Created
January 1, 2012 16:55
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Plotting mammal dataset
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## Response to | |
## http://r-ecology.blogspot.com/2011/12/weecology-can-has-new-mammal-dataset.html | |
## Code from R-ecology | |
# URLs for datasets | |
comm <- "http://esapubs.org/archive/ecol/E092/201/data/MCDB_communities.csv" | |
refs <- "http://esapubs.org/archive/ecol/E092/201/data/MCDB_references.csv" | |
sites <- "http://esapubs.org/archive/ecol/E092/201/data/MCDB_sites.csv" | |
spp <- "http://esapubs.org/archive/ecol/E092/201/data/MCDB_species.csv" | |
trap <- "http://esapubs.org/archive/ecol/E092/201/data/MCDB_trapping.csv" | |
# read them | |
require(plyr) | |
datasets <- llply(list(comm, refs, sites, spp, trap), read.csv, .progress='text') | |
str(datasets[[1]]); head(datasets[[1]]) # cool, worked | |
llply(datasets, head) # see head of all data.frame's | |
# Map the communities | |
require(ggplot2) | |
require(maps) | |
sitesdata <- datasets[[3]] | |
sitesdata <- sitesdata[!sitesdata$Latitude == 'NULL',] | |
sitesdata$Latitude <- as.numeric(as.character(sitesdata$Latitude)) | |
sitesdata$Longitude <- as.numeric(as.character(sitesdata$Longitude)) | |
sitesdata$Elevation_high <- as.numeric(as.character(sitesdata$Elevation_high)) | |
sitesdata <- sitesdata[sitesdata$Longitude > -140,] | |
## Alternative plot with Google Vis. API | |
## Add a new column with lat-long coordinates merged | |
sitesdata$LatLong <- with(sitesdata, paste(Latitude, Longitude, sep=":")) | |
require(googleVis) | |
## display the data with interactive geo charts | |
world <- gvisGeoChart(sitesdata, "LatLong", colorvar="Elevation_high", sizevar="Elevation_low", | |
options=list(displayMode="markers", sizeAxis="{minValue: 0, maxSize: 10}", | |
colorAxis="{minValue: 0, colors: ['#BDC9E1', '#045A8D']}", | |
width=700, height=500), chartid="World") | |
plot(world) | |
us <- gvisGeoChart(sitesdata, "LatLong", colorvar="Elevation_high", sizevar="Elevation_low", | |
options=list(region="US", | |
displayMode="markers", sizeAxis="{minValue: 0, maxSize: 10}", | |
colorAxis="{minValue: 0, colors: ['#BDC9E1', '#045A8D']}"), | |
chartid="US") | |
plot(us) | |
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