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.

Value

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

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.

Author

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")
#> $plot

#> 
#> $text
#> [1] "von Bertalanffy growth function coefficients:  \n Linf (asymptotic average length) = 91.2 cm +/- 88.3 - 94.6 (95% CIs)  \n K (growth rate coefficient) = 0.0633 +/- 0.059 - 0.068 (95% CIs)  \n t0 (age at length 0) = -3.04 (years) +/- -3.337 - -2.769 (95% CIs)  \n tmax (life span; t0 + 3/K) = 44.4 years  \n Number of included specimens = 10401  \n Total number of measured = 618779  \n Excluded (length or age missing):  \n Length = 0; age = 608378"
#> 
#> $params
#> # A tibble: 3 × 7
#>   term  estimate std.error statistic   p.value conf.low conf.high
#>   <chr>    <dbl>     <dbl>     <dbl>     <dbl>    <dbl>     <dbl>
#> 1 Sinf   91.2      1.51         60.3 0          88.3      94.6   
#> 2 K       0.0633   0.00231      27.4 4.90e-160   0.0586    0.0680
#> 3 t0     -3.04     0.139       -21.8 1.71e-103  -3.34     -2.77  
#> 
# \donttest{
# Split by sex
plot_growth(survey_ghl, split.by.sex = TRUE)$plot

# Data as points. Forcing zero group to 10 cm
plot_growth(survey_ghl, force.zero.group.length = 10, boxplot = FALSE)$plot

# }