https://github.com/cran/palmerpenguins
Tip revision: 62438cf5919bde9c762b23b01f6efa2907ab297c authored by Allison Horst on 15 August 2022, 06:40:07 UTC
version 0.1.1
version 0.1.1
Tip revision: 62438cf
README.md
<!-- README.md is generated from README.Rmd. Please edit that file -->
# palmerpenguins <a href='https://allisonhorst.github.io/palmerpenguins/'><img src='man/figures/logo.png' align="right" height="138.5" /></a>
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The goal of palmerpenguins is to provide a great dataset for data
exploration & visualization, as an alternative to `iris`.
<img src="man/figures/README-flipper-bill-1.png" width="75%" style="display: block; margin: auto;" />
## Installation
You can install the released version of palmerpenguins from
[CRAN](https://CRAN.R-project.org) with:
``` r
install.packages("palmerpenguins")
```
To install the development version from [GitHub](https://github.com/)
use:
``` r
# install.packages("remotes")
remotes::install_github("allisonhorst/palmerpenguins")
```
## About the data
Data were collected and made available by [Dr. Kristen
Gorman](https://www.uaf.edu/cfos/people/faculty/detail/kristen-gorman.php)
and the [Palmer Station, Antarctica
LTER](https://pallter.marine.rutgers.edu/), a member of the [Long Term
Ecological Research Network](https://lternet.edu/).
The palmerpenguins package contains two datasets.
``` r
library(palmerpenguins)
data(package = 'palmerpenguins')
```
One is called `penguins`, and is a simplified version of the raw data;
see `?penguins` for more info:
``` r
head(penguins)
#> # A tibble: 6 × 8
#> species island bill_length_mm bill_depth_mm flipper_length_… body_mass_g sex
#> <fct> <fct> <dbl> <dbl> <int> <int> <fct>
#> 1 Adelie Torge… 39.1 18.7 181 3750 male
#> 2 Adelie Torge… 39.5 17.4 186 3800 fema…
#> 3 Adelie Torge… 40.3 18 195 3250 fema…
#> 4 Adelie Torge… NA NA NA NA <NA>
#> 5 Adelie Torge… 36.7 19.3 193 3450 fema…
#> 6 Adelie Torge… 39.3 20.6 190 3650 male
#> # … with 1 more variable: year <int>
```
The second dataset is `penguins_raw`, and contains all the variables and
original names as downloaded; see `?penguins_raw` for more info.
``` r
head(penguins_raw)
#> # A tibble: 6 × 17
#> studyName `Sample Number` Species Region Island Stage `Individual ID`
#> <chr> <dbl> <chr> <chr> <chr> <chr> <chr>
#> 1 PAL0708 1 Adelie Penguin … Anvers Torge… Adul… N1A1
#> 2 PAL0708 2 Adelie Penguin … Anvers Torge… Adul… N1A2
#> 3 PAL0708 3 Adelie Penguin … Anvers Torge… Adul… N2A1
#> 4 PAL0708 4 Adelie Penguin … Anvers Torge… Adul… N2A2
#> 5 PAL0708 5 Adelie Penguin … Anvers Torge… Adul… N3A1
#> 6 PAL0708 6 Adelie Penguin … Anvers Torge… Adul… N3A2
#> # … with 10 more variables: `Clutch Completion` <chr>, `Date Egg` <date>,
#> # `Culmen Length (mm)` <dbl>, `Culmen Depth (mm)` <dbl>,
#> # `Flipper Length (mm)` <dbl>, `Body Mass (g)` <dbl>, Sex <chr>,
#> # `Delta 15 N (o/oo)` <dbl>, `Delta 13 C (o/oo)` <dbl>, Comments <chr>
```
Both datasets contain data for 344 penguins. There are 3 different
species of penguins in this dataset, collected from 3 islands in the
Palmer Archipelago, Antarctica.
``` r
str(penguins)
#> tibble [344 × 8] (S3: tbl_df/tbl/data.frame)
#> $ species : Factor w/ 3 levels "Adelie","Chinstrap",..: 1 1 1 1 1 1 1 1 1 1 ...
#> $ island : Factor w/ 3 levels "Biscoe","Dream",..: 3 3 3 3 3 3 3 3 3 3 ...
#> $ bill_length_mm : num [1:344] 39.1 39.5 40.3 NA 36.7 39.3 38.9 39.2 34.1 42 ...
#> $ bill_depth_mm : num [1:344] 18.7 17.4 18 NA 19.3 20.6 17.8 19.6 18.1 20.2 ...
#> $ flipper_length_mm: int [1:344] 181 186 195 NA 193 190 181 195 193 190 ...
#> $ body_mass_g : int [1:344] 3750 3800 3250 NA 3450 3650 3625 4675 3475 4250 ...
#> $ sex : Factor w/ 2 levels "female","male": 2 1 1 NA 1 2 1 2 NA NA ...
#> $ year : int [1:344] 2007 2007 2007 2007 2007 2007 2007 2007 2007 2007 ...
```
We gratefully acknowledge Palmer Station LTER and the US LTER Network.
Special thanks to Marty Downs (Director, LTER Network Office) for help
regarding the data license & use.
## Examples
You can find these and more code examples for exploring palmerpenguins
in `vignette("examples")`.
Penguins are fun to summarize! For example:
``` r
library(tidyverse)
penguins %>%
count(species)
#> # A tibble: 3 × 2
#> species n
#> <fct> <int>
#> 1 Adelie 152
#> 2 Chinstrap 68
#> 3 Gentoo 124
penguins %>%
group_by(species) %>%
summarize(across(where(is.numeric), mean, na.rm = TRUE))
#> # A tibble: 3 × 6
#> species bill_length_mm bill_depth_mm flipper_length_mm body_mass_g year
#> <fct> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 Adelie 38.8 18.3 190. 3701. 2008.
#> 2 Chinstrap 48.8 18.4 196. 3733. 2008.
#> 3 Gentoo 47.5 15.0 217. 5076. 2008.
```
Penguins are fun to visualize! For example:
<img src="man/figures/README-mass-flipper-1.png" width="75%" style="display: block; margin: auto;" />
<img src="man/figures/README-flipper-hist-1.png" width="75%" style="display: block; margin: auto;" />
## Artwork
You can download palmerpenguins art (useful for teaching with the data)
in `vignette("art")`. If you use this artwork, please cite with:
“Artwork by @allison_horst”.
### Meet the Palmer penguins
<img src="man/figures/lter_penguins.png" width="75%" style="display: block; margin: auto;" />
### Bill dimensions
The culmen is the upper ridge of a bird’s bill. In the simplified
`penguins` data, culmen length and depth are renamed as variables
`bill_length_mm` and `bill_depth_mm` to be more intuitive.
For this penguin data, the culmen (bill) length and depth are measured
as shown below (thanks Kristen Gorman for clarifying!):
<img src="man/figures/culmen_depth.png" width="75%" style="display: block; margin: auto;" />
## License
Data are available by
[CC-0](https://creativecommons.org/share-your-work/public-domain/cc0/)
license in accordance with the [Palmer Station LTER Data
Policy](https://pallter.marine.rutgers.edu/data/) and the [LTER Data
Access Policy for Type I data](https://lternet.edu/data-access-policy/).
## Citation
To cite the palmerpenguins package, please use:
``` r
citation("palmerpenguins")
#>
#> To cite palmerpenguins in publications use:
#>
#> Horst AM, Hill AP, Gorman KB (2020). palmerpenguins: Palmer
#> Archipelago (Antarctica) penguin data. R package version 0.1.0.
#> https://allisonhorst.github.io/palmerpenguins/. doi:
#> 10.5281/zenodo.3960218.
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Manual{,
#> title = {palmerpenguins: Palmer Archipelago (Antarctica) penguin data},
#> author = {Allison Marie Horst and Alison Presmanes Hill and Kristen B Gorman},
#> year = {2020},
#> note = {R package version 0.1.0},
#> doi = {10.5281/zenodo.3960218},
#> url = {https://allisonhorst.github.io/palmerpenguins/},
#> }
```
## Additional data use information
Anyone interested in publishing the data should contact [Dr. Kristen
Gorman](https://www.uaf.edu/cfos/people/faculty/detail/kristen-gorman.php)
about analysis and working together on any final products. From Gorman
et al. (2014): “Individuals interested in using these data are expected
to follow the US LTER Network’s Data Access Policy, Requirements and Use
Agreement: <https://lternet.edu/data-access-policy/>.”
## References
**Data originally published in:**
- Gorman KB, Williams TD, Fraser WR (2014). Ecological sexual
dimorphism and environmental variability within a community of
Antarctic penguins (genus *Pygoscelis*). PLoS ONE 9(3):e90081.
<https://doi.org/10.1371/journal.pone.0090081>
**Data citations:**
Adélie penguins:
- Palmer Station Antarctica LTER and K. Gorman, 2020. Structural size
measurements and isotopic signatures of foraging among adult male
and female Adélie penguins (*Pygoscelis adeliae*) nesting along the
Palmer Archipelago near Palmer Station, 2007-2009 ver 5.
Environmental Data Initiative.
<https://doi.org/10.6073/pasta/98b16d7d563f265cb52372c8ca99e60f>
(Accessed 2020-06-08).
Gentoo penguins:
- Palmer Station Antarctica LTER and K. Gorman, 2020. Structural size
measurements and isotopic signatures of foraging among adult male
and female Gentoo penguin (*Pygoscelis papua*) nesting along the
Palmer Archipelago near Palmer Station, 2007-2009 ver 5.
Environmental Data Initiative.
<https://doi.org/10.6073/pasta/7fca67fb28d56ee2ffa3d9370ebda689>
(Accessed 2020-06-08).
Chinstrap penguins:
- Palmer Station Antarctica LTER and K. Gorman, 2020. Structural size
measurements and isotopic signatures of foraging among adult male
and female Chinstrap penguin (*Pygoscelis antarcticus*) nesting
along the Palmer Archipelago near Palmer Station, 2007-2009 ver 6.
Environmental Data Initiative.
<https://doi.org/10.6073/pasta/c14dfcfada8ea13a17536e73eb6fbe9e>
(Accessed 2020-06-08).