prioritizr: marxan_problem – R documentation

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marxan_problem

Marxan conservation problem

Description

Create a conservation planning problem() following the mathematical formulations used in Marxan (detailed in Beyer et al. 2016). Note that these problems are solved using exact algorithms and not simulated annealing (i.e. the Marxan software).

Usage

marxan_problem(x, ...)

## Default S3 method:
marxan_problem(x, ...)

## S3 method for class 'data.frame'
marxan_problem(x, spec, puvspr, bound = NULL, blm = 0, ...)

## S3 method for class 'character'
marxan_problem(x, ...)

Arguments

`x`	`character` file path for a Marxan input file (typically called `"input.dat"`), or `data.frame` containing planning unit data (typically called `"pu.dat"`). If the argument to `x` is a `data.frame`, then each row corresponds to a different planning unit, and it must have the following columns: id `integer` unique identifier for each planning unit. These identifiers are used in the argument to `puvspr`. cost `numeric` cost of each planning unit. status `integer` indicating if each planning unit should not be locked in the solution (0) or if it should be locked in (2) or locked out (3) of the solution. Although Marxan allows planning units to be selected in the initial solution (using values of 1), these values have no effect here. This column is optional.
`...`	not used.
`spec`	`data.frame` containing information on the features. The argument to `spec` must follow the conventions used by Marxan for the species data file (conventionally called `"spec.dat"`). Each row corresponds to a different feature and each column corresponds to different information about the features. It must contain the columns listed below. Note that the argument to `spec` must contain at least one column named `"prop"` or `"amount"`—but not both columns with both of these names—to specify the target for each feature. id `integer` unique identifier for each feature These identifiers are used in the argument to `puvspr`. name `character` name for each feature. prop `numeric` relative target for each feature (optional). ' amount `numeric` absolute target for each feature (optional).
`puvspr`	`data.frame` containing information on the amount of each feature in each planning unit. The argument to `puvspr` must follow the conventions used in the Marxan input data file (conventionally called `"puvspr.dat"`). It must contain the following columns: pu `integer` planning unit identifier. species `integer` feature identifier. amount `numeric` amount of the feature in the planning unit.
`bound`	`NULL` object indicating that no boundary data is required for the conservation planning problem, or a `data.frame` containing information on the planning units' boundaries. The argument to `bound` must follow the conventions used in the Marxan input data file (conventionally called `"bound.dat"`). It must contain the following columns: id1 `integer` planning unit identifier. id2 `integer` planning unit identifier. boundary `numeric` length of shared boundary between the planning units identified in the previous two columns.
`blm`	`numeric` boundary length modifier. This argument only has an effect when argument to `x` is a `data.frame`. The default argument is zero.

Details

This function is provided as a convenient wrapper for solving Marxan problems using prioritizr.

Value

problem() (i.e. ConservationProblem) object.

Notes

In early versions, this function could accommodate asymmetric connectivity data. This functionality is no longer supported. To specify asymmetric connectivity, please see the add_connectivity_penalties() function.

References

Ball IR, Possingham HP, and Watts M (2009) Marxan and relatives: Software for spatial conservation prioritisation in Spatial conservation prioritisation: Quantitative methods and computational tools. Eds Moilanen A, Wilson KA, and Possingham HP. Oxford University Press, Oxford, UK.

Beyer HL, Dujardin Y, Watts ME, and Possingham HP (2016) Solving conservation planning problems with integer linear programming. Ecological Modelling, 228: 14–22.

Examples

# create Marxan problem using Marxan input file
input_file <- system.file("extdata/input.dat", package = "prioritizr")
p1 <- marxan_problem(input_file) %>%
      add_default_solver(verbose = FALSE)
## Not run: 
# solve problem
s1 <- solve(p1)

# print solution
head(s1)

## End(Not run)
# create Marxan problem using data.frames that have been loaded into R
## load in planning unit data
pu_path <- system.file("extdata/input/pu.dat", package = "prioritizr")
pu_dat <- data.table::fread(pu_path, data.table = FALSE)
head(pu_dat)

## load in feature data
spec_path <- system.file("extdata/input/spec.dat", package = "prioritizr")
spec_dat <- data.table::fread(spec_path, data.table = FALSE)
head(spec_dat)

## load in planning unit vs feature data
puvspr_path <- system.file("extdata/input/puvspr.dat",
                           package = "prioritizr")
puvspr_dat <- data.table::fread(puvspr_path, data.table = FALSE)
head(puvspr_dat)

## load in the boundary data
bound_path <- system.file("extdata/input/bound.dat", package = "prioritizr")
bound_dat <- data.table::fread(bound_path, data.table = FALSE)
head(bound_dat)

# create problem without the boundary data
p2 <- marxan_problem(pu_dat, spec_dat, puvspr_dat) %>%
      add_default_solver(verbose = FALSE)
## Not run: 
# solve problem
s2 <- solve(p2)

# print solution
head(s2)

## End(Not run)
# create problem with the boundary data and a boundary length modifier
# set to 5
p3 <- marxan_problem(pu_dat, spec_dat, puvspr_dat, bound_dat, 5) %>%
      add_default_solver(verbose = FALSE)
## Not run: 
# solve problem
s3 <- solve(p3)

# print solution
head(s3)

## End(Not run)

prioritizr

Systematic Conservation Prioritization in R

v7.0.1

GPL-3

Authors

Jeffrey O Hanson [aut] (<https://orcid.org/0000-0002-4716-6134>), Richard Schuster [aut, cre] (<https://orcid.org/0000-0003-3191-7869>), Nina Morrell [aut], Matthew Strimas-Mackey [aut] (<https://orcid.org/0000-0001-8929-7776>), Matthew E Watts [aut], Peter Arcese [aut] (<https://orcid.org/0000-0002-8097-482X>), Joseph Bennett [aut] (<https://orcid.org/0000-0002-3901-9513>), Hugh P Possingham [aut] (<https://orcid.org/0000-0001-7755-996X>)

Initial release