plot_growth {ggFishPlots}

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"
)

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.

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.

Value

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

Author(s)

Mikko Vihtakari // Institute of Marine Research.

Examples

# Simple plot. Note that a list is returned.
data(survey_ghl)
plot_growth(survey_ghl, length = "length", age = "age")

# 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