Help for package TroublemakeR

Title:

Generates Spatial Problems in R for 'AMPL'

Version:

0.0.1

Description:

Provides methods for generating .dat files for use with the 'AMPL' software using spatial data, particularly rasters. It includes support for various spatial data formats and different problem types. By automating the process of generating 'AMPL' datasets, this package can help streamline optimization workflows and make it easier to solve complex optimization problems. The methods implemented in this package are described in detail in a publication by Fourer et al. (<doi:10.1287/mnsc.36.5.519>).

License:

GPL (≥ 3)

Encoding:

UTF-8

RoxygenNote:

7.2.3

Depends:

R (≥ 4.1.0)

LazyData:

true

Imports:

purrr, terra

URL:

https://github.com/Sustainscapes/TroublemakeR

BugReports:

https://github.com/Sustainscapes/TroublemakeR/issues

NeedsCompilation:

Packaged:

2023-04-03 03:17:13 UTC; au687614

Author:

Derek Corcoran [aut, cre]

Maintainer:

Derek Corcoran <derek.corcoran.barrios@gmail.com>

Repository:

CRAN

Date/Publication:

2023-04-03 16:00:02 UTC

A PackedSpatRaster of 4 species with its projected distribution for current conditions

Description

A PackedSpatRaster of 4 species with its projected distribution for current conditions

Usage

Current

Format

A PackedSpatRaster with 4 layer:

Spp1: Predicted presence absence for species 1 in current coditions
Spp2: Predicted presence absence for species 1 in current conditions
Spp3: Predicted presence absence for species 1 in current conditions
Spp4: Predicted presence absence for species 1 in current conditions

A PackedSpatRaster of the current landuse

Description

A PackedSpatRaster of the current landuse

Usage

CurrentLanduse

Format

A PackedSpatRaster with 1 layer:

Landuse: current landuse

A list of 4 species with its projected distribution for 4 landuses

Description

A list of 4 species with its projected distribution for 4 landuses

Usage

Species

Format

A list of 4 Spatrasters with 4 layers each:

Species 1: Predicted presence absence for species 1 in current, forest, agriculture, and urban landuse
Species 2: Predicted presence absence for species 1 in current, forest, agriculture, and urban landuse
Species 3: Predicted presence absence for species 1 in current, forest, agriculture, and urban landuse
Species 4: Predicted presence absence for species 1 in current, forest, agriculture, and urban landuse

A list of 4 species with its projected distribution for 4 landuses

Description

A list of 4 species with its projected distribution for 4 landuses

Usage

Species_Landuse

Format

A list of 4 Spatrasters with 4 layers each:

Species 1: Predicted presence absence for species 1 in forest, agriculture, and urban landuse
Species 2: Predicted presence absence for species 1 in forest, agriculture, and urban landuse
Species 3: Predicted presence absence for species 1 in forest, agriculture, and urban landuse
Species 4: Predicted presence absence for species 1 in forest, agriculture, and urban landuse

Create budget

Description

This function generates or appends the budget and transition cost to a .dat file for ampl. The file will be written to the location specified by the name argument. If the file already exists, it will be overwritten. The file format is plain text, with each line terminated by a newline character.

Usage

create_budget(
  budget,
  Rastercurrentlanduse,
  landuses,
  name = "Problem",
  verbose = FALSE
)

Arguments

budget

maximum cost for the problem

Rastercurrentlanduse

raster object of current landuses

landuses

character vector with all landuses

name

The name of the output file

verbose

Logical whether messages will be written while the function is generating calculations, defaults to FALSE

Value

A .dat file. This function is used for the side-effect of writing values to a file.

Author(s)

Derek Corcoran

Examples


data(CurrentLanduse)
CurrentLU <- terra::unwrap(CurrentLanduse)


TroublemakeR::create_budget(budget = 2,
Rastercurrentlanduse = CurrentLU,
landuses = c("Agriculture", "Forest", "Urban"),
name = "Problem",
verbose = TRUE)

# delete the file so the test on cran can pass this

file.remove("Problem.dat")

Define Cells

Description

This function takes a Raster object and identifies non NA cells and writes them to a .dat file. The file will be written to the location specified by the name argument. If the file already exists, it will be overwritten. The file format is plain text, with each line terminated by a newline character.

Usage

define_cells(Rasterdomain, name = "Problem")

Arguments

Rasterdomain

A Raster object with any value in the cells that are part of the problem and NA values where the problem is not to be solved

name

The name of the output file

Value

.dat file. This function is used for the side-effect of writing values to a file.

Author(s)

Derek Corcoran

Examples

data(Species)
library(terra)
Test <- Species[[1]] |>
terra::unwrap()

# Generate the "Problem.dat" file

define_cells(Test[[1]])

file.remove("Problem.dat")

Landuse names

Description

This function takes a vector of landuse names and writes them to a .dat file. The file will be written to the location specified by the name argument. If the file already exists, it will be overwritten. The file format is plain text, with each line terminated by a newline character.

Usage

landuse_names(landuses = NULL, name = "Problem")

Arguments

landuses

a vector with the names of the landuses

name

The name of the output file

Value

.dat file. This function is used for the side-effect of writing values to a file.

Author(s)

Derek Corcoran

Examples


landuse_names(landuses =  c("Agriculture", "Forest", "Urban"))

# delete the file so the test on cran can pass this

file.remove("Problem.dat")

Species names

Description

This function takes a vector of species names and writes them to a .dat file. The file will be written to the location specified by the name argument. If the file already exists, it will be overwritten. The file format is plain text, with each line terminated by a newline character.

Usage

species_names(species_names = NULL, name = "Problem")

Arguments

species_names

a vector with the names of species

name

The name of the output file

Value

.dat file. This function is used for the side-effect of writing values to a file.

Author(s)

Derek Corcoran

Examples


species_names(species_names = c("Spp1", "Spp2"))
file.remove("Problem.dat")

Calculate species suitability

Description

Calculate species suitability from a given raster and species names and writes them to a .dat file. The file will be written to the location specified by the name argument. If the file already exists, it will be overwritten. The file format is plain text, with each line terminated by a newline character.

Usage

species_suitability(
  Rastercurrent,
  species_names,
  name = "Problem",
  verbose = FALSE
)

Arguments

Rastercurrent

raster object of current suitability

species_names

character vector of species names

name

The name of the output file

verbose

Logical whether messages will be written while the function is generating calculations, defaults to FALSE

Value

.dat file. This function is used for the side-effect of writing values to a file.

Examples

library(terra)
data(Current)
Current <- terra::unwrap(Current)
species_suitability(Rastercurrent = Current, species_names = c("Spp1", "Spp2", "Spp3", "Spp4"))

file.remove("Problem.dat")

Calculate species suitability for each landuse

Description

Calculate species suitability from a given raster, species names and landuse and writes them to a .dat file. The file will be written to the location specified by the name argument. If the file already exists, it will be overwritten. The file format is plain text, with each line terminated by a newline character.

Usage

species_suitability_landuse(
  Rasterspecieslanduse,
  species_names,
  landuses,
  name = "Problem",
  verbose = FALSE
)

Arguments

Rasterspecieslanduse

a list of species suitability for each landuse

species_names

character vector of species names

landuses

character vector with all landuses

name

The name of the output file

verbose

Logical whether messages will be written while the function is generating calculations, defaults to FALSE

Value

.dat file. This function is used for the side-effect of writing values to a file.

Examples

library(terra)
data("Species_Landuse")
Species_Landuse <- Species_Landuse |> purrr::map(terra::unwrap)
species_suitability_landuse(Rasterspecieslanduse = Species_Landuse,
species_names = c("Spp1", "Spp2", "Spp3", "Spp4"),
landuses = c("Agriculture", "Forest", "Urban"), name = "Test")
file.remove("Test.dat")

Troublemaker

Description

This function is a metafunction with several functions inside of it it takes several spatial objects and generates a .dat file with a spatial dataset for AMPL

Usage

troublemaker(
  Rasterdomain = NULL,
  Rastercurrent = NULL,
  species_names = NULL,
  Rasterspecieslanduse = NULL,
  landuses = NULL,
  budget = NULL,
  Rastercurrentlanduse = NULL,
  name = "Problem",
  verbose = FALSE
)

Arguments

Rasterdomain

A Raster object with any value in the cells that are part of the problem and NA values where the problem is not to be solved

Rastercurrent

raster object of current suitability

species_names

a vector with the names of species

Rasterspecieslanduse

a list of species suitability for each landuse

landuses

character vector with all landuses

budget

maximum cost for the problem

Rastercurrentlanduse

raster object of current landuses

name

The name of the output file

verbose

Logical whether messages will be written while the function is generating calculations, defaults to FALSE

Value

A .dat file with the spatial problem formated for AMPL. This function is used for the side-effect of writing values to a file.

Author(s)

Derek Corcoran

Examples

# Example 1 with current suitabilities
data(Species)
data(Current)
library(terra)
Test <- Species[[1]] |>
terra::unwrap()

Current <- terra::unwrap(Current)

# Generate the "Problem.dat" file

TroublemakeR::troublemaker(Rasterdomain =Test[[1]],
Rastercurrent = Current,
species_names = c("Spp1", "Spp2", "Spp3", "Spp4"),
name = "Problem")

# delete the file so the test on cran can pass this

file.remove("Problem.dat")

# Example 2 with landuse suitabilities

data(Species)
data("Species_Landuse")

library(terra)
Test <- Species[[1]] |>
terra::unwrap()

Species_Landuse <- Species_Landuse |> purrr::map(terra::unwrap)

# Generate the "Problem2.dat" file

TroublemakeR::troublemaker(Rasterdomain =Test[[1]],
Rasterspecieslanduse = Species_Landuse,
species_names = c("Spp1", "Spp2", "Spp3", "Spp4"),
landuses = c("Agriculture", "Forest", "Urban"),
name = "Problem2")

# delete the file so the test on cran can pass this

file.remove("Problem2.dat")

 # Example 3 with budget and transition cost

 data("CurrentLanduse")
 CurrentLU <- terra::unwrap(CurrentLanduse)
 TroublemakeR::troublemaker(Rasterdomain =Test[[1]],
 Rasterspecieslanduse = Species_Landuse,
 species_names = c("Spp1", "Spp2", "Spp3", "Spp4"),
 landuses = c("Agriculture", "Forest", "Urban"),
 Rastercurrentlanduse = CurrentLU,
 budget = 2,
 name = "Problem3",
 verbose = FALSE)

 file.remove("Problem3.dat")

Writes an AMPL line

Description

This function takes a character and writes them to a .dat file. The file will be written to the location specified by the name argument. If the file already exists, it will be overwritten. The file format is plain text, with each line terminated by a newline character.

Usage

write_ampl_lines(line, name = "Problem")

Arguments

line

line to be written to .dat file

name

The name of the output file

Value

.dat file. This function is used for the side-effect of writing values to a file.

Examples


write_ampl_lines("param s:= 1")

file.remove("Problem.dat")

Write cell parameters

Description

This function takes a Raster object, uses its values as a parameter and writes them to a .dat file. The file will be written to the location specified by the name argument. If the file already exists, it will be overwritten. The file format is plain text, with each line terminated by a newline character.

Usage

write_cell_param(
  Rasterparam,
  parameter,
  default = NULL,
  name = "Problem",
  verbose = FALSE
)

Arguments

Rasterparam

A Raster object with the values for the parameter

parameter

The name of the parameter to use

default

The value of the default value for the parameter if there is one, otherwise keep it as NULL

name

The name of the output file

verbose

Logical whether messages will be written while the function is generating calculations, defaults to FALSE

Value

.dat file. This function is used for the side-effect of writing values to a file.

Examples


library(terra)

A <- TroublemakeR::Current |> terra::unwrap()
A <- A[[1]]

write_cell_param(Rasterparam = A, parameter = "Suitability", name = "Problem")

 write_cell_param(Rasterparam = A, parameter = "Carbon", default = 1,
 name = "Problem")

 write_cell_param(Rasterparam = A, parameter = "Cost", default = 0,
 name = "Problem")

 file.remove("Problem.dat")