inspect_apsimx: Inspect an .apsimx (JSON) file

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

Inspect an .apsimx (JSON) file

Description

inspect a JSON apsimx file. It does not replace the GUI, but it can save time by quickly checking parameters and values.

Usage

inspect_apsimx(
  file = "",
  src.dir = ".",
  node = c("Clock", "Weather", "Soil", "SurfaceOrganicMatter", "MicroClimate", "Crop",
    "Manager", "Report", "Operations", "Other"),
  soil.child = c("Metadata", "Water", "InitialWater", "Chemical", "Physical", "Analysis",
    "SoilWater", "InitialN", "CERESSoilTemperature", "SoilTemperature", "Sample",
    "Solute", "NO3", "NH4", "Urea", "Nutrient", "Organic", "Swim3"),
  parm = NULL,
  digits = 3,
  print.path = FALSE,
  root
)

Arguments

file	file ending in .apsimx to be inspected (JSON)
src.dir	directory containing the .apsimx file to be inspected; defaults to the current working directory
node	specific node to be inspected either ‘Clock’, ‘Weather’, ‘Soil’, ‘SurfaceOrganicMatter’, ‘MicroClimate’, ‘Crop’, ‘Manager’, ‘Operations’ or ‘Other’
soil.child	specific soil component to be inspected. The options vary depending on what is available (see details)
parm	parameter to refine the inspection of the ‘manager’ list(‘parm’,‘position’), use ‘NA’ for all the positions. ‘parm’ can be a regular expression for partial matching.
digits	number of decimals to print (default 3). Not used now because everything is a character.
print.path	whether to print the path to the specific parameter. Useful to give the later editing. (Also returned as ‘invisible’)
root	root node label. In simulation structures such as factorials there will be multiple possible nodes. This can be specified by supplying an appropriate character.

Details

In general, this function is used to inspect one parameter at a time. There are some exceptions.

When node equals ‘Other’ there are several options. If ‘parm’ is not specified the structure of the simulation file will be returned. In this case, the parameter to print is typically just ‘Simulations’. This option is useful when the intention is to show the simulation structure to pick a root presumably. ‘parm’ can be set as 0, 1, 2 or 3 for different levels. ‘parm’ can also be a list with integers, such as ‘list(1, 2, 3)’. If zero is included, available elements If a parameter is specified the function will try to ‘guess’ the root elements from the parameter path supplied.

This is simply a script that prints the relevant parameters which are likely to need editing. It does not print all information from an .apsimx file. To investigate the available ‘soil.childs’ specify ‘Soil’ for ‘node’ and do not specify the ‘soil.child’.

Value

prints a table with inspected parameters and values (and ‘parm path’ when ‘print.path’ = TRUE).

Examples

extd.dir <- system.file("extdata", package = "apsimx")
inspect_apsimx("Wheat.apsimx", src.dir = extd.dir, node = "Clock")
inspect_apsimx("Wheat.apsimx", src.dir = extd.dir, node = "Weather")
inspect_apsimx("Wheat.apsimx", src.dir = extd.dir, node = "Soil", soil.child = "Metadata")
inspect_apsimx("Wheat.apsimx", src.dir = extd.dir, node = "Soil", soil.child = "Physical")
inspect_apsimx("Wheat.apsimx", src.dir = extd.dir, node = "Soil", soil.child = "SoilWater")
inspect_apsimx("Wheat.apsimx", src.dir = extd.dir, node = "Soil", soil.child = "Organic")
inspect_apsimx("Wheat.apsimx", src.dir = extd.dir, node = "Soil", soil.child = "Chemical")
inspect_apsimx("Wheat.apsimx", src.dir = extd.dir, node = "Soil", soil.child = "InitialWater")
inspect_apsimx("Wheat.apsimx", src.dir = extd.dir, node = "Soil", soil.child = "InitialN")
inspect_apsimx("Wheat.apsimx", src.dir = extd.dir, node = "SurfaceOrganicMatter")
inspect_apsimx("Wheat.apsimx", src.dir = extd.dir, node = "MicroClimate")
inspect_apsimx("Wheat.apsimx", src.dir = extd.dir, node = "Crop")
inspect_apsimx("Wheat.apsimx", src.dir = extd.dir, node = "Manager")
inspect_apsimx("Wheat.apsimx", src.dir = extd.dir, node = "Report")

## Examples of using node = "Other"
extd.dir <- system.file("extdata", package = "apsimx")

## When parm is not provided
inspect_apsimx("maize-manager-folder.apsimx", src.dir = extd.dir, node = "Other")
## When parm = 2
inspect_apsimx("maize-manager-folder.apsimx", src.dir = extd.dir,
               node = "Other", parm = 2)
## When parm = 3
inspect_apsimx("maize-manager-folder.apsimx", src.dir = extd.dir,
               node = "Other", parm = 3)
## When parm is a path
inspect_apsimx("maize-manager-folder.apsimx", src.dir = extd.dir,
               node = "Other", parm = ".Simulations.Simulation")
## When parm is a list with numbers (integers)
pp <- inspect_apsimx("maize-manager-folder.apsimx", src.dir = extd.dir,
                     node = "Other", parm = list(1, 1, 5),
                     print.path = TRUE)
## Same as above, but with zero prints possible options
inspect_apsimx("maize-manager-folder.apsimx", src.dir = extd.dir,
                node = "Other", parm = list(1, 1, 5, 0))

## It is possible to look into folders using this method
inspect_apsimx("maize-manager-folder.apsimx", node = "Other", src.dir = extd.dir,
               parm = list("Manager", "Fertiliser", "Amount"))

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