View source: R/detectionMaps.R
detectionMaps | R Documentation |
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
)
CTtable |
data.frame. contains station IDs and coordinates |
Xcol |
character. name of the column specifying x coordinates in |
Ycol |
character. name of the column specifying y coordinates in |
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 |
recordTable |
data.frame. the record table created by |
speciesCol |
character. name of the column specifying species in |
speciesToShow |
character. Species to include in the maps. If missing, all species in |
writePNG |
logical. Create PNGs of the plots? |
plotR |
logical. Create plots in R graphics device? |
plotDirectory |
character. Directory in which to save the PNGs |
createPlotDir |
logical. Create |
richnessPlot |
logical. Generate a species richness plot? |
speciesPlots |
logical. Generate plots of all species number of independent events? |
printLabels |
logical. Add station labels to the plots? |
smallPoints |
numeric. Number by which to decrease point sizes in plots (optional). |
addLegend |
logical. Add legends to the plots? |
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. |
The column name stationCol
must be identical in CTtable
and recordTable
and station IDs must match.
Shapefile creation depends on the packages sp and rgdal. shapefileProjection
must be a valid argument of CRS
. If shapefileProjection
is undefined, the resulting shapefile will lack a coordinate reference system.
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.
Juergen Niedballa
A great resource for CRS
arguments is http://spatialreference.org/. Use the Proj4 string as shapefileProjection
argument.
# 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
)
## Not run:
# with a polygon in the background
# make a dummy polygon for the background
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
stationCol = "Station",
speciesCol = "Species",
writePNG = FALSE,
plotR = TRUE,
printLabels = TRUE,
richnessPlot = TRUE,
addLegend = TRUE
)
## End(Not run)
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