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

## Documentation for package ‘apsimx’ version 2.8.270

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A C D E G I M N O P R S T U V W X misc

## -- A --

add_column_apsim_met | Add a column to an object of class 'met'
amp_apsim_met | Calculates attribute amp for an object of class 'met'
apsim | Run an APSIM (7.x) 'Classic' simulation
apsim.options | Environment which stores APSIM options
apsimx | Run an APSIM-X simulation
apsimx.options | Environment which stores APSIM-X options
apsimx_example | Access Example APSIM-X Simulations
apsimx_filetype | Test file format for .apsimx files
apsimx_options | Setting some options for the package
apsimx_soil_profile | Create APSIM-X Soil Profiles
apsim_example | Access Example APSIM Simulations
apsim_options | Setting some options specific to APSIM (7.x) 'Classic'
apsim_version | Display available APSIM 'Classic' and APSIM-X versions
as_apsim_met | Conversion from data frame to met object
auto_detect_apsimx_examples | Auto detect where apsimx examples are located
auto_detect_apsim_examples | Auto detect where apsim examples are located
available_water_content | Calculate available water content

## -- C --

carbon_stocks | Calculate soil carbon stocks
check_apsimx | Partial checking of an apsimx file for possible issues.
check_apsimx_soil_profile | Create APSIM-X Soil Profiles
check_apsim_met | Check a met file for possible errors
coef.optim_apsim | Optimize parameters in an APSIM simulation
compare_apsim | Compare two or more apsim output objects
compare_apsim_met | Compare two or more 'met' files
compare_apsim_soil_profile | Compare two or more soil profiles
confint.optim_apsim | Optimize parameters in an APSIM simulation

## -- D --

date2doy | Converts from doy to date
doy2date | Converts from doy to date

## -- E --

edit_apsim | Edit an APSIM (Classic) Simulation
edit_apsimx | Edit an APSIM-X (JSON) Simulation
edit_apsimx_batch | Edit an APSIM-X (JSON) Simulation in Batch mode
edit_apsimx_replacement | Edit a replacement component in an .apsimx (JSON) file
edit_apsimx_replace_soil_profile | Edit APSIM-X file with a replaced soil profile
edit_apsim_replace_soil_profile | Edit APSIM 'Classic' file with a replaced soil profile
edit_apsim_xml | Edit an APSIM (Classic) Simulation auxiliary xml file
extract_data_apsimx | Extract data from an .apsimx (JSON) file
extract_values_apsimx | Extract values from a parameter path

## -- G --

get_apsimx_json | fetches the json file for a specific model from APSIMX github
get_chirps_apsim_met | Get CHIRPS data for an APSIM met file
get_daymet2_apsim_met | Get DAYMET data for an APSIM met file
get_daymet_apsim_met | Get DAYMET data for an APSIM met file
get_gsod_apsim_met | Get GSOD data for an APSIM met file
get_iemre_apsim_met | Get weather data from Iowa Environmental Mesonet Reanalysis
get_iem_apsim_met | Get weather data from Iowa Environmental Ag Weather Stations
get_isric_soil_profile | Generate a synthetic APSIM soil profile from the ISRIC soil database
get_power_apsim_met | Get NASA-POWER data for an APSIM met file
get_slga_soil | Retrieve soil profile data from SLGA (Soils for Australia)
get_slga_soil_profile | Generate a synthetic APSIM soil profile from the SLGA soil database
get_ssurgo_soil_profile | Retrieve soil profile data and convert it to an object of class 'soil_profile'
get_ssurgo_tables | Retrieve soil profile data and return a (list) with data frames (tables)
get_worldmodeler_apsim_met | Obtain a weather APSIM met from the World Modeler database
get_worldmodeler_soil_profile | Obtain a synthetic APSIM soil profile from the World Modeler database
grep_json_list | grep but for json list

## -- I --

impute_apsim_met | Perform imputation for missing data in a met file
initialwater_parms | Helper function to supply additional Initial Soil Water parameters
insert_replacement_node | Inserts a replacement node in a simple apsimx simulation file
inspect_apsim | Inspect an .apsim (XML) file
inspect_apsimx | Inspect an .apsimx (JSON) file
inspect_apsimx_json | Inspect an .apsimx or .json (JSON) file
inspect_apsimx_replacement | Inspect a replacement component in an .apsimx (JSON) file
inspect_apsim_xml | Inspect an APSIM Classic auxiliary (XML) file

## -- M --

mcmc.apsim.env | Environment to store data for apsim MCMC
mcmc.apsimx.env | Environment to store data for apsimx MCMC

## -- N --

napad_apsim_met | Pad a met file with NAs when there are date discontinuities

## -- O --

obsWheat | Observed wheat phenology, LAI and biomass
optim_apsim | Optimize parameters in an APSIM simulation
optim_apsimx | Optimize parameters in an APSIM Next Generation simulation

## -- P --

plot.carbon.stocks | Plot carbon stocks (function in progress)
plot.met | Plot method for object of class 'met'
plot.met_mrg | Compare two or more 'met' files
plot.out_mrg | Compare two or more apsim output objects
plot.soil_profile | Create APSIM-X Soil Profiles
plot.soil_profile_mrg | Compare two or more soil profiles
print.met | Printer-friendly version of a metfile
print.met_mrg | Compare two or more 'met' files
print.optim_apsim | Optimize parameters in an APSIM simulation
print.out_mrg | Compare two or more apsim output objects
print.sens_apsim | Sensitivity Analysis for APSIM Next Generation simulation
print.soil_profile_mrg | Compare two or more soil profiles

## -- R --

read_apsim | Read APSIM generated .out files
read_apsimx | Read APSIM-X generated .db files
read_apsimx_all | Read all APSIM-X generated .db files in a directory
read_apsim_all | Read all APSIM generated .out files in a directory
read_apsim_met | Read in an APSIM met file
read_apsim_soils | Read in a soils (XML) file into a list of 'soil_profile' objects
remove_column_apsim_met | Add a column to an object of class 'met'

## -- S --

sens_apsim | Sensitivity Analysis for APSIM Next Generation simulation
sens_apsimx | Sensitivity Analysis for APSIM Next Generation simulation
soilorganicmatter_parms | Helper function to supply additional Soil Organic Matter parameters
soilwat_parms | Helper function to supply SoilWat parameters
solutes_parms | Helper function to supply additional Solute parameters
ssurgo2sp | Take in SSURGO csv files and create a soil profile
summary.met | Summary for an APSIM met file
summary.sens_apsim | Sensitivity Analysis for APSIM Next Generation simulation
swim_parms | Helper function to supply SWIM parameters

## -- T --

tav_apsim_met | Calculates attribute amp for an object of class 'met'
tt_apsim_met | Calculates Thermal Time taking a 'met' object

## -- U --

unit_conv | performs common unit conversions

## -- V --

vcov.optim_apsim | Optimize parameters in an APSIM simulation
view_apsim | Viewing an APSIM Classic file interactively
view_apsimx | Viewing an APSIM-X file interactively
view_apsim_xml | View an APSIM Classic auxiliary (XML) file

## -- W --

wop | Wheat example optimization results
wop.h | Wheat example optimization results plus Hessian
write_apsim_met | Write an APSIM met file

## -- X --

xargs_apsimx | Provide extra arguments for APSIM-X

## -- misc --

$<-.met | Add a column to an object of class 'met'
[.met | Extract or Replace Part of a 'met' object
[<-.met | Add a column to an object of class 'met'
[[<-.met | Add a column to an object of class 'met'