Change the availability matrix to simplify automated ATLANTIS calibrations.

Change the availability of predator XXX on specific preygroups.

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), ]
#>   pred pred_stanza prey_stanza       code FPS FVS    CEP  BML PL DL DR DC DLsed
#> 6  FPS           1           1 pPREY1FPS1   0   0 0.1234 0.01  0  0  0  0     0
#> 7  FPS           1           2 pPREY2FPS1   0   0 0.1234 0.01  0  0  0  0     0
#>   DRsed DCsed
#> 6     0     0
#> 7     0     0

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), ]
#>    pred pred_stanza prey_stanza       code    FPS    FVS   CEP  BML    PL    DL
#> 6   FPS           1           1 pPREY1FPS1 0.1111 0.2222 0e+00 0.01 0.000 0.000
#> 7   FPS           1           2 pPREY2FPS1 0.1111 0.2222 0e+00 0.01 0.000 0.000
#> 12  FVS           2           1 pPREY1FVS2 0.3333 0.4444 1e-03 0.00 0.020 0.001
#> 13  FVS           2           2 pPREY2FVS2 0.3333 0.4444 5e-04 0.00 0.004 0.000
#>       DR DC DLsed DRsed DCsed
#> 6  0e+00  0 0.000  0.00     0
#> 7  0e+00  0 0.000  0.00     0
#> 12 0e+00  0 0.004  0.01     0
#> 13 1e-04  0 0.008  0.01     0