edit_apsimx: Edit an APSIM-X (JSON) Simulation

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

Edit an APSIM-X (JSON) Simulation

Description

This function allows editing of an APSIM-X (JSON) simulation file.

Usage

edit_apsimx(
  file,
  src.dir = ".",
  wrt.dir = NULL,
  node = c("Clock", "Weather", "Soil", "SurfaceOrganicMatter", "MicroClimate", "Crop",
    "Manager", "Report", "Operations", "Other"),
  soil.child = c("Metadata", "Water", "SoilWater", "Organic", "Physical", "Analysis",
    "Chemical", "InitialWater", "Sample", "Solute", "NO3", "NH4", "Urea", "Swim3"),
  manager.child = NULL,
  parm = NULL,
  value = NULL,
  overwrite = FALSE,
  edit.tag = "-edited",
  parm.path = NULL,
  root = NULL,
  verbose = TRUE
)

Arguments

file	file ending in .apsimx to be edited (JSON)
src.dir	directory containing the .apsimx file to be edited; defaults to the current working directory
wrt.dir	should be used if the destination directory is different from the src.dir
node	either ‘Clock’, ‘Weather’, ‘Soil’, ‘SurfaceOrganicMatter’, ‘MicroClimate’, ‘Crop’, ‘Manager’, ‘Report’, ‘Operations’ or ‘Other’
soil.child	specific soil component to be edited
manager.child	specific manager component to be edited
parm	parameter to be edited. It can be a regular expression.
value	new values for the parameter to be edited
overwrite	logical; if TRUE the old file is overwritten, a new file is written otherwise
edit.tag	if the file is edited a different tag from the default ‘-edited’ can be used.
parm.path	path to the attribute to edit when node is ‘Other’
root	supply the node position in the case of multiple simulations such as factorials.
verbose	whether to print information about successful edit

Details

The variables specified by parm within the .apsimx file specified by file in the source directory src.dir are edited. The old values are replaced with value, which is a list that has the same number of elements as the length of the vector parm. The current .apsimx file will be overwritten if overwrite is set to TRUE; otherwise the file ‘file’ -edited.apsimx will be created. If (verbose = TRUE) then the name of the written file is returned.

When node equals ‘Report’, the editing allows to add variables, but not to remove them at the moment.

When node equals Operations, ‘parm’ should have a list with two elements. The first should be the line(s) to edit and the second should be the component(s) to edit. Either ‘Date’, ‘Action’ or ‘Line’. When more than one line is edited, ‘value’ should be a character vector of the same length as the number of lines to edit. It is possible to remove, say, line 10 by using ‘parm = list(-10, NA)’. It is safer to remove lines at the end of ‘Operations’. To remove several use the following ‘parm = list(-c(10:12), NA)’. This assumes that ‘12’ is the maximum number of lines present. Trying to remove lines in the middle will have unexpected effects. It is possible to create additional lines, but only by using ‘Date’ first. This feature has not been tested much so use it carefully.

Value

(when verbose=TRUE) complete file path to edited .apsimx file is returned as a character string. As a side effect this function creates a new (JSON) .apsimx file.

Examples

## This example will read one of the examples distributed with APSIM-X
## but write to a temporary directory
tmp.dir <- tempdir()

## Edit Bulk density
extd.dir <- system.file("extdata", package = "apsimx")
bds <- c(1.02, 1.03, 1.09, 1.16, 1.18, 1.19, 1.20)
edit_apsimx("Wheat.apsimx", src.dir = extd.dir,
            wrt.dir = tmp.dir,
            node = "Soil",
            soil.child = "Physical", 
            parm = "BD", value = bds,
            verbose = FALSE)
## Inspect file
inspect_apsimx("Wheat-edited.apsimx", src.dir = tmp.dir,
                node = "Soil", soil.child = "Physical")
## To delete the file...
file.remove(file.path(tmp.dir, "Wheat-edited.apsimx"))

## Edit the fertilizer amount in 'Maize.apsimx'
edit_apsimx("Maize.apsimx", src.dir = extd.dir,
             wrt.dir = tmp.dir, node = "Manager",
             manager.child = "SowingFertiliser",
             parm = "Amount", value = 200, verbose = TRUE)
             
## Make sure it worked
inspect_apsimx("Maize-edited.apsimx", src.dir = tmp.dir, 
               node = "Manager",
               parm = list("SowingFertiliser", NA))

## Remove the file
file.remove(file.path(tmp.dir, "Maize-edited.apsimx"))

apsimx documentation built on Sept. 11, 2024, 5:42 p.m.