ggFishPlots (version 0.2.2)

plot_lw: Plot length-weight relationships

Description

Plot length-weight relationships

Usage

plot_lw(
  dt,
  length = "length",
  weight = "weight",
  sex = "sex",
  female.sex = "F",
  male.sex = "M",
  length.unit = "cm",
  weight.unit = "kg",
  split.by.sex = FALSE,
  xlab = "Total length",
  ylab = "Weight",
  use.nls = FALSE,
  init.a = NULL,
  init.b = NULL,
  log.axes = FALSE,
  base_size = 8,
  legend.position = "bottom",
  correct.units = FALSE,
  verbose = TRUE
)

Value

A ggplot together with the a and b parameters.

Arguments

dt

A data.frame, tibble or data.table

length

Character argument giving the name of the length column in dt

weight

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

A character denoting female sex in the sex column of dt

male.sex

A character denoting male sex in the sex column of dt

length.unit

Character argument giving the unit of length. Will be used in the labels of the figure and for conversion of the a parameter. Allowed values for the conversion: "mm" (millimmeters), "cm" (centimeters), and "m" (meters).

weight.unit

Character argument giving the unit of weight. Will be used in the labels of the figure and for conversion of the a parameter. Allowed values: "g" (grams), "kg" (kilograms), and "t" (metric tons).

split.by.sex

Logical indicating whether the result should be split by sex.

xlab

Character giving the x-axis label without unit

ylab

Character giving the x-axis label without unit.

use.nls

Logical indicating whether the parameters should be calculated using the nonlinear least squares (nls; TRUE) method over the log-log transformed linear model (lm; FALSE) method.

init.a, init.b

Numeric values giving the starting value for a and b parameters respecitively for non-linear least-squares estimation (i.e. when use.nls = TRUE). If NULL, default values are guessed.

log.axes

Logical indicating whether logarithmic axes should be used instead of cartesian ones.

base_size

Base size parameter for ggplot. See ggtheme.

legend.position

Position of the ggplot legend as a character. See ggtheme.

correct.units

Logical indicating whether a and b parameters should be converted for centimeters and grams as in FishBase.

verbose

Logical indicating whether to return warnings and messages.

Author

Mikko Vihtakari // Institute of Marine Research.

Details

It is crucial to get the units right when calculating length-weight relationships. In models, the length and weight units should often match those of the data going into the model, while in comparisons with FishBase, the units of length and weight should be centimetres and grams, respectively. If the units are wrong, the intercept, a, will be off the FishBase scale by orders of magnitude (see FishBase). If correct.units = TRUE, plot_lw() attempts to correct for the units to the FishBase standard (cm and g). The function also returns a warning when the returned parameters are not within expected bounds for cm and g estimation. You can ignore this warning if you want to estimate values. Comparing your a and b with those in FishBase for the species is a good idea. This function may contain bugs.

Examples

data(survey_ghl)

# Simple plot
plot_lw(survey_ghl, length = "length", weight = "weight")
# \donttest{
# Split by sex
plot_lw(survey_ghl, split.by.sex = TRUE)$plot
# }