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README.Rmd
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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "75%",
warning = FALSE,
message = FALSE,
fig.retina = 2,
fig.align = 'center'
)
library(tidyverse)
library(palmerpenguins)
```
# palmerpenguins <a href='https://allisonhorst.github.io/palmerpenguins/'><img src='man/figures/logo.png' align="right" height="138.5" /></a>
<!-- badges: start -->
[](https://doi.org/10.5281/zenodo.3960218)
[](https://cran.r-project.org/package=palmerpenguins)
<!-- badges: end -->
The goal of palmerpenguins is to provide a great dataset for data exploration & visualization, as an alternative to `iris`.
```{r flipper-bill, echo=FALSE}
flipper_bill <- ggplot(data = penguins,
aes(x = flipper_length_mm,
y = bill_length_mm)) +
geom_point(aes(color = species,
shape = species),
size = 3,
alpha = 0.8) +
geom_smooth(method = "lm", se = FALSE, aes(color = species)) +
theme_minimal() +
scale_color_manual(values = c("darkorange","purple","cyan4")) +
labs(title = "Flipper and bill length",
subtitle = "Dimensions for Adelie, Chinstrap and Gentoo Penguins at Palmer Station LTER",
x = "Flipper length (mm)",
y = "Bill length (mm)",
color = "Penguin species",
shape = "Penguin species") +
theme(legend.position = c(0.85, 0.15),
plot.title.position = "plot",
plot.caption = element_text(hjust = 0, face= "italic"),
plot.caption.position = "plot")
flipper_bill
```
## 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 showdata}
library(palmerpenguins)
data(package = 'palmerpenguins')
```
One is called `penguins`, and is a simplified version of the raw data; see `?penguins` for more info:
```{r example-penguins}
head(penguins)
```
The second dataset is `penguins_raw`, and contains all the variables and original names as downloaded; see `?penguins_raw` for more info.
```{r example-penguins-raw}
head(penguins_raw)
```
Both datasets contain data for `r nrow(penguins)` penguins. There are `r length(unique(penguins$species))` different species of penguins in this dataset, collected from `r length(unique(penguins$island))` islands in the Palmer Archipelago, Antarctica.
```{r}
str(penguins)
```
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 example, warning=FALSE, message=FALSE}
library(tidyverse)
penguins %>%
count(species)
penguins %>%
group_by(species) %>%
summarize(across(where(is.numeric), mean, na.rm = TRUE))
```
Penguins are fun to visualize! For example:
```{r mass-flipper, warning = FALSE, message = FALSE, echo = FALSE, out.width='75%', fig.retina=2}
mass_flipper <- ggplot(data = penguins,
aes(x = flipper_length_mm,
y = body_mass_g)) +
geom_point(aes(color = species,
shape = species),
size = 3,
alpha = 0.8) +
theme_minimal() +
scale_color_manual(values = c("darkorange","purple","cyan4")) +
labs(title = "Penguin size, Palmer Station LTER",
subtitle = "Flipper length and body mass for Adelie, Chinstrap, and Gentoo Penguins",
x = "Flipper length (mm)",
y = "Body mass (g)",
color = "Penguin species",
shape = "Penguin species") +
theme(legend.position = c(0.2, 0.7),
plot.title.position = "plot",
plot.caption = element_text(hjust = 0, face= "italic"),
plot.caption.position = "plot")
mass_flipper
```
```{r flipper-hist, echo=FALSE}
flipper_hist <- ggplot(data = penguins, aes(x = flipper_length_mm)) +
geom_histogram(aes(fill = species),
alpha = 0.5,
position = "identity") +
scale_fill_manual(values = c("darkorange","purple","cyan4")) +
theme_minimal() +
labs(x = "Flipper length (mm)",
y = "Frequency",
title = "Penguin flipper lengths")
flipper_hist
```
## 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
```{r, echo = FALSE, fig.align='center'}
knitr::include_graphics("man/figures/lter_penguins.png", dpi = 300)
```
### 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!):
```{r, echo = FALSE, fig.align='center'}
knitr::include_graphics("man/figures/culmen_depth.png", dpi = 300)
```
## 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")
```
## 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).