Repeat at the genus and family levels

[wcornwell]

important function is table or summarize and n_distinct

also word

[wcornwell]

Goal 1: Table with percentage endemics for each group

[wcornwell]

getting started:

countries<-read_csv("intermediate_data/country_dataset.csv")
countries$genus<-word(countries$species,1,1)

length(unique(countries$genus))
length(unique(countries$species))

Pollia<-filter(countries,genus=="Pollia")

group_by(genus) %>%
  summarize()

[wcornwell]

for joining in family names: https://github.com/traitecoevo/taxonlookup

[wcornwell]

install.packages("readr")

library(readr)
library(stringr)
library(dplyr)

countries <- read_csv("intermediate_data/country_dataset.csv")
countries$genus  <- word(countries$species,1,1)

length(unique(countries$genus))
length(unique(countries$species))

Pollia <- filter(countries, genus == "Pollia")

countries %>%
group_by(genus) %>%
  summarize(genus_endemic=all(aus_endemic),
            prop_sp_endemic=sum(aus_endemic)/n()) -> genera

genera %>%
  ggplot(aes(x=prop_sp_endemic))+geom_histogram()

devtools::install_github("wcornwell/taxonlookup")
library(taxonlookup)
lt<-lookup_table(genera$genus, by_species=TRUE)

genera %>%
  left_join(lt) ->genus_with_family

genus_with_family %>%
  group_by(family) %>%
  summarize(prop_endemic=sum(genus_endemic)/n(),n()) ->family_summary

family_summary %>%
  ggplot(aes(x=prop_endemic))+geom_histogram()

lt<-lookup_table(countries$species, by_species=TRUE)
lt<-rownames_to_column(lt,"species")

  left_join(countries,lt) -> species_with_family

species_with_family %>%
  group_by(group) %>%
  summarize(prop_endemic=sum(aus_endemic)/n(),n=n())

[shufoldof]

not sure how to fix this.

[wcornwell]

hi @shufoldof it's loading the libraries. if you load the libraries first it should fix it.

remotes::install_github("wcornwell/taxonlookup")
library(taxonlookup)
library(tidyverse)

[shufoldof]

hi @wcornwell that part worked, thanks. But also have problems with this code. searched but couldn't fix it:

[wcornwell]

hmmm can you post the whole script here?

[shufoldof]

Yes. Here it is:

#install.packages("readr")
#install.packages("rlang")
#install.packages("dplyr")

remotes::install_github("wcornwell/taxonlookup")
library(taxonlookup)
library(readr)
library(tidyverse)
library(stringr)
library(dplyr)
library(ggplot2)

countries <- read_csv("intermediate_data/country_dataset.csv")
countries$genus <- word(countries$species,1,1)

Pollia <- filter(countries, genus == "Pollia")

countries %>%
  group_by(genus) %>%
  summarize(genus_endemic = all(aus_endemic),
            prop_sp_endemic = sum(aus_endemic)/n()) -> genera

genera %>%
  ggplot(aes(x=prop_sp_endemic))+geom_histogram()

devtools::install_github("wcornwell/taxonlookup")

library(taxonlookup)
lt <- lookup_table(genera$genus, by_species = TRUE)

genera %>%
  left_join(lt) -> genus_with_family

genus_with_family %>%
  group_by(family) %>%
  summarize(prop_endemic = sum(genus_endemic)/n(),n()) -> family_summary

family_summary %>%
  ggplot(aes(x=prop_endemic)) + geom_histogram()

lt <- lookup_table(countries$species, by_species = TRUE)
lt <- rownames_to_column(lt, "species")

left_join(countries, lt) -> species_family

species_with_family %>%
  group_by(group) %>%
  summarize(prop_endemic = sum(aus_endemic)/n(), n=n())

[wcornwell]

change:

left_join(countries, lt) -> species_family

to:

left_join(countries, lt) -> species_with_family

[shufoldof]

@wcornwell thank you so much. It worked like a charm. What would be my next step?

[wcornwell]

I think you should make final results tables and write the captions for them.

[shufoldof]

@wcornwell should I do it on the MS word program or should I search how to do it in R?

[wcornwell]

up to you :)