swfscDAS (version 0.4.0)

das_effort_sight: Summarize DAS sightings by effort segment

Description

Summarize number of sightings and animals for selected species by segment

Usage

das_effort_sight(
  x.list,
  sp.codes,
  sp.events = c("S", "G", "K", "M", "t", "p"),
  gs.columns = c("GsSpBest", "GsSpLow", "GsSpHigh")
)

Arguments

x.list

output of das_effort; a list of three data frames named 'segdata', 'sightinfo', and 'randpicks', respectively

sp.codes

character; species code(s) to include in segdata output. These must exactly match the species codes in the data, such as including leading zeros

sp.events

character; event code(s) to include in the sightinfo output. This argument supersedes the 'included' value when determining whether a sighting is included in the segment summaries. Must be one or more of: "S", "K", "M", "G", "t", "p" (case-sensitive). The default is that all of these event codes are kept

gs.columns

character; the column(s) to use to get the group size values that will be summarized in the segdata output. Must be one or more of 'GsSpBest', 'GsSpLow', and 'GsSpBest' (case-sensitive). See Details section for more information

Value

A list, identical to x.list except for 1) the nSI and ANI columns added to x.list$segdata, one each for each element of sp.codes, and 2) the 'included' column of x.list$sightinfo, which has been set as FALSE for sightings of species not listed in sp.codes. Thus, the 'included' column in the output accurately reflects the sightings that were included in the effort segment summaries

Details

This function takes the output of das_effort and adds columns for the number of sightings (nSI) and number of animals (ANI) for selected species (selected via sp.codes) for each segment to the segdata element of x.list. However, only sightings with an included value of TRUE (included is a column in sightinfo) are included in the summaries. Having this step separate from das_effort allows users to personalize the included values as desired for their analysis.

The ANI columns are the sum of the 'GsSp...' column(s) from das_sight specified using gs.columns. If gs.columns specifies more than one column, then the secondary columns will only be used if the values for the previous columns are NA. For instance, if gs.columns = c('GsSpBest', 'GsSpLow'), then for each row in sightinfo, the value from GsSpLow will be used only if the value from GsSpBest is NA

Examples

# NOT RUN {
y <- system.file("das_sample.das", package = "swfscDAS")
y.proc <- das_process(y)
y.eff.cond <- das_effort(
  y.proc, method = "condition", conditions = "Bft", seg.min.km = 0.05,
  num.cores = 1
)

das_effort_sight(y.eff.cond, sp.codes = c("013", "076", "DC"), sp.events = c("S", "t"))

# }