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summarize_bird_dets.R
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summarize_bird_dets.R
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library(tidyverse)
library(WikipediR)
`%notin%` <- Negate(`%in%`)
# goal of this dataset is to get the wikipedia details about each species/family
bdf = read_csv("data/vabirds.csv")
dict = readxl::read_excel("data/FeederWatch_Data_Dictionary.xlsx",5,skip = 1) %>% janitor::clean_names()
get_html <- function(pg){
txt = WikipediR::page_content("en","wikipedia",page_name = pg)$parse$text$`*`
return(txt)
}
get_redirect <- function(html){
detect = html %>% str_detect(.,"redirectMsg")
if(detect==TRUE){
return(TRUE)
} else{
return(FALSE)
}
}
get_redirect_name <- function(html){
title = html %>% read_html() %>% html_node("a") %>% html_attr("title") %>% str_trim()
return(title)
}
get_lead <- function(html,val=3){
paras = html %>% read_html() %>% html_node("body") %>% html_nodes("p")
lead = paras %>% .[[val]] %>% html_text() %>% str_trim()
return(lead)
}
get_status <- function(html){
status = html %>% read_html() %>% toString() %>% str_extract("src.*iucn.*svg.*decoding") %>% str_extract("\\_[A-Z]{1,}\\.svg") %>% str_replace("_","") %>% str_replace(".svg","")
return(status)
}
bdf = bdf %>%
mutate(scientific_name = case_when(
scientific_name == 'Setophaga coronata coronata' ~ 'Setophaga coronata',
scientific_name == 'Setophaga palmarum palmarum' ~ 'Setophaga palmarum',
scientific_name == 'Setophaga palmarum hypochrysea' ~ 'Setophaga palmarum',
TRUE ~ scientific_name
))
df = tibble()
for(i in 1:nrow(bdf)){
name = bdf %>% slice(i) %>% select(scientific_name) %>% pull()
species_code = bdf %>% slice(i) %>% select(species_code) %>% pull()
if(!str_detect(name,"\\(family\\/genus\\)")){
cat(paste0(as.character(i)," - ",name,"\n"))
html = get_html(name)
rTF = get_redirect(html)
if(rTF==TRUE){
name = get_redirect_name(html)
html = get_html(name)
cat(paste0("- redirecting... ",name,"\n"))
}
url = str_replace_all(name,"\\s","_")
image_url = html %>% read_html() %>% html_nodes("img") %>% .[[2]] %>% html_attr("src")
lead = get_lead(html)
status = get_status(html)
tmp_df = tibble(species_code,common_name=name,lead,status,url,image_url)
df = rbind(df,tmp_df)
}
}
# get it with the lead one para before
bdf2 = df %>% mutate(check=str_detect(tolower(lead),paste0("^the ",tolower(common_name)))|str_detect(tolower(lead),paste0("^",tolower(common_name)))) %>% dplyr::filter(check!=TRUE) %>% select(-c(lead,status,url,image_url,check))
df2 = tibble()
for(i in 1:nrow(bdf2)){
name = bdf2 %>% slice(i) %>% select(common_name) %>% pull()
species_code = bdf2 %>% slice(i) %>% select(species_code) %>% pull()
if(!str_detect(name,"\\(family\\/genus\\)")){
cat(paste0(as.character(i)," - ",name,"\n"))
html = get_html(name)
rTF = get_redirect(html)
if(rTF==TRUE){
name = get_redirect_name(html)
html = get_html(name)
cat(paste0("- redirecting... ",name,"\n"))
}
url = str_replace_all(name,"\\s","_")
image_url = html %>% read_html() %>% html_nodes("img") %>% .[[2]] %>% html_attr("src")
lead = get_lead(html,2)
status = get_status(html)
tmp_df = tibble(species_code,common_name=name,lead,status,url,image_url)
df2 = rbind(df2,tmp_df)
}
}
bdf3 = df2 %>% mutate(check=str_detect(tolower(lead),paste0("^the ",tolower(common_name)))|str_detect(tolower(lead),paste0("^",tolower(common_name)))) %>% dplyr::filter(check!=TRUE) %>% select(-c(lead,status,url,image_url,check))
df3 = tibble()
for(i in 1:nrow(bdf3)){
name = bdf3 %>% slice(i) %>% select(common_name) %>% pull()
species_code = bdf3 %>% slice(i) %>% select(species_code) %>% pull()
if(!str_detect(name,"\\(family\\/genus\\)")){
cat(paste0(as.character(i)," - ",name,"\n"))
html = get_html(name)
rTF = get_redirect(html)
if(rTF==TRUE){
name = get_redirect_name(html)
html = get_html(name)
cat(paste0("- redirecting... ",name,"\n"))
}
url = str_replace_all(name,"\\s","_")
image_url = html %>% read_html() %>% html_nodes("img") %>% .[[2]] %>% html_attr("src")
lead = get_lead(html,4)
status = get_status(html)
tmp_df = tibble(species_code,common_name=name,lead,status,url,image_url)
df3 = rbind(df3,tmp_df)
}
}
df3 %>% mutate(check=str_detect(tolower(lead),paste0("^the ",tolower(common_name)))|str_detect(tolower(lead),paste0("^",tolower(common_name)))) %>% dplyr::filter(check!=TRUE) %>% select(-c(lead,status,url,image_url,check))
df3 = df3 %>% mutate(lead=case_when(
common_name=='Merlin (bird)' ~ get_lead(get_html('Merlin (bird)'),4),
common_name=='American yellow warbler' ~ get_lead(get_html('American yellow warbler'),3),
common_name=='Northern pintail' ~ get_lead(get_html('Northern pintail'),3),
TRUE ~ lead
))
final_birds = rbind(df %>% dplyr::filter(species_code %notin% bdf2$species_code),
df2 %>% dplyr::filter(species_code %notin% bdf3$species_code),
df3)
final_birds = final_birds %>% rowwise() %>% mutate(image_url=case_when(
str_detect(image_url,"Status\\_") ~ '',
TRUE ~ image_url
)) %>% ungroup()
final_birds %>% dplyr::filter(image_url=='')
final_birds = final_birds %>% rowwise() %>% mutate(image_url=case_when(
image_url=='' ~ get_html(common_name) %>% read_html() %>% html_nodes("img") %>% .[[1]] %>% html_attr("src"),
TRUE ~ image_url
)) %>% ungroup()
final_birds = final_birds %>% rowwise() %>% mutate(image_url=case_when(
str_detect(image_url,"Red\\_Pencil\\_Icon\\.png") ~ get_html(common_name) %>% read_html() %>% html_nodes("img") %>% .[[3]] %>% html_attr("src"),
TRUE ~ image_url
)) %>% ungroup()
final_birds = final_birds %>% mutate(status=case_when(
species_code=='hoared' ~ "LC",
species_code=='foxsp1' ~ "LC",
TRUE ~ status
))
# add statistics ----------------------------------------------------------
bird_stats = read_csv("data/species_summary.csv")
final_birds2 = bird_stats %>%
left_join(final_birds %>% mutate(species_grp='birds'),by="species_code") %>%
left_join(bdf %>% select(species_code,scientific_name,order,family,native),by="species_code") %>%
rename("cons_status"="status") %>% rename("description"="lead") %>%
mutate(website=paste0("https://en.wikipedia.org/wiki/",common_name %>% str_replace_all("\\s","_") %>% str_replace_all("'","%27"))) %>%
mutate(image_url=paste0("https:",image_url)) %>%
select(species_grp,order,family,species_code,common_name,scientific_name,count_2021,count_2020,count_5yr,cons_status,cons_score,
cons_desc,diff,abs_diff,perc_diff,peak_month,native,description,image_url,website) %>%
mutate(cons_status=case_when(
cons_status=="LC" ~ "Least Concern",
cons_status=="NT" ~ "Near Threatened",
cons_status=="VU" ~ "Vulnerable",
TRUE ~ NA_character_
))
final_birds2 = final_birds2 %>% left_join(dict %>% select(species_code,order1,family) %>% rename("family1"="family"),by="species_code") %>%
mutate(order=ifelse(!is.na(order),order,order1),family=ifelse(!is.na(family),family,family1)) %>% select(-c(order1,family1))
final_birds2 = final_birds2 %>% mutate(perc_diff=case_when(
abs_diff==0 ~ 0,
is.infinite(perc_diff) ~ 1,
TRUE ~ perc_diff
))
final_birds2 %>% write_csv("data/out_infobox.csv")