das_intersects_strata {swfscDAS}

DAS strata - points

Description

Determine if swfscDAS outputs intersect with strata polygons

Usage

das_intersects_strata(x, ...)

## S3 method for class 'list'
das_intersects_strata(x, strata.files, ...)

## S3 method for class 'data.frame'
das_intersects_strata(
  x,
  strata.files,
  x.lon = "Lon",
  x.lat = "Lat",
  strata.which = FALSE,
  ...
)

Arguments

x

a data frame (such as an object of class das_df) or a list. If x is a list, then it must be the output of das_effort or das_effort_sight. If x is a data frame, the user must also specify the coordinate columns of x using x.lon and x.lat

...

ignored

strata.files

list of path(s) of the CSV file(s) with points defining each stratum. The CSV files must contain headers and be a closed polygon. The list may be named; see 'Value' section for how these names are used

x.lon

character; name of the longitude column of x. Ignored if x is a list; default is "Lon"

x.lat

character; name of the latitude column of x. Ignored if x is a list; default is "Lat"

strata.which

logical; indicates if the numeric column 'strata_which' should be included in the output data frame. Ignored if x is a list; default is FALSE. See 'Value' section for more details

Details

Assigns DAS event points or segment midpoints to strata polygons using st_intersects.

If x is a list, then 1) it must be the output of das_effort or das_effort_sight and 2) the segment midpoints (column names mlon and mlat, respectively) are the points checked if they intersect with each provided stratum. If x is a data frame, then the user must provide the columns that specify the point coordinates to check.

x should not be an object of class das_dfr, or an object of class das_df created with add.dtll.sight = FALSE, because the ? and numeric event codes will have NA latitude and longitude values.

Value

If x is a data frame, then logical columns are added to x indicating if each point intersected with the corresponding stratum polygon. The names of these columns are the names of strata.files; the element(s) of strata.files will have the name InPoly#, where '#' is the index of that stratum polygon in strata.files. If strata.which, then the column 'strata_which' is added to the end of the data frame. This column contains either a 0 if the point intersects with no strata or 2) a numeric indicating the index (in strata.files) of the (first) strata polygon that the point intersects with.

Otherwise, i.e. if x is a list and thus the output of one of the effort functions, then the stratum columns are added to both the segdata and sightinfo data frames. However, note that the columns added to the sightinfo data frame still indicate whether or not the segment midpoint was in the corresponding stratum, rather than the sighting point itself.

Examples

y <- system.file("das_sample.das", package = "swfscDAS")
y.proc <- das_process(y)
y.eff <- das_effort(y.proc, method = "section", num.cores = 1)

stratum.file <- system.file("das_sample_stratum.csv", package = "swfscDAS")
das_intersects_strata(y.eff, list(InPoly = stratum.file), x.lon = "Lon", x.lat = "Lat")

das_intersects_strata(y.proc, list(stratum.file))

# Visualize effort midpoints and stratum polygon
require(sf)
y.eff.strata <- das_intersects_strata(y.eff, list(InPoly = stratum.file))
segdata <- st_as_sf(y.eff.strata$segdata, coords = c("mlon", "mlat"), crs = 4326)

# Make stratum polygon
stratum.df <- read.csv(stratum.file)
stratum.sfc <- st_sfc(
  st_polygon(list(matrix(c(stratum.df$Lon, stratum.df$Lat), ncol = 2))),
  crs = 4326
)

plot(segdata["InPoly"], axes = TRUE, reset = FALSE,
     xlim = c(-137, -142.5), ylim = c(42, 47))
plot(stratum.sfc, add = TRUE)