Package 'apsimx'

Description

The usual way of adding a column to a data frame might not work for an object of class ‘met’, so this method is recommended

Usage

add_column_apsim_met(met, value, name, units)

## S3 replacement method for class 'met'
x$name <- value

remove_column_apsim_met(met, name)

Arguments

Value

an object of class ‘met’ with the additional column

an object of class ‘met’ without the variable (column) in ‘name’

Examples

extd.dir <- system.file("extdata", package = "apsimx")
ames <- read_apsim_met("Ames.met", src.dir = extd.dir)

## The recommended method is
val <- abs(rnorm(nrow(ames), 10))
ames <- add_column_apsim_met(ames, value = val, name = "vp", units = "(hPa)")

## This is also possible
vp <- data.frame(vp = abs(rnorm(nrow(ames), 10)))
attr(vp, "units") <- "(hPa)"
ames$vp <- vp$vp

## This is needed to ensure that units and related attributes are also removed
ames <- remove_column_apsim_met(ames, "vp")
## However, ames$vp <- NULL will also work

Description

This function can re-calculate annual mean monthly amplitude for an object of class ‘met’

Usage

amp_apsim_met(met, by.year = TRUE)

Arguments

Value

an object of class ‘met’ with a recalculation of annual amplitude in mean monthly temperature

Description

Run apsim from R. It's for Windows only. It uses ‘shell’.

Usage

apsim(
  file = "",
  src.dir = ".",
  silent = FALSE,
  value = "report",
  cleanup = FALSE,
  simplify = TRUE
)

Arguments

Details

Run an APSIM (7.x) ‘Classic’ Simulation

A valid apsim file can be run from within R. The main goal is to make running APSIM-X simple, especially for large scale simulations or parameter optimization

Value

This function returns a data frame with APSIM output, but it depends on the argument ‘value’ above.

Examples

## See function 'apsim_example'

Description

simple function to run some of the built-in APSIM examples

Usage

apsim_example(example = "Millet", silent = FALSE, tmp.dir = NULL)

Arguments

Details

This function creates a temporary copy of the example file distributed with APSIM to avoid writing a .out file to the directory where the ‘Examples’ are located. It is not a good practice and there is no guarantee that the user has read/write permissions in that directory.

Value

This function returns a data frame with APSIM output

Note

This function creates a new column ‘Date’ which is in the R ‘Date’ format which is convenient for graphics.

Examples

## Not run: 
## Only run these if you have APSIM 'Classic' installed (Windows only)
millet <- apsim_example("Millet")
potato <- apsim_example("Potato")
sugar <- apsim_example("Sugar")
## The 'Date' column is created by this function, based on apsim output.
require(ggplot2)
ggplot(data = millet , aes(x = Date, y = millet_biomass)) + 
  geom_line()

## End(Not run)

Description

Set the path to the APSIM executable, examples and warning suppression.

Usage

apsim_options(exe.path = NA, examples.path = NA, warn.versions = TRUE)

Arguments

Details

Set apsim options

Value

It modifies the ‘apsim.options’ environment as a side effect.

Note

It is possible that APSIM 7.x ‘Classic’ is installed in some alternative location other than the defaults ones. Guessing this can be difficult and then the auto_detect functions might fail. Also, if multiple versions of APSIM are installed apsim will choose the newest one but it will issue a warning. Suppress the warning by setting warn.versions = FLASE.

Examples

## Not run: 
names(apsim.options)
apsim_options(exe.path = "some-new-path-to-executable")
apsim.options$exe.path

## End(Not run)

Description

Display available APSIM ‘Classic’ and APSIM-X versions

Usage

apsim_version(which = c("all", "inuse"), verbose = TRUE)

Arguments

Value

a data frame (all) or a vector (inuse) with APSIM-X and/or APSIM versions

Examples

## Not run: 
## Check which apsim version are avialable
ava <- apsim_version(verbose = TRUE)

## End(Not run)

Description

Environment which can store the path to the executable and where examples are located. Creating an environment avoids the use of global variables or other similar practices which would have possible undesriable consequences.

Usage

apsim.options

Format

An object of class environment of length 3.

Details

Environment which stores APSIM options

Value

This is an environment, so nothing to return.

Examples

## Not run: 
names(apsim.options)
apsim_options(exe.path = "some-new-path-to-executable")
apsim.options$exe.path

## End(Not run)

Description

Run apsimx from R. It uses system (unix) or shell (windows) and it attempts to be platform independent.

Usage

apsimx(
  file = "",
  src.dir = ".",
  silent = FALSE,
  intern = FALSE,
  value = "report",
  cleanup = FALSE,
  simplify = TRUE,
  xargs
)

Arguments

Details

Run an APSIM-X Simulation

A valid apsimx file can be run from within R. The main goal is to make running APSIM-X simple, especially for large scale simulations or parameter optimization

Value

a data frame with the ‘Report’ from the APSIM-X simulation. The return value depends on the argument ‘value’ above.

Examples

## See function 'apsimx_example' and vignette 'apsimx'

Description

simple function to run some of the built-in APSIM-X examples

Usage

apsimx_example(example = "Wheat", silent = FALSE)

Arguments

Details

This function creates a temporary copy of the example file distributed with APSIM-X to avoid writing a .db file to the directory where the ‘Examples’ are located. It is not a good practice and there is no guarantee that the user has read/write permissions in that directory.

Value

It returns a data frame

Note

This function creates a new column ‘Date’ which is in the R ‘Date’ format which is convenient for graphics.

Examples

## Not run: 
wheat <- apsimx_example("Wheat")
maize <- apsimx_example("Maize")
barley <- apsimx_example("Barley")
## The 'Date' column is created by this function, based on apsim output.
require(ggplot2)
ggplot(data = wheat , aes(x = Date, y = Yield)) + 
  geom_point()

## End(Not run)

Description

Test whether an .apsimx file is XML or json

Usage

apsimx_filetype(file = "", src.dir = ".")

Arguments

Value

‘xml’, ‘json’ or ‘unknown’

Note

Minimal function which reads only the first line in a file and tries to guess whether it is an ‘xml’ or ‘json’ file type.

Examples

extd.dir <- system.file("extdata", package = "apsimx")
apsimx_filetype("Wheat.apsimx", src.dir = extd.dir)

Description

Set the path to the APSIM-X executable, examples and warning suppression.

Usage

apsimx_options(
  exe.path = NA,
  dotnet = FALSE,
  mono = FALSE,
  examples.path = NA,
  warn.versions = TRUE,
  warn.find.apsimx = TRUE,
  allow.path.spaces = FALSE,
  system.intern = FALSE
)

Arguments

Details

Set apsimx options

Value

as a side effect it modifies the ‘apsimx.options’ environment.

Note

It is possible that APSIM-X is installed in some alternative location other than the defaults ones. Guessing this can be difficult and then the auto_detect functions might fail. Also, if multiple versions of APSIM-X are installed apsimx will choose the newest one but it will issue a warning. Suppress the warning by setting warn.versions = FLASE.

Examples

names(apsimx.options)
apsimx_options(exe.path = "some-new-path-to-executable")
apsimx.options$exe.path

Description

Generates a soil profile that can then replace the existing one in an ‘.apsimx’ or ‘.apsim’ simulation file

plotting function for a soil profile, it requires ‘ggplot2’

checking an apsimx soil profile for reasonable values

Usage

apsimx_soil_profile(
  nlayers = 10,
  Depth = NULL,
  Thickness = NULL,
  BD = NULL,
  AirDry = NULL,
  LL15 = NULL,
  DUL = NULL,
  SAT = NULL,
  KS = NULL,
  crop.LL = NULL,
  crop.KL = NULL,
  crop.XF = NULL,
  Carbon = NULL,
  SoilCNRatio = NULL,
  FOM = NULL,
  FOM.CN = NULL,
  FBiom = NULL,
  FInert = NULL,
  NO3N = NULL,
  NH4N = NULL,
  PH = NULL,
  ParticleSizeClay = NULL,
  ParticleSizeSilt = NULL,
  ParticleSizeSand = NULL,
  soil.bottom = 150,
  water.table = 200,
  soil.type = 0,
  crops = c("Maize", "Soybean", "Wheat"),
  metadata = NULL,
  soilwat = NA,
  swim = NA,
  initialwater = NA,
  solutes = NA,
  soilorganicmatter = NA,
  dist.parms = list(a = 0, b = 0.2),
  check = TRUE
)

## S3 method for class 'soil_profile'
plot(
  x,
  ...,
  property = c("all", "water", "initialwater", "BD", "AirDry", "LL15", "DUL", "SAT",
    "KS", "Carbon", "SoilCNRatio", "FOM", "FOM.CN", "FBiom", "FInert", "NO3N", "NH4N",
    "PH", "ParticleSizeClay", "ParticleSizeSilt", "ParticleSizeSand", "texture")
)

check_apsimx_soil_profile(x, particle.density = 2.65)

Arguments

Details

Soil Profiles

Real soils might have discontinuities, but for APSIM it might be beneficial to be able to create a soil profile with an arbitrary number of layers and have flexibility in the distribution of soil physical and chemical properties. Steps:

1. apsimx_soil_profile is a function which can create a soil matrix with many layers
2. It allows for creating a smooth distribution for Physical (or Water), Chemical, InitialWater, Analysis, InitialN, Organic or SoilOrganicMatter
3. The distribution can be specified with the ‘a’ and ‘c’ parameter of an exponential decay function, using a list. E.g. DUL = list(0.35, 0, -0.1). This means that the top value for DUL will be 0.35 and it will decay with a rate of -0.1.
4. If an increase and then a decay is needed the Ricker function can be used. See ‘SSricker’ in the ‘nlraa’ package.

The value of soil particle density (2.65 g/cm3) is hard coded in APSIM. https://en.wikipedia.org/wiki/Bulk_density

Value

a soil profile with class ‘soil_profile’ with elements ‘soil’, ‘crops’, ‘metadata’, ‘soilwat’ and ‘swim’.

it produces a plot

It does not produce output unless potential issues are found. Only warnings are produced and it returns an object of class ‘soil_profile’.

Examples

sp <- apsimx_soil_profile()
 require(ggplot2)
 plot(sp)

Description

Environment which can store the path to the executable, warning settings and where examples are located. Creating an environment avoids the use of global variables or other similar practices which would have possible undesriable consequences.

Usage

apsimx.options

Format

An object of class environment of length 9.

Details

Environment which stores APSIM-X options

Value

This is an environment, not a function, so nothing is returned.

Examples

names(apsimx.options)
apsimx_options(exe.path = "some-new-path-to-executable")
apsimx.options$exe.path

Description

It makes minimum assumptions about the data so it is recommended to change defaults

Usage

as_apsim_met(
  x,
  filename = "noname.met",
  site = "nosite",
  latitude = 0,
  longitude = 0,
  tav = NA,
  amp = NA,
  colnames = c("year", "day", "radn", "maxt", "mint", "rain"),
  units = c("()", "()", "(MJ/m2/day)", "(oC)", "(oC)", "(mm)"),
  constants = NA,
  comments = NA,
  check = TRUE
)

Arguments

Details

Simple utility for converting a data frame to an object of class met

Value

it returns an object of class ‘met’.

Description

simple function to detect where APSIM ‘Classic’ examples are located

Usage

auto_detect_apsim_examples()

Details

Auto detect where APSIM (7.x) ‘Classic’ examples are located

Value

will create a directory pointing to APSIM ‘Classic’ distributed examples

Examples

## Not run: 
ex.dir <- auto_detect_apsim_examples()

## End(Not run)

Description

simple function to detect where APSIM-X examples are located

Usage

auto_detect_apsimx_examples()

Details

Auto detect where apsimx examples are located

Value

will create a directory (character string) pointing to APSIM-X distributed examples

Examples

## Not run: 
ex.dir <- auto_detect_apsimx_examples()

## End(Not run)

Description

Calculation of available water content based on an object of class ‘soil_profile’

Usage

available_water_content(
  x,
  depth,
  area = c("m", "m2", "ha"),
  method = c("linear", "constant"),
  weights,
  ...
)

Arguments

Details

Function to calculate available water content. The output units depend on the choice of area. If ‘m’ is used, then the output units will be ‘mm’. If the ‘area’ is ‘m2’, then the output units will be in ‘m3’. If the ‘area’ is ‘ha’, then the output units will be ‘kg/ha’.

Value

returns a value with attribute ‘units’ and ‘depth’

Examples

## Not run: 
sp <- apsimx_soil_profile()
available_water_content(sp)

## End(Not run)

Description

Calculation of carbon stocks based on an object of class ‘soil_profile’

Usage

carbon_stocks(
  x,
  depth,
  area = c("m2", "ha"),
  method = c("linear", "constant"),
  ...
)

Arguments

Details

Function to calculate carbon stocks. The output units depend on the choice of area. If ‘m2’ is used, then the output units will be ‘kg/m2’. If the ‘area’ is ‘ha’, then the output units will be ‘Mg/ha’.

Note that the bulk density (which is needed in the calculation) is available as part of the ‘soil_profile’ object.

Value

returns a value with attribute ‘units’ and ‘depth’

Examples

## Not run: 
sp <- apsimx_soil_profile()
carbon_stocks(sp)
carbon_stocks(sp, depth = 0.1)
carbon_stocks(sp, depth = 0.2)
carbon_stocks(sp, depth = 0.3)
carbon_stocks(sp, depth = 0.4)

## End(Not run)

Description

Takes in an object of class ‘met’ and checks for missing/valid/reasonable values

Usage

check_apsim_met(met)

Arguments

Details

It will only check for missing values and reasonable (within range) values for: ‘year’: range (1500 to 3000);
‘day’: range (1 to 366);
‘maxt’: range (-60 to 60) – units (C);
‘mint’: range (-60 to 40) – units (C);
‘radn’: range (0 to 40) – units (MJ/m2/day);
‘rain’: range (0 to 100) – units (mm/day)

Value

does not return anything unless possible errors are found

Description

Partial checking of an apsimx file for possible issues.

Usage

check_apsimx(
  file = "",
  src.dir = ".",
  node = c("all", "Clock", "Weather", "Soil"),
  soil.child = c("all", "Physical", "InitialWater", "SoilWater", "Solute", "Organic"),
  check.apsim.met = FALSE,
  root = NULL,
  verbose = TRUE
)

Arguments

Value

It does not return an object, but it prints messages useful for diagnosing issues.

Examples

## Check file distributed with the package
extd.dir <- system.file("extdata", package = "apsimx")

check_apsimx("Wheat.apsimx", src.dir = extd.dir)
## This throws warnings but it should not produce errors

Description

Function which allows for a simple comparison between APSIM output objects

print method for ‘out_mrg’

plotting function for compare_apsim, it requires ggplot2

Usage

compare_apsim(
  ...,
  variable,
  index = "Date",
  by,
  labels,
  cRSS = FALSE,
  weights,
  verbose = FALSE
)

## S3 method for class 'out_mrg'
print(x, ..., digits = 2)

## S3 method for class 'out_mrg'
plot(
  x,
  ...,
  plot.type = c("vs", "diff", "resid", "ts", "density"),
  pairs = c(1, 2),
  cumulative = FALSE,
  variable,
  id,
  id.label,
  by,
  facet = FALSE,
  span = 0.75,
  dodge.width = NULL
)

Arguments

Details

Plotting function for observed and simulated data

Value

object of class ‘out_mrg’, which can be used for further plotting

it prints the index.table data.frame

it produces a plot

Note

‘Con Corr’ is the concordance correlation coefficient (https://en.wikipedia.org/wiki/Concordance_correlation_coefficient); ‘ME’ is the model efficiency (https://en.wikipedia.org/wiki/Nash

Examples

## Directory with files
extd.dir <- system.file("extdata", package = "apsimx")
## Comparing observed and simulated for Wheat
data(obsWheat)
sim.opt <- read.csv(file.path(extd.dir, "wheat-sim-opt.csv"))
sim.opt$Date <- as.Date(sim.opt$Date)

cap <- compare_apsim(obsWheat, sim.opt, labels = c("obs", "sim"))

plot(cap)
plot(cap, plot.type = "diff")
plot(cap, plot.type = "resid")
plot(cap, plot.type = "ts")

plot(cap, variable = "AboveGround")
plot(cap, variable = "AboveGround", plot.type = "diff")
plot(cap, variable = "AboveGround", plot.type = "ts")

## Selecting a variable
cap <- compare_apsim(obsWheat, sim.opt, variable = "AboveGround", 
                     labels = c("obs", "sim"))
                     
## Using id
plot(cap, variable = "AboveGround", id = 0.05)

Description

Helper function which allows for a simple comparison among ‘met’ objects

print method for ‘met_mrg’

plotting function for compare_apsim_met, it requires ggplot2

Usage

compare_apsim_met(
  ...,
  met.var = c("all", "radn", "maxt", "mint", "rain", "rh", "wind_speed", "vp"),
  labels,
  check = FALSE,
  verbose = FALSE
)

## S3 method for class 'met_mrg'
print(x, ..., digits = 2)

## S3 method for class 'met_mrg'
plot(
  x,
  ...,
  plot.type = c("vs", "diff", "ts", "density"),
  pairs = c(1, 2),
  cumulative = FALSE,
  met.var = c("radn", "maxt", "mint", "rain"),
  id,
  span = 0.75
)

Arguments

Value

object of class ‘met_mrg’, which can be used for further plotting

it prints the index.table data.frame

it produces a plot

Note

I have only tested this for 2 or 3 objects. The code is set up to be able to compare more, but I'm not sure that would be all that useful.

Examples

## Not run: 
require(nasapower)
## Specify the location
lonlat <- c(-93, 42)
## dates
dts <- c("2017-01-01","2017-12-31")
## Get pwr
pwr <- get_power_apsim_met(lonlat = lonlat, dates = dts)
## Get data from IEM
iem <- get_iem_apsim_met(lonlat = lonlat, dates = dts)
## Compare them
cmet <- compare_apsim_met(pwr[,1:6], iem, labels = c("pwr","iem"))
## Visualize radiation
plot(cmet, met.var = "radn")
plot(cmet, plot.type = "diff")
plot(cmet, plot.type = "ts")
## Visualize maxt
plot(cmet, met.var = "maxt")
plot(cmet, met.var = "maxt", plot.type = "diff")
plot(cmet, met.var = "maxt", plot.type = "ts")
## Cumulative rain
plot(cmet, met.var = "rain", plot.type = "ts", cumulative = TRUE)

## End(Not run)

Description

Helper function which allows for a simple comparison among soil_profile objects

print method for ‘soil_profile_mrg’

plotting function for compare_apsim_soil_profile, it requires ggplot2

Usage

compare_apsim_soil_profile(
  ...,
  soil.var = c("all", "Thickness", "BD", "AirDry", "LL15", "DUL", "SAT", "KS", "Carbon",
    "SoilCNRatio", "FOM", "FOM.CN", "FBiom", "FInert", "NO3N", "NH4N", "PH"),
  property,
  labels,
  merge.wide = TRUE,
  check = FALSE,
  verbose = FALSE
)

## S3 method for class 'soil_profile_mrg'
print(x, ..., format = c("wide", "long"), digits = 2)

## S3 method for class 'soil_profile_mrg'
plot(
  x,
  ...,
  plot.type = c("depth", "vs", "diff", "density"),
  pairs = c(1, 2),
  soil.var = c("all", "Thickness", "BD", "AirDry", "LL15", "DUL", "SAT", "KS", "Carbon",
    "SoilCNRatio", "FOM", "FOM.CN", "FBiom", "FInert", "NO3N", "NH4N", "PH"),
  span = 0.75
)

Arguments

Value

object of class ‘soil_profile_mrg’, which can be used for further plotting

a table with indexes for the soil profiles

it produces a plot

Note

I have only tested this for 2 or 3 objects. The code is set up to be able to compare more, but I'm not sure that would be all that useful.

Examples

## Not run: 
require(soilDB)
require(sp)
require(sf)
require(spData)
# Get two soil profiles
sp1 <- get_ssurgo_soil_profile(lonlat = c(-93, 42))
sp2 <- get_ssurgo_soil_profile(lonlat = c(-92, 41))
# Compare them
cmp <- compare_apsim_soil_profile(sp1[[1]], sp2[[1]], labels = c("sp1", "sp2"))
# Plot the variables
plot(cmp)

## End(Not run)

Description

Given a day of the year as julian (1-366) it converts to ‘Date’

Given a ‘Date’ it converts to julian day (1-366) or day of the year

Usage

doy2date(x, year = 2001, inverse = FALSE)

date2doy(x, year = 2001, inverse = FALSE)

Arguments

Value

an object of class ‘Date’ or a numeric if inverse equals TRUE.

an numeric or an object of class ‘Date’ if inverse equals TRUE.

Examples

doy2date(120)
date2doy("04-30")

Description

This function allows editing of an APSIM (Classic) simulation file.

Usage

edit_apsim(
  file,
  src.dir = ".",
  wrt.dir = NULL,
  node = c("Clock", "Weather", "Soil", "SurfaceOrganicMatter", "MicroClimate", "Crop",
    "Manager", "Outputfile", "Other"),
  soil.child = c("Metadata", "Water", "Physical", "OrganicMatter", "Chemical",
    "Analysis", "InitialWater", "Sample", "SWIM"),
  manager.child = NULL,
  parm = NULL,
  value = NULL,
  overwrite = FALSE,
  edit.tag = "-edited",
  parm.path = NULL,
  root,
  verbose = TRUE,
  check.length = TRUE
)

Arguments

Details

The variables specified by parm within the .apsim 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 .apsim file will be overwritten if overwrite is set to TRUE; otherwise the file ‘file’ -edited.apsim will be created. If (verbose = TRUE) then the name of the written file is returned.

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

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 (XML) .apsimx file.

Note

The components that can be edited are restricted becuase this is better in preventing errors of editing unintended parts of the file. The disadvantage is that there is less flexibility compared to the similar function in the 'apsimr' package.

Examples

## This example will read one of the examples distributed with APSIM
## but write to a temporary directory

tmp.dir <- tempdir()

extd.dir <- system.file("extdata", package = "apsimx")
edit_apsim("Millet", src.dir = extd.dir, wrt.dir = tmp.dir, 
           node = "Clock",
           parm = "start_date", value = "01/02/1940")

## Editing all of the KL values for Millet
pp.KL <- inspect_apsim_xml("Millet.apsim", src.dir = extd.dir, 
                  parm = "SoilCrop[8]/KL")
                 
kls <- seq(0.08, 0.2, length.out = 11)

edit_apsim("Millet.apsim", 
           src.dir = extd.dir,
           wrt.dir = tmp.dir,
           node = "Other", 
           parm.path = pp.KL,
           value = kls)
           
## Check that it was properly edited

inspect_apsim("Millet-edited.apsim", 
              src.dir = tmp.dir,
              node = "Soil",
              soil.child = "Water",
              parm = "KL")

Description

Edits an APSIM Classic simulation by replacing the soil profile

Usage

edit_apsim_replace_soil_profile(
  file = "",
  src.dir = ".",
  wrt.dir = NULL,
  soil.profile = NULL,
  swim = NULL,
  soilwat = NULL,
  initialwater = NULL,
  edit.tag = "-edited",
  overwrite = FALSE,
  verbose = TRUE,
  root
)

Arguments

Details

This function is designed to batch replace the whole soil in an APSIM simulation.

Value

writes an APSIM file to disk with the supplied soil profile

Note

There is no such thing as a default soil, carefully build the profile for each simulation. This function replaces values and it can grow an XML node, but it cannot edit a property which is not present in the original file.

Examples

sp <- apsimx_soil_profile(nlayers = 20,
                          crops = c("Barley", "Chickpea", "Lucerne", 
                          "Maize", "Perennial Grass", "Sorghum", 
                          "Wheat", "Millet"))

extd.dir <- system.file("extdata", package = "apsimx")

## Writing to a temp directory
tmp.dir <- tempdir()
edit_apsim_replace_soil_profile("Millet.apsim", soil.profile = sp, 
                                edit.tag = "-newsoil",
                                src.dir = extd.dir, 
                                wrt.dir = tmp.dir)
                                
inspect_apsim("Millet-newsoil.apsim", src.dir = tmp.dir,
              node = "Soil", soil.child = "Water")

Description

This function allows editing of an APSIM (Classic) simulation xml file.

Usage

edit_apsim_xml(
  file,
  src.dir = ".",
  wrt.dir = NULL,
  parm.path = NULL,
  value = NULL,
  overwrite = FALSE,
  edit.tag = "-edited",
  verbose = TRUE
)

Arguments

Details

The variables specified by parm within the .apsim 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 .xml file will be overwritten if overwrite is set to TRUE; otherwise the file ‘file’ -edited.xml will be created. If (verbose = TRUE) then the name of the written file is returned. The function is similar to the edit_sim_file functin in the ‘apsimr’ package, but with the difference that here the xml2 package is used instead.

Value

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

Note

This function cannot check whether replacement is of the correct length. Also, there is an inspect equivalent. It is more flexible than ‘edit_apsim’ and (perhaps) similar to ‘apsimr::edit_sim_file’.

Examples

## This example changes the RUE values

extd.dir <- system.file("extdata", package = "apsimx")

values <- paste(rep(1.7, 12), collapse = " ")

## Writing to a temp directory, but replace as needed
tmp.dir <- tempdir()

edit_apsim_xml("Maize75.xml", 
               src.dir = extd.dir,
               wrt.dir = tmp.dir,
               parm.path = ".//Model/rue",
               value = values)

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

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"))

Description

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

Usage

edit_apsimx_batch(
  file,
  src.dir = ".",
  wrt.dir = NULL,
  parms = NULL,
  silent = FALSE,
  verbose = TRUE
)

Arguments

Details

from hol430

This allows the user to specify an .apsimx file and a config file when running Models.exe. The .apsimx file will not be run but instead, the changes listed in the config file will be applied to the .apsimx file, which will then be written to disk under the same filename.

The config file should contain lines of the form ‘path = value’

e.g.

[Clock].StartDate = 2019-1-20 .Simulations.Sim1.Name = SimulationVariant35 .Simulations.Sim2.Enabled = false .Simulations.Sim1.Paddock.Soil.Thickness[1] = 50 Notes:

Command line arguments should look like: Models.exe file.apsimx /Edit /path/to/config/file.conf

Relative paths will be resolved to the first match. ie [Clock].StartDate will match the first clock found in the file.

Dates can be specified as yyyy-mm-dd or mm/dd/yyyy.

Strings should not be quoted

Array indices will be interpted as 1-indexed (mad face). So the first element in the array should have index 1 in the config file.

The file will be upgraded to the latest file version as part of this process.

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 InitialResidueMass
extd.dir <- system.file("extdata", package = "apsimx")
parms <- list(`.Simulations.Simulation.Field.SurfaceOrganicMatter.InitialResidueMass` = 600)
edit_apsimx_batch("Wheat.apsimx", src.dir = extd.dir, wrt.dir = tmp.dir, parms = parms)

Description

Edits an APSIM-X simulation by replacing the soil profile

Usage

edit_apsimx_replace_soil_profile(
  file = "",
  src.dir = ".",
  wrt.dir = NULL,
  soil.profile = NULL,
  edit.tag = "-edited",
  overwrite = FALSE,
  verbose = TRUE,
  root = NULL
)

Arguments

Details

This function is designed to batch replace the whole soil in an APSIM simulation file.

Value

writes a file to disk with the supplied soil profile

Note

There is no such thing as a default soil, carefully build the profile for each simulation.

Examples

sp <- apsimx_soil_profile()
extd.dir <- system.file("extdata", package = "apsimx")

## I write to a temp directory but replace as needed
tmp.dir <- tempdir()

edit_apsimx_replace_soil_profile("Maize.apsimx", soil.profile = sp, 
                                  src.dir = extd.dir, wrt.dir = tmp.dir)
inspect_apsimx("Maize-edited.apsimx", src.dir = tmp.dir,
                 node = "Soil")

Description

edit the replacement componenet of an JSON apsimx file. It does not replace the GUI, but it can save time by quickly editing parameters and values.

Usage

edit_apsimx_replacement(
  file = "",
  src.dir = ".",
  wrt.dir = ".",
  node = NULL,
  node.child = NULL,
  node.subchild = NULL,
  node.subsubchild = NULL,
  node.sub3child = NULL,
  node.sub4child = NULL,
  node.sub5child = NULL,
  node.string = NULL,
  root = list("Models.Core.Replacements", NA),
  parm = NULL,
  value = NULL,
  overwrite = FALSE,
  edit.tag = "-edited",
  verbose = TRUE,
  grep.options
)

Arguments

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 .apsimx file.

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.

Note

The components that can be edited are restricted becuase this is better in preventing errors of editing unintended parts of the file.

Examples

extd.dir <- system.file("extdata", package = "apsimx")
## Writing to a temp directory, but change as needed
tmp.dir <- tempdir()

## Inspect original values
inspect_apsimx_replacement("MaizeSoybean.apsimx", 
                           src.dir = extd.dir,
                           node = "Maize", 
                           node.child = "Phenology",
                           node.subchild = "ThermalTime", 
                           node.subsubchild = "BaseThermalTime",
                           node.sub3child = "Response")

edit_apsimx_replacement("MaizeSoybean.apsimx", 
                        src.dir = extd.dir, wrt.dir = tmp.dir,
                        node = "Maize", 
                        node.child = "Phenology",
                        node.subchild = "ThermalTime", 
                        node.subsubchild = "BaseThermalTime",
                        node.sub3child = "Response",
                        parm = "X",
                        value = c(10, 20, 30, 40, 50)) 
## inspect it
inspect_apsimx_replacement("MaizeSoybean-edited.apsimx", 
                           src.dir = tmp.dir,
                           node = "Maize", 
                           node.child = "Phenology",
                           node.subchild = "ThermalTime", 
                           node.subsubchild = "BaseThermalTime",
                           node.sub3child = "Response")

## Illustrating using 'node.string'
## Equivalent to the code to edit above

edit_apsimx_replacement("MaizeSoybean-edited.apsimx", 
                        src.dir = tmp.dir, wrt.dir = tmp.dir,
                        node.string = "Maize.Phenology.ThermalTime.BaseThermalTime.Response",
                        parm = "X",
                        value = c(11, 21, 31, 41, 51),
                        edit.tag = "-ns") 
                        
inspect_apsimx_replacement("MaizeSoybean-edited-ns.apsimx", 
                           src.dir = tmp.dir,
                           node = "Maize", 
                           node.child = "Phenology",
                           node.subchild = "ThermalTime", 
                           node.subsubchild = "BaseThermalTime",
                           node.sub3child = "Response")

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", "Solute", "NO3", "NH4",
    "Urea", "Nutrient", "Organic", "Swim3"),
  parm = NULL,
  digits = 3,
  root = NULL
)

Arguments

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"))

Description

Extract initial values from a parameter path

Usage

extract_values_apsimx(file, src.dir, parm.path)

Arguments

Value

a vector with extracted parameter values from an APSIM file.

Examples

## Find examples
extd.dir <- system.file("extdata", package = "apsimx")
## Extract parameter path
pp <- inspect_apsimx("Maize.apsimx", src.dir = extd.dir,
                     node = "Manager", parm = list("Fert", 1))
ppa <- paste0(pp, ".Amount")
## Extract value
extract_values_apsimx("Maize.apsimx", src.dir = extd.dir, parm.path = ppa)

Description

Retrieves the json replacement file for a specific model

Usage

get_apsimx_json(model = "Wheat", wrt.dir = ".", cleanup = FALSE)

Arguments

Details

Get APSIM-X Model Replacement from github

Value

a list read through the jsonlite package

See Also

insert_replacement_node

Examples

tmp.dir <- tempdir()
wheat <- get_apsimx_json(model = "Wheat", wrt.dir = tmp.dir)

Description

Uses get_chirps from the chirps package to download data to create an APSIM met file.

Usage

get_chirps_apsim_met(
  lonlat,
  dates,
  wrt.dir = ".",
  filename = NULL,
  fillin.radn = TRUE,
  silent = FALSE
)

Arguments

Details

This function requires the chirps package, version 0.1.4.

If the filename is not provided it will not write the file to disk, but it will return an object of class ‘met’. This is useful in case manipulation is required before writing to disk.

Value

returns an object of class ‘met’ and writes a file to disk when filename is supplied.

Examples

## Not run: 
require(chirps)
## This will not write a file to disk
chrp <- get_chirps_apsim_met(lonlat = c(-93,42), dates = c("2012-01-01","2012-12-31"))

## End(Not run)

Description

Uses download_daymet from the daymetr package to download data to create an APSIM met file.

Usage

get_daymet_apsim_met(lonlat, years, wrt.dir = ".", filename, silent = FALSE)

Arguments

Details

This function requires the daymetr package. This function should replace the get_daymet_apsim_met function.

If the filename is not provided it will not write the file to disk, but it will return an object of class ‘met’. This is useful in case manipulation is required before writing to disk. The variable ‘srad’ as downloaded from daymet is average solar radiation, so it is converted to total. Daily total radiation (MJ/m2/day) can be calculated as follows: ((srad (W/m2) * dayl (s/day)) / 1,000,000)
Vapor Pressure Deficit (vp) should be in hecto Pascals

Value

It returns an object of class ‘met’ and writes a file to disk when filename is supplied.

Source

The data is retrieved using the daymetr package. For the original source see: https://daymet.ornl.gov/

Examples

## Not run: 
require(daymetr)
## I write to a temp directory but replace as needed
dmet12 <- get_daymet_apsim_met(lonlat = c(-93,42), years = 2012)
summary(dmet12)
## Check for reasonable ranges 
check_apsim_met(dmet12)

## End(Not run)

Description

Uses download_daymet from the daymetr package to download data to create an APSIM met file.

Usage

get_daymet2_apsim_met(lonlat, years, wrt.dir = ".", filename, silent = FALSE)

Arguments

Details

This function requires the daymetr package. This function should replace the get_daymet_apsim_met function.

If the filename is not provided it will not write the file to disk, but it will return an object of class ‘met’. This is useful in case manipulation is required before writing to disk. The variable ‘srad’ as downloaded from daymet is average solar radiation, so it is converted to total. Daily total radiation (MJ/m2/day) can be calculated as follows: ((srad (W/m2) * dayl (s/day)) / 1,000,000)
Vapor Pressure Deficit (vp) should be in hecto Pascals

Value

It returns an object of class ‘met’ and writes a file to disk when filename is supplied.

Source

The data is retrieved using the daymetr package. For the original source see: https://daymet.ornl.gov/

Examples

## Not run: 
require(daymetr)
## I write to a temp directory but replace as needed
dmet12 <- get_daymet2_apsim_met(lonlat = c(-93,42), years = 2012)
summary(dmet12)
## Check for reasonable ranges 
check_apsim_met(dmet12)

## End(Not run)

Description

Uses get_GSOD from the GSODR package to download data to create an APSIM met file.

Usage

get_gsod_apsim_met(
  lonlat,
  dates,
  wrt.dir = ".",
  filename = NULL,
  distance = 100,
  station,
  fillin.radn = FALSE
)

Arguments

Details

This function requires the GSODR package.

If the filename is not provided it will not write the file to disk, but it will return an object of class ‘met’. This is useful in case manipulation is required before writing to disk.

Value

returns an object of class ‘met’ and writes a file to disk when filename is supplied.

Note

This source of data does not provide solar radiation. If ‘fillin.radn’ is TRUE it fill in radiation data using the nasapower package.

Examples

## Not run: 
require(GSODR)
## This will not write a file to disk
gsd <- get_gsod_apsim_met(lonlat = c(-93,42), dates = c("2012-01-01","2012-12-31"),
                          fillin.radn = TRUE)
summary(gsd)
## Check for reasonable ranges
check_apsim_met(gsd)

## End(Not run)

Description

Retrieves weather data from Iowa Environmental Mesonet (AgWeather) into an APSIM met file

Usage

get_iem_apsim_met(lonlat, dates, wrt.dir = ".", state, station, filename)

Arguments

Details

The original data can be obtained from: https://mesonet.agron.iastate.edu/request/coop/fe.phtml

If the filename is not provided it will not write the file to disk, but it will return an object of class ‘met’. This is useful in case manipulation is required before writing to disk. For this function either provide the longitude and latitude or the state and station, but not both. In fact, ‘state’ and ‘station’ will be ignored if ‘lonlat’ is supplied.

Value

returns an object of class ‘met’ and writes a file to disk when filename is supplied.

Examples

## Not run: 
## This will not write a file to disk
iem.met <- get_iem_apsim_met(state = "IA", 
                             station = "IA0200", 
                             dates = c("2012-01-01","2012-12-31"))

summary(iem.met)

## Alternatively, coordinates can be used
## This should be equivalent to the previous request
iem.met2 <- get_iem_apsim_met(lonlat = c(-93.77, 42.02), 
                              dates = c("2012-01-01","2012-12-31"))

summary(iem.met2)

## End(Not run)

Description

Retrieves weather data from Iowa Environmental Mesonet Reanalysis into an APSIM met file

Usage

get_iemre_apsim_met(
  lonlat,
  dates,
  wrt.dir = ".",
  filename = NULL,
  fillin.radn = FALSE
)

Arguments

Details

The original data can be obtained from: https://mesonet.agron.iastate.edu/iemre/

If the filename is not provided it will not write the file to disk, but it will return an object of class ‘met’. This is useful in case manipulation is required before writing to disk.

Value

returns an object of class ‘met’ and writes a file to disk when filename is supplied.

Note

Multi-year query is not supported for this product.

Examples

## Not run: 
## This will not write a file to disk
iemre <- get_iemre_apsim_met(lonlat = c(-93,42), dates = c("2012-01-01","2012-12-31"))
## Note that solar radiation is not available, but can be filled in
## using the nasapower package
iemre2 <- get_iemre_apsim_met(lonlat = c(-93,42), 
                             dates = c("2012-01-01","2012-12-31"), 
                             fillin.radn = TRUE)
summary(iemre)
summary(iemre2)

## Still it is important to check this object
check_apsim_met(iemre2)

## End(Not run)

Description

Retrieves soil data from the ISRIC global database and converts it to an APSIM soil_profile object

Usage

get_isric_soil_profile(
  lonlat,
  statistic = c("mean", "Q0.5"),
  soil.profile,
  find.location.name = TRUE,
  fix = FALSE,
  verbose = TRUE,
  check = TRUE,
  physical = c("default", "SR"),
  xargs = NULL
)

Arguments

Details

Source: https://www.isric.org/
Details: https://www.isric.org/explore/soilgrids/faq-soilgrids

Pedotransfer functions: Saxton and Rawls, 2006. Soil Water Characteristic Estimates by Texture and Organic Matter for Hydrologic Solutions. Soil Sci. Soc. Am. J. 70:1569–1578.

TODO: need to look into how this is done in APSIM NG https://github.com/APSIMInitiative/ApsimX/pull/3994/files

NOTE: Eric Zurcher provided help by sending me an R file originally written by Andrew Moore. It provides a bit of context for how some of the decisions were made for constructing the synthetic soil profiles in APSIM. (email from june 3 2021).

Variable which are directly retrieved and a simple unit conversion is performed:
* Bulk density - bdod
* Carbon - soc
* Clay - clay
* Sand - sand
* PH - phh2o
* Nitrogen - nitrogen
Variables which are optionally estimated using pedotransfer functions:
LL15, DUL, SAT, KS, AirDry
TO-DO:
What do I do with nitrogen?
Can I use CEC?
How can I have a guess at FBiom and Finert?
FBiom does not depend on any soil property at the moment, should it?

Value

it generates an object of class ‘soil_profile’.

Author(s)

Fernando E. Miguez, Eric Zurcher (CSIRO) and Andrew Moore (CSIRO)

See Also

apsimx_soil_profile, edit_apsim_replace_soil_profile, edit_apsimx_replace_soil_profile.

Examples

## Not run: 
## Only run this if rest.isric.org is working
rest.isric.on <- suppressWarnings(try(readLines("http://rest.isric.org", 
n = 1, warn = FALSE), silent = TRUE))

## Get soil profile properties for a single point
if(!inherits(rest.isric.on, "try-error")){
  sp1 <- get_isric_soil_profile(lonlat = c(-93, 42), fix = TRUE, verbose = FALSE)
  ## Visualize
  plot(sp1)
  plot(sp1, property = "water")
 }

## End(Not run)

Description

Uses get_power from the nasapower package to download data to create an APSIM met file.

Usage

get_power_apsim_met(lonlat, dates, wrt.dir = ".", filename = NULL)

Arguments

Details

This function requires the nasapower package version 4.0.0.

It looks like the earliest year you can request data for is 1984.

If the filename is not provided it will not write the file to disk, but it will return an object of class ‘met’. This is useful in case manipulation is required before writing to disk.

Value

returns an object of class ‘met’ and writes a file to disk when filename is supplied.

Examples

## Not run: 
require(nasapower)
## This will not write a file to disk
pwr <- get_power_apsim_met(lonlat = c(-93,42), dates = c("2012-01-01","2012-12-31"))
## Let's insert a missing value
pwr[100, "radn"] <- NA
summary(pwr)
## Check the met file 
check_apsim_met(pwr)
## Impute using linear interpolation
pwr.imptd <- impute_apsim_met(pwr, verbose = TRUE)
summary(pwr.imptd)
check_apsim_met(pwr.imptd)

## End(Not run)

Description

Generate a synthetic soil profile based on the information in SSURGO database

Usage

get_ssurgo_soil_profile(
  lonlat,
  shift = -1,
  nmapunit = 1,
  nsoil = 1,
  xout = NULL,
  soil.bottom = 200,
  method = c("constant", "linear"),
  nlayers = 10,
  check = TRUE,
  fix = FALSE,
  verbose = FALSE,
  xargs = NULL
)

Arguments

Details

Data source is USDA-NRCS Soil Data Access. See package soilDB for more details

Value

this function will always return a list. Each element of the list will be an object of class ‘soil_profile’

Examples

## Not run: 
require(soilDB)
require(sp)
require(sf)
require(spData)
require(ggplot2)
## Soil inforation for a single point
sp <- get_ssurgo_soil_profile(lonlat = c(-93, 42))
## The initial attempt throws warnings, so better to use 'fix'
sp <- get_ssurgo_soil_profile(lonlat = c(-93, 42), fix = TRUE)
plot(sp[[1]])
plot(sp[[1]], property = "water")
## Add initial water
iwat <- initialwater_parms(Thickness = sp[[1]]$soil$Thickness,
                           InitialValues = sp[[1]]$soil$DUL * 0.8)
sp[[1]]$initialwater <- iwat
plot(sp[[1]], property = "initialwater")

## End(Not run)

Description

This function does partially what get_ssurgo_soil_profile does, but it returns a list with tables for mapunit, component, chorizon and mapunit.shp (object of class sf)

Usage

get_ssurgo_tables(lonlat, shift = -1, aoi, verbose = FALSE)

Arguments

Details

Data source is USDA-NRCS Soil Data Access. See package soilDB for more details

* If a point is requested then an object of class ‘sf’ is returned (for mapunit.shp) with the MUKEY and AREASYMBOL with GEOMETRY type: POINT.

* If a the request is for a spatial polygon, then an object of class ‘sf’ is returned with gid, mukey and area_ac with GEOMETRY type: POLYGON.

Value

a list with elements: mapunit, component, chorizon and mapunit.shp

Examples

## Not run: 
require(soilDB)
require(sp)
require(sf)
require(spData)
## retrieve data from lon -93, lat = 42
stbls <- get_ssurgo_tables(lonlat = c(-93, 42)) 

stbls2 <- get_ssurgo_tables(lonlat = c(-93, 42), shift = 200)


## End(Not run)

Description

Retrieves met data from the World Modeler global database and (optionally) saves it to a file

Usage

get_worldmodeler_apsim_met(
  lonlat,
  dates,
  wrt.dir,
  filenames,
  check = FALSE,
  verbose = FALSE
)

Arguments

Value

it creates a list with objects of class ‘met’. If it fails, then the objects will be of class ‘try-error’.

Examples

## Not run: 
## Get soil profile properties for a single point
  am1 <- get_worldmodeler_apsim_met(lonlat = c(-93, 42), 
                                    dates = c("2010-01-01", "2013-12-31"))
  if(inherits(am1, 'met')){
     plot(am1[[1]], met.var = "rain", cumulative = TRUE)
  }
 
## End(Not run)

Description

Retrieves soil data from the World Modeler global database and (optionally) saves it to a soils file

Usage

get_worldmodeler_soil_profile(
  lonlat,
  soil.name,
  wrt.dir,
  filename,
  verbose = FALSE
)

Arguments

Value

it returns a list with objects of class ‘soil_profile’. If ‘filename’ is specified it also creates a file with extension ‘soils’, which can be read using function read_apsim_soils.

Author(s)

Brian Collins (University of Southern Queensland) and Fernando Miguez

Examples

## Not run: 
## Get soil profile properties for a single point
  sp1 <- get_worldmodeler_soil_profile(lonlat = c(-93, 42))
  
  if(inherits(sp1[[1]], 'soil_profile')){
    plot(sp1[[1]], property = "Carbon")
  }

## End(Not run)

Description

recursive grep adapted for a json list

Usage

grep_json_list(
  pattern,
  x,
  ignore.case = FALSE,
  search.depth = 10,
  how = c("unlist", "replace", "list")
)

Arguments

Value

It returns a list with the found object, the json path and the positions in the list.

Description

Takes in an object of class ‘met’ and imputes values

Usage

impute_apsim_met(
  met,
  method = c("approx", "spline", "mean"),
  verbose = FALSE,
  ...
)

Arguments

Value

an object of class ‘met’ with attributes

Description

Creates a list with specific components for the Initial Soil Water module

Usage

initialwater_parms(
  Depth = NA,
  Thickness = NA,
  InitialValues = NA,
  InitialPAWmm = NA,
  PercentFull = NA,
  RelativeTo = NA,
  FilledFromTop = NA,
  DepthWetSoil = NA
)

Arguments

Description

Inserts a replacement node in a simple apsimx simulation file

Usage

insert_replacement_node(
  file,
  src.dir,
  wrt.dir,
  rep.node,
  edit.tag = "-edited",
  overwrite = FALSE,
  verbose = FALSE
)

Arguments

Value

it does not return an R object but it writes an apsimx file to disk

Examples

## Not run: 
## It is not trivial to produce a reproducible example
## because the model and file versions need to align.
## The steps are:
## 1. Get model: 
##    wheat <- get_apsimx_json(model = "Wheat", wrt.dir = tmp.dir)
## 2. Create file that matches current model version
## 3. Edit the file by inserting the 'replacements' node
##    insert_replacement_node("Wheat.apsimx", rep.node = wheat)
                        

## End(Not run)

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

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")

Description

inspect an auxiliary XML apsim file.

Usage

inspect_apsim_xml(
  file = "",
  src.dir = ".",
  parm,
  verbose = TRUE,
  print.path = TRUE
)

Arguments

Value

it returns an absolute parameter path(s)

Note

the behavior has changed from previous verions (earlier than 1.977). Before, if more than match was found it would return an error. Now it returns a list with all possible matches. This can be useful when trying to find a parameter.

Examples

extd.dir <- system.file("extdata", package = "apsimx")

inspect_apsim_xml("Maize75.xml", src.dir = extd.dir,
                  parm = "leaf_no_rate_change")
                  
pp <- inspect_apsim_xml("Maize75.xml", src.dir = extd.dir,
                        parm = "leaf_no_rate_change",
                        verbose = FALSE, 
                        print.path = FALSE)

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

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"))

Description

inspect an .apsimx or .json (JSON) file. It does not replace the GUI, but it can save time by quickly checking parameters and values.

Usage

inspect_apsimx_json(
  file = "",
  src.dir = ".",
  parm,
  search.depth = 15,
  print.path = FALSE,
  verbose = FALSE
)

Arguments

Details

This function is a work in progress. There are many instances for which it will not work.

It will probably only find the first instance that matches.

Value

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

Examples

extd.dir <- system.file("extdata", package = "apsimx")
## It seems to work for simple search
inspect_apsimx_json("Wheat.apsimx", src.dir = extd.dir, parm = "Version")
inspect_apsimx_json("Wheat.apsimx", src.dir = extd.dir, parm = "Simulations")
inspect_apsimx_json("Wheat.apsimx", src.dir = extd.dir, parm = "Clock")
inspect_apsimx_json("Wheat.apsimx", src.dir = extd.dir, parm = "Weather")
## Does return soil components
inspect_apsimx_json("Wheat.apsimx", src.dir = extd.dir, parm = "DUL")
## Or cultivar
inspect_apsimx_json("Wheat.apsimx", src.dir = extd.dir, parm = "Hartog")

Description

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

Usage

inspect_apsimx_replacement(
  file = "",
  src.dir = ".",
  node = NULL,
  node.child = NULL,
  node.subchild = NULL,
  node.subsubchild = NULL,
  node.sub3child = NULL,
  node.sub4child = NULL,
  node.sub5child = NULL,
  node.string = NULL,
  root = list("Models.Core.Replacements", NA),
  parm = NULL,
  display.available = FALSE,
  digits = 3,
  print.path = FALSE,
  verbose = TRUE,
  grep.options
)

Arguments

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 .apsimx file.

Value

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

Note

I need to make some changes in order to be able to handle multiple parameters. At this point, it might work but it will generate warnings.

Examples

extd.dir <- system.file("extdata", package = "apsimx")
inspect_apsimx_replacement("MaizeSoybean.apsimx", src.dir = extd.dir,
                           node = "Maize", node.child = "Phenology",
                           node.subchild = "ThermalTime", 
                           node.subsubchild = "BaseThermalTime",
                           node.sub3child = "Response") 
## For Wheat
## getting down to 'XYPairs'
inspect_apsimx_replacement("WheatRye.apsimx", 
                           src.dir = extd.dir,
                           node = "Wheat",
                           node.child = "Structure",
                           node.subchild = "BranchingRate",
                           node.subsubchild = "PotentialBranchingRate",
                           node.sub3child = "Vegetative",
                           node.sub4child = "PotentialBranchingRate",
                           node.sub5child = "XYPairs")

Description

Environment which stores data for MCMC

Usage

mcmc.apsim.env

Format

An object of class environment of length 0.

Details

Create an apsim environment for MCMC

Value

This is an environment, so nothing to return.

Description

Environment which stores data for MCMC

Usage

mcmc.apsimx.env

Format

An object of class environment of length 0.

Details

Create an apsimx environment for MCMC

Value

This is an environment, so nothing to return.

Description

It will fill in or ‘pad’ a met object with NAs

Usage

napad_apsim_met(met)

Arguments

Details

Fill in with missing data date discontinuities in a met file

Value

It returns an object of class ‘met’ with padded NAs.

Note

The purpose of this function is to allow for imputation using impute_apsim_met

Description

Artificial observed data for Wheat

Usage

obsWheat

Format

A data frame with 10 rows and 4 variables:

Date

-date- date starting Oct 1 2016 and ending June 6 2017

Wheat.Phenology.Stage

-numeric- phenology stage of wheat

Wheat.Leaf.LAI

-numeric- Leaf Area Index

Wheat.AboveGround.Wt

-numeric- above ground biomass (g/m2)

Details

A dataset containing the Date, phenology stage, LAI and above ground biomass for Wheat

Source

These are simulated data. For details see the APSIM documentation

Description

It is a wrapper for running APSIM and optimizing parameters using optim

Friendly printing of optim_apsim

Variance-Covariance for an ‘optim_apsim’ object

Parameter estimates for an ‘optim_apsim’ object

Confidence intervals for parameter estimates for an ‘optim_apsim’ object

Usage

optim_apsim(
  file,
  src.dir = ".",
  crop.file,
  parm.paths,
  data,
  type = c("optim", "nloptr", "mcmc", "ucminf"),
  weights,
  index = "Date",
  parm.vector.index,
  xml.parm,
  ...
)

## S3 method for class 'optim_apsim'
print(x, ..., digits = 3, level = 0.95)

## S3 method for class 'optim_apsim'
vcov(object, ..., scaled = TRUE)

## S3 method for class 'optim_apsim'
coef(object, ..., scaled = FALSE)

## S3 method for class 'optim_apsim'
confint(object, parm, level = 0.95, ...)

Arguments

Details

Simple optimization for APSIM Classic

* This function assumes that you want to optimize parameters which are stored in an auxiliary XML file. These are typically crop or cultivar specific parameters. However, it is possible to optimize parameters present in the main simulation file.

* Only one observation per day is allowed in the data.

* Given how APSIM Classic works, this can only be run when the main simulation file is in the current directory and the crop file (or XML) should be in the same directory as the main simulation.

* The initial values for the optimization should be the ones in the stored crop parameter file.

* It is suggested that you keep a backup of the original file. This function will edit and overwrite the file during the optimization.

* When you use the parm.vector.index you cannot edit two separate elements of a vector at the same time. This should be used to target a single element of a vector only.

* Internally, the optimization is done around the scaled value of the initial parameter values. A value of 1 would correspond to the inital value of the parameter. The ‘lower’ and ‘upper’ (or ‘ub’ and ‘lb’) are also scaled to the initial values of the parameters. So, for example, if your initial value is 20 and you provide an upper bound of 5, it means that the actual upper value that you are allowing for is 100.

Value

object of class ‘optim_apsim’, but really just a list with results from optim and additional information.

prints to console

it returns the variance-covariance matrix for an object of class ‘optim_apsim’.

a numeric vector with the value of the parameter estimates.

a matrix with lower and upper limits and the point estimate (coef)

Note

When computing the objective function (residual sum-of-squares) different variables are combined. It is common to weight them since they are in different units. If the argument weights is not supplied no weighting is applied. It can be ‘mean’, ‘var’ or a numeric vector of appropriate length.

This in the scale of the optimized parameters which are scaled to be around 1.