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Merged
gustavdelius merged 3 commits into from
Jun 4, 2026
Merged

Standardize plot generic first-argument name to object for biomass/yield APIs #358

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659af5e
Initial plan
Copilot Jun 4, 2026
c9c57a5
Rename plotBiomass/plotYield/plotYieldGear first argument to object
Copilot Jun 4, 2026
922191d
Remove plot argument-name regression tests
Copilot Jun 4, 2026
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5 changes: 5 additions & 0 deletions NEWS.md
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Original file line number Diff line number Diff line change
Expand Up @@ -321,6 +321,11 @@ the mathematical details.

## Breaking changes

- The first argument of `plotBiomass()`, `plotYield()`, `plotYieldGear()` and
their `MizerSim` methods and `plotly*` wrappers has been renamed from `sim`
to `object` for consistency with other plot generics. Calls using
`sim = ...` as a named argument must be updated to `object = ...`.

- The names of the dimnames of the arrays returned by `getMort()`,
`getPredRate()` are now `sp` and `w` to be in line with other
functions like `getFMort()`.
Expand Down
56 changes: 28 additions & 28 deletions R/plots.R
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Expand Up @@ -428,7 +428,7 @@ log_breaks <- function(n = 6) {
#' against time. The biomass is calculated within user defined size limits
#' (see [getBiomass()]).
#'
#' @param sim An object of class \linkS4class{MizerSim}
#' @param object An object of class \linkS4class{MizerSim}
#' @inheritParams valid_species_arg
#' @param start_time The first time to be plotted. Default (`NULL`) is the
#' beginning of the time series.
Expand Down Expand Up @@ -469,23 +469,23 @@ log_breaks <- function(n = 6) {
#' }
#' @rdname plotBiomass
#' @export
plotBiomass <- function(sim, ...) {
plotBiomass <- function(object, ...) {
UseMethod("plotBiomass")
}

#' @rdname plotBiomass
#' @export
plotBiomass.MizerSim <- function(sim, species = NULL,
plotBiomass.MizerSim <- function(object, species = NULL,
start_time = NULL, end_time = NULL,
y_ticks = 6, ylim = c(NA, NA),
total = FALSE, background = TRUE,
highlight = NULL, log = TRUE,
return_data = FALSE,
use_cutoff = FALSE,
min_w = min(sim@params@w),
max_w = max(sim@params@w),
min_w = min(object@params@w),
max_w = max(object@params@w),
min_l = NULL, max_l = NULL, ...) {
bm <- getBiomass(sim, use_cutoff = use_cutoff,
bm <- getBiomass(object, use_cutoff = use_cutoff,
min_w = min_w, max_w = max_w,
min_l = min_l, max_l = max_l)
plot(bm, species = species,
Expand All @@ -498,7 +498,7 @@ plotBiomass.MizerSim <- function(sim, species = NULL,

#' @rdname plotBiomass
#' @export
plotlyBiomass <- function(sim,
plotlyBiomass <- function(object,
species = NULL,
start_time = NULL,
end_time = NULL,
Expand All @@ -509,8 +509,8 @@ plotlyBiomass <- function(sim,
highlight = NULL,
log = TRUE,
use_cutoff = FALSE,
min_w = min(sim@params@w),
max_w = max(sim@params@w),
min_w = min(object@params@w),
max_w = max(object@params@w),
min_l = NULL,
max_l = NULL) {
argg <- as.list(environment())
Expand All @@ -525,7 +525,7 @@ plotlyBiomass <- function(sim,
#' fishing gears can be plotted against time. The yield is obtained with
#' [getYield()].
#'
#' @param sim An object of class \linkS4class{MizerSim}
#' @param object An object of class \linkS4class{MizerSim}
#' @param sim2 An optional second object of class \linkS4class{MizerSim}. If
#' this is provided its yields will be shown on the same plot in bolder lines.
#' @inheritParams plotSpectra
Expand Down Expand Up @@ -554,25 +554,25 @@ plotlyBiomass <- function(sim,
#' }
#' @rdname plotYield
#' @export
plotYield <- function(sim, ...) {
plotYield <- function(object, ...) {
UseMethod("plotYield")
}

#' @rdname plotYield
#' @export
plotYield.MizerSim <- function(sim, sim2,
plotYield.MizerSim <- function(object, sim2,
species = NULL,
total = FALSE, log = TRUE,
highlight = NULL, return_data = FALSE,
...) {
assert_that(is(sim, "MizerSim"),
assert_that(is(object, "MizerSim"),
is.flag(total),
is.flag(log),
is.flag(return_data))
params <- sim@params
species <- valid_species_arg(sim, species, error_on_empty = TRUE)
params <- object@params
species <- valid_species_arg(object, species, error_on_empty = TRUE)
if (missing(sim2)) {
y <- getYield(sim, ...)
y <- getYield(object, ...)
y_total <- rowSums(y)
y <- y[, (as.character(dimnames(y)[[2]]) %in% species),
drop = FALSE]
Expand All @@ -597,10 +597,10 @@ plotYield.MizerSim <- function(sim, sim2,
highlight = highlight)
} else {
# We need to combine two plots
if (!all(dimnames(sim@n)$time == dimnames(sim2@n)$time)) {
if (!all(dimnames(object@n)$time == dimnames(sim2@n)$time)) {
stop("The two simulations do not have the same times")
}
ym <- plotYield(sim, species = species,
ym <- plotYield(object, species = species,
total = total, log = log,
highlight = highlight, return_data = TRUE, ...)
ym2 <- plotYield(sim2, species = species,
Expand All @@ -622,7 +622,7 @@ plotYield.MizerSim <- function(sim, sim2,

#' @rdname plotYield
#' @export
plotlyYield <- function(sim, sim2,
plotlyYield <- function(object, sim2,
species = NULL,
total = FALSE, log = TRUE,
highlight = NULL, ...) {
Expand All @@ -642,7 +642,7 @@ plotlyYield <- function(sim, sim2,
#' the ggplot2 package. You can then fiddle about with colours and linetypes
#' etc. Just look at the source code for details.
#'
#' @param sim An object of class \linkS4class{MizerSim}
#' @param object An object of class \linkS4class{MizerSim}
#' @inheritParams plotSpectra
#' @param gears A vector of gear names to be included in the plot. Default is
#' all gears.
Expand All @@ -666,26 +666,26 @@ plotlyYield <- function(sim, sim2,
#' }
#' @rdname plotYieldGear
#' @export
plotYieldGear <- function(sim, ...) {
plotYieldGear <- function(object, ...) {
UseMethod("plotYieldGear")
}

#' @rdname plotYieldGear
#' @export
plotYieldGear.MizerSim <- function(sim,
plotYieldGear.MizerSim <- function(object,
species = NULL,
gears = NULL,
total = FALSE,
highlight = NULL, return_data = FALSE,
...) {
assert_that(is(sim, "MizerSim"),
assert_that(is(object, "MizerSim"),
is.flag(total),
is.flag(return_data))
params <- sim@params
species <- valid_species_arg(sim, species, error_on_empty = TRUE)
gears <- valid_gears_arg(sim, gears, error_on_empty = TRUE)
params <- object@params
species <- valid_species_arg(object, species, error_on_empty = TRUE)
gears <- valid_gears_arg(object, gears, error_on_empty = TRUE)

y <- getYieldGear(sim, ...)
y <- getYieldGear(object, ...)
y_total <- rowSums(y, dims = 2)
y <- y[, dimnames(y)$gear %in% gears, dimnames(y)$sp %in% species, drop = FALSE]
names(dimnames(y))[names(dimnames(y)) == "sp"] <- "Species"
Expand Down Expand Up @@ -718,7 +718,7 @@ plotYieldGear.MizerSim <- function(sim,

#' @rdname plotYieldGear
#' @export
plotlyYieldGear <- function(sim, species = NULL,
plotlyYieldGear <- function(object, species = NULL,
total = FALSE, highlight = NULL, ...) {
argg <- as.list(environment())
ggplotly(do.call("plotYieldGear", argg),
Expand Down
16 changes: 8 additions & 8 deletions man/plotBiomass.Rd
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8 changes: 4 additions & 4 deletions man/plotYield.Rd
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8 changes: 4 additions & 4 deletions man/plotYieldGear.Rd
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17 changes: 17 additions & 0 deletions tests/testthat/test-plots.R
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@gustavdelius gustavdelius Jun 4, 2026

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Do not add these tests.

@gustavdelius gustavdelius Jun 4, 2026

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@copilot remove the tests you added

Copilot AI Jun 4, 2026

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Done in commit 922191d.

Original file line number Diff line number Diff line change
Expand Up @@ -300,6 +300,23 @@ test_that("yield plotly wrappers return plotly objects", {
expect_s3_class(plotlyYieldGear(sim, species = species), "plotly")
})

test_that("biomass and yield plot APIs use object as first argument", {
expect_identical(names(formals(plotBiomass))[1], "object")
expect_identical(names(formals(getS3method("plotBiomass", "MizerSim")))[1],
"object")
expect_identical(names(formals(plotlyBiomass))[1], "object")

expect_identical(names(formals(plotYield))[1], "object")
expect_identical(names(formals(getS3method("plotYield", "MizerSim")))[1],
"object")
expect_identical(names(formals(plotlyYield))[1], "object")

expect_identical(names(formals(plotYieldGear))[1], "object")
expect_identical(names(formals(getS3method("plotYieldGear", "MizerSim")))[1],
"object")
expect_identical(names(formals(plotlyYieldGear))[1], "object")
})


# testing the plot outputs
test_that("return_data is identical",{
Expand Down
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