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Monitoring and Analysis","monthly_downloads":153675,"total_dependent_repos":151,"total_dependent_packages":39,"readme":"---\noutput: github_document\n---\n\n\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n\n```{r, include = FALSE}\nknitr::opts_chunk$set(\n  collapse = TRUE,\n  comment = \"#\u003e\",\n  fig.path = \"man/figures/README-\",\n  out.width = \"75%\",\n  warning = FALSE,\n  message = FALSE,\n  fig.retina = 2,\n  fig.align = 'center'\n)\nlibrary(tidyverse)\nlibrary(palmerpenguins)\n```\n\n# palmerpenguins \u003ca href='https://allisonhorst.github.io/palmerpenguins/'\u003e\u003cimg src='man/figures/logo.png' align=\"right\" height=\"138.5\" /\u003e\u003c/a\u003e\n\n\u003c!-- badges: start --\u003e\n\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3960218.svg)](https://doi.org/10.5281/zenodo.3960218)\n[![CRAN](https://www.r-pkg.org/badges/version/palmerpenguins)](https://cran.r-project.org/package=palmerpenguins)\n\n\u003c!-- badges: end --\u003e\n\nThe goal of palmerpenguins is to provide a great dataset for data exploration \u0026 visualization, as an alternative to `iris`. \n\n```{r flipper-bill, echo=FALSE}\nflipper_bill \u003c- ggplot(data = penguins,\n                         aes(x = flipper_length_mm,\n                             y = bill_length_mm)) +\n  geom_point(aes(color = species, \n                 shape = species),\n             size = 3,\n             alpha = 0.8) +\n  geom_smooth(method = \"lm\", se = FALSE, aes(color = species)) +\n  theme_minimal() +\n  scale_color_manual(values = c(\"darkorange\",\"purple\",\"cyan4\")) +\n  labs(title = \"Flipper and bill length\",\n       subtitle = \"Dimensions for Adelie, Chinstrap and Gentoo Penguins at Palmer Station LTER\",\n       x = \"Flipper length (mm)\",\n       y = \"Bill length (mm)\",\n       color = \"Penguin species\",\n       shape = \"Penguin species\") +\n  theme(legend.position = c(0.85, 0.15),\n        plot.title.position = \"plot\",\n        plot.caption = element_text(hjust = 0, face= \"italic\"),\n        plot.caption.position = \"plot\")\n\nflipper_bill\n```\n\n\n\n## Installation\n\nYou can install the released version of palmerpenguins from [CRAN](https://CRAN.R-project.org) with:\n\n``` r\ninstall.packages(\"palmerpenguins\")\n```\n\nTo install the development version from [GitHub](https://github.com/) use:\n\n``` r\n# install.packages(\"remotes\")\nremotes::install_github(\"allisonhorst/palmerpenguins\")\n```\n\n## About the data\n\nData 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/). \n\nThe palmerpenguins package contains two datasets. \n\n```{r showdata}\nlibrary(palmerpenguins)\ndata(package = 'palmerpenguins')\n``` \n\nOne is called `penguins`, and is a simplified version of the raw data; see `?penguins` for more info: \n\n```{r example-penguins}\nhead(penguins)\n```\n\n\nThe second dataset is `penguins_raw`, and contains all the variables and original names as downloaded; see `?penguins_raw` for more info.\n\n```{r example-penguins-raw}\nhead(penguins_raw)\n```\n\nBoth 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. \n\n```{r}\nstr(penguins)\n```\n\n\nWe 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 \u0026 use. \n\n\n## Examples\n\nYou can find these and more code examples for exploring palmerpenguins in `vignette(\"examples\")`.\n\nPenguins are fun to summarize! For example:\n\n```{r example, warning=FALSE, message=FALSE}\nlibrary(tidyverse)\npenguins %\u003e% \n  count(species)\npenguins %\u003e% \n  group_by(species) %\u003e% \n  summarize(across(where(is.numeric), mean, na.rm = TRUE))\n```\n\nPenguins are fun to visualize! For example:\n\n```{r mass-flipper, warning = FALSE, message = FALSE, echo = FALSE, out.width='75%', fig.retina=2}\nmass_flipper \u003c- ggplot(data = penguins, \n                       aes(x = flipper_length_mm,\n                           y = body_mass_g)) +\n  geom_point(aes(color = species, \n                 shape = species),\n             size = 3,\n             alpha = 0.8) +\n  theme_minimal() +\n  scale_color_manual(values = c(\"darkorange\",\"purple\",\"cyan4\")) +\n  labs(title = \"Penguin size, Palmer Station LTER\",\n       subtitle = \"Flipper length and body mass for Adelie, Chinstrap, and Gentoo Penguins\",\n       x = \"Flipper length (mm)\",\n       y = \"Body mass (g)\",\n       color = \"Penguin species\",\n       shape = \"Penguin species\") +\n  theme(legend.position = c(0.2, 0.7),\n        plot.title.position = \"plot\",\n        plot.caption = element_text(hjust = 0, face= \"italic\"),\n        plot.caption.position = \"plot\")\n\nmass_flipper\n```\n\n```{r flipper-hist, echo=FALSE}\nflipper_hist \u003c- ggplot(data = penguins, aes(x = flipper_length_mm)) +\n  geom_histogram(aes(fill = species), \n                 alpha = 0.5, \n                 position = \"identity\") +\n  scale_fill_manual(values = c(\"darkorange\",\"purple\",\"cyan4\")) +\n  theme_minimal() +\n  labs(x = \"Flipper length (mm)\",\n       y = \"Frequency\",\n       title = \"Penguin flipper lengths\")\n\nflipper_hist\n```\n\n## Artwork\n\nYou 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\".\n\n### Meet the Palmer penguins\n\n```{r, echo = FALSE, fig.align='center'}\nknitr::include_graphics(\"man/figures/lter_penguins.png\", dpi = 300)\n```\n\n### Bill dimensions\n\nThe 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.  \n\nFor this penguin data, the culmen (bill) length and depth are measured as shown below (thanks Kristen Gorman for clarifying!):\n\n```{r, echo = FALSE, fig.align='center'}\nknitr::include_graphics(\"man/figures/culmen_depth.png\", dpi = 300)\n```\n\n## License\n\nData 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/).\n\n## Citation\n\nTo cite the palmerpenguins package, please use:\n\n```{r}\ncitation(\"palmerpenguins\")\n```\n\n\n## Additional data use information\n\nAnyone 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/.\"\n\n## References\n\n**Data originally published in:** \n\n+ 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\n\n\n**Data citations:**\n\nAdélie penguins: \n\n+ 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).\n\nGentoo penguins:\n\n+ 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).\n\nChinstrap penguins: \n\n+ 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).\n","funding_links":[],"readme_doi_urls":["https://doi.org/10.5281/zenodo.3960218","https://doi.org/10.1371/journal.pone.0090081","https://doi.org/10.6073/pasta/98b16d7d563f265cb52372c8ca99e60f","https://doi.org/10.6073/pasta/7fca67fb28d56ee2ffa3d9370ebda689","https://doi.org/10.6073/pasta/c14dfcfada8ea13a17536e73eb6fbe9e"],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":["dynamic","ecology"],"project_url":"https://ost.ecosyste.ms/api/v1/projects/20324","html_url":"https://ost.ecosyste.ms/projects/20324"}