Taxonomic Group Treemap

Taxonomic groups from gmbi package used in bbnj analysis

suppressPackageStartupMessages({
  library(dplyr)
  library(treemap)
  library(ggplot2)
  library(kableExtra)
})

## filter spp dataset by groups number
filter_group <- function (df, groupnumber) {
    df %>%
    filter(!is.na(UQ(sym(groupnumber))))
}

## summarise by taxonomic group name

summarise_group <- function(df, groupnumber) {
  groupnumber<- as.symbol(groupnumber)
  groupnumber<- enquo(groupnumber)
  df %>% 
  group_by((!!groupnumber)) %>%
  summarize(n = n())
}

# Read in spp_bbnj.csv with groupings:
  # groups00: All original AquaMaps species 
  # groups01: 1st taxonomic grouping [n = 23]
  # groups02: 1st grouping, species (prob≥ 0.5) in high seas
  # groups03: 1st grouping, species (prob ≥ 0.5) and 25% of its range in high seas
  # groups04: 2nd taxonomic grouping [n = 9]
  # groups05: 2nd grouping, species (prob≥ 0.5) in high seas
  # groups06: 2nd grouping, species (prob ≥ 0.5) and 25% of its range in high seas

spp <- readr::read_csv("extdata/spp_bbnj.csv")

groupnumber<-"groups01"

spp_grp<-filter_group(spp,groupnumber)
nspp_grp<-nrow(spp_grp)
taxa_grp <-summarise_group(spp_grp,groupnumber)
ngrp_grp <-nrow(taxa_grp)

Groups v01

All AquaMaps (no HS filter)
24 Taxonomic Groups
24904 Species

#Create treemap where size of rectangle corresponds to number of species in each group

taxa_treemap<- treemap(taxa_grp,
                       index=groupnumber,
                       vSize="n",
                       type="index",
                       force.print.labels = TRUE,
                       title="Number of species per group"
)

#Create table of nspp for each taxonomic group
knitr::kable(taxa_grp,
             col.names = c("Group",
                           "Number of Species")) %>% 
  kable_styling(bootstrap_options = "striped")

Group	Number of Species
Bivalves	1018
Bony fishes	11409
Cephalopods	295
Cetaceans	82
Chitons	81
Corals	918
Crustaceans	3058
Echinoderms	956
Euphausiids	43
Forams	16
Gastropods	2852
Hydrozoans	321
Jellyfish	19
Mangroves	1
Other	973
Pinnipeds	32
Reptiles	34
Sea spiders	332
Seagrasses	10
Sharks & rays	834
Sponges	440
Tunas & billfishes	63
Tunicates	666
Worms	451

groupnumber<-"groups02"

spp_grp<-filter_group(spp,groupnumber)
nspp_grp<-nrow(spp_grp)
taxa_grp <-summarise_group(spp_grp,groupnumber)
ngrp_grp <-nrow(taxa_grp)

Groups v02

AquaMaps species (prob≥ 0.5) in high seas
23 Taxonomic Groups
12013 Species

#Create treemap where size of rectangle corresponds to number of species in each group

taxa_treemap<- treemap(taxa_grp,
                       index=groupnumber,
                       vSize="n",
                       type="index",
                       force.print.labels = TRUE,
                       title="Number of species per group"
)

#Create table of nspp for each taxonomic group
knitr::kable(taxa_grp,
             col.names = c("Group",
                           "Number of Species")) %>% 
  kable_styling(bootstrap_options = "striped")

Group	Number of Species
Bivalves	469
Bony fishes	5101
Cephalopods	155
Cetaceans	69
Chitons	19
Corals	435
Crustaceans	1913
Echinoderms	440
Euphausiids	35
Forams	6
Gastropods	962
Hydrozoans	260
Jellyfish	13
Other	546
Pinnipeds	25
Reptiles	20
Sea spiders	229
Seagrasses	3
Sharks & rays	396
Sponges	135
Tunas & billfishes	39
Tunicates	446
Worms	297

groupnumber<-"groups03"

spp_grp<-filter_group(spp,groupnumber)
nspp_grp<-nrow(spp_grp)
taxa_grp <-summarise_group(spp_grp,groupnumber)
ngrp_grp <-nrow(taxa_grp)

Groups v03

AquaMaps species (prob≥ 0.5) in high seas and 25% of its range in high seas
22 Taxonomic Groups
2673 Species

#Create treemap where size of rectangle corresponds to number of species in each group

taxa_treemap<- treemap(taxa_grp,
                       index=groupnumber,
                       vSize="n",
                       type="index",
                       force.print.labels = TRUE,
                       title="Number of species per group"
)

#Create table of nspp for each taxonomic group
knitr::kable(taxa_grp,
             col.names = c("Group",
                           "Number of Species")) %>% 
  kable_styling(bootstrap_options = "striped")

Group	Number of Species
Bivalves	43
Bony fishes	1395
Cephalopods	42
Cetaceans	52
Chitons	2
Corals	12
Crustaceans	340
Echinoderms	61
Euphausiids	3
Forams	3
Gastropods	114
Hydrozoans	59
Jellyfish	3
Other	94
Pinnipeds	10
Reptiles	1
Sea spiders	128
Sharks & rays	52
Sponges	25
Tunas & billfishes	21
Tunicates	160
Worms	53

groupnumber<-"groups04"

spp_grp<-filter_group(spp,groupnumber)
nspp_grp<-nrow(spp_grp)
taxa_grp <-summarise_group(spp_grp,groupnumber)
ngrp_grp <-nrow(taxa_grp)

Groups v04

All AquaMaps (no HS filter)
9 Taxonomic Groups
24904 Species

#Create treemap where size of rectangle corresponds to number of species in each group

taxa_treemap<- treemap(taxa_grp,
                       index=groupnumber,
                       vSize="n",
                       type="index",
                       force.print.labels = TRUE,
                       title="Number of species per group"
)

#Create table of nspp for each taxonomic group
knitr::kable(taxa_grp,
             col.names = c("Group",
                           "Number of Species")) %>% 
  kable_styling(bootstrap_options = "striped")

Group	Number of Species
Bony fishes	11409
Cephalopods	295
Corals	918
Invertebrates	10550
Marine Mammals	119
Other	706
Seagrasses	10
Sharks & rays	834
Tunas & billfishes	63

groupnumber<-"groups05"

spp_grp<-filter_group(spp,groupnumber)
nspp_grp<-nrow(spp_grp)
taxa_grp <-summarise_group(spp_grp,groupnumber)
ngrp_grp <-nrow(taxa_grp)

Groups v05

AquaMaps species (prob≥ 0.5) in high seas
9 Taxonomic Groups
12013 Species

#Create treemap where size of rectangle corresponds to number of species in each group

taxa_treemap<- treemap(taxa_grp,
                       index=groupnumber,
                       vSize="n",
                       type="index",
                       force.print.labels = TRUE,
                       title="Number of species per group"
)

#Create table of nspp for each taxonomic group
knitr::kable(taxa_grp,
             col.names = c("Group",
                           "Number of Species")) %>% 
  kable_styling(bootstrap_options = "striped")

Group	Number of Species
Bony fishes	5101
Cephalopods	155
Corals	435
Invertebrates	5437
Marine Mammals	95
Other	352
Seagrasses	3
Sharks & rays	396
Tunas & billfishes	39

groupnumber<-"groups06"

spp_grp<-filter_group(spp,groupnumber)
nspp_grp<-nrow(spp_grp)
taxa_grp <-summarise_group(spp_grp,groupnumber)
ngrp_grp <-nrow(taxa_grp)

Groups v06

AquaMaps species (prob≥ 0.5) in high seas and 25% of its range in high seas
8 Taxonomic Groups
2673 Species

#Create treemap where size of rectangle corresponds to number of species in each group

taxa_treemap<- treemap(taxa_grp,
                       index=groupnumber,
                       vSize="n",
                       type="index",
                       force.print.labels = TRUE,
                       title="Number of species per group"
)

#Create table of nspp for each taxonomic group
knitr::kable(taxa_grp,
             col.names = c("Group",
                           "Number of Species")) %>% 
  kable_styling(bootstrap_options = "striped")

Group	Number of Species
Bony fishes	1395
Cephalopods	42
Corals	12
Invertebrates	1037
Marine Mammals	62
Other	52
Sharks & rays	52
Tunas & billfishes	21

Taxonomic Group Treemap

11/8/2019

Taxonomic groups from gmbi package used in bbnj analysis

Groups v01

Groups v02

Groups v03

Groups v04

Groups v05

Groups v06