Package 'rapsimng' reference manual

Title:	APSIM Next Generation
Description:	The Agricultural Production Systems sIMulator ('APSIM') is a widely used to simulate the agricultural systems for multiple crops. This package is designed to create, modify and run 'apsimx' files in the 'APSIM' Next Generation <https://www.apsim.info/>.
Authors:	Bangyou Zheng [aut, cre]
Maintainer:	Bangyou Zheng <[email protected]>
License:	MIT + file LICENSE
Version:	0.4.5
Built:	2025-02-15 02:39:17 UTC
Source:	https://github.com/byzheng/rapsimng

append a model into apsimx

Description

append a model into apsimx

Usage

append_model(l, path, model)
append_model(l, path, model)

Arguments

`l`	the list of apsimx file
`path`	If numeric, the path returned by search_path or search_node. If character, the path supported by apsimx
`model`	A new model which should be a list of new models

Value

The modified list with new value

Examples

wheat <- read_apsimx(system.file("extdata/wheat.apsimx", package = "rapsimng"))
replacements <- new_model("Core.Replacements")
wheat_new <- insert_model(wheat, 1, replacements)
replacements_node <- search_path(wheat_new, ".Simulations.Replacements")
replacements_node$path
# Add a cultivar folder under replacements
cultivar_folder <- new_model("PMF.CultivarFolder", "Cultivars")
wheat_new <- insert_model(wheat_new, replacements_node$path, cultivar_folder)
cultivar_folder_node <- search_path(wheat_new,
                                    ".Simulations.Replacements.Cultivars")
cultivar_folder_node$path
# Add an new cultivar
cultivar <- new_model("PMF.Cultivar", "Hartog")
wheat_new <- insert_model(wheat_new, cultivar_folder_node$path, cultivar)
cultivar_node <- search_path(wheat_new,
                             ".Simulations.Replacements.Cultivars.Hartog")
cultivar_node$path
# Append another cultivar
cultivar2 <- new_model("PMF.Cultivar", "Axe")
wheat_new <- append_model(wheat_new, cultivar_node$path, list(cultivar2))
cultivar2_node <- search_path(wheat_new,
                              ".Simulations.Replacements.Cultivars.Axe")
cultivar2_node$path
wheat <- read_apsimx(system.file("extdata/wheat.apsimx", package = "rapsimng"))
replacements <- new_model("Core.Replacements")
wheat_new <- insert_model(wheat, 1, replacements)
replacements_node <- search_path(wheat_new, ".Simulations.Replacements")
replacements_node$path
# Add a cultivar folder under replacements
cultivar_folder <- new_model("PMF.CultivarFolder", "Cultivars")
wheat_new <- insert_model(wheat_new, replacements_node$path, cultivar_folder)
cultivar_folder_node <- search_path(wheat_new,
                                    ".Simulations.Replacements.Cultivars")
cultivar_folder_node$path
# Add an new cultivar
cultivar <- new_model("PMF.Cultivar", "Hartog")
wheat_new <- insert_model(wheat_new, cultivar_folder_node$path, cultivar)
cultivar_node <- search_path(wheat_new,
                             ".Simulations.Replacements.Cultivars.Hartog")
cultivar_node$path
# Append another cultivar
cultivar2 <- new_model("PMF.Cultivar", "Axe")
wheat_new <- append_model(wheat_new, cultivar_node$path, list(cultivar2))
cultivar2_node <- search_path(wheat_new,
                              ".Simulations.Replacements.Cultivars.Axe")
cultivar2_node$path

List all available models in APSIM NG

Description

List all available models in APSIM NG

Usage

available_models()
available_models()

Value

a character vector of available models

Examples

a <- available_models()
a[1:10]
a <- available_models()
a[1:10]

Disable models in apsimx

Description

Disable models in apsimx

Usage

disable_models(l, paths)
disable_models(l, paths)

Arguments

`l`	the list of apsimx file
`paths`	If numeric, the path returned by search_path or search_node. If character, the path supported by apsimx

Value

The modified list with new value

Examples

wheat <- read_apsimx(system.file("extdata/Wheat.json", package = "rapsimng"))
a <- disable_models(wheat, '[Wheat].Phenology.ThermalTime')
wheat <- read_apsimx(system.file("extdata/Wheat.json", package = "rapsimng"))
a <- disable_models(wheat, '[Wheat].Phenology.ThermalTime')

Get all cultivar parameters in a model

Description

Get all cultivar parameters in a model

Usage

get_cultivar(l, alias = TRUE)
get_cultivar(l, alias = TRUE)

Arguments

`l`	The list of apsimx file
`alias`	Whether to export alias

Value

A data frame for all cultivar parameters

Examples

wheat <- read_apsimx(system.file("extdata/Wheat.json", package = "rapsimng"))
get_cultivar(wheat)
get_cultivar(wheat, alias = FALSE)

wheat <- read_apsimx(system.file("extdata/Wheat.json", package = "rapsimng"))
get_cultivar(wheat)
get_cultivar(wheat, alias = FALSE)

Get the met file name for an experiment

Description

Get the met file name for an experiment

Usage

get_metfile(l, is_stop = TRUE)
get_metfile(l, is_stop = TRUE)

Arguments

`l`	A list or apsimxNode red by read_apsimx
`is_stop`	Whether stop the function when error

Value

The met file name in a experiment

Examples

wheat <- read_apsimx(system.file("extdata/wheat.apsimx", package = "rapsimng"))
exp <- search_path(wheat, path = "[Experiment]")
get_metfile(exp)
wheat <- read_apsimx(system.file("extdata/wheat.apsimx", package = "rapsimng"))
exp <- search_path(wheat, path = "[Experiment]")
get_metfile(exp)

Get the parent node from a path

Description

Get the parent node from a path

Usage

get_parent(l, path)
get_parent(l, path)

Arguments

`l`	the list of apsimx file
`path`	If numeric, the path returned by search_path or search_node. If character, the path supported by apsimx

Value

A new list for parent

Examples

wheat <- read_apsimx(system.file("extdata/Wheat.json", package = "rapsimng"))
a <- search_path(wheat, '[Structure].BranchingRate')
get_parent(wheat, a$path)
wheat <- read_apsimx(system.file("extdata/Wheat.json", package = "rapsimng"))
a <- search_path(wheat, '[Structure].BranchingRate')
get_parent(wheat, a$path)

Get simulations for a factorial experiment

Description

Get simulations for a factorial experiment

Usage

get_simulations(l)
get_simulations(l)

Arguments

`l`	A list from read_apsim with Factorial.Permutation as root.

Value

A list with Factor as name and Levels as values

Examples

wheat <- read_apsimx(system.file("extdata/wheat.apsimx", package = "rapsimng"))
permutation <- search_path(wheat, path = "[Factors].Permutation")
get_simulations(permutation$node)
wheat <- read_apsimx(system.file("extdata/wheat.apsimx", package = "rapsimng"))
permutation <- search_path(wheat, path = "[Factors].Permutation")
get_simulations(permutation$node)

Insert a model into apsimx

Description

Insert a model into apsimx

Usage

insert_model(l, path, model)
insert_model(l, path, model)

Arguments

`l`	the list of apsimx file
`path`	If numeric, the path returned by search_path or search_node. If character, the path supported by apsimx
`model`	A new model

Value

The modified list with new value

Examples

wheat <- read_apsimx(system.file("extdata/wheat.apsimx", package = "rapsimng"))
replacements <- new_model("Core.Replacements")
wheat_new <- insert_model(wheat, 1, replacements)
replacements_node <- search_path(wheat_new, ".Simulations.Replacements")
replacements_node$path
# Add a cultivar folder under replacements
cultivar_folder <- new_model("PMF.CultivarFolder", "Cultivars")
wheat_new <- insert_model(wheat_new, replacements_node$path, cultivar_folder)
cultivar_folder_node <- search_path(wheat_new,
                                    ".Simulations.Replacements.Cultivars")
cultivar_folder_node$path
# Add an new cultivar
cultivar <- new_model("PMF.Cultivar", "Hartog")
wheat_new <- insert_model(wheat_new, cultivar_folder_node$path, cultivar)
cultivar_node <- search_path(wheat_new,
                             ".Simulations.Replacements.Cultivars.Hartog")
cultivar_node$path
wheat <- read_apsimx(system.file("extdata/wheat.apsimx", package = "rapsimng"))
replacements <- new_model("Core.Replacements")
wheat_new <- insert_model(wheat, 1, replacements)
replacements_node <- search_path(wheat_new, ".Simulations.Replacements")
replacements_node$path
# Add a cultivar folder under replacements
cultivar_folder <- new_model("PMF.CultivarFolder", "Cultivars")
wheat_new <- insert_model(wheat_new, replacements_node$path, cultivar_folder)
cultivar_folder_node <- search_path(wheat_new,
                                    ".Simulations.Replacements.Cultivars")
cultivar_folder_node$path
# Add an new cultivar
cultivar <- new_model("PMF.Cultivar", "Hartog")
wheat_new <- insert_model(wheat_new, cultivar_folder_node$path, cultivar)
cultivar_node <- search_path(wheat_new,
                             ".Simulations.Replacements.Cultivars.Hartog")
cultivar_node$path

Insert models into apsimx

Description

Insert models into apsimx

Usage

insert_models(l, path, models)
insert_models(l, path, models)

Arguments

`l`	the list of apsimx file
`path`	If numeric, the path returned by search_path or search_node. If character, the path supported by apsimx
`models`	New models

Value

The modified list with new value

Examples

wheat <- read_apsimx(system.file("extdata/wheat.apsimx", package = "rapsimng"))
replacements <- new_model("Core.Replacements")
wheat_new <- insert_model(wheat, 1, replacements)
replacements_node <- search_path(wheat_new, ".Simulations.Replacements")
replacements_node$path
# Add a cultivar folder under replacements
cultivar_folder <- new_model("PMF.CultivarFolder", "Cultivars")
wheat_new <- insert_model(wheat_new, replacements_node$path, cultivar_folder)
cultivar_folder_node <- search_path(wheat_new,
                                    ".Simulations.Replacements.Cultivars")
cultivar_folder_node$path
# Add an new cultivar
cultivar <- new_model("PMF.Cultivar", "Hartog")
wheat_new <- insert_model(wheat_new, cultivar_folder_node$path, cultivar)
cultivar_node <- search_path(wheat_new,
                             ".Simulations.Replacements.Cultivars.Hartog")
cultivar_node$path
wheat <- read_apsimx(system.file("extdata/wheat.apsimx", package = "rapsimng"))
replacements <- new_model("Core.Replacements")
wheat_new <- insert_model(wheat, 1, replacements)
replacements_node <- search_path(wheat_new, ".Simulations.Replacements")
replacements_node$path
# Add a cultivar folder under replacements
cultivar_folder <- new_model("PMF.CultivarFolder", "Cultivars")
wheat_new <- insert_model(wheat_new, replacements_node$path, cultivar_folder)
cultivar_folder_node <- search_path(wheat_new,
                                    ".Simulations.Replacements.Cultivars")
cultivar_folder_node$path
# Add an new cultivar
cultivar <- new_model("PMF.Cultivar", "Hartog")
wheat_new <- insert_model(wheat_new, cultivar_folder_node$path, cultivar)
cultivar_node <- search_path(wheat_new,
                             ".Simulations.Replacements.Cultivars.Hartog")
cultivar_node$path

Keep simulations for a factorial experiment

Description

Keep simulations for a factorial experiment

Usage

keep_simulations(l, s)
keep_simulations(l, s)

Arguments

`l`	A list from read_apsim with Factorial.Permutation as root.
`s`	a list with factor as name and levels as value to keep. The factor is kept if it is not specified.

Value

A new list with removed simulations.

Examples

wheat <- read_apsimx(system.file("extdata/wheat.apsimx", package = "rapsimng"))
permutation <- search_path(wheat, path = "[Factors].Permutation")
permutation_new <- keep_simulations(permutation$node, list(V = "2"))
get_simulations(permutation_new)

permutation_new <- keep_simulations(permutation$node, list(Cv = c("Axe", "Bolac")))
get_simulations(permutation_new)

permutation_new <- keep_simulations(permutation$node,
                                    list(V = "1", Cv = c("Axe", "Bolac")))
get_simulations(permutation_new)
wheat <- read_apsimx(system.file("extdata/wheat.apsimx", package = "rapsimng"))
permutation <- search_path(wheat, path = "[Factors].Permutation")
permutation_new <- keep_simulations(permutation$node, list(V = "2"))
get_simulations(permutation_new)

permutation_new <- keep_simulations(permutation$node, list(Cv = c("Axe", "Bolac")))
get_simulations(permutation_new)

permutation_new <- keep_simulations(permutation$node,
                                    list(V = "1", Cv = c("Axe", "Bolac")))
get_simulations(permutation_new)

List all reports in the database

Description

List all reports in the database

Usage

list_report(file)
list_report(file)

Arguments

file

the file path to apsimx or db file

Value

a vector of all reports

Examples

## Not run: 
file <- system.file("extdata/wheat.apsimx", package = "rapsimng")
list_report(file)

## End(Not run)
## Not run: 
file <- system.file("extdata/wheat.apsimx", package = "rapsimng")
list_report(file)

## End(Not run)

Set the log level of apsimx file

Description

Set the log level of apsimx file

Usage

log_level(l, level = c("Error", "Warning", "Information", "Diagnostic", "All"))
log_level(l, level = c("Error", "Warning", "Information", "Diagnostic", "All"))

Arguments

`l`	the list of apsimx file
`level`	log level with option Error, Warning, Information, Diagnostic, All

Value

a new apsimx file

Create the minimum requirements to run an APSIM Next Generation

Description

Create the minimum requirements to run an APSIM Next Generation

Usage

minimum_apsimng(install_path, output)
minimum_apsimng(install_path, output)

Arguments

`install_path`	The installed path of APSIM Next Generation
`output`	The output folder

Examples

## Not run: 
 minimum_apsimng("C:/ProgramFiles/APSIMNG", "minimum_apsimng")

## End(Not run)
## Not run: 
 minimum_apsimng("C:/ProgramFiles/APSIMNG", "minimum_apsimng")

## End(Not run)

Create a new model

Description

Create a new model

Usage

new_model(model, name = model)
new_model(model, name = model)

Arguments

`model`	The name of new model
`name`	The new name

Examples

new_model(model = "PMF.Cultivar")
new_model(model = "PMF.Cultivar", name = "example")
new_model(model = "PMF.Cultivar")
new_model(model = "PMF.Cultivar", name = "example")

Read APSIMX file

Description

Read APSIMX file

Usage

read_apsimx(path)
read_apsimx(path)

Arguments

path

The file path or URL to apsimx file

Value

A list object of apsimx file

Examples

file <- system.file("extdata/wheat.apsimx", package = "rapsimng")
m <- read_apsimx(file)
file <- system.file("extdata/wheat.apsimx", package = "rapsimng")
m <- read_apsimx(file)

Read apsimx database in db file format

Description

Read apsimx database in db file format

Usage

read_report(file, report)
read_report(file, report)

Arguments

`file`	the file path to apsimx or db file
`report`	the report name

Value

a data.frame for a report

Examples

## Not run: 
file <- system.file("extdata/wheat.apsimx", package = "rapsimng")
read_report(file, "HarvestReport")

## End(Not run)
## Not run: 
file <- system.file("extdata/wheat.apsimx", package = "rapsimng")
read_report(file, "HarvestReport")

## End(Not run)

Remove a model with new values

Description

Remove a model with new values

Usage

remove_model(l, path)
remove_model(l, path)

Arguments

`l`	the list of apsimx file
`path`	If numeric, the path returned by search_path or search_node. If character, the path supported by apsimx

Value

The modified list with new value

Examples

wheat <- read_apsimx(system.file("extdata/Wheat.json", package = "rapsimng"))
a <- search_path(wheat, '[Wheat].Phenology.ThermalTime')
wheat_new <- remove_model(wheat, a$path)
b <- search_path(wheat_new, '[Wheat].Phenology.ThermalTime')
b
wheat <- read_apsimx(system.file("extdata/Wheat.json", package = "rapsimng"))
a <- search_path(wheat, '[Wheat].Phenology.ThermalTime')
wheat_new <- remove_model(wheat, a$path)
b <- search_path(wheat_new, '[Wheat].Phenology.ThermalTime')
b

Replace a model with new values

Description

Replace a model with new values

Usage

replace_model(l, path, model)
replace_model(l, path, model)

Arguments

`l`	the list of apsimx file
`path`	If numeric, the path returned by search_path or search_node. If character, the path supported by apsimx
`model`	A new model

Value

The modified list with new value

Examples

wheat <- read_apsimx(system.file("extdata/Wheat.json", package = "rapsimng"))

a <- search_path(wheat, '[Wheat].Phenology.ThermalTime')
a$node$Children[[1]]$X[[2]] <- 27
wheat_new <- replace_model(wheat, a$path, a$node)
b <- search_path(wheat_new, '[Wheat].Phenology.ThermalTime')
b$node$Children[[1]]$X
wheat <- read_apsimx(system.file("extdata/Wheat.json", package = "rapsimng"))

a <- search_path(wheat, '[Wheat].Phenology.ThermalTime')
a$node$Children[[1]]$X[[2]] <- 27
wheat_new <- replace_model(wheat, a$path, a$node)
b <- search_path(wheat_new, '[Wheat].Phenology.ThermalTime')
b$node$Children[[1]]$X

Run apsimx file using Models.exe

Description

Run apsimx file using Models.exe

Usage

run_models(
  models_exe,
  path,
  pattern = NULL,
  recurse = FALSE,
  csv = FALSE,
  parallel = NULL,
  ncpus = NULL,
  verbose = FALSE
)
run_models(
  models_exe,
  path,
  pattern = NULL,
  recurse = FALSE,
  csv = FALSE,
  parallel = NULL,
  ncpus = NULL,
  verbose = FALSE
)

Arguments

`models_exe`	path to Models.exe
`path`	The path to an .apsimx file. May include wildcard.
`pattern`	Use to filter simulation names to run.
`recurse`	Recursively search subdirectories for files matching ApsimXFileSpec. FALSE in default.
`csv`	Export all reports to .csv files. FALSE in default.
`parallel`	Use the multi-process job runner. If FALSE, use single threaded; if TRUE, use the multi-process job runner
`ncpus`	Set the number of processors to use. All processes in default
`verbose`	Write messages to StdOut when a simulation starts/finishes. Only has an effect when running a directory of .apsimx files (*.apsimx).

Find element(s) in apsimx file

Description

Find element(s) in apsimx file

Usage

search_node(l, all = FALSE, max_depth = 1e+06, case_insensitive = TRUE, ...)
search_node(l, all = FALSE, max_depth = 1e+06, case_insensitive = TRUE, ...)

Arguments

`l`	The list of apsimx file
`all`	Whether to find all elements
`max_depth`	The maximum depth to search
`case_insensitive`	Whether case sensitive
`...`	Other names arguments for property to match

Value

A list matching all criteria if all equals to TRUE, A list with node and path if all equals to FALSE (default)

Examples

wheat <- read_apsimx(system.file("extdata/Wheat.json", package = "rapsimng"))
# Return empty list if not found
search_node(wheat, Name = "Simulations1")
# Find root level
a <- search_node(wheat, Name = "Simulations")
a$path
# Find sub-level
a <- search_node(wheat, Name = "Wheat")
a$path
a <- search_node(wheat, `$type` = "Models.PMF.Cultivar, Models")
a$path

# Find multiple attributes
a <- search_node(wheat,
            Name = 'PotentialBranchingRate',
            `$type` = "Models.Functions.PhaseLookup, Models")
a$path
a$node$Name
# Find all cultivar nodes
 a <- search_node(wheat, `$type` = "Models.PMF.Cultivar, Models", all = TRUE)
length(a)
wheat <- read_apsimx(system.file("extdata/Wheat.json", package = "rapsimng"))
# Return empty list if not found
search_node(wheat, Name = "Simulations1")
# Find root level
a <- search_node(wheat, Name = "Simulations")
a$path
# Find sub-level
a <- search_node(wheat, Name = "Wheat")
a$path
a <- search_node(wheat, `$type` = "Models.PMF.Cultivar, Models")
a$path

# Find multiple attributes
a <- search_node(wheat,
            Name = 'PotentialBranchingRate',
            `$type` = "Models.Functions.PhaseLookup, Models")
a$path
a$node$Name
# Find all cultivar nodes
 a <- search_node(wheat, `$type` = "Models.PMF.Cultivar, Models", all = TRUE)
length(a)

Find a model in the apsimx file using specified path

Description

Find a model in the apsimx file using specified path

Usage

search_path(l, path, case_insensitive = TRUE)
search_path(l, path, case_insensitive = TRUE)

Arguments

`l`	the list of apsimx file
`path`	The specified path (See details)
`case_insensitive`	Whether case sensitive

Value

The list for the specified path.

Absolute Paths

Absolute paths have a leading ‘.’ e.g.

.Simulations.Test.Clock - absolute path - refers to the clock model in the 'Test' simulation.

Scoped Paths

Scoped paths have a leading model type in square brackets. A model of the specified name, in scope, is located before applying the rest of the path.

[Soil].Water - scoped path - refers to the Water model that is a child of a model that has the name 'Soil' that is in scope

Examples

wheat <- read_apsimx(system.file("extdata/Wheat.json", package = "rapsimng"))
# Return empty list if not found
search_path(wheat, "[Simulations1]")
# Search root path
a <- search_path(wheat, '.Simulations')
a$path
a$node$Name
# Level one
a <- search_path(wheat, '.Simulations.Wheat1')
a$path
a$node$Name
# Level two
a <- search_path(wheat, '.Simulations.Wheat')
a$path
a$node$Name
# Level three
a <- search_path(wheat, '.Simulations.Wheat.BranchingRate')
a$path
a$node$Name
a <- search_path(wheat, '.Simulations.Wheat.Structure')
a$path
a$node$Name
# Level four
a <- search_path(wheat, '.Simulations.Wheat.Structure.BranchingRate')
a$path
a$node$Name
a <- search_path(wheat, '.Simulations.Wheat.Structure.BranchingRate1')
a$path
a$node$Name
# scoped
# Root path
a <- search_path(wheat, '[Simulations1]')
a <- search_path(wheat, '[Simulations]')
a$path
a$node$Name
# Level two
a <- search_path(wheat, '[Simulations].Wheat1')
a <- search_path(wheat, '[Simulations1].Wheat')
a$path
a$node$Name
a <- search_path(wheat, '[Whea]')
a <- search_path(wheat, '[Wheat]')
a$path
a$node$Name
# Level three
a <- search_path(wheat, '[Wheat].BranchingRate')
a <- search_path(wheat, '[Wheat].Structure')
a$path
a$node$Name
a <- search_path(wheat, '[Structure]')
a$path
a$node$Name
# Level four
a <- search_path(wheat, '[Structure].BranchingRate')
a$path
a$node$Name
a <- search_path(wheat, '[Structure].BranchingRate1')
a <- search_path(wheat, '[Structure1].BranchingRate')
wheat <- read_apsimx(system.file("extdata/Wheat.json", package = "rapsimng"))
# Return empty list if not found
search_path(wheat, "[Simulations1]")
# Search root path
a <- search_path(wheat, '.Simulations')
a$path
a$node$Name
# Level one
a <- search_path(wheat, '.Simulations.Wheat1')
a$path
a$node$Name
# Level two
a <- search_path(wheat, '.Simulations.Wheat')
a$path
a$node$Name
# Level three
a <- search_path(wheat, '.Simulations.Wheat.BranchingRate')
a$path
a$node$Name
a <- search_path(wheat, '.Simulations.Wheat.Structure')
a$path
a$node$Name
# Level four
a <- search_path(wheat, '.Simulations.Wheat.Structure.BranchingRate')
a$path
a$node$Name
a <- search_path(wheat, '.Simulations.Wheat.Structure.BranchingRate1')
a$path
a$node$Name
# scoped
# Root path
a <- search_path(wheat, '[Simulations1]')
a <- search_path(wheat, '[Simulations]')
a$path
a$node$Name
# Level two
a <- search_path(wheat, '[Simulations].Wheat1')
a <- search_path(wheat, '[Simulations1].Wheat')
a$path
a$node$Name
a <- search_path(wheat, '[Whea]')
a <- search_path(wheat, '[Wheat]')
a$path
a$node$Name
# Level three
a <- search_path(wheat, '[Wheat].BranchingRate')
a <- search_path(wheat, '[Wheat].Structure')
a$path
a$node$Name
a <- search_path(wheat, '[Structure]')
a$path
a$node$Name
# Level four
a <- search_path(wheat, '[Structure].BranchingRate')
a$path
a$node$Name
a <- search_path(wheat, '[Structure].BranchingRate1')
a <- search_path(wheat, '[Structure1].BranchingRate')

Set a parameter with a new value

Description

Set a parameter with a new value

Usage

set_parameter_value(l, parameter, value)
set_parameter_value(l, parameter, value)

Arguments

`l`	the list of apsimx file
`parameter`	the name of parameter with APSIM NG specification
`value`	the new value

Value

A list with replaced value

Examples

 wheat <- read_apsimx(system.file("extdata/Wheat.json", package = "rapsimng"))
 new_wheat <- set_parameter_value(wheat,
  "[Structure].BranchingRate.PotentialBranchingRate.Reproductive.Zero.FixedValue",
  1)
new_wheat2 <- search_path(new_wheat,
    "[Structure].BranchingRate.PotentialBranchingRate.Reproductive.Zero")
new_wheat2$node$FixedValue

new_wheat <- set_parameter_value(
    wheat,
    "[Structure].HeightModel.WaterStress.XYPairs.Y",
    "0.1,1.1")
new_wheat2 <- search_path(new_wheat,
    "[Structure].HeightModel.WaterStress.XYPairs")
new_wheat2$node$Y
wheat <- read_apsimx(system.file("extdata/Wheat.json", package = "rapsimng"))
 new_wheat <- set_parameter_value(wheat,
  "[Structure].BranchingRate.PotentialBranchingRate.Reproductive.Zero.FixedValue",
  1)
new_wheat2 <- search_path(new_wheat,
    "[Structure].BranchingRate.PotentialBranchingRate.Reproductive.Zero")
new_wheat2$node$FixedValue

new_wheat <- set_parameter_value(
    wheat,
    "[Structure].HeightModel.WaterStress.XYPairs.Y",
    "0.1,1.1")
new_wheat2 <- search_path(new_wheat,
    "[Structure].HeightModel.WaterStress.XYPairs")
new_wheat2$node$Y

Test whether all files under published folder of apsimx are required

Description

Test whether all files under published folder of apsimx are required

Usage

test_apsimx(base, example)
test_apsimx(base, example)

Arguments

`base`	the base folder path to apsimx publish
`example`	an example apsimx file

Value

A vector a required files

Title Update the cultivar parameters

Description

This function assumes the file is apsimx format. A new Replacements node is added if it is not exist. The existing cultivar parameters are updated. New cultivar is created.

Usage

update_cultivar(
  l,
  df,
  add = TRUE,
  use_folder = TRUE,
  cultivar_folder = "Cultivars"
)
update_cultivar(
  l,
  df,
  add = TRUE,
  use_folder = TRUE,
  cultivar_folder = "Cultivars"
)

Arguments

`l`	The list of apsimx file
`df`	A data frame for new parameters with three columns, i.e. name, parameter and value.
`add`	Whether to add extra nodes (e.g. replacements, Cultivars folder and new cultivar)
`use_folder`	use cultivar folder to add new cultivars
`cultivar_folder`	folder name for cultivars

Value

The modified apsimx file

Examples

wheat <- read_apsimx(system.file("extdata/wheat.apsimx", package = "rapsimng"))
# Update cultivars
df <- data.frame(name = rep("Hartog", 3),
                 parameter = c("[Phenology].MinimumLeafNumber.FixedValue",
                              "[Phenology].VrnSensitivity.FixedValue",
                              "[Phenology].PpSensitivity.FixedValue"),
                value = c(9, 7, 3))

wheat_cultivar <- update_cultivar(wheat, df)
hartog <- search_path(wheat_cultivar, "[Replacements].Hartog")
hartog$path
wheat <- read_apsimx(system.file("extdata/wheat.apsimx", package = "rapsimng"))
# Update cultivars
df <- data.frame(name = rep("Hartog", 3),
                 parameter = c("[Phenology].MinimumLeafNumber.FixedValue",
                              "[Phenology].VrnSensitivity.FixedValue",
                              "[Phenology].PpSensitivity.FixedValue"),
                value = c(9, 7, 3))

wheat_cultivar <- update_cultivar(wheat, df)
hartog <- search_path(wheat_cultivar, "[Replacements].Hartog")
hartog$path

Run APSIM Next Generation Simulations in a Temporary Folder

Description

The 'with_apsimx' function automates the process of setting up and running APSIM Next Generation (NG) simulations in a temporary or specified folder. This approach helps reduce I/O overhead, particularly in high-performance computing (HPC) environments with network file systems (NFS). The frequent file I/O operations performed by APSIM NG (e.g., writing to SQLite databases) can strain file systems, and redirecting simulations to a local folder mitigates this issue. The function can also perform optional post-processing of the simulation results.

Usage

with_apsimx(
  models,
  file,
  mets = NULL,
  target = tempdir(),
  clean = c("none", "simulations", "mets", "all"),
  post_process = NULL,
  ...
)
with_apsimx(
  models,
  file,
  mets = NULL,
  target = tempdir(),
  clean = c("none", "simulations", "mets", "all"),
  post_process = NULL,
  ...
)

Arguments

`models`	A character string specifying the path to the APSIM NG executable ('Models.exe' on Windows or 'Models' on Linux).
`file`	A character string specifying the path to the '.apsimx' simulation file.
`mets`	A character vector specifying paths to meteorological data ('.met' files) used in the simulation. Currently, only '.met' files located in the same folder as the '.apsimx' file are supported (optional).
`target`	A character string specifying the target directory where simulations will be run. Defaults to the R system temporary directory ('tempdir()').
`clean`	A character string specifying which files or directories to clean after the simulation. Options are: '"none"': No files are cleaned (default). '"simulations"': Cleans only simulation-related files (e.g., '.apsimx', '.db', '.db-shm', '.db-wal', '.csv'). '"mets"': Cleans only meteorological files (e.g., '.met'). '"all"': Cleans all files, including APSIM NG executable files, simulations, and meteorological files.
`post_process`	An optional function for post-processing simulation results. The function must accept a 'folder' argument specifying the directory containing the simulation results.
`...`	Additional arguments passed to both the 'run_models' and 'post_process' functions.

Value

If a 'post_process' function is provided, its return value is returned. Otherwise, the function returns 'NULL'.

Examples

## Not run: 
# Run simulations without post-processing
with_apsimx(
    models = "path/to/apsimx",
    file = "path/to/input.apsimx",
    mets = c("path/to/met1.met", "path/to/met2.met"),
    clean = "all"
)

# Run simulations with post-processing
post_process_function <- function(folder) {
    output_files <- list.files(folder, full.names = TRUE)
    message("Output files:", paste(output_files, collapse = "\n"))
}

result <- with_apsimx(
    models = "path/to/apsimx",
    file = "path/to/input.apsimx",
    mets = c("path/to/met1.met", "path/to/met2.met"),
    post_process = post_process_function
)

## End(Not run)

## Not run: 
# Run simulations without post-processing
with_apsimx(
    models = "path/to/apsimx",
    file = "path/to/input.apsimx",
    mets = c("path/to/met1.met", "path/to/met2.met"),
    clean = "all"
)

# Run simulations with post-processing
post_process_function <- function(folder) {
    output_files <- list.files(folder, full.names = TRUE)
    message("Output files:", paste(output_files, collapse = "\n"))
}

result <- with_apsimx(
    models = "path/to/apsimx",
    file = "path/to/input.apsimx",
    mets = c("path/to/met1.met", "path/to/met2.met"),
    post_process = post_process_function
)

## End(Not run)

Write APSIMX file

Description

Write APSIMX file

Usage

write_apsimx(l, file)
write_apsimx(l, file)

Arguments

`l`	the list of apsimx file
`file`	The file path to apsimx file

Value

A list object of apsimx file

Package 'rapsimng'

Help Index

append a model into apsimx

Description

Usage

Arguments

Value

Examples

List all available models in APSIM NG

Description

Usage

Value

Examples

Disable models in apsimx

Description

Usage

Arguments

Value

Examples

Get all cultivar parameters in a model

Description

Usage

Arguments

Value

Examples

Get the met file name for an experiment

Description

Usage

Arguments

Value

Examples

Get the parent node from a path

Description

Usage

Arguments

Value

Examples

Get simulations for a factorial experiment

Description

Usage

Arguments

Value

Examples

Insert a model into apsimx

Description

Usage

Arguments

Value

Examples

Insert models into apsimx

Description

Usage

Arguments

Value

Examples

Keep simulations for a factorial experiment

Description

Usage

Arguments

Value

Examples

List all reports in the database

Description

Usage

Arguments

Value

Examples

Set the log level of apsimx file

Description

Usage

Arguments

Value

Create the minimum requirements to run an APSIM Next Generation

Description

Usage

Arguments

Examples

Create a new model

Description

Usage