Package: apsimx 2.8.207

Fernando Miguez

apsimx: Inspect, Read, Edit and Run 'APSIM' "Next Generation" and 'APSIM' Classic

The functions in this package inspect, read, edit and run files for 'APSIM' "Next Generation" ('JSON') and 'APSIM' "Classic" ('XML'). The files with an 'apsim' extension correspond to 'APSIM' Classic (7.x) - Windows only - and the ones with an 'apsimx' extension correspond to 'APSIM' "Next Generation". For more information about 'APSIM' see (<https://www.apsim.info/>) and for 'APSIM' next generation (<https://apsimnextgeneration.netlify.app/>).

Authors:Fernando Miguez [aut, cre]

apsimx_2.8.207.tar.gz
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apsimx_2.8.207.tgz(r-4.4-any)apsimx_2.8.207.tgz(r-4.3-any)
apsimx_2.8.207.tar.gz(r-4.5-noble)apsimx_2.8.207.tar.gz(r-4.4-noble)
apsimx_2.8.207.tgz(r-4.4-emscripten)apsimx_2.8.207.tgz(r-4.3-emscripten)
apsimx.pdf |apsimx.html✨
apsimx/json (API)
NEWS

# Install 'apsimx' in R:
install.packages('apsimx', repos = c('https://femiguez.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/femiguez/apsimx/issues

Datasets:
  • obsWheat - Observed wheat phenology, LAI and biomass
  • wop - Wheat example optimization results
  • wop.h - Wheat example optimization results plus Hessian

On CRAN:

apsimapsimx

9.30 score 53 stars 1 packages 56 scripts 724 downloads 84 exports 23 dependencies

Last updated 5 days agofrom:cbe2e9c124. Checks:OK: 1 ERROR: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 18 2024
R-4.5-winERRORNov 18 2024
R-4.5-linuxERRORNov 18 2024
R-4.4-winERRORNov 18 2024
R-4.4-macERRORNov 18 2024
R-4.3-winERRORNov 18 2024
R-4.3-macERRORNov 18 2024

Exports:add_column_apsim_metamp_apsim_metapsimapsim_exampleapsim_optionsapsim_versionapsim.optionsapsimxapsimx_exampleapsimx_filetypeapsimx_optionsapsimx_soil_profileapsimx.optionsas_apsim_metauto_detect_apsim_examplesauto_detect_apsimx_examplesavailable_water_contentcarbon_stockscheck_apsim_metcheck_apsimxcheck_apsimx_soil_profilecompare_apsimcompare_apsim_metcompare_apsim_soil_profiledate2doydoy2dateedit_apsimedit_apsim_replace_soil_profileedit_apsim_xmledit_apsimxedit_apsimx_batchedit_apsimx_replace_soil_profileedit_apsimx_replacementextract_data_apsimxextract_values_apsimxget_apsimx_jsonget_chirps_apsim_metget_daymet_apsim_metget_daymet2_apsim_metget_gsod_apsim_metget_iem_apsim_metget_iemre_apsim_metget_isric_soil_profileget_power_apsim_metget_ssurgo_soil_profileget_ssurgo_tablesget_worldmodeler_apsim_metget_worldmodeler_soil_profilegrep_json_listimpute_apsim_metinitialwater_parmsinsert_replacement_nodeinspect_apsiminspect_apsim_xmlinspect_apsimxinspect_apsimx_jsoninspect_apsimx_replacementmcmc.apsim.envmcmc.apsimx.envnapad_apsim_metoptim_apsimoptim_apsimxread_apsimread_apsim_allread_apsim_metread_apsim_soilsread_apsimxread_apsimx_allremove_column_apsim_metsens_apsimsens_apsimxsoilorganicmatter_parmssoilwat_parmssolutes_parmsssurgo2spswim_parmstav_apsim_mettt_apsim_metunit_convview_apsimview_apsim_xmlview_apsimxwrite_apsim_metxargs_apsimx

Dependencies:bitbit64blobcachemclicpp11DBIevaluatefastmapgluehighrjsonliteknitrlifecyclememoisepkgconfigplogrrlangRSQLitevctrsxfunxml2yaml

apsimx: An R package for APSIM Next Generation (and Classic)

Fernando Miguez

Rendered fromapsimx.Rmdusingknitr::rmarkdownon Nov 18 2024.

Last update: 2024-06-06
Started: 2019-06-29

apsimx: writing scripts

Fernando Miguez

Rendered fromapsimx-scripts.Rmdusingknitr::rmarkdownon Nov 18 2024.

Last update: 2024-08-07
Started: 2019-07-26

Parameter Optimization

Fernando Miguez

Rendered fromoptim-apsim.Rmdusingknitr::rmarkdownon Nov 18 2024.

Last update: 2024-05-06
Started: 2020-09-16

Sensitivity Analysis

Fernando Miguez

Rendered fromsensitivity-apsim.Rmdusingknitr::rmarkdownon Nov 18 2024.

Last update: 2024-05-06
Started: 2021-07-28

Readme and manuals

Help Manual

Help pageTopics
Add a column to an object of class 'met'$<-.met add_column_apsim_met remove_column_apsim_met
Calculates attribute amp for an object of class 'met'amp_apsim_met
Run an APSIM (7.x) 'Classic' simulationapsim
Access Example APSIM Simulationsapsim_example
Setting some options specific to APSIM (7.x) 'Classic'apsim_options
Display available APSIM 'Classic' and APSIM-X versionsapsim_version
Environment which stores APSIM optionsapsim.options
Run an APSIM-X simulationapsimx
Access Example APSIM-X Simulationsapsimx_example
Test file format for .apsimx filesapsimx_filetype
Setting some options for the packageapsimx_options
Create APSIM-X Soil Profilesapsimx_soil_profile check_apsimx_soil_profile plot.soil_profile
Environment which stores APSIM-X optionsapsimx.options
Conversion from data frame to met objectas_apsim_met
Auto detect where apsim examples are locatedauto_detect_apsim_examples
Auto detect where apsimx examples are locatedauto_detect_apsimx_examples
Calculate available water contentavailable_water_content
Calculate soil carbon stockscarbon_stocks
Check a met file for possible errorscheck_apsim_met
Partial checking of an apsimx file for possible issues.check_apsimx
Compare two or more apsim output objectscompare_apsim plot.out_mrg print.out_mrg
Compare two or more metfilescompare_apsim_met plot.met_mrg print.met_mrg
Compare two or more soil profilescompare_apsim_soil_profile plot.soil_profile_mrg print.soil_profile_mrg
Converts from doy to datedate2doy doy2date
Edit an APSIM (Classic) Simulationedit_apsim
Edit APSIM 'Classic' file with a replaced soil profileedit_apsim_replace_soil_profile
Edit an APSIM (Classic) Simulation auxiliary xml fileedit_apsim_xml
Edit an APSIM-X (JSON) Simulationedit_apsimx
Edit an APSIM-X (JSON) Simulation in Batch modeedit_apsimx_batch
Edit APSIM-X file with a replaced soil profileedit_apsimx_replace_soil_profile
Edit a replacement component in an .apsimx (JSON) fileedit_apsimx_replacement
Extract data from an .apsimx (JSON) fileextract_data_apsimx
Extract values from a parameter pathextract_values_apsimx
fetches the json file for a specific model from APSIMX githubget_apsimx_json
Get CHIRPS data for an APSIM met fileget_chirps_apsim_met
Get DAYMET data for an APSIM met fileget_daymet_apsim_met
Get DAYMET data for an APSIM met fileget_daymet2_apsim_met
Get GSOD data for an APSIM met fileget_gsod_apsim_met
Get weather data from Iowa Environmental Ag Weather Stationsget_iem_apsim_met
Get weather data from Iowa Environmental Mesonet Reanalysisget_iemre_apsim_met
Generate a synthetic APSIM soil profile from the ISRIC soil databaseget_isric_soil_profile
Get NASA-POWER data for an APSIM met fileget_power_apsim_met
Retrieve soil profile data and convert it to an object of class 'soil_profile'get_ssurgo_soil_profile
Retrieve soil profile data and return a (list) with data frames (tables)get_ssurgo_tables
Obtain a weather APSIM met from the World Modeler databaseget_worldmodeler_apsim_met
Obtain a synthetic APSIM soil profile from the World Modeler databaseget_worldmodeler_soil_profile
grep but for json listgrep_json_list
Perform imputation for missing data in a met fileimpute_apsim_met
Helper function to supply additional Initial Soil Water parametersinitialwater_parms
Inserts a replacement node in a simple apsimx simulation fileinsert_replacement_node
Inspect an .apsim (XML) fileinspect_apsim
Inspect an APSIM Classic auxiliary (XML) fileinspect_apsim_xml
Inspect an .apsimx (JSON) fileinspect_apsimx
Inspect an .apsimx or .json (JSON) fileinspect_apsimx_json
Inspect a replacement component in an .apsimx (JSON) fileinspect_apsimx_replacement
Environment to store data for apsim MCMCmcmc.apsim.env
Environment to store data for apsimx MCMCmcmc.apsimx.env
Pad a met file with NAs when there are date discontinuitiesnapad_apsim_met
Observed wheat phenology, LAI and biomassobsWheat
Optimize parameters in an APSIM simulationcoef.optim_apsim confint.optim_apsim optim_apsim print.optim_apsim vcov.optim_apsim
Optimize parameters in an APSIM Next Generation simulationoptim_apsimx
Plot method for object of class 'met'plot.met
Printer-friendly version of a metfileprint.met
Read APSIM generated .out filesread_apsim
Read all APSIM generated .out files in a directoryread_apsim_all
Read in an APSIM met fileread_apsim_met
Read in a soils (XML) file into a list of 'soil_profile' objectsread_apsim_soils
Read APSIM-X generated .db filesread_apsimx
Read all APSIM-X generated .db files in a directoryread_apsimx_all
Sensitivity Analysis for APSIM Next Generation simulationsens_apsim
Sensitivity Analysis for APSIM Next Generation simulationprint.sens_apsim sens_apsimx summary.sens_apsim
Helper function to supply additional Soil Organic Matter parameterssoilorganicmatter_parms
Helper function to supply SoilWat parameterssoilwat_parms
Helper function to supply additional Solute parameterssolutes_parms
Take in SSURGO csv files and create a soil profilessurgo2sp
Summary for an APSIM met filesummary.met
Helper function to supply SWIM parametersswim_parms
Calculates attribute amp for an object of class 'met'tav_apsim_met
Calculates Thermal Time taking a 'met' objecttt_apsim_met
performs common unit conversionsunit_conv
Viewing an APSIM Classic file interactivelyview_apsim
View an APSIM Classic auxiliary (XML) fileview_apsim_xml
Viewing an APSIM-X file interactivelyview_apsimx
Wheat example optimization resultswop
Wheat example optimization results plus Hessianwop.h
Write an APSIM met filewrite_apsim_met
Provide extra arguments for APSIM-Xxargs_apsimx