detectionMaps: Generate maps of observed species richness and species...

In camtrapR: Camera Trap Data Management and Preparation of Occupancy and Spatial Capture-Recapture Analyses

Generate maps of observed species richness and species presences by station

Description

Generates maps of observed species richness and species presence by species and station. Output can be R graphics, PNG graphics or a shapefile for use in GIS software.

Usage

detectionMaps(
  CTtable,
  recordTable,
  Xcol,
  Ycol,
  backgroundPolygon,
  stationCol = "Station",
  speciesCol = "Species",
  speciesToShow,
  richnessPlot = TRUE,
  speciesPlots = TRUE,
  addLegend = TRUE,
  printLabels = FALSE,
  smallPoints,
  plotR = TRUE,
  writePNG = FALSE,
  plotDirectory,
  createPlotDir = FALSE,
  pngMaxPix = 1000,
  writeShapefile = FALSE,
  shapefileName,
  shapefileDirectory,
  shapefileProjection
)

Arguments

CTtable	data.frame. contains station IDs and coordinates
recordTable	data.frame. the record table created by recordTable
Xcol	character. name of the column specifying x coordinates in CTtable
Ycol	character. name of the column specifying y coordinates in CTtable
backgroundPolygon	SpatialPolygons or SpatialPolygonsDataFrame. Polygon to be plotted in the background of the map (e.g. project area boundary)
stationCol	character. name of the column specifying station ID in CTtable and recordTable
speciesCol	character. name of the column specifying species in recordTable
speciesToShow	character. Species to include in the maps. If missing, all species in recordTable will be included.
richnessPlot	logical. Generate a species richness plot?
speciesPlots	logical. Generate plots of all species number of independent events?
addLegend	logical. Add legends to the plots?
printLabels	logical. Add station labels to the plots?
smallPoints	numeric. Number by which to decrease point sizes in plots (optional).
plotR	logical. Create plots in R graphics device?
writePNG	logical. Create PNGs of the plots?
plotDirectory	character. Directory in which to save the PNGs
createPlotDir	logical. Create plotDirectory?
pngMaxPix	integer. number of pixels in pngs on the longer side
writeShapefile	logical. Create a shapefile from the output?
shapefileName	character. Name of the shapefile to be saved. If empty, a name will be generated automatically.
shapefileDirectory	character. Directory in which to save the shapefile.
shapefileProjection	character. A character string of projection arguments to use in the shapefile.

Details

The column name stationCol must be identical in CTtable and recordTable and station IDs must match.

Shapefile creation depends on the packages sf. Argument shapefileProjection must be a valid argument of st_crs (one of (i) character: a string accepted by GDAL, (ii) integer, a valid EPSG value (numeric), or (iii) an object of class crs. If shapefileProjection is undefined, the resulting shapefile will lack a coordinate reference system.

Value

An invisible data.frame with station coordinates, numbers of events by species at each station and total species number by station. In addition and optionally, R graphics or png image files.

Author(s)

Juergen Niedballa

References

A great resource for coordinate system information is https://spatialreference.org/. Use the Proj4 string as shapefileProjection argument.

Examples

# load station information
data(camtraps)

# load record table
data(recordTableSample)


# create maps
Mapstest <- detectionMaps(CTtable           = camtraps,
                          recordTable       = recordTableSample,
                          Xcol              = "utm_x",
                          Ycol              = "utm_y",
                          stationCol        = "Station",
                          speciesCol        = "Species",
                          writePNG          = FALSE,
                          plotR             = TRUE,
                          printLabels       = TRUE,
                          richnessPlot      = TRUE,
                          addLegend         = TRUE
)



# with a polygon in the background, and for one species only

# make a dummy polygon for the background
library(sf)

Sr1 = st_polygon(list(cbind(c(521500,526500,527000, 521500, 521500),
                            c(607500, 608000, 603500, 603500, 607500))))
aoi <- data.frame(name = "My AOI")
st_geometry(aoi) <- st_geometry(Sr1)
st_crs(aoi) <- 32650  # assign CRS: UTM50N

Mapstest2 <- detectionMaps(CTtable           = camtraps,
                           recordTable       = recordTableSample,
                           Xcol              = "utm_x",
                           Ycol              = "utm_y",
                           backgroundPolygon = aoi,               # this was added
                           speciesToShow     = c("PBE", "VTA"),   # this was added
                           stationCol        = "Station",
                           speciesCol        = "Species",
                           writePNG          = FALSE,
                           plotR             = TRUE,
                           printLabels       = TRUE,
                           richnessPlot      = TRUE,
                           addLegend         = TRUE
)

camtrapR documentation built on May 29, 2024, 6:45 a.m.