STICS general parameters xml file(s) from a template file according to a STICS version", "topics": [ "gen_general_param_xml" ] }, { "page": "gen_ini_xml", "title": "Generate STICS ini xml file(s) from a template or an input file", "topics": [ "gen_ini_xml" ] }, { "page": "gen_obs", "title": "Generating observation data files from a data.frame", "topics": [ "gen_obs" ] }, { "page": "gen_obs_sd", "title": "Generating observation data standard deviation files from a data.frame as for generating observations data files ('gen_obs')", "topics": [ "gen_obs_sd" ] }, { "page": "gen_sols_xml", "title": "Generate STICS sols xml file from a template or an input file", "topics": [ "gen_sols_xml" ] }, { "page": "gen_sta_xml", "title": "Generate STICS sta xml file(s) from a template or an input file", "topics": [ "gen_sta_xml" ] }, { "page": "gen_tec_xml", "title": "Generate STICS tec xml file(s) from a template or an input file", "topics": [ "gen_tec_xml" ] }, { "page": "gen_usms_xml", "title": "Generate STICS usms xml file from a template or an input file", "topics": [ "gen_usms_xml" ] }, { "page": "gen_usms_xml2txt", "title": "Generating one or several usms directories with STICS input files from a javastics workspace content", "topics": [ "gen_usms_xml2txt" ] }, { "page": "gen_varmod", "title": "Generating a var.mod type file", "topics": [ "gen_varmod" ] }, { "page": "get_climate_txt", "title": "Read STICS input meteorology file", "topics": [ "get_climate_txt" ] }, { "page": "get_cultivars_list", "title": "Get the cultivar names for an xml plant file (*_plt.xml)", "topics": [ "get_cultivars_list" ] }, { "page": "get_cultivars_param", "title": "Get the values of cultivar-specific parameters from an xml plant file (*_plt.xml)", "topics": [ "get_cultivars_param" ] }, { "page": "get_dev_stages", "title": "Get developmental stages from simulations", "topics": [ "get_dev_stages" ] }, { "page": "get_examples_path", "title": "Getting examples files path attached to a STICS version for a given file type", "topics": [ "get_examples_path" ] }, { "page": "get_files_list", "title": "Getting existing xml files path list per usm from an usms.xml file", "topics": [ "get_files_list" ] }, { "page": "get_lai_forcing", "title": "Getting LAI forcing for each usm", "topics": [ "get_lai_forcing" ] }, { "page": "get_obs", "title": "Read STICS observation files (*.obs)", "topics": [ "get_obs" ] }, { "page": "get_obs_sd", "title": "Read STICS observation standard deviation files (*.sd)", "topics": [ "get_obs_sd" ] }, { "page": "get_param_info", "title": "Finding parameters information using partial search words", "topics": [ "get_param_info" ] }, { "page": "get_param_txt", "title": "Read STICS input parameters from text files", "topics": [ "get_general_txt", "get_ini_txt", "get_param_txt", "get_plant_txt", "get_soil_txt", "get_station_txt", "get_tec_txt", "get_tmp_txt", "get_usm_txt" ] }, { "page": "get_param_xml", "title": "Getting parameter values from xml files", "topics": [ "get_param_xml" ] }, { "page": "get_plants_nb", "title": "Getting plants number per usm for all usms or selected from a usm name vector", "topics": [ "get_plants_nb" ] }, { "page": "get_report_results", "title": "Extracting data from the STICS report file", "topics": [ "get_report_results" ] }, { "page": "get_sim", "title": "Load and format STICS daily output file(s)", "topics": [ "get_sim" ] }, { "page": "get_soils_list", "title": "Get the soil names for an usms.xml or sols.xml file", "topics": [ "get_soils_list" ] }, { "page": "get_stics_versions_compat", "title": "Get the compatible STICS versions", "topics": [ "get_stics_versions_compat" ] }, { "page": "get_usms_list", "title": "Getting usms names list for an usms.xml file", "topics": [ "get_usms_list" ] }, { "page": "get_var_info", "title": "Find STICS output variable names and description", "topics": [ "get_var_info" ] }, { "page": "get_varmod", "title": "Get desired STICS outputs", "topics": [ "get_varmod" ] }, { "page": "get_xml_files_param_df", "title": "Extracting a data.frame of parameters values for an xml file or a set of (whatever the xml file kind)", "topics": [ "get_xml_files_param_df" ] }, { "page": "is_mac", "title": "Evaluating if the OS is a Mac OS type", "topics": [ "is_mac" ] }, { "page": "is_stics_param", "title": "Search if a STICS parameter exist", "topics": [ "is_stics_param" ] }, { "page": "is_stics_var", "title": "Search if a STICS variable exist", "topics": [ "is_stics_var" ] }, { "page": "is_unix", "title": "Evaluating if the OS is a unix like type", "topics": [ "is_unix" ] }, { "page": "is_windows", "title": "Evaluating if the OS is a windows type", "topics": [ "is_windows" ] }, { "page": "read_params_table", "title": "Getting parameters data from tables files (Excel sheet, csv)", "topics": [ "read_params_table" ] }, { "page": "set_param_txt", "title": "Set (replace) STICS input file parameters", "topics": [ "set_general_txt", "set_ini_txt", "set_param_txt", "set_plant_txt", "set_soil_txt", "set_station_txt", "set_tec_txt", "set_tmp_txt", "set_usm_txt" ] }, { "page": "set_param_xml", "title": "Setting parameter values into xml files", "topics": [ "set_param_xml" ] }, { "page": "upgrade_ini_xml", "title": "Upgrade _ini.xml file(s) to a next major version", "topics": [ "upgrade_ini_xml" ] }, { "page": "upgrade_param_gen_xml", "title": "Upgrade a param_gen.xml file to a next major version", "topics": [ "upgrade_param_gen_xml" ] }, { "page": "upgrade_param_newform_xml", "title": "Upgrade a param_newform.xml file to a next major version", "topics": [ "upgrade_param_newform_xml" ] }, { "page": "upgrade_plt_xml", "title": "Upgrade _plt.xml file(s) to a next major version", "topics": [ "upgrade_plt_xml" ] }, { "page": "upgrade_sols_xml", "title": "Upgrade a sols.xml file to a next major version", "topics": [ "upgrade_sols_xml" ] }, { "page": "upgrade_sta_xml", "title": "Upgrade _sta.xml file(s) to a next major version", "topics": [ "upgrade_sta_xml" ] }, { "page": "upgrade_tec_xml", "title": "Upgrade _tec.xml file(s) to a next major version", "topics": [ "upgrade_tec_xml" ] }, { "page": "upgrade_usms_xml", "title": "Upgrade a usms.xml file to a next major version", "topics": [ "upgrade_usms_xml" ] }, { "page": "upgrade_workspace_xml", "title": "Upgrade a Javastics STICS xml workspace directory to a next major version", "topics": [ "upgrade_workspace_xml" ] } ], "_readme": "https://github.com/SticsRPacks/SticsRFiles/raw/HEAD/README.md", "_rundeps": [ "askpass", "assertthat", "cli", "codetools", "cpp11", "crayon", "curl", "data.table", "doParallel", "dplyr", "foreach", "generics", "glue", "httr", "iterators", "jsonlite", "lifecycle", "lubridate", "magrittr", "mime", "openssl", "pillar", "pkgconfig", "purrr", "R6", "Rcpp", "rlang", "rstudioapi", "semver", "stringi", "stringr", "sys", "tibble", "tidyr", "tidyselect", "timechange", "utf8", "vctrs", "withr", "XML", "xml2", "xslt" ], "_vignettes": [ { "source": "Generating_Stics_text_files.Rmd", "filename": "Generating_Stics_text_files.html", "title": "Generating STICS text files from XML files", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Converting JavaSTICS workspace files", "Converting files into separated folders (one per usm)", "Converting files into one folder (overwriting case)" ], "created": "2020-01-20 04:54:02", "modified": "2025-06-03 14:21:17", "commits": 20 }, { "source": "Generating_Stics_XML_files.Rmd", "filename": "Generating_Stics_XML_files.html", "title": "Generating STICS XML files from tabulated data", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Package functions to be used", "Getting a table file example", "Getting inputs Excel example file from the SticsRFiles package", "Getting 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