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Style code and document #217

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37 changes: 20 additions & 17 deletions R/plot_abundance_at_age.R
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Original file line number Diff line number Diff line change
Expand Up @@ -97,7 +97,7 @@ plot_abundance_at_age <- function(
ggplot2::ggplot()
)
}

data <- data |>
dplyr::mutate(age = as.numeric(age))

Expand All @@ -114,31 +114,34 @@ plot_abundance_at_age <- function(
)
# export figure to rda if argument = T
if (make_rda == TRUE) {

# Obtain relevant key quantities for captions/alt text
pop.naa.start.year <- min(data$year)
pop.naa.end.year <- max(data$year)
pop.naa.age.min <- min(data$age)
pop.naa.age.max <- max(data$age)
pop.naa.fish.min <- min(data$estimate) |> round(digits = 3)
pop.naa.fish.max <- max(data$estimate) |> round(digits = 3)

# calculate & export key quantities
export_kqs(pop.naa.start.year,
pop.naa.end.year,
pop.naa.age.min,
pop.naa.age.max,
pop.naa.fish.min,
pop.naa.fish.max)

export_kqs(
pop.naa.start.year,
pop.naa.end.year,
pop.naa.age.min,
pop.naa.age.max,
pop.naa.fish.min,
pop.naa.fish.max
)

# Add key quantities to captions/alt text
insert_kqs(pop.naa.start.year,
pop.naa.end.year,
pop.naa.age.min,
pop.naa.age.max,
pop.naa.fish.min,
pop.naa.fish.max)

insert_kqs(
pop.naa.start.year,
pop.naa.end.year,
pop.naa.age.min,
pop.naa.age.max,
pop.naa.fish.min,
pop.naa.fish.max
)

create_rda(
object = plot,
# get name of function and remove "plot_" from it
Expand Down
38 changes: 20 additions & 18 deletions R/plot_biomass.R
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -148,8 +148,7 @@ plot_biomass <- function(

### Make RDA ----
if (make_rda) {

if (relative){
if (relative) {
# pulling out the 2nd df in 'data' works for several datasets
rel.B.min <- ggplot2::ggplot_build(final)@data[[2]] |>
as.data.frame() |>
Expand All @@ -159,36 +158,39 @@ plot_biomass <- function(
as.data.frame() |>
dplyr::pull(y) |>
max()

# calculate & export key quantities
export_kqs(rel.B.min, rel.B.max)

# Add key quantities to captions/alt text
insert_kqs(rel.B.min, rel.B.max)

} else {
B.min <- min(prepared_data$estimate)
B.max <- max(prepared_data$estimate)

export_kqs(B.min, B.max)
insert_kqs(B.min, B.max)
}

B.ref.pt <- as.character(ref_line)
B.units <- as.character(unit_label)
B.start.year <- min(prepared_data$year) |> round(digits = 3)
B.end.year <- max(prepared_data$year) |> round(digits = 3)

export_kqs(B.ref.pt,
B.units,
B.start.year,
B.end.year)

insert_kqs(B.ref.pt,
B.units,
B.start.year,
B.end.year)


export_kqs(
B.ref.pt,
B.units,
B.start.year,
B.end.year
)

insert_kqs(
B.ref.pt,
B.units,
B.start.year,
B.end.year
)

create_rda(
object = final,
topic_label = ifelse(relative, "relative_biomass", "biomass"),
Expand Down
37 changes: 20 additions & 17 deletions R/plot_biomass_at_age.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -84,7 +84,7 @@ plot_biomass_at_age <- function(

data <- data |>
dplyr::mutate(age = as.numeric(age))

# Plot data
plot <- plot_aa(
dat = data,
Expand All @@ -98,31 +98,34 @@ plot_biomass_at_age <- function(
)
# export figure to rda if argument = T
if (make_rda == TRUE) {

# Obtain relevant key quantities for captions/alt text
pop.baa.start.year <- min(data$year)
pop.baa.end.year <- max(data$year)
pop.baa.age.min <- min(data$age)
pop.baa.age.max <- max(data$age)
pop.baa.fish.min <- min(data$estimate) |> round(digits = 3)
pop.baa.fish.max <- max(data$estimate) |> round(digits = 3)

# calculate & export key quantities
export_kqs(pop.baa.start.year,
pop.baa.end.year,
pop.baa.age.min,
pop.baa.age.max,
pop.baa.fish.min,
pop.baa.fish.max)

export_kqs(
pop.baa.start.year,
pop.baa.end.year,
pop.baa.age.min,
pop.baa.age.max,
pop.baa.fish.min,
pop.baa.fish.max
)

# Add key quantities to captions/alt text
insert_kqs(pop.baa.start.year,
pop.baa.end.year,
pop.baa.age.min,
pop.baa.age.max,
pop.baa.fish.min,
pop.baa.fish.max)

insert_kqs(
pop.baa.start.year,
pop.baa.end.year,
pop.baa.age.min,
pop.baa.age.max,
pop.baa.fish.min,
pop.baa.fish.max
)

create_rda(
object = plot,
# get name of function and remove "plot_" from it
Expand Down
39 changes: 21 additions & 18 deletions R/plot_catch_comp.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -100,10 +100,10 @@ plot_catch_comp <- function(
group <- processed_data[[2]]
facet <- processed_data[[3]]
}

data <- data |>
dplyr::mutate(age = as.numeric(age))

# Plot data
plot <- plot_aa(
dat = data,
Expand All @@ -115,31 +115,34 @@ plot_catch_comp <- function(

# export figure to rda if argument = T
if (make_rda == TRUE) {

# Obtain relevant key quantities for captions/alt text
caa.start.year <- min(data$year)
caa.end.year <- max(data$year)
caa.age.min <- min(data$age)
caa.age.max <- max(data$age)
tot.catch.min <- min(data$estimate) |> round(digits = 3)
tot.catch.max <- max(data$estimate) |> round(digits = 3)

# calculate & export key quantities
export_kqs(caa.start.year,
caa.end.year,
caa.age.min,
caa.age.max,
tot.catch.min,
tot.catch.max)

export_kqs(
caa.start.year,
caa.end.year,
caa.age.min,
caa.age.max,
tot.catch.min,
tot.catch.max
)

# Add key quantities to captions/alt text
insert_kqs(caa.start.year,
caa.end.year,
caa.age.min,
caa.age.max,
tot.catch.min,
tot.catch.max)

insert_kqs(
caa.start.year,
caa.end.year,
caa.age.min,
caa.age.max,
tot.catch.min,
tot.catch.max
)

create_rda(
object = plot,
# get name of function and remove "plot_" from it
Expand Down
36 changes: 19 additions & 17 deletions R/plot_fishing_mortality.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -95,9 +95,8 @@ plot_fishing_mortality <- function(

### Make RDA ----
if (make_rda) {

if (relative){
# Obtain relevant key quantities for captions/alt text
if (relative) {
# Obtain relevant key quantities for captions/alt text
# pulling out the 2nd df in 'data' works for several datasets
rel.F.min <- ggplot2::ggplot_build(final)@data[[2]] |>
as.data.frame() |>
Expand All @@ -109,33 +108,36 @@ plot_fishing_mortality <- function(
dplyr::pull(y) |>
max() |>
round(digits = 2)

# calculate & export key quantities
export_kqs(rel.F.min, rel.F.max)

# Add key quantities to captions/alt text
insert_kqs(rel.F.min, rel.F.max)

} else {
F.min <- min(prepared_data$estimate) |> round(digits = 3)
F.max <- max(prepared_data$estimate) |> round(digits = 3)

export_kqs(F.min, F.max)
insert_kqs(F.min, F.max)
}

F.ref.pt <- as.character(ref_line)
F.start.year <- min(prepared_data$year)
F.end.year <- max(prepared_data$year)

export_kqs(F.ref.pt,
F.start.year,
F.end.year)

insert_kqs(F.ref.pt,
F.start.year,
F.end.year)


export_kqs(
F.ref.pt,
F.start.year,
F.end.year
)

insert_kqs(
F.ref.pt,
F.start.year,
F.end.year
)

create_rda(
object = final,
topic_label = ifelse(relative, "relative_fishing_mortality", "fishing_mortality"),
Expand Down
34 changes: 19 additions & 15 deletions R/plot_indices.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -114,30 +114,34 @@ plot_indices <- function(

### Make RDA ----
if (make_rda) {

# Obtain relevant key quantities for captions/alt text
cpue.start.year <- min(prepared_data$year)
cpue.end.year <- max(prepared_data$year)
cpue.min <- min(prepared_data$estimate) |> round(digits = 3)
cpue.max <- max(prepared_data$estimate) |> round(digits = 3)
cpue.units <- ifelse(unit_label == "",
"an estimated index ratio", # default if empty
unit_label)
"an estimated index ratio", # default if empty
unit_label
)

# calculate & export key quantities
export_kqs(cpue.start.year,
cpue.end.year,
cpue.min,
cpue.max,
cpue.units)

export_kqs(
cpue.start.year,
cpue.end.year,
cpue.min,
cpue.max,
cpue.units
)

# Add key quantities to captions/alt text
insert_kqs(cpue.start.year,
cpue.end.year,
cpue.min,
cpue.max,
cpue.units)

insert_kqs(
cpue.start.year,
cpue.end.year,
cpue.min,
cpue.max,
cpue.units
)

create_rda(
object = plt,
# get name of function and remove "plot_" from it
Expand Down
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