LongevityTables_Test.R

# code from Demo Derby.R
# testing if it works with the ELC API instead of the pbdb packagelibrary(RColorBrewer) #to make pretty colors
library(ggplot2) #for plottinglibrary(RColorBrewer) #to make pretty colors
library(dplyr) #for plotting

# decide what genus/family to get info about
input<-"felidae"

# download the data using the ELC API
occurrences<-read.csv(paste("http://earthlifeconsortium.org/api_v1/occ?taxon=",input,"&ageunits=Ka&output=csv",sep=""))

# not necessary when we have only one taxa that we're showing
x <- list(occurrences) # each taxonomic group into a list

####  function to GENERATE LONGEVITY TABLES ####
GenerateLongevities <- function(x){ #where x is a matrix of pbdb occurrence data fetched via pbdb_occurrences
  
      x <- as.data.frame(x)  # turn x into a data frame (holdover from version where multiple families are included)
      x<-x[!is.na(x$min_age),] # remove rows that have a NA for either min age or max age
      x<-x[!is.na(x$max_age),] # remove rows that have a NA for either min age or max age
      
      taxon_split<-strsplit(as.character(x$taxon)," ")  # split the taxon name on spaces
      genera<-NA 
      
      for(row in 1:length(taxon_split)) {
          genera[row]<-taxon_split[[row]][1]
      }
      
      x$genera<-genera  # add the genus column to the data frame
      
      genus.names<-unique(genera) #What are the unique genus names?
      num.genera<-length(genus.names) #How many genera are there? (will be number of rows in the results matrix)
      
      outTable<-data.frame(matrix(NA,nrow=num.genera,ncol=4))  
      colnames(outTable)<-c("Taxa","FAD","LAD","Duration")
      outTable$Taxa<-genus.names
      
      for(species in 1:nrow(outTable)){
          this.taxon <- outTable[species,1] #Define the taxa
          all.occ.this.taxon <- dplyr::filter(x, x$genera == this.taxon) #Select all rows of that taxon
          FAD <- max(all.occ.this.taxon$max_age, na.rm = T) #Find the max value (FAD) of that taxon...
          outTable[species,2] <- FAD #...and insert it into column 2 (FAD)
          LAD <- min(all.occ.this.taxon$min_age, na.rm = T) #Find the min value (LAD) of that taxon...
          outTable[species,3] <- LAD #...and insert it into column 3
          longevity <- FAD - LAD #Calulate the species longevity...
          outTable[species,4] <- longevity #...and insert it into column 4
          outTable<-outTable
          }

df <- as.data.frame(outTable) #Save Result to list

# Plot the longevities
g <- ggplot(df, aes(x = Longevity, y = Taxa)) +
  geom_segment(aes(x = as.numeric(as.character(LAD)), y = Taxa, xend = as.numeric(as.character(FAD)), yend = Taxa)) +
  geom_text(aes(x = as.numeric(as.character(FAD)), y = Taxa, label = Taxa), nudge_x = 1, nudge_y = 1) +
  theme(axis.text.y=element_blank(),
        axis.ticks.y=element_blank()) +
  ggtitle("Longevities")
g

} #end function

Longevities <- lapply(x, GenerateLongevities)

Longevities