################################################################################ #Project: Hanna Basin Plant/insect ecological indicies #Purpose: PeerJ Manuscript #File: Paleobot_analysis_2018 #By: Lauren Azevedo Schmidt #Start date (02/20/19): #R Version: 3.4.3 ################################################################################ #Libraries---- #LOAD PACKAGES require(vegan) #Working directory---- ##Set wd setwd("/Users/Babycakes/Desktop/HB MS Project /HB 2017 Field Work/Hanna WD") getwd() #Read in data to calculate diversity and evenness #Stat level data data.pd<- read.table("PDX.Update.csv", header=T, sep=",", na.strings= "NA", dec=".", strip.white=TRUE) row.names(data.pd) <- data.pd$X data.pd$X <- NULL data.site<- read.table("PD.Site.Updated.csv", header=T, sep=",", na.strings= "NA", dec=".", strip.white=TRUE) row.names(data.site) <- data.site$X data.site$X <- NULL ############################################################################ #Analysis: Plant Diversity by strat level---- ## Species richness (S) and Pielou's evenness (J): STRAT level H.strat <- diversity(data.pd) #Shannon diversity index invsimp.strat <- diversity(data.pd, "inv") #inverse-Simp index S.strat <- specnumber(data.pd) ## rowSums(PDXT > 0) does the same... J.strat <- H.strat/log(S.strat) #evenness matric #Analysis: Plant Diversity by site level---- ## Species richness (S) and Pielou's evenness (J): STRAT level H.site <- diversity(data.site) #Shannon diversity index invsimp.site <- diversity(data.site, "inv") #inverse-Simp index S.site <- specnumber(data.site) ## rowSums(PDXT > 0) does the same... J.site <- H.site/log(S.site) #evenness matric