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getDiet() now also includes the contribution of the external encoun…
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…ter rate to the diet.
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@gustavdelius
gustavdelius committed Aug 19, 2024
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2 changes: 2 additions & 0 deletions NEWS.md
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@@ -1,5 +1,7 @@
# Development version

- `getDiet()` now also includes the contribution of the external encounter rate
to the diet.
- Improved scaling of the y-axis in `plotGrowthCurves()`.
- `steadySingleSpecies()` no longer requires species to grow to `w_max`.
- `matchGrowth()` now also rescales the external encounter rate.
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41 changes: 23 additions & 18 deletions R/summary_methods.R
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Expand Up @@ -38,11 +38,12 @@ NULL
#' Get diet of predator at size, resolved by prey species
#'
#' Calculates the rate at which a predator of a particular species and size
#' consumes biomass of each prey species and resource.
#' The diet has units of grams/year.
#' consumes biomass of each prey species, resource, and other components of the
#' ecosystem. Returns either the rates in grams/year or the proportion of the
#' total consumption rate.
#'
#' Returns the rates \eqn{D_{ij}(w)} at which a predator of species \eqn{i}
#' and size \eqn{w} consumes biomass from prey species \eqn{j}. This is
#' The rates \eqn{D_{ij}(w)} at which a predator of species \eqn{i}
#' and size \eqn{w} consumes biomass from prey species \eqn{j} are
#' calculated from the predation kernel \eqn{\phi_i(w, w_p)},
#' the search volume \eqn{\gamma_i(w)}, the feeding level \eqn{f_i(w)}, the
#' species interaction matrix \eqn{\theta_{ij}} and the prey abundance density
Expand All @@ -51,25 +52,27 @@ NULL
#' D_{ij}(w, w_p) = (1-f_i(w)) \gamma_i(w) \theta_{ij}
#' \int N_j(w_p) \phi_i(w, w_p) w_p dw_p.
#' }
#' The prey index \eqn{j} runs over all species and the resource. It also runs
#' over any extra ecosystem components in your model for which you have
#' defined an encounter rate function. This encounter rate is multiplied by
#' \eqn{1-f_i(w)} to give the rate of consumption of biomass from these extra
#' components.
#' The prey index \eqn{j} runs over all species and the resource.
#'
#' This function performs the same integration as
#' [getEncounter()] but does not aggregate over prey species, and
#' multiplies by \eqn{1-f_i(w)} to get the consumed biomass rather than the
#' available biomass. Outside the range of sizes for a predator species the
#' returned rate is zero.
#' Extra columns are added for the external encounter rate and for any extra
#' ecosystem components in your model for which you have defined an encounter
#' rate function. These encounter rates are multiplied by \eqn{1-f_i(w)} to give
#' the rate of consumption of biomass from these extra components.
#'
#' This function performs the same integration as [getEncounter()] but does not
#' aggregate over prey species, and multiplies by \eqn{1-f_i(w)} to get the
#' consumed biomass rather than the available biomass. Outside the range of
#' sizes for a predator species the returned rate is zero.
#'
#' @inheritParams getEncounter
#' @param proportion If TRUE (default) the function returns the diet as a
#' proportion of the total consumption rate. If FALSE it returns the
#' consumption rate in grams per year.
#'
#' @return An array (predator species x predator size x
#' (prey species + resource + other components) )
#' (prey species + resource + other components). Dimnames are "prey", "w",
#' and "predator".
#'
#' @export
#' @family summary functions
#' @concept summary_function
Expand All @@ -92,11 +95,11 @@ getDiet <- function(params,
other_names <- names(params@other_encounter)
assert_that(identical(dim(n), c(no_sp, no_w)),
length(n_pp) == no_w_full)
diet <- array(0, dim = c(no_sp, no_w, no_sp + 1 + no_other),
diet <- array(0, dim = c(no_sp, no_w, no_sp + 2 + no_other),
dimnames = list("predator" = species,
"w" = dimnames(params@initial_n)$w,
"prey" = c(as.character(species),
"Resource",
"Resource", "External",
other_names)))
# idx_sp are the index values of object@w_full such that
# object@w_full[idx_sp] = object@w
Expand Down Expand Up @@ -141,9 +144,11 @@ getDiet <- function(params,
diet[, , 1:(no_sp + 1)] <- sweep(sweep(diet[, , 1:(no_sp + 1), drop = FALSE],
c(1, 3), inter, "*"),
c(1, 2), params@search_vol, "*")
# Add diet from external sources
diet[, , no_sp + 2] <- params@ext_encounter
# Add diet from other components
for (i in seq_along(params@other_encounter)) {
diet[, , no_sp + 1 + i] <-
diet[, , no_sp + 2 + i] <-
do.call(params@other_encounter[[i]],
list(params = params,
n = n, n_pp = n_pp, n_other = n_other,
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32 changes: 17 additions & 15 deletions man/getDiet.Rd
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129 changes: 129 additions & 0 deletions tests/testthat/_snaps/summary_methods.md
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Expand Up @@ -3997,6 +3997,135 @@
Cod 3.002041e+00 4.763716e+00 8.214362e+00 1.294631e+01 2.035887e+01
Saithe 3.407671e+00 5.497502e+00 9.324405e+00 1.491433e+01 2.372086e+01
, , prey = External
w
predator 0.001 0.00119 0.00142 0.0017 0.00203 0.00242 0.00289 0.00345 0.00411
Sprat 0 0 0 0 0 0 0 0 0
Sandeel 0 0 0 0 0 0 0 0 0
N.pout 0 0 0 0 0 0 0 0 0
Herring 0 0 0 0 0 0 0 0 0
Dab 0 0 0 0 0 0 0 0 0
Whiting 0 0 0 0 0 0 0 0 0
Sole 0 0 0 0 0 0 0 0 0
Gurnard 0 0 0 0 0 0 0 0 0
Plaice 0 0 0 0 0 0 0 0 0
Haddock 0 0 0 0 0 0 0 0 0
Cod 0 0 0 0 0 0 0 0 0
Saithe 0 0 0 0 0 0 0 0 0
w
predator 0.00491 0.00586 0.00699 0.00834 0.00995 0.0119 0.0142 0.0169 0.0202
Sprat 0 0 0 0 0 0 0 0 0
Sandeel 0 0 0 0 0 0 0 0 0
N.pout 0 0 0 0 0 0 0 0 0
Herring 0 0 0 0 0 0 0 0 0
Dab 0 0 0 0 0 0 0 0 0
Whiting 0 0 0 0 0 0 0 0 0
Sole 0 0 0 0 0 0 0 0 0
Gurnard 0 0 0 0 0 0 0 0 0
Plaice 0 0 0 0 0 0 0 0 0
Haddock 0 0 0 0 0 0 0 0 0
Cod 0 0 0 0 0 0 0 0 0
Saithe 0 0 0 0 0 0 0 0 0
w
predator 0.0241 0.0288 0.0343 0.0409 0.0489 0.0583 0.0696 0.083 0.0991 0.118
Sprat 0 0 0 0 0 0 0 0 0 0
Sandeel 0 0 0 0 0 0 0 0 0 0
N.pout 0 0 0 0 0 0 0 0 0 0
Herring 0 0 0 0 0 0 0 0 0 0
Dab 0 0 0 0 0 0 0 0 0 0
Whiting 0 0 0 0 0 0 0 0 0 0
Sole 0 0 0 0 0 0 0 0 0 0
Gurnard 0 0 0 0 0 0 0 0 0 0
Plaice 0 0 0 0 0 0 0 0 0 0
Haddock 0 0 0 0 0 0 0 0 0 0
Cod 0 0 0 0 0 0 0 0 0 0
Saithe 0 0 0 0 0 0 0 0 0 0
w
predator 0.141 0.168 0.201 0.24 0.286 0.342 0.408 0.486 0.58 0.693 0.827 0.987
Sprat 0 0 0 0 0 0 0 0 0 0 0 0
Sandeel 0 0 0 0 0 0 0 0 0 0 0 0
N.pout 0 0 0 0 0 0 0 0 0 0 0 0
Herring 0 0 0 0 0 0 0 0 0 0 0 0
Dab 0 0 0 0 0 0 0 0 0 0 0 0
Whiting 0 0 0 0 0 0 0 0 0 0 0 0
Sole 0 0 0 0 0 0 0 0 0 0 0 0
Gurnard 0 0 0 0 0 0 0 0 0 0 0 0
Plaice 0 0 0 0 0 0 0 0 0 0 0 0
Haddock 0 0 0 0 0 0 0 0 0 0 0 0
Cod 0 0 0 0 0 0 0 0 0 0 0 0
Saithe 0 0 0 0 0 0 0 0 0 0 0 0
w
predator 1.18 1.4 1.68 2 2.39 2.85 3.4 4.06 4.84 5.78 6.9 8.23 9.82 11.7 14
Sprat 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Sandeel 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
N.pout 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Herring 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Dab 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Whiting 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Sole 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Gurnard 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Plaice 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Haddock 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Cod 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Saithe 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
w
predator 16.7 19.9 23.8 28.4 33.8 40.4 48.2 57.5 68.7 81.9 97.8 117 139 166
Sprat 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Sandeel 0 0 0 0 0 0 0 0 0 0 0 0 0 0
N.pout 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Herring 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Dab 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Whiting 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Sole 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Gurnard 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Plaice 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Haddock 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Cod 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Saithe 0 0 0 0 0 0 0 0 0 0 0 0 0 0
w
predator 198 237 282 337 402 480 573 683 816 973 1160 1390 1650 1970 2360 2810
Sprat 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Sandeel 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
N.pout 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Herring 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Dab 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Whiting 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Sole 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Gurnard 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Plaice 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Haddock 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Cod 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Saithe 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
w
predator 3350 4000 4780 5700 6800 8120 9690 11600 13800 16500 19600 23400
Sprat 0 0 0 0 0 0 0 0 0 0 0 0
Sandeel 0 0 0 0 0 0 0 0 0 0 0 0
N.pout 0 0 0 0 0 0 0 0 0 0 0 0
Herring 0 0 0 0 0 0 0 0 0 0 0 0
Dab 0 0 0 0 0 0 0 0 0 0 0 0
Whiting 0 0 0 0 0 0 0 0 0 0 0 0
Sole 0 0 0 0 0 0 0 0 0 0 0 0
Gurnard 0 0 0 0 0 0 0 0 0 0 0 0
Plaice 0 0 0 0 0 0 0 0 0 0 0 0
Haddock 0 0 0 0 0 0 0 0 0 0 0 0
Cod 0 0 0 0 0 0 0 0 0 0 0 0
Saithe 0 0 0 0 0 0 0 0 0 0 0 0
w
predator 28000 33400 39900
Sprat 0 0 0
Sandeel 0 0 0
N.pout 0 0 0
Herring 0 0 0
Dab 0 0 0
Whiting 0 0 0
Sole 0 0 0
Gurnard 0 0 0
Plaice 0 0 0
Haddock 0 0 0
Cod 0 0 0
Saithe 0 0 0

# getSSB works

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4 changes: 2 additions & 2 deletions tests/testthat/test-summary_methods.R
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Expand Up @@ -299,8 +299,8 @@ test_that("getDiet works with additional components", {

diet1 <- getDiet(params, proportion = FALSE)
diet2 <- getDiet(p, proportion = FALSE)
expect_identical(diet1[, , 1:13], diet2[, , 1:13])
expect_identical(diet2[1, 1, 14], 111)
expect_identical(diet1[, , 1:14], diet2[, , 1:14])
expect_identical(diet2[1, 1, 15], 111)
})


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