Archive | February, 2017

Mapping Biodiversity data on smaller than one degree scale

23 Feb

Guest Post by Enjie (Jane) LI

I have been using bdvis package (version 0.2.9) to visualize the iNaturalist records of RAScals project (http://www.inaturalist.org/projects/rascals).

Initially, the mapgrid function in the bdvis version 0.2.9 was written to map the number of records, number of species and completeness in a 1-degree cell grid (~111km x 111km resolution).

I applied this function to the RASCals dataset, see the following code. However, the mapping results are not satisfying. The 1 degree cells are too big to reveal the details in the study areas. Also, the raster grid was on top the basemap, which makes it really hard to associate the mapping results with physical locations.

library(rinat)
library(bdvis)

rascals=get_inat_obs_project("rascals")
conf <- list(Latitude="latitude",
             Longitude="longitude",
             Date_collected="Observed.on",
             Scientific_name="Scientific.name")
rascals <- format_bdvis(rascals, config=conf)
## Get rid of a record with weird location log
rascals <- rascals[!(rascals$Id== 4657868),]
rascals <- getcellid(rascals)
rascals <- gettaxo(rascals)
bdsummary(rascals)

a <- mapgrid(indf = rascals, ptype = "records",
             title = "distribution of RASCals records",
             bbox = NA, legscale = 0, collow = "blue",
             colhigh = "red", mapdatabase = "county",
             region = "CA", customize = NULL)

b <- mapgrid(indf = rascals, ptype = "species",
              title = "distribution of species richness of RASCals records",
              bbox = NA, legscale = 0, collow = "blue",
              colhigh = "red", mapdatabase = "county",
              region = "CA", customize = NULL)

rascals01

rascals02

I contacted developers of the package regarding these two issues. They have been very responsive to resolve them. They quickly added the gridscale argument in the mapgrid function. This new argument allows the users to choose scale (0.1 or 1). The default 1-degree cell grid for mapping.

Here are mapping results from using the gridscale argument. Make sure you have bdvis version 0.2.14 or later.

c <- mapgrid(indf = rascals, ptype = "records",
             title = "distribution of RASCals records",
             bbox = NA, legscale = 0, collow = "blue",
             colhigh = "red", mapdatabase = "county",
             region = "CA", customize = NULL,
             gridscale = 0.1)

d <- mapgrid(indf = rascals, ptype = "species",
             title = "distribution of species richness of RASCals records",
             bbox = NA, legscale = 0, collow = "blue",
             colhigh = "red", mapdatabase = "county",
             region = "CA", customize = NULL,
             gridscale = 0.1)

rascals03

rascals04

We can see that the new map with a finer resolution definitely revealed more information within the range of our study area. One more thing to note is that in this version developers have adjusted the basemap to be on top of the raster layer. This has definitely made the map easier to read and reference back to the physical space.

Good job team! Thanks for developing and perfecting the bdvis package.

References