{ "_id": "6a100a93acfb0bcc41c7f630", "Package": "SticsRFiles", "Title": "Read and Modify 'STICS' Input/Output Files", "Version": "1.6.0", "Date": "2025-06-03", "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(\"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. Files are either 'JavaSTICS' XML files or text files\nused by the model 'fortran' executable. Most basic\nfunctionalities are reading or writing parameter names and\nvalues in both XML or text input files, and getting data from\noutput files. Advanced functionalities include XML files\ngeneration from XML templates and/or spreadsheets, or text\nfiles generation from XML files by using '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", "Encoding": "UTF-8", "Language": "en-US", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "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'col_names_to_var.R' 'compute_date_from_day.R'\n'compute_day_number.R' 'convert_xml2txt.R'\n'convert_xml2txt_int.R' 'download_data.R' 'download_usm_xl.R'\n'exist_param_xml.R' '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'\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_ini_xml.R'\n'upgrade_param_gen_xml.R' 'upgrade_param_newform_xml.R'\n'upgrade_plt_xml.R' 'upgrade_sols_xml.R' 'upgrade_sta_xml.R'\n'upgrade_tec_xml.R' 'upgrade_usms_xml.R'\n'upgrade_workspace_xml.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://pecanproject.r-universe.dev", "Date/Publication": "2026-04-22 06:18:14 UTC", "RemoteUrl": "https://github.com/SticsRPacks/SticsRFiles", "RemoteRef": "HEAD", "RemoteSha": "6e5faf0e5ed4158877eeca1d7d50936dde51581f", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-22 07:45:30 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: ),\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 ", "MD5sum": "b5425c9f484f13aa5d1226a7d52bd843", "_user": "pecanproject", "_type": "src", "_file": "SticsRFiles_1.6.0.tar.gz", "_fileid": "c75716782b1632e37785d2f896c35aee692df4bd60cbf2062fa73624a1c63b10", "_filesize": 1761468, "_sha256": "c75716782b1632e37785d2f896c35aee692df4bd60cbf2062fa73624a1c63b10", "_created": "2026-05-22T07:45:30.000Z", "_published": "2026-05-22T07:49:38.955Z", "_distro": "noble", "_jobs": [ { "job": 77337958686, "time": 206, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7155464582" }, { "job": 77337958692, "time": 206, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7155464587" }, { "job": 77337958681, "time": 165, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", 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"6e5faf0e5ed4158877eeca1d7d50936dde51581f", "author": "Patrice Lecharpentier ", "committer": "GitHub ", "message": "Merge pull request #274 from SticsRPacks/plecharpent-patch-1\n\nUpdate pr-checks.yaml", "time": 1776838694 }, "_maintainer": { "name": "Patrice Lecharpentier", "email": "patrice.lecharpentier@inrae.fr", "login": "plecharpent", "description": "", "uuid": 3098097, "orcid": "0000-0002-4044-4322" }, "_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": "lubridate", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": 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}, { "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": 2879854, "type": "organization", "name": "PEcAn Project" }, "_downloads": { "count": 311, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/SticsRFiles" }, "_devurl": "https://github.com/sticsrpacks/sticsrfiles", "_searchresults": 90, "_metadata": { "notes": "Suggested by PEcAn.STICS" }, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/SticsRFiles.html", "manual.pdf" ], "_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" } ], "_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_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_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_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 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_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": "Upgrading _ini.xml file(s) to a newer version", "topics": [ "upgrade_ini_xml" ] }, { "page": "upgrade_param_gen_xml", "title": "Upgrading a param_gen.xml file to a newer version", "topics": [ "upgrade_param_gen_xml" ] }, { "page": "upgrade_param_newform_xml", "title": "Upgrading a param_newform.xml file to a newer version", "topics": [ "upgrade_param_newform_xml" ] }, { "page": "upgrade_plt_xml", "title": "Upgrading _plt.xml file(s) to a newer version", "topics": [ "upgrade_plt_xml" ] }, { "page": "upgrade_sols_xml", "title": "Upgrading a sols.xml file to a newer version", "topics": [ "upgrade_sols_xml" ] }, { "page": "upgrade_sta_xml", "title": "Upgrading _sta.xml file(s) to a newer version", "topics": [ "upgrade_sta_xml" ] }, { "page": "upgrade_tec_xml", "title": "Upgrading _tec.xml file(s) to a newer version", "topics": [ "upgrade_tec_xml" ] }, { "page": "upgrade_usms_xml", "title": "Upgrading a usms.xml file to a newer version", "topics": [ "upgrade_usms_xml" ] }, { "page": "upgrade_workspace_xml", "title": "Upgrading XML files of a JavaSTICS workspace directory to a newer STICS version format", "topics": [ "upgrade_workspace_xml" ] } ], "_readme": 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