Change the availability matrix to simplify automated ATLANTIS calibrations.

Change the availability of predator XXX on specific preygroups.

Usage

change_avail(
  dietmatrix,
  pred = NULL,
  pred_stanza = NULL,
  prey = NULL,
  roc,
  relative = TRUE,
  consecutive = FALSE
)

Arguments

dietmatrix: Dataframe in 'long' format containing information about availabilities with columns 'pred', 'prey', 'pred_stanza', 'prey_stanza', 'code', 'prey_id' and 'avail'. The dataframe should be generated with load_dietmatrix().
pred: Character vector of predator Acronyms (see get_acronyms()). Selecting NULL as pred results in all predators being selected. This can be helpful if you want to increase the feeding pressure on a specific prey item by all groups. Default is NULL.
pred_stanza: Integer vector indicating if the predator is juvenile (= 1) or adult (= 2). pred and pred_stanza need to be of the same length. In rare instances, e.g. pred_stanza being NULL or one single integer either all pred_stanzas are selected or the single pred_stanza is applied to all predators. Default is NULL.
prey: List of character vectors of prey Acronyms (see get_acronyms()). pred and prey need to be of the same length. Selecting NULL as prey results in all prey groups being selected. This can be helpful if you want to increase the available prey for a specific predator overall. Default is NULL.
roc: Vector of multiplication factors which shall be applied to the old set of parameters. Please supply one value per selected group. In case relative is FALSE the new absolute values can be passed as roc.
relative: Logical if TRUE values are changed relative to base values. If FALSE new values can be passed directly. Default is NULL.
consecutive: Boolean indicating if multiple calls to change_avail are performed one after another TRUE. Default is FALSE.

Value

parameterfile *.prm file with the new parameter values.

Examples

d <- system.file("extdata", "setas-model-new-trunk", package = "atlantistools")
dm <- load_dietmatrix(prm_biol = file.path(d, "VMPA_setas_biol_fishing_Trunk.prm"),
                      fgs = file.path(d, "SETasGroupsDem_NoCep.csv"))

dm1 <- change_avail(dietmatrix = dm,
                    pred = "FPS",
                    pred_stanza = 1,
                    prey = "CEP",
                    roc = 0.1234,
                    relative = FALSE)
# Show only rows with availability of 0.1234
dm1[apply(apply(dm1[, 5:ncol(dm1)], MARGIN = 2, function(x) x == 0.1234), MARGIN = 1, any), ]
#> # A tibble: 2 × 15
#>   pred  pred_stanza prey_stanza code     FPS   FVS   CEP   BML    PL    DL    DR
#>   <chr>       <dbl>       <dbl> <chr>  <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 FPS             1           1 pPREY…     0     0 0.123  0.01     0     0     0
#> 2 FPS             1           2 pPREY…     0     0 0.123  0.01     0     0     0
#> # ℹ 4 more variables: DC <dbl>, DLsed <dbl>, DRsed <dbl>, DCsed <dbl>

dm2 <- change_avail(dietmatrix = dm,
                    pred = c("FPS", "FVS"),
                    pred_stanza = c(1, 2),
                    prey = list(c("FPS", "FVS"), c("FPS", "FVS")),
                    roc = list(c(0.1111, 0.2222), c(0.3333, 0.4444)),
                    relative = FALSE)

# Show only rows with availability of 0.1111, 0.2222, 0.3333 or 0.4444
dm2[apply(apply(dm2[, 5:ncol(dm2)], MARGIN = 2,
function(x) is.element(x,  c(0.1111, 0.2222, 0.3333, 0.4444))), MARGIN = 1, any), ]
#> # A tibble: 4 × 15
#>   pred  pred_stanza prey_stanza code     FPS   FVS   CEP   BML    PL    DL    DR
#>   <chr>       <dbl>       <dbl> <chr>  <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 FPS             1           1 pPREY… 0.111 0.222  0     0.01 0     0      0   
#> 2 FPS             1           2 pPREY… 0.111 0.222  0     0.01 0     0      0   
#> 3 FVS             2           1 pPREY… 0.333 0.444  1e-3  0    0.02  0.001  0   
#> 4 FVS             2           2 pPREY… 0.333 0.444  5e-4  0    0.004 0      1e-4
#> # ℹ 4 more variables: DC <dbl>, DLsed <dbl>, DRsed <dbl>, DCsed <dbl>