National phenology network

This data set contains data from the USA National Phenology Network.

In R, we need 2 packages to download and visualize the data. First, check if the packages are already installed. Install them if they are not:

packages <- c("tidyverse", "devtools") 
new.packages <- packages[!(packages %in% installed.packages()[,"Package"])] 
if(length(new.packages)>0) install.packages(new.packages)

Then, load them and install ‘rnpn’, an R client for interacting with the USA National Phenology Network data web services.

lapply(packages, library, character.only = TRUE)

── Attaching packages ─────────────────────────────────────── tidyverse 1.3.0 ──

✔ ggplot2 3.4.1     ✔ purrr   0.3.4
✔ tibble  3.2.1     ✔ dplyr   1.0.9
✔ tidyr   1.1.2     ✔ stringr 1.4.0
✔ readr   1.4.0     ✔ forcats 0.5.0

── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()

Loading required package: usethis

[[1]]
 [1] "forcats"   "stringr"   "dplyr"     "purrr"     "readr"     "tidyr"    
 [7] "tibble"    "ggplot2"   "tidyverse" "stats"     "graphics"  "grDevices"
[13] "utils"     "datasets"  "methods"   "base"     

[[2]]
 [1] "devtools"  "usethis"   "forcats"   "stringr"   "dplyr"     "purrr"    
 [7] "readr"     "tidyr"     "tibble"    "ggplot2"   "tidyverse" "stats"    
[13] "graphics"  "grDevices" "utils"     "datasets"  "methods"   "base"     

install_github("usa-npn/rnpn")

Skipping install of 'rnpn' from a github remote, the SHA1 (0dff444e) has not changed since last install.
  Use `force = TRUE` to force installation

library(rnpn)

Download data about Woodhouse’s toads:

toads <- npn_download_status_data(request_source='Your Name',years = c(2000:2020), species_id=c(237))

using a custom handler function.

opening curl input connection.


 Found 0 records...

closing curl input connection.

using a custom handler function.

opening curl input connection.


 Found 0 records...

closing curl input connection.

using a custom handler function.

opening curl input connection.


 Found 0 records...

closing curl input connection.

using a custom handler function.

opening curl input connection.


 Found 0 records...

closing curl input connection.

using a custom handler function.

opening curl input connection.


 Found 0 records...

closing curl input connection.

using a custom handler function.

opening curl input connection.


 Found 0 records...

closing curl input connection.

using a custom handler function.

opening curl input connection.


 Found 0 records...

closing curl input connection.

using a custom handler function.

opening curl input connection.


 Found 0 records...

closing curl input connection.

using a custom handler function.

opening curl input connection.


 Found 0 records...

closing curl input connection.

using a custom handler function.

opening curl input connection.


 Found 0 records...

closing curl input connection.

using a custom handler function.

opening curl input connection.


 Found 5 records...

closing curl input connection.

using a custom handler function.

opening curl input connection.


 Found 59 records...

closing curl input connection.

using a custom handler function.

opening curl input connection.


 Found 0 records...

closing curl input connection.

using a custom handler function.

opening curl input connection.


 Found 14 records...

closing curl input connection.

using a custom handler function.

opening curl input connection.


 Found 7 records...

closing curl input connection.

using a custom handler function.

opening curl input connection.


 Found 7 records...

closing curl input connection.

using a custom handler function.

opening curl input connection.


 Found 0 records...

closing curl input connection.

using a custom handler function.

opening curl input connection.


 Found 0 records...

closing curl input connection.

using a custom handler function.

opening curl input connection.


 Found 0 records...

closing curl input connection.

using a custom handler function.

opening curl input connection.


 Found 0 records...

closing curl input connection.

using a custom handler function.

opening curl input connection.


 Found 0 records...

closing curl input connection.

Plot phenophases as a function of DOY per state:

ggplot(toads) +
  geom_point(aes(day_of_year, phenophase_description)) +
  facet_wrap(.~state) +
  theme_bw() +
  xlab('Day of year') +
  ylab('Phenophase')