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Change plot_biomass and spawning_biomass plots to work through errors #34

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merged 3 commits into from
Dec 17, 2024
Merged

Change plot_biomass and spawning_biomass plots to work through errors #34

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a92e893
fix(b and sb plots): reformat plots so they still fxn even missing th…
Schiano-NOAA Dec 16, 2024
91a77c3
feature(plot_biomass): add annotation for reference line
Schiano-NOAA Dec 17, 2024
bf38ef8
fix double + in plot_biomass plot
Schiano-NOAA Dec 17, 2024
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56 changes: 42 additions & 14 deletions R/plot_biomass.R
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,10 @@
#' lower-case letters but you must use one of the options specified in the
#' default list to ensure that the label on the figure looks correct
#' regardless of how it is specified in `dat`.
#' @param ref_point A known value of the reference point along with the label
#' for the reference point as specified in the output file. Please use this
#' option if the ref_line cannot find your desired point. Indicate the
#' reference point in the form c("label" = value).
#' @return Plot total biomass from a stock assessment model as found in a NOAA
#' stock assessment report. Units of total biomass can either be manually added
#' or will be extracted from the provided file if possible. In later releases, model will not
Expand All @@ -18,14 +22,17 @@ plot_biomass <- function(
unit_label = "metric tons",
scale_amount = 1,
ref_line = c("target", "MSY", "msy", "unfished"),
ref_point = NULL,
end_year = NULL,
relative = FALSE,
make_rda = FALSE,
rda_dir = getwd()
){

if(length(ref_line)>1){
ref_line = "target"
if (!is.null(ref_point)) {
ref_line <- names(ref_point)
} else if(length(ref_line)>1){
ref_line <- "target"
} else {
ref_line <- match.arg(ref_line, several.ok = FALSE)
}
Expand All @@ -39,22 +46,45 @@ plot_biomass <- function(
# Select value for reference line and label
# update the target option later
# TODO: add option to indicate the reference pt
ref_line_val <- as.numeric(dat[
grep(
pattern = glue::glue("^biomass.*{tolower(ref_line)}$"),
x = dat[["label"]]
),
"estimate"
])
if (!is.null(ref_point)) {
ref_line_val <- as.numeric(ref_point)
} else {
if ( inherits( try( solve(as.numeric(dat[
grep(
pattern = glue::glue("^biomass.*{tolower(ref_line)}$"),
x = dat[["label"]]
),
"estimate"
])), silent = TRUE), "try-error")) {
ref_line_val <- NULL
} else {
ref_line_val <- as.numeric(dat[
grep(
pattern = glue::glue("^biomass.*{tolower(ref_line)}$"),
x = dat[["label"]]
),
"estimate"
])
}
# ref_line_val <- as.numeric(dat[
# grep(
# pattern = glue::glue("^biomass.*{tolower(ref_line)}$"),
# x = dat[["label"]]
# ),
# "estimate"
# ])
}

if (length(ref_line_val) == 0) {
stop(glue::glue(
warning(glue::glue(
"The resulting reference value of `biomass_{ref_line}` was
not found in `dat[[\"label\"]]`."
))
warning("Reference line will not be plotted on the figure.")
} else if (length(ref_line_val) > 1) {
warning(glue::glue(
"More than one of the resulting reference value of 'biomass_{ref_line}` was
not in `dat[[\"label\"]]`."
not in `dat[[\"label\"]]`. \n Both reference points will be plotted on the figure."
))
}

Expand Down Expand Up @@ -99,9 +129,7 @@ plot_biomass <- function(
ymax = estimate_upper),
colour = "grey",
alpha = 0.3) +
ggplot2::geom_hline(
yintercept = ref_line_val / ifelse(relative, ref_line_val, scale_amount),
linetype = 2) +
{if(!is.null(ref_line_val)) ggplot2::geom_hline(yintercept = ref_line_val / ifelse(relative, ref_line_val, scale_amount),linetype = 2)} +
ggplot2::labs(
x = "Year",
y = biomass_label) +
Expand Down
62 changes: 46 additions & 16 deletions R/plot_spawning_biomass.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,10 @@
#' lower-case letters but you must use one of the options specified in the
#' default list to ensure that the label on the figure looks correct
#' regardless of how it is specified in `dat`.
#' @param ref_point A known value of the reference point along with the label
#' for the reference point as specified in the output file. Please use this
#' option if the ref_line cannot find your desired point. Indicate the
#' reference point in the form c("label" = value).
#' @return
#' Plot spawning biomass from the results of an assessment model translated to
#' the standard output. The {ggplot2} object is returned for further
Expand All @@ -22,13 +26,20 @@ plot_spawning_biomass <- function(
unit_label = "metric ton",
scale_amount = 1,
ref_line = c("target", "unfished", "msy"),
ref_point = NULL,
end_year = NULL,
relative = FALSE,
n_projected_years = 10,
make_rda = FALSE,
rda_dir = getwd()
) {
ref_line <- match.arg(ref_line)
if (!is.null(ref_point)) {
ref_line <- names(ref_point)
} else if(length(ref_line)>1){
ref_line <- "target"
} else {
ref_line <- match.arg(ref_line, several.ok = FALSE)
}
# TODO: Fix the unit label if scaling. Maybe this is up to the user to do if
# they want something scaled then they have to supply a better unit name
# or we create a helper function to do this.
Expand All @@ -49,22 +60,44 @@ plot_spawning_biomass <- function(
# Select value for reference line and label
# TODO: add case if ref_line not indicated or hard to find - find one of the
# options and set as ref_line
ref_line_val <- as.numeric(dat[
grep(
pattern = glue::glue("^spawning_biomass.*{tolower(ref_line)}"),
x = dat[["label"]]
),
"estimate"
])
if (!is.null(ref_point)) {
ref_line_val <- as.numeric(ref_point)
} else {
if ( inherits( try( solve(as.numeric(dat[
grep(
pattern = glue::glue("^spawning_biomass.*{tolower(ref_line)}$"),
x = dat[["label"]]
),
"estimate"
])), silent = TRUE), "try-error")) {
ref_line_val <- NULL
} else {
ref_line_val <- as.numeric(dat[
grep(
pattern = glue::glue("^spawning_biomass.*{tolower(ref_line)}$"),
x = dat[["label"]]
),
"estimate"
])
}
# ref_line_val <- as.numeric(dat[
# grep(
# pattern = glue::glue("^biomass.*{tolower(ref_line)}$"),
# x = dat[["label"]]
# ),
# "estimate"
# ])
}
if (length(ref_line_val) == 0) {
stop(glue::glue(
warning(glue::glue(
"The resulting reference value of `spawning_biomass_{ref_line}` was
not found in `dat[[\"label\"]]`."
))
} else if (length(ref_line_val > 1)) {
warning("Reference line will not be plotted on the figure.")
} else if (length(ref_line_val) > 1) {
warning(glue::glue(
"More than one of the resulting reference value of `spawning_biomass_{ref_line}` was
not in `dat[[\"label\"]]`."
"More than one of the resulting reference value of 'spawing_biomass_{ref_line}` was
not in `dat[[\"label\"]]`. \n Both reference points will be plotted on the figure."
))
}
sb <- dat |>
Expand Down Expand Up @@ -99,10 +132,7 @@ plot_spawning_biomass <- function(
),
linewidth = 1
) +
ggplot2::geom_hline(
yintercept = ref_line_val / ifelse(relative, ref_line_val, scale_amount),
linetype = 2
) +
{if(!is.null(ref_line_val)) ggplot2::geom_hline(yintercept = ref_line_val / ifelse(relative, ref_line_val, scale_amount),linetype = 2)} +
# Only add confidence intervals for the non NA estimates
# which allows for no warnings if uncertainty = NA
ggplot2::geom_ribbon(
Expand Down
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