lfqCreate {TropFishR}

Create lfq data from length measurements

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))