lfqCreate: Create lfq data from length measurements

In TropFishR: Tropical Fisheries Analysis

Description

Convert raw length measurements to length frequency data (lfq class).

Usage

lfqCreate(
  data,
  Lname,
  Dname,
  Fname = NA,
  bin_size = 1,
  species = NA,
  stock = NA,
  comment = "",
  Lmin = 0,
  length_unit = "cm",
  plus_group = FALSE,
  aggregate_dates = FALSE,
  plot = FALSE
)

Arguments

data	data with at least two columns, one with the length measurements, one with the sampling date
Lname	name of the length column
Dname	name of the date column
Fname	optional; name of column with frequency, in case each length was measured more than one time
bin_size	size of the bins in cm (Default: 2)
species	character; to store species name in lfq list
stock	character; to store stock ID or name in lfq list
comment	optional character; to store comments conerning the lfq list
Lmin	minimum length for the midLengths vector (default: 0)
length_unit	unit of length measurements, either "cm" (default), "mm" or "m"
plus_group	logical; should a plus group be created? If yes you will be asked to insert the length for the plus group in the console (default: FALSE). Instead of inserting the length of the plus group via the console, the value can be incorporated in a vector, e.g. plus_group = c(TRUE, 30).
aggregate_dates	logical; indicating whether dates should be lumped in monthly sampling times (assuming sampling always aound the 15th of each month; default is FALSE). More exact lumping can only done manually and then sampling dates provided in data.
plot	logical; should a graph of lfq data be displayed? (Default: FALSE)

Value

A list of "lfq" class with

• dates dates of sampling times (class Date),

• midLengths midpoints of the length classes,

• catch matrix with catches/counts per length class (row) and sampling date (column).

Examples

# create random data
set.seed(1)
data <- data.frame(length.mm. = sample(c(rpois(300, lambda = 60),
           rpois(200, lambda = 100), rpois(100, lambda = 150)),
           size = 1000, replace = TRUE),
           dates = seq.Date(as.Date("2015-10-02"),as.Date("2016-08-28"),
           length.out = 1000))
# create lfq data
lfq_dat <- lfqCreate(data,Lname = "length.mm.", Dname = "dates", aggregate_dates = TRUE,
   length_unit = "mm", bin_size = 0.5, plot=TRUE, plus_group=c(TRUE,15.75))

TropFishR documentation built on Oct. 4, 2021, 9:06 a.m.