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
11900 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	468
Bony fishes	5095
Cephalopods	153
Cetaceans	69
Chitons	19
Corals	435
Crustaceans	1871
Echinoderms	438
Euphausiids	35
Forams	5
Gastropods	935
Hydrozoans	247
Jellyfish	13
Other	540
Pinnipeds	25
Reptiles	20
Sea spiders	217
Seagrasses	3
Sharks & rays	396
Sponges	134
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
2051 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	12
Bony fishes	1325
Cephalopods	33
Cetaceans	52
Chitons	1
Corals	10
Crustaceans	175
Echinoderms	33
Euphausiids	1
Forams	2
Gastropods	52
Hydrozoans	9
Jellyfish	2
Other	62
Pinnipeds	8
Reptiles	1
Sea spiders	64
Sharks & rays	49
Sponges	9
Tunas & billfishes	21
Tunicates	84
Worms	46

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
11900 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	5095
Cephalopods	153
Corals	435
Invertebrates	5339
Marine Mammals	95
Other	345
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
2051 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	1325
Cephalopods	33
Corals	10
Invertebrates	527
Marine Mammals	60
Other	26
Sharks & rays	49
Tunas & billfishes	21

Taxonomic Group Treemap

7/31/2019

Taxonomic groups from gmbi package used in bbnj analysis

Groups v01

Groups v02

Groups v03

Groups v04

Groups v05

Groups v06