Marxan conservation problem

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). Please note that the vroom package is required to import Marxan data files.

Usage

marxan_problem(x, ...)

# S3 method for default
marxan_problem(x, ...)

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

# S3 method for 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.

symmetric

logical does the boundary data (i.e., argument to bound) describe symmetric relationships between planning units? If the boundary data contain asymmetric connectivity data, this parameter should be set to FALSE. Defaults to TRUE.

Value

A problem() object.

Details

This function is provided as a convenient interface for solving Marxan problems using the prioritizr package. Note that this function does not support all of the functionality provided by the Marxan software. In particular, only the following parameters supported: "INPUTDIR", "SPECNAME", "PUNAME", "PUVSPRNAME", "BOUNDNAME", "BLM", and "ASYMMETRICCONNECTIVITY". Additionally, for the species data (i.e., argument to spec), only the "id", "name", "prop", and "amount"` columns are considered.

Notes

In previous versions, this function could not accommodate asymmetric connectivity data. It has now been updated to handle asymmetric connectivity data.

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.

Serra N, Kockel A, Game ET, Grantham H, Possingham HP, and McGowan J (2020) Marxan User Manual: For Marxan version 2.43 and above. The Nature Conservancy (TNC), Arlington, Virginia, United States and Pacific Marine Analysis and Research Association (PacMARA), Victoria, British Columbia, Canada.

Examples

# create Marxan problem using Marxan input file
# (note this example requires the vroom package to be installed)
# \dontrun{
input_file <- system.file("extdata/marxan/input.dat", package = "prioritizr")
p1 <-
  marxan_problem(input_file) %>%
  add_default_solver(verbose = FALSE)

# solve problem
s1 <- solve(p1)

# print solution
head(s1)
#>   id       cost status    xloc     yloc locked_in locked_out solution_1
#> 1  3      0.000      0 1116623 -4493479     FALSE      FALSE          0
#> 2 30   7527.275      3 1110623 -4496943     FALSE       TRUE          0
#> 3 56  37349.075      0 1092623 -4500408     FALSE      FALSE          0
#> 4 58  16959.021      0 1116623 -4500408     FALSE      FALSE          0
#> 5 84  34220.256      0 1098623 -4503872     FALSE      FALSE          0
#> 6 85 178907.584      0 1110623 -4503872     FALSE      FALSE          0

# create Marxan problem using data.frames that have been loaded into R
# (note this example also requires the vroom package to be installed)
## load in planning unit data
pu_path <- system.file("extdata/marxan/input/pu.dat", package = "prioritizr")
pu_dat <- vroom::vroom(pu_path)
#> Rows: 1751 Columns: 5
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: ","
#> dbl (5): id, cost, status, xloc, yloc
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
head(pu_dat)
#> # A tibble: 6 × 5
#>      id    cost status     xloc      yloc
#>   <dbl>   <dbl>  <dbl>    <dbl>     <dbl>
#> 1     3      0       0 1116623. -4493479.
#> 2    30   7527.      3 1110623. -4496943.
#> 3    56  37349.      0 1092623. -4500408.
#> 4    58  16959.      0 1116623. -4500408.
#> 5    84  34220.      0 1098623. -4503872.
#> 6    85 178908.      0 1110623. -4503872.

## load in feature data
spec_path <- system.file(
  "extdata/marxan/input/spec.dat", package = "prioritizr"
)
spec_dat <- vroom::vroom(spec_path)
#> Rows: 17 Columns: 4
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: ","
#> chr (1): name
#> dbl (3): id, prop, spf
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
head(spec_dat)
#> # A tibble: 6 × 4
#>      id  prop   spf name  
#>   <dbl> <dbl> <dbl> <chr> 
#> 1    10   0.3     1 bird1 
#> 2    11   0.3     1 nvis2 
#> 3    12   0.3     1 nvis8 
#> 4    13   0.3     1 nvis9 
#> 5    14   0.3     1 nvis14
#> 6    15   0.3     1 nvis20

## load in planning unit vs feature data
puvspr_path <- system.file(
  "extdata/marxan/input/puvspr.dat", package = "prioritizr"
)
puvspr_dat <- vroom::vroom(puvspr_path)
#> Rows: 4662 Columns: 3
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: ","
#> dbl (3): species, pu, amount
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
head(puvspr_dat)
#> # A tibble: 6 × 3
#>   species    pu amount
#>     <dbl> <dbl>  <dbl>
#> 1      26    56 120.  
#> 2      26    58  45.2 
#> 3      26    84  68.0 
#> 4      26    85   9.74
#> 5      26    86   7.80
#> 6      26   111 478.  

## load in the boundary data
bound_path <- system.file(
  "extdata/marxan/input/bound.dat", package = "prioritizr"
)
bound_dat <- vroom::vroom(bound_path)
#> Rows: 5256 Columns: 3
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> dbl (3): id1, id2, boundary
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
head(bound_dat)
#> # A tibble: 6 × 3
#>     id1   id2 boundary
#>   <dbl> <dbl>    <dbl>
#> 1     3     3    16000
#> 2     3    30     4000
#> 3     3    58     4000
#> 4    30    30    12000
#> 5    30    58     4000
#> 6    30    85     4000

# create problem without the boundary data
p2 <-
  marxan_problem(pu_dat, spec_dat, puvspr_dat) %>%
  add_default_solver(verbose = FALSE)

# solve problem
s2 <- solve(p2)

# print solution
head(s2)
#>   id       cost status    xloc     yloc locked_in locked_out solution_1
#> 1  3      0.000      0 1116623 -4493479     FALSE      FALSE          0
#> 2 30   7527.275      3 1110623 -4496943     FALSE       TRUE          0
#> 3 56  37349.075      0 1092623 -4500408     FALSE      FALSE          1
#> 4 58  16959.021      0 1116623 -4500408     FALSE      FALSE          0
#> 5 84  34220.256      0 1098623 -4503872     FALSE      FALSE          0
#> 6 85 178907.584      0 1110623 -4503872     FALSE      FALSE          0

# 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, blm = 5) %>%
  add_default_solver(verbose = FALSE)

# solve problem
s3 <- solve(p3)

# print solution
head(s3)
#>   id       cost status    xloc     yloc locked_in locked_out solution_1
#> 1  3      0.000      0 1116623 -4493479     FALSE      FALSE          0
#> 2 30   7527.275      3 1110623 -4496943     FALSE       TRUE          0
#> 3 56  37349.075      0 1092623 -4500408     FALSE      FALSE          0
#> 4 58  16959.021      0 1116623 -4500408     FALSE      FALSE          0
#> 5 84  34220.256      0 1098623 -4503872     FALSE      FALSE          0
#> 6 85 178907.584      0 1110623 -4503872     FALSE      FALSE          0
# }