Looking at the Weecology mammal dataset

mammaldataset.R

# setwd("/Mac/R_stuff/Blog_etc/Mammal_Dataset")

# 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,]
world_map <- map_data("world")
us <- world_map[world_map$region=='USA',]

  # World map
ggplot(world_map, aes(long, lat)) +
  theme_bw(base_size=16) +
  geom_polygon(aes(group = group), colour="grey60", fill = 'white', size = .3) +
  ylim(-55, 85) +
  geom_jitter(data = sitesdata, aes(Longitude, Latitude, size=Elevation_high), alpha=0.3)
ggsave("worldmap.png")

  # US only
ggplot(us, aes(long, lat)) +
  theme_bw(base_size=16) +
  geom_polygon(aes(group = group), colour="grey60", fill = 'white', size = .3) +
  ylim(25, 50) +
  xlim(-130, -60) +
  geom_jitter(data = sitesdata, aes(Longitude, Latitude, size=Elevation_high), alpha=0.3)
ggsave("usmap.png")

# What phylogenies can we get for these species?
install.packages("treebase")
require(treebase); require(RCurl)
datasets[[4]]$gensp <- as.factor(paste(datasets[[4]]$Genus, datasets[[4]]$Species))

trees <- llply(datasets[[4]]$gensp, function(x) search_treebase(paste("\"", x, '\"', sep=''), 
          by="taxon", max_trees=1, exact_match=TRUE, curl=getCurlHandle()))
spwithtrees <- data.frame(datasets[[4]]$gensp, 
           laply(trees, function(x) if(length(unlist(x)) > 0){1} else{0}))
names(spwithtrees) <- c('species', 'trees')
length(spwithtrees[spwithtrees$trees == 1, 2])