plot_growth: Plot age-length relationships and growth curves

Description

Plot age-length relationships and growth curves

Usage

plot_growth(
  dt,
  length = "length",
  age = "age",
  sex = "sex",
  female.sex = "F",
  male.sex = "M",
  length.unit = "cm",
  split.by.sex = FALSE,
  growth.model = 1,
  force.zero.group.length = NA,
  force.zero.group.strength = 10,
  force.zero.group.cv = 0,
  show.Linf = TRUE,
  boxplot = TRUE,
  base_size = 8,
  legend.position = "bottom"
)

Value

A list containing the plot, text for Rmarkdown and Shiny applications, and estimated parameters (params).

Arguments

dt: A data.frame, tibble or data.table
length: Character argument giving the name of the length column in dt
age: Character argument giving the name of the age column in dt
sex: Character argument giving the name of the sex column in dt. Ignored if split.by.sex == FALSE.
female.sex, male.sex: A character or integer denoting female and male sex in the sex column of dt, respectively.
length.unit: A character argument giving the unit of length. Will be used in the labels of the figure.
split.by.sex: Logical indicating whether the result should be split by sex.
growth.model: Integer defining the growth model. 1 = von Bertalanffy, 2 = Gompertz, 3 = Logistic.
force.zero.group.length: Numeric indicating the length to which 0-group should be forced. Use NA ignore the forcing.
force.zero.group.strength: Numeric indicating how many percent of total fish should be added to the specified force.zero.group.length.
force.zero.group.cv: Numeric indicating the coefficient of variation for the forced 0-group length. Resulting lengths will be randomly generated from a normal distribution.
show.Linf: Logical indicating whether Linf values should be shown as dashed vertical lines.
boxplot: Logical indicating whether boxplots (TRUE) should be used to show data over points (FALSE)
base_size: Base size parameter for ggplot. See ggtheme.
legend.position: Position of the ggplot legend as a character. See ggtheme.

Author

Mikko Vihtakari // Institute of Marine Research.

Details

Uses the fishmethods::growth function to calculate the growth curves. Zero group length can be forced to the growth functions using the force.zero.group.* parameters.

Examples

Run this code

# Simple plot. Note that a list is returned.
data(survey_ghl)
plot_growth(survey_ghl, length = "length", age = "age")
# \donttest{
# Split by sex
plot_growth(survey_ghl, split.by.sex = TRUE)$plot
# Data as points. Forcing zero group to 10 cm
plot_growth(survey_ghl, force.zero.group.length = 10, boxplot = FALSE)$plot
# }

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