Search birds by geography

the ebird website categorizes some popular locations as “Hotspots”. These are areas where there are both lots of birds and lots of birders. Once such location is at Iona Island, near Vancouver. You can see data for this site at http://ebird.org/ebird/hotspot/L261851

At that link, you can see a page like this:

The data already look to be organized in a data frame! rebird allows us to read these data directly into R. (The ID code for Iona Island is **“L261851**)

ebirdhotspot(locID = "L261851") %>%
  head() %>%
  kable()

## Warning: `rbind_all()` is deprecated. Please use `bind_rows()` instead.

We can use the function ebirdgeo to get a list for an area. (Note that South and West are negative):

vanbirds <- ebirdgeo(lat = 49.2500, lng = -123.1000)

## Warning: `rbind_all()` is deprecated. Please use `bind_rows()` instead.

vanbirds %>%
  head %>%
    kable

We can also search by “region”, which refers to short codes which serve as common shorthands for different political units. For example, France is represented by the letters FR

frenchbirds <- ebirdregion("FR")

frenchbirds %>%
  head() %>%
  kable()

Find out WHEN a bird has been seen in a certain place! Choosing a name from vanbirds above (the Bald Eagle):

eagle <- ebirdgeo(species = 'Haliaeetus leucocephalus', lat = 42, lng = -76)

eagle %>%
  head() %>%
  kable()

rebird knows where you are:

ebirdgeo(species = 'Buteo lagopus')

remixing geonames and rebird:

What are the cities of France?

francedata <- countryInfo %>%
    filter(countryName == "France")

frenchcities <- with(francedata,
             GNcities(north = north, east = east, south = south,
                             west = west, maxRows = 500))
frenchcities %>% 
  head %>% 
  kable

Wikipedia searching

We can use geonames to search for georeferenced Wikipedia articles. Here are those within 20 Km of Rio de Janerio, comparing results for English-language Wikipedia (lang = "en") and Portuguese-language Wikipedia (lang = "pt"):

rio_english <- GNfindNearbyWikipedia(lat = -22.9083, lng = -43.1964,
                                                                         radius = 20, lang = "en", maxRows = 500)
rio_portuguese <- GNfindNearbyWikipedia(lat = -22.9083, lng = -43.1964,
                                                                                radius = 20, lang = "pt", maxRows = 500)

nrow(rio_english)

## [1] 305

nrow(rio_portuguese)

## [1] 349

alternate strategy for keeping keys: .Rprofile

Remember to protect your key! it is important for your privacy. You know, like a key * Now we follow the ROpenSci tutorial on API keys * Add .Rprofile to your .gitignore !! * Make a .Rprofile file windows tips mac tips * Write the following in it:

options(PlosApiKey = "YOUR_KEY")

• restart R (e.g. reopen your Rstudio project)

This code adds another element to the list of options, which you can see by calling options(). Part of the work done by rplos::searchplos() and friends is to go and obtain the value of this option with the function getOption("PlosApiKey"). This indicates two things: 1. Spelling is important when you set the option in your .Rprofile 2. you can do a similar process for an arbitrary package or key. For example:

## in .Rprofile
options("this_is_my_key" = XXXX)

## later, in the R script:
key <- getOption("this_is_my_key")

This is a simple means to keep your keys private, especially if you are sharing the same authentication across several projects.

A few timely reminders about your .Rprofile

print("This is Andrew's Rprofile and you can't have it!")
options(PlosApiKey = "XXXXXXXXX")

• Note that it must end with a blank line!
• It lives in the project’s working directory, i.e. the location of your .Rproj
• It must be gitignored

Remember that using .Rprofile makes your code un-reproducible. In this case, that is exactly what we want!

take a highbrow look!

out <- highplos(q='alcohol', hl.fl = 'abstract', rows=10, , key = key)
highbrow(out)