###BQI sensitivity
suppressMessages(suppressWarnings(library(readxl)))
mtm <- read.csv('LumpedAggedInfPCMet2017-01-18.csv',na='empty')
suppressMessages(suppressWarnings(library(tidyverse)))
sp <- mtm %>% select(11:190)
sp <- ceiling(sp) #to round-up decimal point in abundance
f <- data.frame(taxa=colnames(sp),
freq=colSums(sp!=0),
row.names = 1:180)#get the number of cores were each taxon occur#
f1 <- f %>%
dplyr::filter(freq>20) ##list of taxa taxa that occur in >20 cores
suppressMessages(suppressWarnings(library(vegan)))#for rarefy function
sp1 <- sp %>%
dplyr::filter(rowSums(.)>10) %>% ##remove core with < 10 individuals
mutate(ES50 = rarefy(.,50)) %>% #get the ES50 rarefied richness based on Hurlbert's (1971) formulation.
select(match(f1$taxa,names(sp)),ES50) %>% ##select taxa that occur in >20 cores
gather(sp,abund,-ES50) ##convert into long format
## Warning in rarefy(., 50): Requested 'sample' was larger than smallest site
## maximum (11)
sensi <-
sp1 %>%
group_by(sp) %>%
dplyr::filter(abund>0) %>%
arrange(ES50) %>%
mutate(p=percent_rank(cumsum(abund))) %>%
slice(which.min(abs(p - .05))) %>%
data.frame(.) %>%
select(ES50,sp) %>%
rename(sensitivity = ES50) %>%
arrange(sensitivity) %>%
print()
## sensitivity sp
## 1 2.834466 insecta
## 2 3.000000 austrohelice.crassa
## 3 3.077834 acari
## 4 3.490246 halopyrgus.pupoides
## 5 3.529997 platyhelminthes
## 6 3.529997 scolecolepides
## 7 3.536116 potamopyrgus
## 8 3.946303 amphibola.crenata
## 9 4.000000 amphipoda
## 10 4.000000 nereididae
## 11 4.041686 oligochaeta
## 12 4.137612 arthritica.bifurca
## 13 4.205882 perrierina.turneri
## 14 4.289742 hemiplax.hirtipes
## 15 4.345280 cyclomactra.ovata
## 16 4.389320 isopoda
## 17 4.518259 cossura.consimilis
## 18 4.601518 paphies.australis
## 19 4.759824 austrovenus.stutchburyi
## 20 4.821661 hemigrapsus
## 21 4.854189 capitellidae
## 22 4.912292 austrominius.modestus
## 23 4.941088 halicarcinus
## 24 4.946660 mysida
## 25 5.000000 aonides
## 26 5.000000 copepoda
## 27 5.000000 crustacea
## 28 5.000000 edwardsia
## 29 5.000000 paraonidae
## 30 5.000000 polydora
## 31 5.000000 scolelepis
## 32 5.000000 sipuncula
## 33 5.000000 spionidae
## 34 5.193795 scoloplos.cylindrifer
## 35 5.254085 cominella.glandiformis
## 36 5.269761 arcuatula.senhousia
## 37 5.277008 neoguraleus
## 38 5.301273 heteromastus.filiformis
## 39 5.319901 nematoda
## 40 5.411891 tanaidacea
## 41 5.413415 bivalvia
## 42 5.447561 boccardia
## 43 5.461037 nephtyidae
## 44 5.501570 nemertea
## 45 5.514867 macomona.liliana
## 46 5.591030 theora.lubrica
## 47 5.592201 mytilidae
## 48 5.645542 glyceridae
## 49 5.649394 ostreidae
## 50 5.756257 acanthochitona.zelandica
## 51 5.793631 phyllochaetopterus.socialis
## 52 5.960030 notoacmea
## 53 6.000000 alpheidae
## 54 6.000000 chaetognatha
## 55 6.000000 diloma
## 56 6.000000 hesionidae
## 57 6.000000 ostracoda
## 58 6.000000 prionospio
## 59 6.051427 cumacea
## 60 6.116779 chiton
## 61 6.185118 syllidae
## 62 6.461486 actiniidae
## 63 6.524159 manayunkia
## 64 6.566734 micrelenchus
## 65 6.629825 gastropoda
## 66 6.640793 cirratulidae
## 67 6.653736 fellaster.zelandiae
## 68 6.666177 magelona
## 69 6.671291 pectinaria
## 70 6.748442 notomastus
## 71 6.748442 sphaerodoridae
## 72 6.808314 orbinia.papillosa
## 73 6.884615 cominella.adspersa
## 74 6.980392 goniadidae
## 75 7.000000 hiatula
## 76 7.000000 lumbrineridae
## 77 7.000000 maldanidae
## 78 7.000000 nuculidae
## 79 7.000000 phyllodocidae
## 80 7.000000 polychaeta
## 81 7.000000 sabellidae
## 82 7.000000 travisia
## 83 7.000000 zeacumantus
## 84 7.014095 pseudarcopagia
## 85 7.014095 xymene
## 86 7.026593 haminoea.zelandiae
## 87 7.050644 sigalionidae
## 88 7.063788 opisthobranchia
## 89 7.177206 cirripedia
## 90 7.378918 lasaea
## 91 7.546874 orbiniidae
## 92 7.803396 holothuroidea
## 93 7.834791 amalda
## 94 7.850135 polynoidae
## 95 8.000000 crangonidae
## 96 8.009559 armandia.maculata
## 97 8.009559 turbonilla
## 98 8.104911 stomatopoda
## 99 8.252611 venerida
## 100 8.362918 dorvilleidae
## 101 8.600554 owenia
## 102 8.751210 mysella
## 103 8.800419 phoronida
## 104 8.855065 diplodonta
## 105 8.988635 euterebra.tristis
## 106 9.141197 nassarius.burchardi
## 107 9.449098 anthozoa
## 108 9.606022 scalibregmatidae
## 109 9.606022 terebellidae
## 110 9.629968 nebaliacea