Rmacdiv:

#'
#' Create summaries of the proportion of species uniquely found
#' on each Island, Plot, Habitat. The function does not have any arguments
#' yet. I may change this at a later stage.
#'
#'

specprop<-function(.){

dat %>%
    dplyr::select(Species,Coloniz,IND.NON.IND,Island) %>%
    unique() %>%
    rename(species=Species) ->statusinfo

#------ Island scale: all species

pardat %>%
    gather(species,abundance,-c(Archip,Island,habitat,MACDIVCode,sampleno)) %>%
    group_by(Archip,Island,species) %>%
    summarise(ab=sum(abundance)) %>%
    mutate(ab=ifelse(ab > 0,1,ab)) %>%
    group_by(Archip,Island,species) %>%
    summarise(abflag=sum(ab)) %>%
    filter(abflag > 0)  %>%
    dplyr::select(Archip,Island,species) %>%
    ungroup() -> tmp1
tmp1 %>%
    mutate(counter=1) %>%
    group_by(Archip,species) %>%
    summarise(tot=sum(counter)) %>%
    filter(tot==1)  %>%
    left_join(unique(tmp1))  %>%
    group_by(Archip,Island) %>%
    summarise(nsp=n_distinct(species)) %>%
    ungroup() ->tmp2
pardat %>%
    gather(species,abundance,-c(Archip,Island,habitat,MACDIVCode,sampleno))  %>%
    filter(abundance > 0) %>%
    group_by(Archip) %>%
    summarise(tot=n_distinct(species)) %>%
    ungroup() %>%
    left_join(tmp2) %>%
    mutate(prop=nsp/tot) %>%
    dplyr::select(Island,tot,nsp,prop) %>%
    mutate(group="All species") ->prop.allsp

#------ Island scale: other groups

# get data in the right format
pardat %>%
    gather(species,abundance,-c(Archip,Island,habitat,MACDIVCode,sampleno)) %>%
    group_by(Archip,Island,species) %>%
    summarise(ab=sum(abundance)) %>%
    mutate(ab=ifelse(ab > 0,1,ab)) %>%
    group_by(Archip,Island,species) %>%
    summarise(abflag=sum(ab)) %>%
    filter(abflag > 0) %>%
    inner_join(statusinfo) %>%
    dplyr::select(species,Coloniz,IND.NON.IND,Island,Archip) %>%
    ungroup() %>%
    gather(origin1,origin,-c(species,Island,Archip)) %>%
    filter(origin!="NON-IND" & origin!="IND?" & origin!="??") %>%
    dplyr::select(-c(origin1)) -> tmp1
# unique species per Island
tmp1 %>%
    mutate(counter=1) %>%
    group_by(Archip,species,origin) %>%
    summarise(tot=sum(counter)) %>%
    filter(tot==1) %>%
    left_join(unique(tmp1))  %>%
    group_by(Archip,Island,origin) %>%
    summarise(nsp=n_distinct(species)) %>%
    ungroup() ->tmp2
# division with totals by Island
tmp1 %>%
    group_by(Archip,origin) %>%
    summarise(tot=n_distinct(species))  %>%
    ungroup() %>%
    left_join(tmp2) %>%
    mutate(prop=nsp/tot)  %>%
    dplyr::select(Island,tot,nsp,prop,origin) %>%
    rename(group=origin) %>%
    bind_rows(prop.allsp) ->prop.allsp1


writeWorksheetToFile(data=prop.allsp1,file="/mnt/data1tb/Dropbox/macdiv/betaprops/betatprops.xlsx",
sheet = "summary", header = TRUE,startCol=1,startRow=1,styleAction =XLC$"STYLE_ACTION.NONE")



#------ Plot scale: all species

pardat %>%
    gather(species,abundance,-c(Archip,Island,habitat,MACDIVCode,sampleno))  %>%
    group_by(Archip,Island,species,MACDIVCode) %>%
    summarise(ab=sum(abundance)) %>%
    mutate(ab=ifelse(ab > 0,1,ab))  %>%
    group_by(Archip,Island,species,MACDIVCode) %>%
    summarise(abflag=sum(ab))  %>%
    filter(abflag > 0)  %>%
    dplyr::select(Archip,Island,species,MACDIVCode) %>%
    ungroup() -> tmp1
tmp1 %>%
    mutate(counter=1)  %>%
    group_by(Island,species) %>%
    summarise(tot=sum(counter))  %>%
    filter(tot==1)  %>%
    left_join(unique(tmp1))  %>%
    group_by(Archip,Island,MACDIVCode) %>%
    summarise(nsp=n_distinct(species)) %>%
    ungroup() ->tmp2
pardat %>%
    gather(species,abundance,-c(Archip,Island,habitat,MACDIVCode,sampleno))  %>%
    filter(abundance > 0) %>%
    group_by(Archip,Island) %>%
    summarise(tot=n_distinct(species)) %>%
    ungroup() %>%
    left_join(tmp2) %>%
    mutate(prop=nsp/tot) %>%
    dplyr::select(Island,tot,nsp,prop,MACDIVCode) %>%
    mutate(group="All species") ->prop.allsp.plots

#------ Plot scale: other groups

pardat %>%
    gather(species,abundance,-c(Archip,Island,habitat,MACDIVCode,sampleno)) %>%
    group_by(Archip,Island,species,MACDIVCode) %>%
    summarise(ab=sum(abundance)) %>%
    mutate(ab=ifelse(ab > 0,1,ab)) %>%
    group_by(Archip,Island,species,MACDIVCode) %>%
    summarise(abflag=sum(ab)) %>%
    filter(abflag > 0) %>%
    inner_join(statusinfo) %>%
    dplyr::select(species,Coloniz,IND.NON.IND,Island,Archip,MACDIVCode) %>%
    ungroup() %>%
    gather(origin1,origin,-c(species,Island,Archip,MACDIVCode)) %>%
    filter(origin!="NON-IND" & origin!="IND?" & origin!="??") %>%
    dplyr::select(-c(origin1)) -> tmp1
# unique species per plot
tmp1 %>%
    mutate(counter=1) %>%
    group_by(Island,species,origin) %>%
    summarise(tot=sum(counter)) %>%
    filter(tot==1)  %>%
    left_join(unique(tmp1))  %>%
    group_by(Archip,Island,origin,MACDIVCode) %>%
    summarise(nsp=n_distinct(species)) %>%
    ungroup() ->tmp2
# division with totals by plot
tmp1 %>%
    group_by(Archip,Island,origin) %>%
    summarise(tot=n_distinct(species))  %>%
    ungroup() %>%
    left_join(tmp2) %>%
    mutate(prop=nsp/tot)  %>%
    dplyr::select(Island,tot,nsp,prop,MACDIVCode,origin)  %>%
    rename(group=origin) %>%
    bind_rows(prop.allsp.plots) ->prop.allsp.plots1


writeWorksheetToFile(data=prop.allsp.plots1,file="/mnt/data1tb/Dropbox/macdiv/betaprops/betatprops.xlsx",
sheet = "summary", header = TRUE,startCol=7,startRow=1,styleAction =XLC$"STYLE_ACTION.NONE")


#------ Habitat scale: all species
pardat %>%
    gather(species,abundance,-c(Archip,Island,habitat,MACDIVCode,sampleno))  %>%
    filter(habitat!="Herbaceous") %>%
    group_by(Archip,Island,species,MACDIVCode,habitat) %>%
    summarise(ab=sum(abundance)) %>%
    mutate(ab=ifelse(ab > 0,1,ab)) %>%
    group_by(Archip,Island,species,MACDIVCode,habitat) %>%
    summarise(abflag=sum(ab)) %>%
    filter(abflag > 0)  %>%
    dplyr::select(Archip,Island,species,MACDIVCode,habitat) %>%
    ungroup() -> tmp1
tmp1 %>%
    mutate(counter=1) %>%
    group_by(Island,species,MACDIVCode) %>%
    summarise(tot=sum(counter)) %>%
    filter(tot==1)  %>%
    left_join(unique(tmp1))  %>%
    group_by(Archip,Island,MACDIVCode,habitat) %>%
    summarise(nsp=n_distinct(species)) %>%
    ungroup() ->tmp2
pardat %>%
    gather(species,abundance,-c(Archip,Island,habitat,MACDIVCode,sampleno,habitat))  %>%
    filter(habitat!="Herbaceous") %>%
    filter(abundance > 0) %>%
    group_by(Archip,Island,MACDIVCode) %>%
    summarise(tot=n_distinct(species)) %>%
    ungroup() %>%
    left_join(tmp2) %>%
    mutate(prop=nsp/tot) %>%
    dplyr::select(Island,tot,nsp,prop,MACDIVCode,habitat) %>%
    mutate(group="All species") ->prop.allsp.plots.habitats

#------ Habitat scale: other groups


pardat %>%
    gather(species,abundance,-c(Archip,Island,habitat,MACDIVCode,sampleno)) %>%
    filter(habitat!="Herbaceous") %>%
    group_by(Archip,Island,species,MACDIVCode,habitat) %>%
    summarise(ab=sum(abundance)) %>%
    mutate(ab=ifelse(ab > 0,1,ab)) %>%
    group_by(Archip,Island,species,MACDIVCode,habitat) %>%
    summarise(abflag=sum(ab)) %>%
    filter(abflag > 0) %>%
    inner_join(statusinfo) %>%
    dplyr::select(species,Coloniz,IND.NON.IND,Island,Archip,MACDIVCode,habitat) %>%
    ungroup() %>%
    gather(origin1,origin,-c(species,Island,Archip,MACDIVCode,habitat)) %>%
    filter(origin!="NON-IND" & origin!="IND?" & origin!="??") %>%
    dplyr::select(-c(origin1)) -> tmp1
# unique species per plot
tmp1 %>%
    mutate(counter=1) %>%
    group_by(Island,species,MACDIVCode) %>%
    summarise(tot=sum(counter)) %>%
    filter(tot==1)  %>%
    left_join(unique(tmp1))  %>%
    group_by(Archip,Island,origin,MACDIVCode,habitat) %>%
    summarise(nsp=n_distinct(species)) %>%
    ungroup() ->tmp2
# division with totals by plot
tmp1 %>%
    group_by(Archip,Island,origin,MACDIVCode) %>%
    summarise(tot=n_distinct(species))  %>%
    ungroup() %>%
    left_join(tmp2) %>%
    mutate(prop=nsp/tot)  %>%
    dplyr::select(Island,tot,nsp,prop,MACDIVCode,habitat,origin)  %>%
    rename(group=origin)  %>%
    bind_rows(prop.allsp.plots.habitats) ->prop.allsp.plots.habitats1

writeWorksheetToFile(data=prop.allsp.plots.habitats1,file="/mnt/data1tb/Dropbox/macdiv/betaprops/betatprops.xlsx",
sheet = "summary", header = TRUE,startCol=14,startRow=1,styleAction =XLC$"STYLE_ACTION.NONE")

}