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.
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 )
data.frame. contains station IDs and coordinates
data.frame. the record table created by
character. name of the column specifying x coordinates in
character. name of the column specifying y coordinates in
SpatialPolygons or SpatialPolygonsDataFrame. Polygon to be plotted in the background of the map (e.g. project area boundary)
character. name of the column specifying station ID in
character. name of the column specifying species in
character. Species to include in the maps. If missing,
all species in
recordTable will be included.
logical. Generate a species richness plot?
logical. Generate plots of all species number of independent events?
logical. Add legends to the plots?
logical. Add station labels to the plots?
numeric. Number by which to decrease point sizes in plots (optional).
logical. Create plots in R graphics device?
logical. Create PNGs of the plots?
character. Directory in which to save the PNGs
integer. number of pixels in pngs on the longer side
logical. Create a shapefile from the output?
character. Name of the shapefile to be saved. If empty, a name will be generated automatically.
character. Directory in which to save the shapefile.
character. A character string of projection arguments to use in the shapefile.
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.
The column name
stationCol must be identical in
recordTable and station IDs must match.
Shapefile creation depends on the packages sf.
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.
shapefileProjection is undefined,
the resulting shapefile will lack a coordinate reference system.
A great resource for coordinate system information
is https://spatialreference.org/. Use the Proj4 string as
# 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(sp) poly1 <- Polygon(cbind(c(521500,526500,527000, 521500),c(607500, 608000, 603500, 603500))) poly2 <- Polygons(list(poly1), "s1") poly3 <- SpatialPolygons(list(poly2)) Mapstest2 <- detectionMaps(CTtable = camtraps, recordTable = recordTableSample, Xcol = "utm_x", Ycol = "utm_y", backgroundPolygon = poly3, # this was added speciesToShow = c("PBE", "VTA"), # this was added stationCol = "Station", speciesCol = "Species", writePNG = FALSE, plotR = TRUE, printLabels = TRUE, richnessPlot = TRUE, addLegend = TRUE )