extract_data_apsimx {apsimx}

Extract data from an .apsimx (JSON) file

Description

Extract data from a JSON apsimx file.

Usage

extract_data_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", "Sample", "Nutrient", "Organic",
    "Swim3"),
  parm = NULL,
  digits = 3,
  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 used 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 inspect_apsimx)

parm

parameter to refine the extraction 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.

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 function does not print anything (compared to inspect_apsimx). The purpose is to return data contained in the APSIM simulation as a data.frame. It will return a ‘list’ when a data frame does not naturally accommodate the result. For example, the complete manager node does not naturally fit into a data frame structure. In some cases, multiple data frames are returned as part of lists.

Have not written this section yet

Value

a data.frame or a list. It does not return a path.

Examples

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