Palmer Penguins

The Palmer penguins dataset by Allison Horst, Alison Hill, and Kristen Gorman was first made publicly available as an R package. The goal of the Palmer Penguins dataset is to replace the highly overused Iris dataset for data exploration & visualization. However, now you can use Palmer penguins on huggingface!

  License

Data are available by CC-0 license in accordance with the Palmer Station LTER Data Policy and the LTER Data Access Policy for Type I data.… See the full description on the dataset page: https://huggingface.co/datasets/SIH/palmer-penguins.

Measurements for three penguin species observed in the Palmer Archipelago, Antarctica.

These data were collected from 2007 - 2009 by Dr. Kristen Gorman with the Palmer Station Long Term Ecological Research Program, part of the US Long Term Ecological Research Network. The data were originally imported from the Environmental Data Initiative (EDI) Data Portal, and are available for use by CC0 license ("No Rights Reserved") in accordance with the Palmer Station Data Policy. This copy was imported from Allison Horst's GitHub repository.

To use this dataset:

import tensorflow_datasets as tfds

ds = tfds.load('penguins', split='train')
for ex in ds.take(4):
 print(ex)

See the guide for more informations on tensorflow_datasets.

Analysis of ‘Palmer Archipelago (Antarctica) penguin data ’ provided by Analyst-2 (analyst-2.ai), based on source dataset retrieved from https://www.kaggle.com/parulpandey/palmer-archipelago-antarctica-penguin-data on 12 November 2021.

--- Dataset description provided by original source is as follows ---

Please refer to the official Github page for details and license information. The details below have also been taken from there.

Artwork: @allison_horst

Palmer Archipelago (Antarctica) penguin data

Data were collected and made available by Dr. Kristen Gorman and the Palmer Station, Antarctica LTER, a member of the Long Term Ecological Research Network.

Thank you to Dr. Gorman, Palmer Station LTER and the LTER Network! Special thanks to Marty Downs (Director, LTER Network Office) for help regarding the data license & use.

License & citation

• Data are available by CC-0 license in accordance with the Palmer Station LTER Data Policy and the LTER Data Access Policy for Type I data.

• Please cite this data using: 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. doi:10.1371/journal.pone.0090081

Summary:

The data folder contains two CSV files. For intro courses/examples, you probably want to use the first one (penguins_size.csv).

• penguins_size.csv: Simplified data from original penguin data sets. Contains variables:

  • species: penguin species (Chinstrap, Adélie, or Gentoo)
  • culmen_length_mm: culmen length (mm)
  • culmen_depth_mm: culmen depth (mm)
  • flipper_length_mm: flipper length (mm)
  • body_mass_g: body mass (g)
  • island: island name (Dream, Torgersen, or Biscoe) in the Palmer Archipelago (Antarctica)
  • sex: penguin sex

• penguins_lter.csv: Original combined data for 3 penguin species (aggregated from individual links below)

Meet the penguins:

https://github.com/allisonhorst/penguins/raw/master/figures/lter_penguins.png" alt="">

What are culmen length & depth?

The culmen is "the upper ridge of a bird's beak" (definition from Oxford Languages).

For this penguin data, the culmen length and culmen depth are measured as shown below (thanks Kristen Gorman for clarifying!):

https://github.com/allisonhorst/penguins/raw/master/figures/culmen_depth.png" alt="">

Data:

These data are 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. doi:10.1371/journal.pone.0090081

Anyone interested in publishing the data should contact Dr. Kristen Gorman about analysis and working together on any final products.

From Gorman et al. (2014): "Data reported here are publicly available within the PAL-LTER data system (datasets #219, 220, and 221): http://oceaninformatics.ucsd.edu/datazoo/data/pallter/datasets. These data are additionally archived within the United States (US) LTER Network’s Information System Data Portal: https://portal.lternet.edu/. Individuals interested in using these data are therefore expected to follow the US LTER Network’s Data Access Policy, Requirements and Use Agreement: https://lternet.edu/data-access-policy/."

From the LTER data access policy: "The consumer of these data (“Data User” herein) has an ethical obligation to cite it appropriately in any publication that results from its use. The Data User should realize that these data may be actively used by others for ongoing research and that coordination may be necessary to prevent duplicate publication. The Data User is urged to contact the authors of these data if any questions about methodology or results occur. Where appropriate, the Data User is encouraged to consider collaboration or coauthorship with the authors. The Data User should realize that misinterpretation of data may occur if used out of context of the original study. While substantial efforts are made to ensure the accuracy of data and associated documentation, complete accuracy of data sets cannot be guaranteed. All data are made available “as is.” The Data User should be aware, however, that data are updated periodically and it is the responsibility of the Data User to check for new versions of the data. The data authors and the repository where these data were obtained shall not be liable for damages resulting from any use or misinterpretation of the data. Thank you."

Links to original data & metadata:

Original data accessed via the Environmental Data Initiative:

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).

--- Original source retains full ownership of the source dataset ---

We evaluated regional variation in reproductive isotopic niche among breeding populations of Adélie (Pygoscelis adeliae), chinstrap (P. antarctica), and gentoo (P. papua) penguins west of the Antarctic Peninsula (AP) to test a hypothesis for sea ice-associated food-web correlates of breeding population change. We rely on signatures of naturally occurring carbon (13C/12C, δ13C) and nitrogen (15N/14N, δ15N) stable isotopes (SI) as integrated proxies of penguin trophic foraging and food-web structure. Each season, study nests, where pairs of adults were present, were individually marked and chosen before the onset of egg-laying, and consistently monitored. When study nests were found at the one-egg stage, both adults were captured to obtain blood samples used for molecular sexing and stable isotope analyses, and measurements of structural size and body mass. At the time of capture, each adult penguin was quickly blood sampled (~1 ml) from the brachial vein. After handling, individuals at study nests were further monitored to ensure the pair reached clutch completion, i.e., two eggs. At approximate an average nest age of five and 15 days, offspring from study nests were captured and quickly blood sampled (≤ ~500 μl for day five chicks, and ≤ ~1 ml for day 15 chicks) from the tarsus vein using a sterile needle and heparinized capillary tubes for day five chicks, and a sterile 3 ml syringe and heparinized infusion needle for day 15 chicks, again to obtain blood tissue for SI analyses. Study nests were monitored for chick survival to 25 days. At five weeks into chick-rearing, older crèched chicks of all three species were captured and quickly blood sampled from study rookeries near Anvers Island. Handling of crèched chicks occurred over a one or two day period, which varied seasonally and by species depending on nest initiation dates. Adélie penguin chicks at Avian Island were sampled on the same day Anvers Island Adélie penguin chicks were sampled. Adélie penguin chicks at Charcot Island, sampled during one season only on 25 January 2010, were handled three days after Anvers Island and Avian Island Adélie penguin chicks were sampled that year, i.e., 22 January 2010. Blood samples from crèched chicks (~1 ml) were taken from the brachial vein using a sterile 3 ml syringe and heparinized infusion needle following sampling procedures used for adult penguins to obtain blood tissue for SI analyses. Stable isotope analyses were conducted at the Stable Isotope Facility at the University of California, Davis using an elemental analyzer interfaced with an isotope ratio mass spectrometer

Abstract: The Antarctic Site Inventory Project has collected biological data and site-descriptive information in the Antarctic Peninsula region since 1994. This research effort has provided data on those sites which are visited by tourists on shipboard expeditions in the region. The aim is to obtain data on the population status of several key species of Antarctic seabirds, which might be affected by the cumulative impact resulting from visits to the sites. This project will continue the effort by focusing on two heavily-visited Antarctic Peninsula sites: Paulet Island, in the northwestern Weddell Sea and Petermann Island, in the Lemaire Channel near Anvers Island. These sites were selected because both rank among the ten most visited sites in Antarctica each year in terms of numbers of visitors and zodiac landings; both are diverse in species composition, and both are sensitive to potential environmental disruptions from visitors. These data collected focus on two important biological parameters for penguins and blue-eyed shags: (1) breeding population size (number of occupied nests) and (2) breeding success (number of chicks per occupied nests). A long-term data program will be supported, with studies at the two sites over a five-year period. The main focus will be at Petermann Island, selected for intensive study due to its visitor status and location in the region near Palmer Station. This will allow for comparative data with the Palmer Long Term Ecological Research program. Demographic data will be collected in accordance with Standard Methods established by the Convention for the Conservation of Antarctic Marine Living Resources Ecosystem Monitoring Program and thus will be comparable with similar data sets being collected by other international Antarctic Treaty nation research programs. While separating human-induced change from change resulting from a combination of environmental factors will be difficult, this work will provide a first step to identify potential impacts. These long-term data sets will contribute to a better understanding of biological processes in the entire region and will contribute valuable information to be used by the Antarctic Treaty Parties as they address issues in environmental stewardship in Antarctica.

Adelie penguin diet composition, secondary prey items, 1991 - present.\t. The fundamental long-term objective of the seabird component of the Palmer LTER (PAL) has been to identify and understand the mechanistic processes that regulate the mean fitness (population growth rate) of regional penguin populations. Two hypotheses have guided this research, with one suggesting that population mean fitness is best explained by changes in regional krill biomass, and the other proposing that long-term changes in sea ice affects mean fitness by tipping the balance in favor of one species over another in accordance with species-specific evolved life history affinities to sea ice. Although these hypotheses are not mutually exclusive, current evidence in the PAL region tends to favor the latter over the former. Since the inception of PAL, Adélie penguin populations have effectively collapsed, while those of gentoo and chinstrap penguins have increased dramatically, trends that are spatially and temporally coherent with decreasing regional sea ice duration. Adélie penguins are an ice-obligate polar species whose life history is intimately linked to the presence of sea ice, while chinstrap and gentoo penguins are ice-intolerant species whose life histories evolved in the sub-Antarctic, where sea ice is a less permanent feature of the marine ecosystem. In contrast, although krill constitute the most important component of the summer diets by mass of these three penguin species, changes in PAL krill abundances have exhibited no long-term trends, and thus fail to explain the divergent patterns in penguin populations evident in our time series.

Besides krill and fish, a number of secondary prey items (see DIET) can be found in Adélie penguin diets, including octopus, squid, amphipods, mysid shrimp, limpets and small clams. One or more of these prey types may occur frequently in the samples, but very rarely in abundance, hence recorded metrics are limited to detailing the number of specimens observed and obtaining weights if warranted by the sample size. One exception concerns squid and octopus beaks, which like fish otoliths can be identified to species and the size and mass of individuals reconstituted based on regressions that use beak length to determine relational metrics. Like otoliths, beaks are also processed by experts outside PAL (see FISH), hence similar time lags exist in database integration. What role these less abundant prey items have in Adélie penguin diets is unknown, but paleoecological evidence suggests that squid in particular were once consumed much more frequently in the PAL region than they are now.

_NCProperties=version=1|netcdflibversion=4.6.1|hdf5libversion=1.10.6 acknowledgement=Funding and support provided by the National Science Foundation cdm_data_type=Other comment=The Palmer, Antarctica, Long-Term Ecological Research project is a member site of the Long-Term Ecological Research program, a network of sites investigating diverse biomes. A team of researchers seeks to understand the structure and function of the Western Antarctic Peninsula's marine and terrestrial ecosystems in the context of seasonal-to-interannual atmospheric and sea ice dynamics, as well as long-term climate change. The PAL measurement system (or grid) is designed to study marine and terrestrial food webs consisting principally of diatom primary producers, the dominant herbivore Antarctic krill, and the apex predator Adelie penguin. An attenuated microbial food web is also a focus. PAL studies these ecosystems annually over a regional scale grid of oceanographic stations and seasonally at Palmer Station.

Palmer Station is located on Anvers Island west of the Antarctic Peninula. The peninsula runs perpendicular to a strong climatic gradient between the cold, dry continental regime to the south, characteristic of the Antarctic interior, and the warm, moist, maritime regime to the north. North-south shifts in the gradient give rise to large environmental variability to climate change. Sea ice extent and variability affects ecosystem changes at all trophic levels. In addition to the long-term field and research activities, information management, graduate student training, education and outreach are an integral part of the program. contributor_email=bfraser@3rivers.net contributor_name=William Fraser contributor_role=PrincipalInvestigator contributor_role_vocabulary=https://vocab.nerc.ac.uk/collection/G04/current/ Conventions=CF-1.8, ACDD-1.3, COARDS datazoo_dataset_id=98 datazoo_datatable_id=98 datazoo_datatable_label=Adelie Penguin Diet Composition, Other Prey datazoo_datatable_name=AdeliePenguinDietPreyotherthanFishandEuphausiasuberba defaultDataQuery=null defaultGraphQuery=time%2Cnum_prey%2Cevidence_size&.draw=markers&.marker=7%7C5&.color=0x000000&.colorBar=%7C%7C%7C%7C%7C&.bgColor=0xffccccff geospatial_bounds_crs=EPSG:4326 geospatial_bounds_vertical_crs=EPSG:5831 geospatial_lat_resolution=0.00001 degree geospatial_lat_units=degree_north geospatial_lon_resolution=0.00001 degree geospatial_lon_units=degree_east geospatial_vertical_positive=down geospatial_vertical_units=EPSG:5831 history=data_pallter_oi_datazoo_datatables.dat_98 infoUrl=https://pal.lternet.edu/ institution=National Science Foundation keywords_vocabulary=LTER Core Areas,LTER Controlled Vocabulary license_link=https://lternet.edu/data-access-policy/ naming_authority=edu.rutgers.rucool program=LTER project=Palmer LTER references=https://pal.lternet.edu/ sea_name=Southern Ocean source=/Users/kerfoot/data/lter/data/tsv/dat_98/dat_98_PAL1718.tsv sourceUrl=(local files) standard_name_vocabulary=CF Standard Name Table v77 subsetVariables=study_name time_coverage_end=2018-01-29T00:00:00Z time_coverage_start=1992-01-25T00:00:00Z