lfqCreate function

Create lfq data from length measurements

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

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)

Returns

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))