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Rinsp_specialisation.R
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##########
#Library
##########
library(RInSp)
library(vegan)
library(dplyr)
###########
#Chichocs
###########
setwd("C:/Users/lstrople/OneDrive - Norwegian University of Life Sciences/Winter_paper/KML files")
safo.df <- read.csv("C:/Users/lstrople/OneDrive - Norwegian University of Life Sciences/Mathias & Leah/Excel files/safo.csv")
winter <- subset(safo.df, Season=="Winter")
summer <- subset(safo.df, Season=="Summer")
########
#winter
########
#Paul
safopauRISWi = import.RInSp(winter, col.header=TRUE, row.names=1, info.cols=c(1:6), data.type = "integer", subset.rows = c("Lake", "Paul"))
resultsPauWi <- WTcMC(safopauRISWi, replicates = 999)
resultsPauWWi= WTcMC(safopauRISWi, weight="N_items", replicates=999)
TroutEPauWi = Eindex(safopauRISWi, index = "saramaki", jackknife = TRUE)
sumMC.RInSp(resultsPauWi)
#Shoener index
PSiPauWi <- PSicalc(safopauRISWi, exclude = FALSE, replicates = 999)
#Cascapedia
safocascRISWi = import.RInSp(winter, col.header=TRUE, row.names=1, info.cols=c(1:6), data.type = "integer", subset.rows = c("Lake", "Cascapedia"))
resultsCascWi <- WTcMC(safocascRISWi, replicates = 999)
resultsCascWWi= WTcMC(safocascRISWi, weight="N_items", replicates=999)
TroutECascWi = Eindex(safocascRISWi, index = "saramaki", jackknife = TRUE)
sumMC.RInSp(resultsCascWWi)
PSiCascWi <- PSicalc(safocascRISWi, exclude = FALSE, replicates = 999)
#Thibault
safothibRISWi = import.RInSp(winter, col.header=TRUE, row.names=1, info.cols=c(1:6), data.type = "integer", subset.rows = c("Lake", "Thibault"))
resultsThibWi <- WTcMC(safothibRISWi, replicates = 999)
resultsThibWWi = WTcMC(safothibRISWi, weight="N_items", replicates=999)
TroutEWi = Eindex(safothibRISWi, index = "saramaki", jackknife = TRUE)
sumMC.RInSp(resultsThibWWi)
PSiThibWi <- PSicalc(safothibRISWi, exclude = FALSE, replicates = 999)
########
#summer
########
#Paul
safopauRISSu = import.RInSp(summer, col.header=TRUE, row.names=1, info.cols=c(1:6), data.type = "integer", subset.rows = c("Lake", "Paul"))
resultsPauSu <- WTcMC(safopauRISSu, replicates = 999)
resultsPauWSu= WTcMC(safopauRISSu, weight="N_items", replicates=999)
TroutEPauSu = Eindex(safopauRISSu, index = "saramaki", jackknife = TRUE)
sumMC.RInSp(resultsPauSu)
PSicascSu <- PSicalc(safocascRISSu, exclude = FALSE, replicates = 999)
#Cascapedia
safocascRISSu = import.RInSp(summer, col.header=TRUE, row.names=1, info.cols=c(1:6), data.type = "integer", subset.rows = c("Lake", "Cascapedia"))
resultsCascSu <- WTcMC(safocascRISSu, replicates = 999)
resultsCascWSu= WTcMC(safocascRISSu, weight="N_items", replicates=999)
TroutECascSu = Eindex(safocascRISSu, index = "saramaki", jackknife = TRUE)
sumMC.RInSp(resultsCascWSu)
PSicascSu <- PSicalc(safocascRISSu, exclude = FALSE, replicates = 999)
#Thibault
safothibRISSu = import.RInSp(summer, col.header=TRUE, row.names=1, info.cols=c(1:6), data.type = "integer", subset.rows = c("Lake", "Thibault"))
resultsThibWi <- WTcMC(safothibRISSu, replicates = 999)
resultsThibWSu = WTcMC(safothibRISSu, weight="N_items", replicates=999)
TroutESu = Eindex(safothibRISSu, index = "saramaki", jackknife = TRUE)
sumMC.RInSp(resultsThibWSu)
PSiThibSu <- PSicalc(safothibRISSu, exclude = FALSE, replicates = 999)
#Haymard
safoHayRISSu = import.RInSp(summer, col.header=TRUE, row.names=1, info.cols=c(1:6), data.type = "integer", subset.rows = c("Lake", "Haymard"))
resultsHay <- WTcMC(safoHayRISSu, replicates = 999)
resultsHayWSu= WTcMC(safoHayRISSu, weight="N_items", replicates=999)
safohayESu = Eindex(safoHayRISSu, index = "saramaki", jackknife = TRUE)
sumMC.RInSp(resultsHayWSu)
PSiHaySu <- PSicalc(safoHayRISSu, exclude = FALSE, replicates = 999)
###########
#Simpson
###########
#0 represents no diversity (only one species present) and 1 represents infinite diversity
summerHay <- subset(summer, Lake=="Haymard")
summerSimpHay <- summerHay %>% select(c(-Date,-Date_Processed,-Season,-Lake, -Specie))
simpsonHaySum <- (mean(diversity(summerSimpHay, index = "simpson")))
summerHay <- subset(summer, Lake=="Haymard")
summerSimpHay <- summerHay %>% select(c(-Date,-Date_Processed,-Season,-Lake, -Specie))
simpsonHaySum <- (mean(diversity(summerSimpHay, index = "simpson")))