lfqModify {TropFishR}

Modify lfq data for further analysis

Description

Modify length-freqeuncy (LFQ) data. Allows to summarise catch matrix of LFQ data to one column per year. This is required for e.g. catchCurve. Allows to change bin size of LFQ data. Allows to ad plus group to catch matrix.

Usage

lfqModify(
  lfq,
  par = NULL,
  bin_size = NA,
  aggregate = NA,
  vectorise_catch = FALSE,
  plus_group = FALSE,
  minDate = NA,
  maxDate = NA,
  years = NA,
  Lmin = NA,
  Lmax = NA,
  lfq2 = NA
)

Arguments

lfq

lfq object with dates, midLengths, and catch

par

growth parameters as resulting from e.g. ELEFAN

bin_size

Bin size for length frequencies (in cm)

aggregate

Factor to aggregate catch per year ("year"), per quarter ("quarter"), or per month ("month"). By default data is not aggregated (NA).

vectorise_catch

logical; indicating if the catch matrix should be summarised to yearly vectors (default: FALSE).

plus_group

logical or numeric; 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 inserted, e.g. plus_group = 85.5.

minDate

minimum date to subset lfq data

maxDate

maximum date to subset lfq data

years

numeric with year(s) to subset lfq data

Lmin

minimum length to subset lfq data

Lmax

maximum length to subset lfq data

lfq2

optional second lfq object which will be merged with lfq. This might be interesting for fleet specific lfq objects. Default: NA. Be aware that catches are combined without weighting!

Value

lfq object with rearranged catch matrix (yearly sums) and growth parameters if provided.

Examples

data(synLFQ4)

## summarise catch matrix per year
lfq_sum <- lfqModify(synLFQ4, vectorise_catch = TRUE)

## change bin size
lfq_bin <- lfqModify(synLFQ4, bin_size = 4)

## add plus_group
lfq_plus <- lfqModify(synLFQ4, plus_group = 85.5)