inspect_apsim: Inspect an .apsim (XML) file

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

Inspect an .apsim (XML) file

Description

inspect an XML apsim file. It does not replace the GUI, but it can save time by quickly checking parameters and values.

Usage

inspect_apsim(
  file = "",
  src.dir = ".",
  node = c("Clock", "Weather", "Soil", "SurfaceOrganicMatter", "Crop", "Manager",
    "Outputfile", "Other"),
  soil.child = c("Metadata", "Water", "OrganicMatter", "Nitrogen", "Analysis",
    "InitialWater", "Sample", "SWIM"),
  parm = NULL,
  digits = 3,
  print.path = FALSE,
  root
)

Arguments

file	file ending in .apsim (Classic) to be inspected (XML)
src.dir	directory containing the .apsim file to be inspected; defaults to the current working directory
node	either ‘Weather’, ‘Soil’, ‘SurfaceOrganicMatter’, ‘MicroClimate’, ‘Crop’, ‘Manager’, ‘Outputfile’ or ‘Other’
soil.child	specific soil component to be inspected
parm	parameter to inspect when node = ‘Crop’, ‘Manager’, ‘Outputfile’ or ‘Other’
digits	number of decimals to print (default 3)
print.path	whether to print the parameter path (default = FALSE)
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

This is simply a script that prints the relevant parameters which are likely to need editing. It does not print all information from an .apsim file. For ‘Crop’, ‘Manager’ and ‘Other’, ‘parm’ should be indicated with a first element to look for and a second with the relative position in case there are multiple results.

Value

It returns the parameter path (when print.path equals TRUE) and table with inspected parameters and values

Note

When multiple folders are present as it is the case when there are factorials. Inspect will find the instance in the first folder unless 'root' is supplied. By providing the name of the folder to root (or a regular expression), the appropriate node can be selected. In this case the printed path will be absolute instead of relative.

Examples

extd.dir <- system.file("extdata", package = "apsimx")
## Testing using 'Millet'
inspect_apsim("Millet.apsim", src.dir = extd.dir, node = "Clock")
inspect_apsim("Millet.apsim", src.dir = extd.dir, node = "Weather") 
inspect_apsim("Millet.apsim", src.dir = extd.dir, node = "Soil", soil.child = "Metadata")
inspect_apsim("Millet.apsim", src.dir = extd.dir, node = "Soil", soil.child = "OrganicMatter")
inspect_apsim("Millet.apsim", src.dir = extd.dir, node = "Soil", soil.child = "Analysis")
inspect_apsim("Millet.apsim", src.dir = extd.dir, node = "Soil", soil.child = "InitialWater")
inspect_apsim("Millet.apsim", src.dir = extd.dir, node = "Soil", soil.child = "Sample")
inspect_apsim("Millet.apsim", src.dir = extd.dir, node = "SurfaceOrganicMatter")
inspect_apsim("Millet.apsim", src.dir = extd.dir, node = "Crop", parm = list("sow",NA)) 
inspect_apsim("Millet.apsim", src.dir = extd.dir, node = "Crop", parm = list("sow",7))

## when soil.child = "Water" there are potentially many crops to chose from 
## This selects LL, KL and XF for Barley
inspect_apsim("Millet.apsim", src.dir = extd.dir, node = "Soil", 
              soil.child = "Water", parm = "Barley")
## This selects LL for all the crops
inspect_apsim("Millet.apsim", src.dir = extd.dir, node = "Soil", 
              soil.child = "Water", parm = "LL")
## To print the parm.path the selection needs to be unique
## but still there will be multiple soil layers
## 'parm' can be a list or a character vector of length equal to two
inspect_apsim("Millet.apsim", src.dir = extd.dir, node = "Soil", 
              soil.child = "Water", parm = list("Barley", "LL"),
              print.path = TRUE)

## Inspect outputfile
inspect_apsim("Millet.apsim", src.dir = extd.dir, node = "Outputfile",
              parm = "filename")
 
inspect_apsim("Millet.apsim", src.dir = extd.dir, node = "Outputfile",
              parm = "variables")

## Testing with maize-soybean-rotation.apsim
inspect_apsim("maize-soybean-rotation.apsim", src.dir = extd.dir, node = "Clock")
inspect_apsim("maize-soybean-rotation.apsim", src.dir = extd.dir, node = "Weather")
inspect_apsim("maize-soybean-rotation.apsim", src.dir = extd.dir, node = "Soil",
              soil.child = "Metadata")
inspect_apsim("maize-soybean-rotation.apsim", src.dir = extd.dir, node = "Soil", 
               soil.child = "OrganicMatter")
inspect_apsim("maize-soybean-rotation.apsim", src.dir = extd.dir, node = "Soil", 
               soil.child = "Analysis")
inspect_apsim("maize-soybean-rotation.apsim", src.dir = extd.dir, node = "Soil", 
               soil.child = "InitialWater")
inspect_apsim("maize-soybean-rotation.apsim", src.dir = extd.dir, node = "Soil", 
               soil.child = "Sample")
inspect_apsim("maize-soybean-rotation.apsim", src.dir = extd.dir, 
               node = "SurfaceOrganicMatter")
inspect_apsim("maize-soybean-rotation.apsim", src.dir = extd.dir, node = "Crop")
## This has many options and a complex structure
## It is possible to select unique managements, but not non-unique ones
## The first element in parm can be a regular expression
inspect_apsim("maize-soybean-rotation.apsim", src.dir = extd.dir, 
               node = "Manager", parm = list("rotat",NA))
inspect_apsim("maize-soybean-rotation.apsim", src.dir = extd.dir, 
               node = "Manager", 
               parm = list("sow on a fixed date - maize",NA))
## Select an individual row by position
inspect_apsim("maize-soybean-rotation.apsim", src.dir = extd.dir, 
              node = "Manager", 
              parm = list("sow on a fixed date - maize",7))
              
## Illustrating the 'print.path' feature.
inspect_apsim("Millet.apsim", src.dir = extd.dir, 
               node = "Soil", soil.child = "Water", 
               parm = "DUL", print.path = TRUE)
## But the path can also be returned as a string
## Which is useful for later editing
pp <-  inspect_apsim("Millet.apsim", src.dir = extd.dir, 
               node = "Soil", soil.child = "Water", 
               parm = "DUL", print.path = TRUE)
               
## Inspecting a factorial
## (or simply a simulation with multiple folders)
## No cover
inspect_apsim("maize-factorial.apsim", src.dir = extd.dir, 
               root = "IA-CC_Canisteo_No-Cover")
               
## Cover
inspect_apsim("maize-factorial.apsim", src.dir = extd.dir, 
               root = "IA-CC_Canisteo_Cover")

apsimx documentation built on March 18, 2022, 7:52 p.m.