estimateLake: Lake-Wide Fish Estimates from Acoustic and Midwater Trawl...

In dmwarn/EchoNet2FishTO: Estimate Fish Abundance from Acoustic Echoes and Net Catch

Description

Estimate lake-wide fish density and total number (in number per ha and millions) and biomass density and total biomass (in g per ha and t) from acoustic and midwater trawl data.

Usage

estimateLake(
  maindir,
  rdat = "ACMT",
  ageSp = NULL,
  region,
  regArea,
  TSrange = c(-60, -30),
  TSthresh = 1,
  psi = 0.01,
  chngBinCntToZero = FALSE,
  BinCntZeroParams = c(depth = 40, TS = -45),
  SpeciesFromDepthTS = FALSE,
  DepthTSParams = c(SpDepth = 40, SpTS = -45, SPECIES = 204),
  rmBycatch = FALSE,
  ByCatchParams = c(bcdepth = 40, bcSPECIES = c(106, 109)),
  soi = c(106, 109, 203, 204),
  spInfo,
  sliceDef,
  short = TRUE,
  IntMeansPlots = FALSE,
  descr = "ACMT Estimates"
)

Arguments

maindir	A character scalar giving the directory where rdat is located and where output will be placed. Use forward slashes, e.g., "C:/temp/".
rdat	A character scalar giving the name of the RData file in maindir with the acoustic and midwater trawl data, typically the output from readAll.
ageSp	A numeric vector giving the species codes for species for which age-length keys should be used, default NULL.
region	A character vector, names of regions used in laying out sampling design.
regArea	A numeric vector, corresponding areas (in ha) of region.
TSrange	A numeric vector of length 2, the target strength range of interest, minimum and maximum in dB, default c(-60, -30).
TSthresh	A numeric scalar, the minimum number of binned targets required to incorporate the TS information from a given (interval by layer) cell.
psi	A numeric scalar, the transducer-specific two-way equivalent beam angle in steradians, default 0.01.
chngBinCntToZero	Logical scalar, indicating if the user wishes to convert the number of targets in specific TS bins to zero so they don't influence sigma.
BinCntZeroParams	A numeric vector, depth and TS ranges below which the number of targets in the specified TS bins will be converted to zero
SpeciesFromDepthTS	Logical scalar indicating if the user wishes to use depth and TS to identify species.
DepthTSParams	A numeric vector of depth (meters) and TS (dB) as in (DepthTSParams = c(40, -45)). Currently this function can only be used to assign density in cells >= the values provided here. Future modifications may provide more flexibility.
rmBycatch	Logical scalar indicating whether or not the user wishes to remove particular species from midwater trawl data because they are believed to be bycatch. One common example of a need for this was reported by Warner et al. (2012), who found that catch observed over the course of three decades varied with fishing depth. At depths > 40 m below the surface, the vast majority (> 70 percent) of fish were bloater > 120 mm.
ByCatchParams	A vector with the first entry being depth, below which the user believes the species (the remaining portion of the vector) are bycatch and should be removed from the fishing data.
soi	A numeric vector, codes of fish species for which estimates will be generated, default c(106, 109, 203, 204).
spInfo	A data frame with five variables sp = numeric, species code, must include all codes listed in soi, may include codes not listed in soi spname = character, species name lcut = numeric, the length cut off (in mm) at which to divide the corresponding species data into two groups (those with fish lengths <= lcut and > lcut) for estimation, use 0 for species with no length cut offs lwa and lwb = numeric parameters of length-weight relations, Wg = lwa * Lmm ^ lwb, where Wg is the weight (in g) and Lmm is the total length (in mm)
sliceDef	A list of at least two named sub-lists defining the slices into which observations will be classified. Each sub-list contains one or more named numeric vectors of length two, identifying the parameter (the name of the vector) and the range of values (see Details) that contribute to the slice definition, with one exception. For slicing by regions, the named vector is character (not numeric), is of length one or more (not necessarily two), and specifies all of the regions that contribute to the slice definition. The name of each sub-list is the name of the slice to be assigned. See Examples.
short	Logical scalar, indicating aspect of map area. If TRUE, the default, the mapped area is assumed to be wider (longitudinally) than tall. Used to better arrange multiple maps on a single page.
descr	A character scalar to be incorporated in the name of the saved output files, default "ACMT Estimates".

Details

The sigma for each acoustic cell is estimated as the mean of the linearized target strength (TS) weighted by the number of targets in each dB bin using the TS frequency distribution.

The number of scatterers per unit volume, Nv, is estimated according to Sawada et al. (1993) (see estNv). So called "biased" sigmas where Nv > 0.1 are replaced with mean "unbiased" sigmas from cells in the same layer and (if possible) transect. Then, Nv is recalculated.

Value

A rich text file (rtf) with a *.doc file extension (so that it will be opened with Word by default) is saved to maindir.

Seven different data frames are saved as objects in an Rdata file and are written to csv files in maindir:

• Lakes = lake-wide totals (in millions and t) and means (in numbers and g per ha), with a row for each species group and estimate type and columns for estimates, standard errors, and relative standard errors.

• Regions = region means (in fish per ha and g per ha), with a row for each region, species group, and estimate type and columns for estimates and corresponding (surface) areas.

• intmeans_nph = interval means (in fish per ha), with a row for each region and interval, a column for each species group, and additional columns for region area, and the interval bottom depth, latitude and longitude.

• intmeans_gph = interval means (in g per ha), similar to intmeans_nph.

• intlaymeans_nph = interval and layer means (in fish per ha), with a row for each region, interval, and layer, a column for each species group, and many additional columns.

• intlaymeans_gph = interval and layer means (in g per ha), similar to intlaymeans_nph.

• svts5 = the result of merging the SV and TS data, with several changes made: subsetted to valid regions, original and modified sigma estimates of n1, nv, fish_ha, depth_botmid (bottom depth range), and identity of slice, nearmt (nearest midwater trawl), region, and region area.

The Rdata and csv files are named using the lake and the year.

dmwarn/EchoNet2FishTO documentation built on March 6, 2021, 12:25 a.m.