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Acknowledgements

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Thomas, R. Q., Boettiger, C., Carey, C. C., Dietze, M. C., Johnson, L. R., Kenney, M. A., et al. (2023). The NEON Ecological Forecasting Challenge. Frontiers in Ecology and the Environment, 21(3), 112–113. https://doi.org/10.1002/fee.2616

We thank NEON for providing the freely available data and the EFI community for feedback on the design of the Challenge. This material is based upon work supported by the National Science Foundation under Grant DEB-1926388.

Page last updated on 2024-03-06

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Thomas, R. Q., Boettiger, C., Carey, C. C., Dietze, M. C., Johnson, L. R., Kenney, M. A., et al. (2023). The NEON Ecological Forecasting Challenge. Frontiers in Ecology and the Environment, 21(3), 112–113. https://doi.org/10.1002/fee.2616

We thank NEON for providing the freely available data and the EFI community for feedback on the design of the Challenge. This material is based upon work supported by the National Science Foundation under Grant DEB-1926388.

Page last updated on 2024-03-08

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diff --git a/search.json b/search.json index 55dccd11aa..bb7ebd3a79 100644 --- a/search.json +++ b/search.json @@ -1,31 +1,73 @@ [ { - "objectID": "performance.html", - "href": "performance.html", - "title": "Forecast performance", + "objectID": "index.html", + "href": "index.html", + "title": "Forecasting Challenge", "section": "", - "text": "This page visualizes the forecasts and forecast performance for the focal target variables. Only forecasts from a subset of NEON sites are shown. If you want to see your forecasts or scores, the links can be found in our forecast catalog and scores catalog" + "text": "We invite you to submit forecasts!\nThe NEON Ecological Forecasting Challenge is an open platform for the ecological and data science communities to forecast data from the National Ecological Observatory Network before they are collected.\nThe Challenge is hosted by the Ecological Forecasting Initiative Research Coordination Network and sponsored by the U.S. National Science Foundation." }, { - "objectID": "performance.html#sec-performance", - "href": "performance.html#sec-performance", - "title": "Forecast performance", - "section": "Most recent forecasts", - "text": "Most recent forecasts\nOnly the top-performing models from the last 30 days are shown.\nForecasts submitted on 2024-03-04\n\nTerrestrial: net ecosystem exchangeTerrestrial: latent heat fluxPhenology: greennessPhenology: rednessAquatics: water temperatureAquatics: dissolved oxygenAquatics: chlorophyll-aBeetle community richnessBeetle community abundanceTicks: Amblyomma americanum\n\n\nForecast summaries are available here\n\n\n\n\n\n\n\n\nForecast summaries are available here\n\n\n\n\n\n\n\n\nForecast summaries are available here\n\n\n\n\n\n\n\n\nForecast summaries are available here\n\n\n\n\n\n\n\n\nForecast summaries are available here\n\n\n\n\n\n\n\n\nForecast summaries are available here\n\n\n\n\n\n\n\n\nForecast summaries are available here\n\n\n\n\n\n\n\n\nForecast summaries are available here\n\n\n\n\n\n\n\n\nForecast summaries are available here\n\n\n\n\n\n\n\n\nForecast summaries are available here" + "objectID": "index.html#why-a-forecasting-challenge", + "href": "index.html#why-a-forecasting-challenge", + "title": "Forecasting Challenge", + "section": "Why a forecasting challenge?", + "text": "Why a forecasting challenge?\nOur vision is to use forecasts to advance theory and to support natural resource management. We can begin to realize this vision by creating and analyzing a catalog of forecasts from a range of ecological systems, spatiotemporal scales, and environmental gradients.\nOur forecasting challenge is platform for the ecological and data science communities to advance skills in forecasting ecological systems and for generating forecasts that contribute to a synthetic understanding of patterns of predictability in ecology. Rewards for contributing are skill advancement, joy, and potential involved in manuscripts. We do not currently crown winner nor offer financial awards.\nThe Challenge is an excellent focal project in university courses.\n \n\n\n\n\n\n\n\n\n\nTotal forecasts submitted to the NEON Challenge\n6193\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nMost recent data for model training\n2024-03-06\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nNumber of years of data for model training\n10.69\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nNumber of variables being forecasted\n10" }, { - "objectID": "performance.html#forecast-analysis", - "href": "performance.html#forecast-analysis", - "title": "Forecast performance", - "section": "Forecast analysis", - "text": "Forecast analysis\nBelow are forecasts submitted 30 days ago and include the observations used to evaluate them. Mouse over to see the team id, scroll to zoom. Only the top five performing models are shown. Information on how to access the scores can be found in our catalog\n\nTerrestrial: net ecosystem exchangeTerrestrial: latent heat fluxPhenology: greennessPhenology: rednessAquatics: water temperatureAquatics: dissolved oxygenAquatics: chlorophyll-aBeetle community richnessBeetle community abundanceTicks: Amblyomma americanum" + "objectID": "index.html#the-challenge-is-a-platform", + "href": "index.html#the-challenge-is-a-platform", + "title": "Forecasting Challenge", + "section": "The Challenge is a platform", + "text": "The Challenge is a platform\nOur platform is designed to empower you to contribute by providing target data, numerical weather forecasts, and tutorials. We automatically score your forecasts using the latest NEON data. All forecasts and scores are publicly available through cloud storage and discoverable through our catalog.\n \nFigure from Thomas et al. 2023" }, { - "objectID": "performance.html#aggregated-scores", - "href": "performance.html#aggregated-scores", - "title": "Forecast performance", - "section": "Aggregated scores", - "text": "Aggregated scores\nAverage skill scores of each model across all sites.\n\nScores are shown by reference date and forecast horizon (in days).\n\nScores are averaged across all submissions of the model with a given horizon or a given reference_datetime using submissions made since in the last 30 days for the daily or sub-daily variables and the past year for the weekly variables\n\nLearn about the continuous ranked probability score here\n\nTerrestrial: Net Ecosystem ExchangeTerrestrial: Latent Heat FluxPhenology: GreenessPhenology: RednessAquatics: water temperatureAquatics: dissolved oxygenAquatics: chrophyll-aBeetle community richnessBeetle community abundanceTicks: Amblyomma americanum" + "objectID": "index.html#contact", + "href": "index.html#contact", + "title": "Forecasting Challenge", + "section": "Contact", + "text": "Contact\neco4cast.initiative@gmail.com" + }, + { + "objectID": "index.html#acknowledgements", + "href": "index.html#acknowledgements", + "title": "Forecasting Challenge", + "section": "Acknowledgements", + "text": "Acknowledgements\nThomas, R. Q., Boettiger, C., Carey, C. C., Dietze, M. C., Johnson, L. R., Kenney, M. A., et al. (2023). The NEON Ecological Forecasting Challenge. Frontiers in Ecology and the Environment, 21(3), 112–113. https://doi.org/10.1002/fee.2616 We thank NEON for providing the freely available data and the EFI community for feedback on the design of the Challenge. This material is based upon work supported by the National Science Foundation under Grant DEB-1926388. Page last updated on 2024-03-08" + }, + { + "objectID": "targets.html", + "href": "targets.html", + "title": "What to forecast", + "section": "", + "text": "The “targets” are time-series of National Ecological Observatory Network (NEON) data for use in model development and forecast evaluation.\nThe targets are updated as new NEON data is made available.\nThe 10 targets were specifically chosen to include ecosystem, community, and population dynamics and are represented by five “themes”. The themes and links to targets files are included below." + }, + { + "objectID": "targets.html#tldr-forecast-the-targets", + "href": "targets.html#tldr-forecast-the-targets", + "title": "What to forecast", + "section": "", + "text": "The “targets” are time-series of National Ecological Observatory Network (NEON) data for use in model development and forecast evaluation.\nThe targets are updated as new NEON data is made available.\nThe 10 targets were specifically chosen to include ecosystem, community, and population dynamics and are represented by five “themes”. The themes and links to targets files are included below." + }, + { + "objectID": "targets.html#sec-starting-sites", + "href": "targets.html#sec-starting-sites", + "title": "What to forecast", + "section": "Where to start", + "text": "Where to start\nIf are you are getting started, we recommend the following focal sites for each of the five “themes”. The first site in the list is the recommended starting site.\n\nTerrestrial: BART, OSBS, KONZ, SRER\nAquatics: BARC, CRAM\nPhenology: HARV, BART, STEI, UKFS, GRSM, DELA, CLBJ\nBeetles: BLAN, OSBS\nTicks: BLAN, TALL\n\nAs you develop your forecasting skills and want to expand to more sites, the targets are available at all 81 NEON sites. You may also consider submitting forecasts to sites that match your interests. For example, a class being taught in the winter may be more interested in forecasting southern sites while a summer class may focus on more northern sites.\nMore information about NEON sites can be found in the site metadata and on NEON’s website" + }, + { + "objectID": "targets.html#sec-targets", + "href": "targets.html#sec-targets", + "title": "What to forecast", + "section": "Explore the targets and themes", + "text": "Explore the targets and themes\nInformation on the targets files for the five “themes” is below. In the tables,\n\n“duration” is the time-step of the variable where PT30M is a 30-minute mean, P1D is a daily mean, and P1W is a weekly total.\nThe “forecast horizon” is the number of days-ahead that we want you to forecast.\nThe “latency” is the time between data collection and data availability in the targets file\n\n\nTerrestrial fluxesAquaticsPhenologyBeetle communitiesTick populations\n\n\n\nThe exchange of water and carbon dioxide between the atmosphere and the land is akin to earth’s terrestrial ecosystems breathing rate and lung capacity. \nThe terrestrial flux theme challenges you to forecast the gas exchange at up to 47 sites across the U.S.\nThere are two variables and two time-steps (or duration) that you can forecast.\n\n\n\n\n\n\n\n\n\n\n\n\nvariable\nduration\nDescription\nforecast horizon\nLatency\n\n\n\n\nle\nP1D\ndaily mean latent heat flux (W/m2)\n30 days\n~ 5 days\n\n\nnee\nP1D\ndaily mean Net ecosystem exchange (gC/m2/day)\n30 days\n~ 5 days\n\n\nle\nPT30M\n30 minute mean latent heat flux (W/m2)\n10 days\n~ 5 days\n\n\nnee\nPT30M\n30 minute mean net ecosystem exchange (umol/m2/s)\n10 days\n~ 5 days\n\n\n\n\n\n\nDaily mean\nThe daily mean target file is located at the following URL.\n\nurl_P1D <- \"https://sdsc.osn.xsede.org/bio230014-bucket01/challenges/targets/project_id=neon4cast/duration=P1D/terrestrial_daily-targets.csv.gz\"\n\nYou can directly load it into R using the following\n\nterrestrial_targets <- read_csv(url_P1D, show_col_types = FALSE)\n\nThe file contains the following columns\n\n\n\n\n\nproject_id\nsite_id\ndatetime\nduration\nvariable\nobservation\n\n\n\n\nneon4cast\nBART\n2017-02-06\nP1D\nle\n11.5794551\n\n\nneon4cast\nBART\n2017-02-07\nP1D\nle\n4.8951620\n\n\nneon4cast\nBART\n2017-02-09\nP1D\nle\n7.5281656\n\n\nneon4cast\nBART\n2017-02-11\nP1D\nle\n1.1577581\n\n\nneon4cast\nBART\n2017-02-12\nP1D\nle\n0.1999174\n\n\nneon4cast\nBART\n2017-02-13\nP1D\nle\n10.9325370\n\n\n\n\n\nand the time series for the focal sites\n\nterrestrial_targets |> \n filter(site_id %in% terrestrial_focal_sites) |> \n ggplot(aes(x = datetime, y = observation)) +\n geom_point() +\n facet_grid(variable~site_id, scales = \"free_y\") +\n theme_bw()\n\n\n\n\n\n\n30 minute\nThe 30 minute duration targets are designed for forecasting sub-daily carbon and water dynamics. The URL is found at:\n\nurl_PT30M <- \"https://sdsc.osn.xsede.org/bio230014-bucket01/challenges/targets/project_id=neon4cast/duration=PT30M/terrestrial_30min-targets.csv.gz\"\n\nLearn more at: https://projects.ecoforecast.org/neon4cast-docs/Terrestrial.html\n\n\n\n\nFreshwater surface water temperature, dissolved oxygen, and chlorophyll-a all influence drinking water quality, are critical for life in aquatic environments, and can represent the health of the ecosystem.\nThe aquatics theme challenges you to forecast daily mean water quality variables at up-to 7 lakes and 27 river/stream NEON sites.\n\n\n\n\n\n\n\n\n\n\n\n\nvariable\nduration\nDescription\nhorizon\nLatency\n\n\n\n\nchla\nP1D\ndaily mean Chlorophyll-a (ug/L)\n30 days\n~ 3 days\n\n\noxygen\nP1D\nSurface Mean Daily Dissolved Oxygen Concentration (mgL)\n30 days\n~ 3 days\n\n\ntemperature\nP1D\nSurface Mean Daily Water Temperature (Celsius)\n30 days\n~ 3 days\n\n\n\n\n\nThe daily mean target file is located at the following URL.\n\nurl <- \"https://sdsc.osn.xsede.org/bio230014-bucket01/challenges/targets/project_id=neon4cast/duration=P1D/aquatics-targets.csv.gz\"\n\nYou can directly load it into R using the following\n\naquatics_targets <- read_csv(url, show_col_types = FALSE)\n\nThe file contains the following columns\n\n\n\n\n\nproject_id\nsite_id\ndatetime\nduration\nvariable\nobservation\n\n\n\n\nneon4cast\nARIK\n2016-08-12\nP1D\noxygen\n3.402153\n\n\nneon4cast\nARIK\n2016-08-13\nP1D\noxygen\n4.156236\n\n\nneon4cast\nARIK\n2016-08-14\nP1D\noxygen\n4.071263\n\n\nneon4cast\nARIK\n2016-08-15\nP1D\noxygen\n3.909114\n\n\nneon4cast\nARIK\n2016-08-16\nP1D\noxygen\n3.862653\n\n\nneon4cast\nARIK\n2016-08-17\nP1D\noxygen\n4.354618\n\n\n\n\n\nand the time series for the focal sites\n\naquatics_targets |> \n filter(site_id %in% aquatics_focal_sites) |> \n ggplot(aes(x = datetime, y = observation)) +\n geom_point() +\n facet_grid(variable~site_id, scales = \"free_y\") +\n theme_bw()\n\nWarning: Removed 941 rows containing missing values or values outside the scale range\n(`geom_point()`).\n\n\n\n\n\nWater temperature at multiple depths measured at the UTC 00 hour are available for the 7 NEON lake sites. These data can be used for model development but will not be used for forecast evaluation.\n\nurl <- \"https://sdsc.osn.xsede.org/bio230014-bucket01/challenges/supporting_data/project_id=neon4cast/aquatics-expanded-observations.csv.gz\"\n\nLearn more at: https://projects.ecoforecast.org/neon4cast-docs/Aquatics.html\n\n\n\nPhenology (the changes in plant canopies over the year) has been identified as one of the primary ecological fingerprints of global climate change.\nThe greenness and redness, as measured by a camera looking down at the top of vegetation are a quantitative measure of phenology. The phenology theme challenges you to forecast daily mean greeness and/or redness at up-to 47 terrestrial NEON sites.\n\nurl <- \"https://sdsc.osn.xsede.org/bio230014-bucket01/challenges/targets/project_id=neon4cast/duration=P1D/phenology-targets.csv.gz\"\nread_csv(url, show_col_types = FALSE) |> \n distinct(variable, duration) |> \n left_join(target_metadata, by = c(\"variable\",\"duration\")) |> \n filter(variable %in% c(\"gcc_90\",\"rcc_90\")) |> \n select(-class) |> \n knitr::kable()\n\n\n\n\n\n\n\n\n\n\n\nvariable\nduration\nDescription\nhorizon\nLatency\n\n\n\n\ngcc_90\nP1D\nGreen chromatic coordinate is the ratio of the green digital number to the sum of the red, green, blue digital numbers from a digital camera.\n30 days\n~ 2 days\n\n\nrcc_90\nP1D\nRed chromatic coordinate is the ratio of the Red digital number to the sum of the red, green, blue digital numbers from a digital camera.\n30 days\n~ 2 days\n\n\n\n\n\nThe daily mean target file is located at the following URL.\n\nurl <- \"https://sdsc.osn.xsede.org/bio230014-bucket01/challenges/targets/project_id=neon4cast/duration=P1D/phenology-targets.csv.gz\"\n\nYou can directly load it into R using the following\n\nphenology_targets <- read_csv(url, show_col_types = FALSE)\n\nThe file contains the following columns\n\n\n\n\n\nproject_id\nsite_id\ndatetime\nduration\nvariable\nobservation\n\n\n\n\nneon4cast\nABBY\n2017-05-30\nP1D\ngcc_90\n0.41659\n\n\nneon4cast\nABBY\n2017-05-31\nP1D\ngcc_90\n0.41570\n\n\nneon4cast\nABBY\n2017-06-01\nP1D\ngcc_90\n0.41780\n\n\nneon4cast\nABBY\n2017-06-02\nP1D\ngcc_90\n0.41539\n\n\nneon4cast\nABBY\n2017-06-03\nP1D\ngcc_90\n0.42216\n\n\nneon4cast\nABBY\n2017-06-04\nP1D\ngcc_90\n0.41659\n\n\n\n\n\nand the time series for the focal sites\n\nphenology_targets |> \n filter(site_id %in% phenology_focal_sites) |> \n ggplot(aes(x = datetime, y = observation)) +\n geom_point() +\n facet_grid(variable~site_id, scales = \"free_y\") +\n theme_bw()\n\nWarning: Removed 8178 rows containing missing values or values outside the scale range\n(`geom_point()`).\n\n\n\n\n\nLearn more at: https://projects.ecoforecast.org/neon4cast-docs/Phenology.html\n\n\n\nSentinel species (such as beetles) can give forewarning of environmental risk to humans, so are particularly useful for such monitoring and forecasting efforts because they can provide surrogates for other co-located components of biodiversity.\nThe beetles theme challenges you to forecast weekly ground beetles (Family: Carabidae) abundance and richness (two measures of biodiversity) at up-to 47 terrestrial NEON sites.\n\n\n\n\n\n\n\n\n\n\n\n\nvariable\nduration\nDescription\nhorizon\nLatency\n\n\n\n\nabundance\nP1W\nTotal number of carabid individuals per trap-night, estimated each week of the year at each NEON site\n1 year\n~ 6 months\n\n\nrichness\nP1W\nTotal number of unique ‘species’ in a sampling bout for each NEON site each week.\n1 year\n~ 6 months\n\n\n\n\n\nThe daily mean target file is located at the following URL.\n\nurl <- \"https://sdsc.osn.xsede.org/bio230014-bucket01/challenges/targets/project_id=neon4cast/duration=P1W/beetles-targets.csv.gz\"\n\nYou can directly load it into R using the following\n\nbeetles_targets <- read_csv(url, show_col_types = FALSE)\n\nThe file contains the following columns\n\n\n\n\n\nproject_id\nsite_id\ndatetime\nduration\nvariable\nobservation\n\n\n\n\nneon4cast\nABBY\n2016-09-12\nP1W\nabundance\n1.0489796\n\n\nneon4cast\nABBY\n2016-09-12\nP1W\nrichness\n14.0000000\n\n\nneon4cast\nABBY\n2016-09-26\nP1W\nabundance\n4.4535714\n\n\nneon4cast\nABBY\n2016-09-26\nP1W\nrichness\n13.0000000\n\n\nneon4cast\nABBY\n2017-05-01\nP1W\nabundance\n0.0553571\n\n\nneon4cast\nABBY\n2017-05-01\nP1W\nrichness\n10.0000000\n\n\n\n\n\nand the time series for the focal sites\n\nbeetles_targets |> \n filter(site_id %in% beetles_focal_sites) |> \n ggplot(aes(x = datetime, y = observation)) +\n geom_point() +\n facet_grid(variable~site_id, scales = \"free_y\") +\n theme_bw()\n\n\n\n\nLearn more at: https://projects.ecoforecast.org/neon4cast-docs/Beetles.html\n\n\n\nTarget species for the tick population forecasts are Amblyomma americanum nymphal ticks. A. americanum is a vector of ehrlichiosis, tularemia, and southern tick-associated rash illness. The species is present in the eastern United States, and their populations are expanding. There is a correlation between tick population abundance and disease incidence, meaning forecasts for tick abundance have the potential to aid in our understanding of disease risk through time and space.\nThe beetles theme challenges you to forecast weekly Amblyomma americanum nymphal tick abundance at up-to 9 terrestrial NEON sites.\n\n\n\n\n\n\n\n\n\n\n\n\nvariable\nduration\nDescription\nhorizon\nLatency\n\n\n\n\namblyomma_americanum\nP1W\nThe density of Amblyomma americanum nymphs per week (ticks per 1600m^2)\n1 year\n~ 6 months\n\n\n\n\n\nThe weekly target file is located at the following URL.\n\n\"https://sdsc.osn.xsede.org/bio230014-bucket01/challenges/targets/project_id=neon4cast/duration=P1W/ticks-targets.csv.gz\"\n\n[1] \"https://sdsc.osn.xsede.org/bio230014-bucket01/challenges/targets/project_id=neon4cast/duration=P1W/ticks-targets.csv.gz\"\n\n\nYou can directly load it into R using the following\n\nticks_targets <- read_csv(url, show_col_types = FALSE)\n\nThe file contains the following columns\n\n\n\n\n\n\n\n\n\n\n\n\n\nproject_id\nsite_id\ndatetime\nduration\nvariable\nobservation\n\n\n\n\nneon4cast\nBLAN\n2015-04-20\nP1W\namblyomma_americanum\n0.000000\n\n\nneon4cast\nBLAN\n2015-05-11\nP1W\namblyomma_americanum\n9.815951\n\n\nneon4cast\nBLAN\n2015-06-01\nP1W\namblyomma_americanum\n10.000000\n\n\nneon4cast\nBLAN\n2015-06-08\nP1W\namblyomma_americanum\n19.393939\n\n\nneon4cast\nBLAN\n2015-06-22\nP1W\namblyomma_americanum\n3.137255\n\n\nneon4cast\nBLAN\n2015-07-13\nP1W\namblyomma_americanum\n3.661327\n\n\n\n\n\nand the time series for the focal sites\n\nticks_targets |> \n filter(site_id %in% ticks_focal_sites) |> \n ggplot(aes(x = datetime, y = observation)) +\n geom_point() +\n facet_grid(variable~site_id, scales = \"free_y\") +\n theme_bw()\n\n\n\n\nLearn more at: https://projects.ecoforecast.org/neon4cast-docs/Ticks.html" + }, + { + "objectID": "targets.html#explore-the-sites", + "href": "targets.html#explore-the-sites", + "title": "What to forecast", + "section": "Explore the sites", + "text": "Explore the sites\n\n\n\n\n\n\n The following table lists all the sites in the NEON Ecological Forecasting Challenge. The columns with “theme” names incidate whether that site is included in that theme’s target file.\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nsite_id\nfield_site_name\nterrestrial\naquatics\nphenology\nticks\nbeetles\n\n\n\n\nABBY\nAbby Road NEON\n1\n0\n1\n0\n1\n\n\nARIK\nArikaree River NEON\n0\n1\n0\n0\n0\n\n\nBARC\nLake Barco NEON\n0\n1\n0\n0\n0\n\n\nBARR\nUtqiaġvik NEON\n1\n0\n1\n0\n1\n\n\nBART\nBartlett Experimental Forest NEON\n1\n0\n1\n0\n1\n\n\nBIGC\nUpper Big Creek NEON\n0\n1\n0\n0\n0\n\n\nBLAN\nBlandy Experimental Farm NEON\n1\n0\n1\n1\n1\n\n\nBLDE\nBlacktail Deer Creek NEON\n0\n1\n0\n0\n0\n\n\nBLUE\nBlue River NEON\n0\n1\n0\n0\n0\n\n\nBLWA\nBlack Warrior River NEON\n0\n1\n0\n0\n0\n\n\nBONA\nCaribou-Poker Creeks Research Watershed NEON\n1\n0\n1\n0\n1\n\n\nCARI\nCaribou Creek NEON\n0\n1\n0\n0\n0\n\n\nCLBJ\nLyndon B. Johnson National Grassland NEON\n1\n0\n1\n0\n1\n\n\nCOMO\nComo Creek NEON\n0\n1\n0\n0\n0\n\n\nCPER\nCentral Plains Experimental Range NEON\n1\n0\n1\n0\n1\n\n\nCRAM\nCrampton Lake NEON\n0\n1\n0\n0\n0\n\n\nCUPE\nRio Cupeyes NEON\n0\n1\n0\n0\n0\n\n\nDCFS\nDakota Coteau Field Site NEON\n1\n0\n1\n0\n1\n\n\nDEJU\nDelta Junction NEON\n1\n0\n1\n0\n1\n\n\nDELA\nDead Lake NEON\n1\n0\n1\n0\n1\n\n\nDSNY\nDisney Wilderness Preserve NEON\n1\n0\n1\n0\n1\n\n\nFLNT\nFlint River NEON\n0\n1\n0\n0\n0\n\n\nGRSM\nGreat Smoky Mountains National Park NEON\n1\n0\n1\n0\n1\n\n\nGUAN\nGuanica Forest NEON\n1\n0\n1\n0\n1\n\n\nGUIL\nRio Guilarte NEON\n0\n1\n0\n0\n0\n\n\nHARV\nHarvard Forest & Quabbin Watershed NEON\n1\n0\n1\n0\n1\n\n\nHEAL\nHealy NEON\n1\n0\n1\n0\n1\n\n\nHOPB\nLower Hop Brook NEON\n0\n1\n0\n0\n0\n\n\nJERC\nThe Jones Center At Ichauway NEON\n1\n0\n1\n0\n1\n\n\nJORN\nJornada Experimental Range NEON\n1\n0\n1\n0\n1\n\n\nKING\nKings Creek NEON\n0\n1\n0\n0\n0\n\n\nKONA\nKonza Prairie Agroecosystem NEON\n1\n0\n1\n0\n1\n\n\nKONZ\nKonza Prairie Biological Station NEON\n1\n0\n1\n1\n1\n\n\nLAJA\nLajas Experimental Station NEON\n1\n0\n1\n0\n1\n\n\nLECO\nLeConte Creek NEON\n0\n1\n0\n0\n0\n\n\nLENO\nLenoir Landing NEON\n1\n0\n1\n1\n1\n\n\nLEWI\nLewis Run NEON\n0\n1\n0\n0\n0\n\n\nLIRO\nLittle Rock Lake NEON\n0\n1\n0\n0\n0\n\n\nMART\nMartha Creek NEON\n0\n1\n0\n0\n0\n\n\nMAYF\nMayfield Creek NEON\n0\n1\n0\n0\n0\n\n\nMCDI\nMcDiffett Creek NEON\n0\n1\n0\n0\n0\n\n\nMCRA\nMcRae Creek NEON\n0\n1\n0\n0\n0\n\n\nMLBS\nMountain Lake Biological Station NEON\n1\n0\n1\n0\n1\n\n\nMOAB\nMoab NEON\n1\n0\n1\n0\n1\n\n\nNIWO\nNiwot Ridge NEON\n1\n0\n1\n0\n1\n\n\nNOGP\nNorthern Great Plains Research Laboratory NEON\n1\n0\n1\n0\n1\n\n\nOAES\nMarvin Klemme Range Research Station NEON\n1\n0\n1\n0\n1\n\n\nOKSR\nOksrukuyik Creek NEON\n0\n1\n0\n0\n0\n\n\nONAQ\nOnaqui NEON\n1\n0\n1\n0\n1\n\n\nORNL\nOak Ridge NEON\n1\n0\n1\n1\n1\n\n\nOSBS\nOrdway-Swisher Biological Station NEON\n1\n0\n1\n1\n1\n\n\nPOSE\nPosey Creek NEON\n0\n1\n0\n0\n0\n\n\nPRIN\nPringle Creek NEON\n0\n1\n0\n0\n0\n\n\nPRLA\nPrairie Lake NEON\n0\n1\n0\n0\n0\n\n\nPRPO\nPrairie Pothole NEON\n0\n1\n0\n0\n0\n\n\nPUUM\nPu’u Maka’ala Natural Area Reserve NEON\n1\n0\n1\n0\n1\n\n\nREDB\nRed Butte Creek NEON\n0\n1\n0\n0\n0\n\n\nRMNP\nRocky Mountains NEON\n1\n0\n1\n0\n1\n\n\nSCBI\nSmithsonian Conservation Biology Institute NEON\n1\n0\n1\n1\n1\n\n\nSERC\nSmithsonian Environmental Research Center NEON\n1\n0\n1\n1\n1\n\n\nSJER\nSan Joaquin Experimental Range NEON\n1\n0\n1\n0\n1\n\n\nSOAP\nSoaproot Saddle NEON\n1\n0\n1\n0\n1\n\n\nSRER\nSanta Rita Experimental Range NEON\n1\n0\n1\n0\n1\n\n\nSTEI\nSteigerwaldt-Chequamegon NEON\n1\n0\n1\n0\n1\n\n\nSTER\nNorth Sterling NEON\n1\n0\n1\n0\n1\n\n\nSUGG\nLake Suggs NEON\n0\n1\n0\n0\n0\n\n\nSYCA\nSycamore Creek NEON\n0\n1\n0\n0\n0\n\n\nTALL\nTalladega National Forest NEON\n1\n0\n1\n1\n1\n\n\nTEAK\nLower Teakettle NEON\n1\n0\n1\n0\n1\n\n\nTECR\nTeakettle Creek - Watershed 2 NEON\n0\n1\n0\n0\n0\n\n\nTOMB\nLower Tombigbee River NEON\n0\n1\n0\n0\n0\n\n\nTOOK\nToolik Lake NEON\n0\n1\n0\n0\n0\n\n\nTOOL\nToolik Field Station NEON\n1\n0\n1\n0\n1\n\n\nTREE\nTreehaven NEON\n1\n0\n1\n0\n1\n\n\nUKFS\nUniversity of Kansas Field Station NEON\n1\n0\n1\n1\n1\n\n\nUNDE\nUniversity of Notre Dame Environmental Research Center NEON\n1\n0\n1\n0\n1\n\n\nWALK\nWalker Branch NEON\n0\n1\n0\n0\n0\n\n\nWLOU\nWest St Louis Creek NEON\n0\n1\n0\n0\n0\n\n\nWOOD\nChase Lake National Wildlife Refuge NEON\n1\n0\n1\n0\n1\n\n\nWREF\nWind River Experimental Forest NEON\n1\n0\n1\n0\n1\n\n\nYELL\nYellowstone National Park NEON\n1\n0\n1\n0\n1" }, { "objectID": "learn-more.html", @@ -49,39 +91,25 @@ "text": "Lewis, A., W. Woelmer, H. Wander, D. Howard, J. Smith, R. McClure, M. Lofton, N. Hammond, R. Corrigan, R.Q. Thomas, C.C. Carey. 2022. Increased adoption of best practices in ecological forecasting enables comparisons of forecastability across systems. Ecological Applications 32: e02500 https://doi.org/10.1002/eap.2500\nLewis, A. S. L., Rollinson, C. R., Allyn, A. J., Ashander, J., Brodie, S., Brookson, C. B., et al. (2023). The power of forecasts to advance ecological theory. Methods in Ecology and Evolution, 14(3), 746–756. https://doi.org/10.1111/2041-210X.13955\n\n\n\nThomas, R. Q., Boettiger, C., Carey, C. C., Dietze, M. C., Johnson, L. R., Kenney, M. A., et al. (2023). The NEON Ecological Forecasting Challenge. Frontiers in Ecology and the Environment, 21(3), 112–113. https://doi.org/10.1002/fee.2616\nThomas, R.Q, R.P. McClure, T.N. Moore, W.M. Woelmer, C. Boettiger, R.J. Figueiredo, R.T. Hensley, C.C. Carey. Near-term forecasts of NEON lakes reveal gradients of environmental predictability across the U.S. Frontiers in Ecology and Environment 21: 220–226. https://doi.org/10.1002/fee.2623\nWheeler, K., M. Dietze, D. LeBauer, J. Peters, A.D. Richardson, R.Q. Thomas, K. Zhu, U. Bhat, S. Munch, R.F Buzbee, M. Chen, B. Goldstein, J.S. Guo, D. Hao, C. Jones, M. Kelly-Fair, H. Liu, C. Malmborg, N. Neupane. D. Pal, A. Ross, V. Shirey, Y. Song, M. Steen, E.A. Vance, W.M. Woelmer, J. Wynne and L. Zachmann. Predicting Spring Phenology in Deciduous Broadleaf Forests: An Open Community Forecast Challenge.\n\n\n\nDietze, M., R.Q. Thomas, J. Peters, C. Boettiger, A. Shiklomanov, and J. Ashander. 2023. A community convention for ecological forecasting: output files and metadata v1.0. Ecosphere 14: e4686 https://doi.org/10.1002/ecs2.4686\n\n\n\nMoore, T.N., R.Q. Thomas, W.M. Woelmer, C.C Carey. 2022. Integrating ecological forecasting into undergraduate ecology curricula with an R Shiny application-based teaching module. Forecasting 4:604-633. https://doi.org/10.3390/forecast4030033\nPeters, J. and R.Q. Thomas. 2021. Going Virtual: What We Learned from the Ecological Forecasting Initiative Research Coordination Network Virtual Workshop. Bulletin of the Ecological Society of America 102: e01828 https://doi.org/10.1002/bes2.1828\nWillson, A.M., H. Gallo, J.A. Peters, A. Abeyta, N. Bueno Watts, C.C. Carey, T.N. Moore, G. Smies, R.Q. Thomas, W.M. Woelmer, and J.S. McLachlan. 2023. Assessing opportunities and inequities in undergraduate ecological forecasting education. Ecology and Evolution 13: e10001. https://doi.org/10.1002/ece3.10001\nWoelmer, W. M., Bradley, L. M., Haber, L. T., Klinges, D. H., Lewis, A. S. L., Mohr, E. J., et al. (2021). Ten simple rules for training yourself in an emerging field. PLOS Computational Biology, 17(10), e1009440. https://doi.org/10.1371/journal.pcbi.1009440\nWoelmer, W.M., T.N. Moore, M.E. Lofton, R.Q. Thomas, and C.C. Carey. 2023. Embedding communication concepts in forecasting training increases students’ understanding of ecological uncertainty Ecosphere 14: e4628 https://doi.org/10.1002/ecs2.4628" }, { - "objectID": "index.html", - "href": "index.html", - "title": "Forecasting Challenge", + "objectID": "catalog.html", + "href": "catalog.html", + "title": "Forecast catalog", "section": "", - "text": "We invite you to submit forecasts!\nThe NEON Ecological Forecasting Challenge is an open platform for the ecological and data science communities to forecast data from the National Ecological Observatory Network before they are collected.\nThe Challenge is hosted by the Ecological Forecasting Initiative Research Coordination Network and sponsored by the U.S. National Science Foundation." - }, - { - "objectID": "index.html#why-a-forecasting-challenge", - "href": "index.html#why-a-forecasting-challenge", - "title": "Forecasting Challenge", - "section": "Why a forecasting challenge?", - "text": "Why a forecasting challenge?\nOur vision is to use forecasts to advance theory and to support natural resource management. We can begin to realize this vision by creating and analyzing a catalog of forecasts from a range of ecological systems, spatiotemporal scales, and environmental gradients.\nOur forecasting challenge is platform for the ecological and data science communities to advance skills in forecasting ecological systems and for generating forecasts that contribute to a synthetic understanding of patterns of predictability in ecology. Rewards for contributing are skill advancement, joy, and potential involved in manuscripts. We do not currently crown winner nor offer financial awards.\nThe Challenge is an excellent focal project in university courses.\n \n\n\n\n\n\n\n\n\n\nTotal forecasts submitted to the NEON Challenge\n6158\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nMost recent data for model training\n2024-03-04\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nNumber of years of data for model training\n10.68\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nNumber of variables being forecasted\n10" - }, - { - "objectID": "index.html#the-challenge-is-a-platform", - "href": "index.html#the-challenge-is-a-platform", - "title": "Forecasting Challenge", - "section": "The Challenge is a platform", - "text": "The Challenge is a platform\nOur platform is designed to empower you to contribute by providing target data, numerical weather forecasts, and tutorials. We automatically score your forecasts using the latest NEON data. All forecasts and scores are publicly available through cloud storage and discoverable through our catalog.\n \nFigure from Thomas et al. 2023" + "text": "Note: This figure will become more complete, as more models register and provide model descriptions" }, { - "objectID": "index.html#contact", - "href": "index.html#contact", - "title": "Forecasting Challenge", - "section": "Contact", - "text": "Contact\neco4cast.initiative@gmail.com" + "objectID": "catalog.html#what-types-of-models-are-submitting-forecasts", + "href": "catalog.html#what-types-of-models-are-submitting-forecasts", + "title": "Forecast catalog", + "section": "", + "text": "Note: This figure will become more complete, as more models register and provide model descriptions" }, { - "objectID": "index.html#acknowledgements", - "href": "index.html#acknowledgements", - "title": "Forecasting Challenge", - "section": "Acknowledgements", - "text": "Acknowledgements\nThomas, R. Q., Boettiger, C., Carey, C. C., Dietze, M. C., Johnson, L. R., Kenney, M. A., et al. (2023). The NEON Ecological Forecasting Challenge. Frontiers in Ecology and the Environment, 21(3), 112–113. https://doi.org/10.1002/fee.2616 We thank NEON for providing the freely available data and the EFI community for feedback on the design of the Challenge. This material is based upon work supported by the National Science Foundation under Grant DEB-1926388. Page last updated on 2024-03-06" + "objectID": "catalog.html#sec-spatiotemporal-asset-catalog", + "href": "catalog.html#sec-spatiotemporal-asset-catalog", + "title": "Forecast catalog", + "section": "Catalog of forecast submissions and evaluations", + "text": "Catalog of forecast submissions and evaluations\nThe catalog of submitted forecasts and the evaluation of the forecasts (“scores”) is available through the SpatioTemporal Asset Catalogs browser (below). \nThe catalog provides the code that you can use to access forecasts and scores. \nA full page version can be found here" }, { "objectID": "instructions.html", @@ -147,59 +175,31 @@ "text": "8 Questions?\nThanks for reading this document!\n\nIf you still have questions about how to submit your forecast to the NEON Ecological Forecasting Challenge, we encourage you to email Dr. Quinn Thomas (rqthomas{at}vt.edu)." }, { - "objectID": "catalog.html", - "href": "catalog.html", - "title": "Forecast catalog", - "section": "", - "text": "Note: This figure will become more complete, as more models register and provide model descriptions" - }, - { - "objectID": "catalog.html#what-types-of-models-are-submitting-forecasts", - "href": "catalog.html#what-types-of-models-are-submitting-forecasts", - "title": "Forecast catalog", - "section": "", - "text": "Note: This figure will become more complete, as more models register and provide model descriptions" - }, - { - "objectID": "catalog.html#sec-spatiotemporal-asset-catalog", - "href": "catalog.html#sec-spatiotemporal-asset-catalog", - "title": "Forecast catalog", - "section": "Catalog of forecast submissions and evaluations", - "text": "Catalog of forecast submissions and evaluations\nThe catalog of submitted forecasts and the evaluation of the forecasts (“scores”) is available through the SpatioTemporal Asset Catalogs browser (below). \nThe catalog provides the code that you can use to access forecasts and scores. \nA full page version can be found here" - }, - { - "objectID": "targets.html", - "href": "targets.html", - "title": "What to forecast", - "section": "", - "text": "The “targets” are time-series of National Ecological Observatory Network (NEON) data for use in model development and forecast evaluation.\nThe targets are updated as new NEON data is made available.\nThe 10 targets were specifically chosen to include ecosystem, community, and population dynamics and are represented by five “themes”. The themes and links to targets files are included below." - }, - { - "objectID": "targets.html#tldr-forecast-the-targets", - "href": "targets.html#tldr-forecast-the-targets", - "title": "What to forecast", + "objectID": "performance.html", + "href": "performance.html", + "title": "Forecast performance", "section": "", - "text": "The “targets” are time-series of National Ecological Observatory Network (NEON) data for use in model development and forecast evaluation.\nThe targets are updated as new NEON data is made available.\nThe 10 targets were specifically chosen to include ecosystem, community, and population dynamics and are represented by five “themes”. The themes and links to targets files are included below." + "text": "This page visualizes the forecasts and forecast performance for the focal target variables. Only forecasts from a subset of NEON sites are shown. If you want to see your forecasts or scores, the links can be found in our forecast catalog and scores catalog" }, { - "objectID": "targets.html#sec-starting-sites", - "href": "targets.html#sec-starting-sites", - "title": "What to forecast", - "section": "Where to start", - "text": "Where to start\nIf are you are getting started, we recommend the following focal sites for each of the five “themes”. The first site in the list is the recommended starting site.\n\nTerrestrial: BART, OSBS, KONZ, SRER\nAquatics: BARC, CRAM\nPhenology: HARV, BART, STEI, UKFS, GRSM, DELA, CLBJ\nBeetles: BLAN, OSBS\nTicks: BLAN, TALL\n\nAs you develop your forecasting skills and want to expand to more sites, the targets are available at all 81 NEON sites. You may also consider submitting forecasts to sites that match your interests. For example, a class being taught in the winter may be more interested in forecasting southern sites while a summer class may focus on more northern sites.\nMore information about NEON sites can be found in the site metadata and on NEON’s website" + "objectID": "performance.html#sec-performance", + "href": "performance.html#sec-performance", + "title": "Forecast performance", + "section": "Most recent forecasts", + "text": "Most recent forecasts\nOnly the top-performing models from the last 30 days are shown.\nForecasts submitted on 2024-03-06\n\nTerrestrial: net ecosystem exchangeTerrestrial: latent heat fluxPhenology: greennessPhenology: rednessAquatics: water temperatureAquatics: dissolved oxygenAquatics: chlorophyll-aBeetle community richnessBeetle community abundanceTicks: Amblyomma americanum\n\n\nForecast summaries are available here\n\n\n\n\n\n\n\n\nForecast summaries are available here\n\n\n\n\n\n\n\n\nForecast summaries are available here\n\n\n\n\n\n\n\n\nForecast summaries are available here\n\n\n\n\n\n\n\n\nForecast summaries are available here\n\n\n\n\n\n\n\n\nForecast summaries are available here\n\n\n\n\n\n\n\n\nForecast summaries are available here\n\n\n\n\n\n\n\n\nForecast summaries are available here\n\n\n\n\n\n\n\n\nForecast summaries are available here\n\n\n\n\n\n\n\n\nForecast summaries are available here" }, { - "objectID": "targets.html#sec-targets", - "href": "targets.html#sec-targets", - "title": "What to forecast", - "section": "Explore the targets and themes", - "text": "Explore the targets and themes\nInformation on the targets files for the five “themes” is below. In the tables,\n\n“duration” is the time-step of the variable where PT30M is a 30-minute mean, P1D is a daily mean, and P1W is a weekly total.\nThe “forecast horizon” is the number of days-ahead that we want you to forecast.\nThe “latency” is the time between data collection and data availability in the targets file\n\n\nTerrestrial fluxesAquaticsPhenologyBeetle communitiesTick populations\n\n\n\nThe exchange of water and carbon dioxide between the atmosphere and the land is akin to earth’s terrestrial ecosystems breathing rate and lung capacity. \nThe terrestrial flux theme challenges you to forecast the gas exchange at up to 47 sites across the U.S.\nThere are two variables and two time-steps (or duration) that you can forecast.\n\n\n\n\n\n\n\n\n\n\n\n\nvariable\nduration\nDescription\nforecast horizon\nLatency\n\n\n\n\nle\nP1D\ndaily mean latent heat flux (W/m2)\n30 days\n~ 5 days\n\n\nnee\nP1D\ndaily mean Net ecosystem exchange (gC/m2/day)\n30 days\n~ 5 days\n\n\nle\nPT30M\n30 minute mean latent heat flux (W/m2)\n10 days\n~ 5 days\n\n\nnee\nPT30M\n30 minute mean net ecosystem exchange (umol/m2/s)\n10 days\n~ 5 days\n\n\n\n\n\n\nDaily mean\nThe daily mean target file is located at the following URL.\n\nurl_P1D <- \"https://sdsc.osn.xsede.org/bio230014-bucket01/challenges/targets/project_id=neon4cast/duration=P1D/terrestrial_daily-targets.csv.gz\"\n\nYou can directly load it into R using the following\n\nterrestrial_targets <- read_csv(url_P1D, show_col_types = FALSE)\n\nThe file contains the following columns\n\n\n\n\n\nproject_id\nsite_id\ndatetime\nduration\nvariable\nobservation\n\n\n\n\nneon4cast\nBART\n2017-02-06\nP1D\nle\n11.5794551\n\n\nneon4cast\nBART\n2017-02-07\nP1D\nle\n4.8951620\n\n\nneon4cast\nBART\n2017-02-09\nP1D\nle\n7.5281656\n\n\nneon4cast\nBART\n2017-02-11\nP1D\nle\n1.1577581\n\n\nneon4cast\nBART\n2017-02-12\nP1D\nle\n0.1999174\n\n\nneon4cast\nBART\n2017-02-13\nP1D\nle\n10.9325370\n\n\n\n\n\nand the time series for the focal sites\n\nterrestrial_targets |> \n filter(site_id %in% terrestrial_focal_sites) |> \n ggplot(aes(x = datetime, y = observation)) +\n geom_point() +\n facet_grid(variable~site_id, scales = \"free_y\") +\n theme_bw()\n\n\n\n\n\n\n30 minute\nThe 30 minute duration targets are designed for forecasting sub-daily carbon and water dynamics. The URL is found at:\n\nurl_PT30M <- \"https://sdsc.osn.xsede.org/bio230014-bucket01/challenges/targets/project_id=neon4cast/duration=PT30M/terrestrial_30min-targets.csv.gz\"\n\nLearn more at: https://projects.ecoforecast.org/neon4cast-docs/Terrestrial.html\n\n\n\n\nFreshwater surface water temperature, dissolved oxygen, and chlorophyll-a all influence drinking water quality, are critical for life in aquatic environments, and can represent the health of the ecosystem.\nThe aquatics theme challenges you to forecast daily mean water quality variables at up-to 7 lakes and 27 river/stream NEON sites.\n\n\n\n\n\n\n\n\n\n\n\n\nvariable\nduration\nDescription\nhorizon\nLatency\n\n\n\n\nchla\nP1D\ndaily mean Chlorophyll-a (ug/L)\n30 days\n~ 3 days\n\n\noxygen\nP1D\nSurface Mean Daily Dissolved Oxygen Concentration (mgL)\n30 days\n~ 3 days\n\n\ntemperature\nP1D\nSurface Mean Daily Water Temperature (Celsius)\n30 days\n~ 3 days\n\n\n\n\n\nThe daily mean target file is located at the following URL.\n\nurl <- \"https://sdsc.osn.xsede.org/bio230014-bucket01/challenges/targets/project_id=neon4cast/duration=P1D/aquatics-targets.csv.gz\"\n\nYou can directly load it into R using the following\n\naquatics_targets <- read_csv(url, show_col_types = FALSE)\n\nThe file contains the following columns\n\n\n\n\n\nproject_id\nsite_id\ndatetime\nduration\nvariable\nobservation\n\n\n\n\nneon4cast\nARIK\n2016-08-12\nP1D\noxygen\n3.402153\n\n\nneon4cast\nARIK\n2016-08-13\nP1D\noxygen\n4.156236\n\n\nneon4cast\nARIK\n2016-08-14\nP1D\noxygen\n4.071263\n\n\nneon4cast\nARIK\n2016-08-15\nP1D\noxygen\n3.909114\n\n\nneon4cast\nARIK\n2016-08-16\nP1D\noxygen\n3.862653\n\n\nneon4cast\nARIK\n2016-08-17\nP1D\noxygen\n4.354618\n\n\n\n\n\nand the time series for the focal sites\n\naquatics_targets |> \n filter(site_id %in% aquatics_focal_sites) |> \n ggplot(aes(x = datetime, y = observation)) +\n geom_point() +\n facet_grid(variable~site_id, scales = \"free_y\") +\n theme_bw()\n\nWarning: Removed 941 rows containing missing values or values outside the scale range\n(`geom_point()`).\n\n\n\n\n\nWater temperature at multiple depths measured at the UTC 00 hour are available for the 7 NEON lake sites. These data can be used for model development but will not be used for forecast evaluation.\n\nurl <- \"https://sdsc.osn.xsede.org/bio230014-bucket01/challenges/supporting_data/project_id=neon4cast/aquatics-expanded-observations.csv.gz\"\n\nLearn more at: https://projects.ecoforecast.org/neon4cast-docs/Aquatics.html\n\n\n\nPhenology (the changes in plant canopies over the year) has been identified as one of the primary ecological fingerprints of global climate change.\nThe greenness and redness, as measured by a camera looking down at the top of vegetation are a quantitative measure of phenology. The phenology theme challenges you to forecast daily mean greeness and/or redness at up-to 47 terrestrial NEON sites.\n\nurl <- \"https://sdsc.osn.xsede.org/bio230014-bucket01/challenges/targets/project_id=neon4cast/duration=P1D/phenology-targets.csv.gz\"\nread_csv(url, show_col_types = FALSE) |> \n distinct(variable, duration) |> \n left_join(target_metadata, by = c(\"variable\",\"duration\")) |> \n filter(variable %in% c(\"gcc_90\",\"rcc_90\")) |> \n select(-class) |> \n knitr::kable()\n\n\n\n\n\n\n\n\n\n\n\nvariable\nduration\nDescription\nhorizon\nLatency\n\n\n\n\ngcc_90\nP1D\nGreen chromatic coordinate is the ratio of the green digital number to the sum of the red, green, blue digital numbers from a digital camera.\n30 days\n~ 2 days\n\n\nrcc_90\nP1D\nRed chromatic coordinate is the ratio of the Red digital number to the sum of the red, green, blue digital numbers from a digital camera.\n30 days\n~ 2 days\n\n\n\n\n\nThe daily mean target file is located at the following URL.\n\nurl <- \"https://sdsc.osn.xsede.org/bio230014-bucket01/challenges/targets/project_id=neon4cast/duration=P1D/phenology-targets.csv.gz\"\n\nYou can directly load it into R using the following\n\nphenology_targets <- read_csv(url, show_col_types = FALSE)\n\nThe file contains the following columns\n\n\n\n\n\nproject_id\nsite_id\ndatetime\nduration\nvariable\nobservation\n\n\n\n\nneon4cast\nABBY\n2017-05-30\nP1D\ngcc_90\n0.41659\n\n\nneon4cast\nABBY\n2017-05-31\nP1D\ngcc_90\n0.41570\n\n\nneon4cast\nABBY\n2017-06-01\nP1D\ngcc_90\n0.41780\n\n\nneon4cast\nABBY\n2017-06-02\nP1D\ngcc_90\n0.41539\n\n\nneon4cast\nABBY\n2017-06-03\nP1D\ngcc_90\n0.42216\n\n\nneon4cast\nABBY\n2017-06-04\nP1D\ngcc_90\n0.41659\n\n\n\n\n\nand the time series for the focal sites\n\nphenology_targets |> \n filter(site_id %in% phenology_focal_sites) |> \n ggplot(aes(x = datetime, y = observation)) +\n geom_point() +\n facet_grid(variable~site_id, scales = \"free_y\") +\n theme_bw()\n\nWarning: Removed 8174 rows containing missing values or values outside the scale range\n(`geom_point()`).\n\n\n\n\n\nLearn more at: https://projects.ecoforecast.org/neon4cast-docs/Phenology.html\n\n\n\nSentinel species (such as beetles) can give forewarning of environmental risk to humans, so are particularly useful for such monitoring and forecasting efforts because they can provide surrogates for other co-located components of biodiversity.\nThe beetles theme challenges you to forecast weekly ground beetles (Family: Carabidae) abundance and richness (two measures of biodiversity) at up-to 47 terrestrial NEON sites.\n\n\n\n\n\n\n\n\n\n\n\n\nvariable\nduration\nDescription\nhorizon\nLatency\n\n\n\n\nabundance\nP1W\nTotal number of carabid individuals per trap-night, estimated each week of the year at each NEON site\n1 year\n~ 6 months\n\n\nrichness\nP1W\nTotal number of unique ‘species’ in a sampling bout for each NEON site each week.\n1 year\n~ 6 months\n\n\n\n\n\nThe daily mean target file is located at the following URL.\n\nurl <- \"https://sdsc.osn.xsede.org/bio230014-bucket01/challenges/targets/project_id=neon4cast/duration=P1W/beetles-targets.csv.gz\"\n\nYou can directly load it into R using the following\n\nbeetles_targets <- read_csv(url, show_col_types = FALSE)\n\nThe file contains the following columns\n\n\n\n\n\nproject_id\nsite_id\ndatetime\nduration\nvariable\nobservation\n\n\n\n\nneon4cast\nABBY\n2016-09-12\nP1W\nabundance\n1.0489796\n\n\nneon4cast\nABBY\n2016-09-12\nP1W\nrichness\n14.0000000\n\n\nneon4cast\nABBY\n2016-09-26\nP1W\nabundance\n4.4535714\n\n\nneon4cast\nABBY\n2016-09-26\nP1W\nrichness\n13.0000000\n\n\nneon4cast\nABBY\n2017-05-01\nP1W\nabundance\n0.0553571\n\n\nneon4cast\nABBY\n2017-05-01\nP1W\nrichness\n10.0000000\n\n\n\n\n\nand the time series for the focal sites\n\nbeetles_targets |> \n filter(site_id %in% beetles_focal_sites) |> \n ggplot(aes(x = datetime, y = observation)) +\n geom_point() +\n facet_grid(variable~site_id, scales = \"free_y\") +\n theme_bw()\n\n\n\n\nLearn more at: https://projects.ecoforecast.org/neon4cast-docs/Beetles.html\n\n\n\nTarget species for the tick population forecasts are Amblyomma americanum nymphal ticks. A. americanum is a vector of ehrlichiosis, tularemia, and southern tick-associated rash illness. The species is present in the eastern United States, and their populations are expanding. There is a correlation between tick population abundance and disease incidence, meaning forecasts for tick abundance have the potential to aid in our understanding of disease risk through time and space.\nThe beetles theme challenges you to forecast weekly Amblyomma americanum nymphal tick abundance at up-to 9 terrestrial NEON sites.\n\n\n\n\n\n\n\n\n\n\n\n\nvariable\nduration\nDescription\nhorizon\nLatency\n\n\n\n\namblyomma_americanum\nP1W\nThe density of Amblyomma americanum nymphs per week (ticks per 1600m^2)\n1 year\n~ 6 months\n\n\n\n\n\nThe weekly target file is located at the following URL.\n\n\"https://sdsc.osn.xsede.org/bio230014-bucket01/challenges/targets/project_id=neon4cast/duration=P1W/ticks-targets.csv.gz\"\n\n[1] \"https://sdsc.osn.xsede.org/bio230014-bucket01/challenges/targets/project_id=neon4cast/duration=P1W/ticks-targets.csv.gz\"\n\n\nYou can directly load it into R using the following\n\nticks_targets <- read_csv(url, show_col_types = FALSE)\n\nThe file contains the following columns\n\n\n\n\n\n\n\n\n\n\n\n\n\nproject_id\nsite_id\ndatetime\nduration\nvariable\nobservation\n\n\n\n\nneon4cast\nBLAN\n2015-04-20\nP1W\namblyomma_americanum\n0.000000\n\n\nneon4cast\nBLAN\n2015-05-11\nP1W\namblyomma_americanum\n9.815951\n\n\nneon4cast\nBLAN\n2015-06-01\nP1W\namblyomma_americanum\n10.000000\n\n\nneon4cast\nBLAN\n2015-06-08\nP1W\namblyomma_americanum\n19.393939\n\n\nneon4cast\nBLAN\n2015-06-22\nP1W\namblyomma_americanum\n3.137255\n\n\nneon4cast\nBLAN\n2015-07-13\nP1W\namblyomma_americanum\n3.661327\n\n\n\n\n\nand the time series for the focal sites\n\nticks_targets |> \n filter(site_id %in% ticks_focal_sites) |> \n ggplot(aes(x = datetime, y = observation)) +\n geom_point() +\n facet_grid(variable~site_id, scales = \"free_y\") +\n theme_bw()\n\n\n\n\nLearn more at: https://projects.ecoforecast.org/neon4cast-docs/Ticks.html" + "objectID": "performance.html#forecast-analysis", + "href": "performance.html#forecast-analysis", + "title": "Forecast performance", + "section": "Forecast analysis", + "text": "Forecast analysis\nBelow are forecasts submitted 30 days ago and include the observations used to evaluate them. Mouse over to see the team id, scroll to zoom. Only the top five performing models are shown. Information on how to access the scores can be found in our catalog\n\nTerrestrial: net ecosystem exchangeTerrestrial: latent heat fluxPhenology: greennessPhenology: rednessAquatics: water temperatureAquatics: dissolved oxygenAquatics: chlorophyll-aBeetle community richnessBeetle community abundanceTicks: Amblyomma americanum" }, { - "objectID": "targets.html#explore-the-sites", - "href": "targets.html#explore-the-sites", - "title": "What to forecast", - "section": "Explore the sites", - "text": "Explore the sites\n\n\n\n\n\n\n The following table lists all the sites in the NEON Ecological Forecasting Challenge. The columns with “theme” names incidate whether that site is included in that theme’s target file.\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nsite_id\nfield_site_name\nterrestrial\naquatics\nphenology\nticks\nbeetles\n\n\n\n\nABBY\nAbby Road NEON\n1\n0\n1\n0\n1\n\n\nARIK\nArikaree River NEON\n0\n1\n0\n0\n0\n\n\nBARC\nLake Barco NEON\n0\n1\n0\n0\n0\n\n\nBARR\nUtqiaġvik NEON\n1\n0\n1\n0\n1\n\n\nBART\nBartlett Experimental Forest NEON\n1\n0\n1\n0\n1\n\n\nBIGC\nUpper Big Creek NEON\n0\n1\n0\n0\n0\n\n\nBLAN\nBlandy Experimental Farm NEON\n1\n0\n1\n1\n1\n\n\nBLDE\nBlacktail Deer Creek NEON\n0\n1\n0\n0\n0\n\n\nBLUE\nBlue River NEON\n0\n1\n0\n0\n0\n\n\nBLWA\nBlack Warrior River NEON\n0\n1\n0\n0\n0\n\n\nBONA\nCaribou-Poker Creeks Research Watershed NEON\n1\n0\n1\n0\n1\n\n\nCARI\nCaribou Creek NEON\n0\n1\n0\n0\n0\n\n\nCLBJ\nLyndon B. Johnson National Grassland NEON\n1\n0\n1\n0\n1\n\n\nCOMO\nComo Creek NEON\n0\n1\n0\n0\n0\n\n\nCPER\nCentral Plains Experimental Range NEON\n1\n0\n1\n0\n1\n\n\nCRAM\nCrampton Lake NEON\n0\n1\n0\n0\n0\n\n\nCUPE\nRio Cupeyes NEON\n0\n1\n0\n0\n0\n\n\nDCFS\nDakota Coteau Field Site NEON\n1\n0\n1\n0\n1\n\n\nDEJU\nDelta Junction NEON\n1\n0\n1\n0\n1\n\n\nDELA\nDead Lake NEON\n1\n0\n1\n0\n1\n\n\nDSNY\nDisney Wilderness Preserve NEON\n1\n0\n1\n0\n1\n\n\nFLNT\nFlint River NEON\n0\n1\n0\n0\n0\n\n\nGRSM\nGreat Smoky Mountains National Park NEON\n1\n0\n1\n0\n1\n\n\nGUAN\nGuanica Forest NEON\n1\n0\n1\n0\n1\n\n\nGUIL\nRio Guilarte NEON\n0\n1\n0\n0\n0\n\n\nHARV\nHarvard Forest & Quabbin Watershed NEON\n1\n0\n1\n0\n1\n\n\nHEAL\nHealy NEON\n1\n0\n1\n0\n1\n\n\nHOPB\nLower Hop Brook NEON\n0\n1\n0\n0\n0\n\n\nJERC\nThe Jones Center At Ichauway NEON\n1\n0\n1\n0\n1\n\n\nJORN\nJornada Experimental Range NEON\n1\n0\n1\n0\n1\n\n\nKING\nKings Creek NEON\n0\n1\n0\n0\n0\n\n\nKONA\nKonza Prairie Agroecosystem NEON\n1\n0\n1\n0\n1\n\n\nKONZ\nKonza Prairie Biological Station NEON\n1\n0\n1\n1\n1\n\n\nLAJA\nLajas Experimental Station NEON\n1\n0\n1\n0\n1\n\n\nLECO\nLeConte Creek NEON\n0\n1\n0\n0\n0\n\n\nLENO\nLenoir Landing NEON\n1\n0\n1\n1\n1\n\n\nLEWI\nLewis Run NEON\n0\n1\n0\n0\n0\n\n\nLIRO\nLittle Rock Lake NEON\n0\n1\n0\n0\n0\n\n\nMART\nMartha Creek NEON\n0\n1\n0\n0\n0\n\n\nMAYF\nMayfield Creek NEON\n0\n1\n0\n0\n0\n\n\nMCDI\nMcDiffett Creek NEON\n0\n1\n0\n0\n0\n\n\nMCRA\nMcRae Creek NEON\n0\n1\n0\n0\n0\n\n\nMLBS\nMountain Lake Biological Station NEON\n1\n0\n1\n0\n1\n\n\nMOAB\nMoab NEON\n1\n0\n1\n0\n1\n\n\nNIWO\nNiwot Ridge NEON\n1\n0\n1\n0\n1\n\n\nNOGP\nNorthern Great Plains Research Laboratory NEON\n1\n0\n1\n0\n1\n\n\nOAES\nMarvin Klemme Range Research Station NEON\n1\n0\n1\n0\n1\n\n\nOKSR\nOksrukuyik Creek NEON\n0\n1\n0\n0\n0\n\n\nONAQ\nOnaqui NEON\n1\n0\n1\n0\n1\n\n\nORNL\nOak Ridge NEON\n1\n0\n1\n1\n1\n\n\nOSBS\nOrdway-Swisher Biological Station NEON\n1\n0\n1\n1\n1\n\n\nPOSE\nPosey Creek NEON\n0\n1\n0\n0\n0\n\n\nPRIN\nPringle Creek NEON\n0\n1\n0\n0\n0\n\n\nPRLA\nPrairie Lake NEON\n0\n1\n0\n0\n0\n\n\nPRPO\nPrairie Pothole NEON\n0\n1\n0\n0\n0\n\n\nPUUM\nPu’u Maka’ala Natural Area Reserve NEON\n1\n0\n1\n0\n1\n\n\nREDB\nRed Butte Creek NEON\n0\n1\n0\n0\n0\n\n\nRMNP\nRocky Mountains NEON\n1\n0\n1\n0\n1\n\n\nSCBI\nSmithsonian Conservation Biology Institute NEON\n1\n0\n1\n1\n1\n\n\nSERC\nSmithsonian Environmental Research Center NEON\n1\n0\n1\n1\n1\n\n\nSJER\nSan Joaquin Experimental Range NEON\n1\n0\n1\n0\n1\n\n\nSOAP\nSoaproot Saddle NEON\n1\n0\n1\n0\n1\n\n\nSRER\nSanta Rita Experimental Range NEON\n1\n0\n1\n0\n1\n\n\nSTEI\nSteigerwaldt-Chequamegon NEON\n1\n0\n1\n0\n1\n\n\nSTER\nNorth Sterling NEON\n1\n0\n1\n0\n1\n\n\nSUGG\nLake Suggs NEON\n0\n1\n0\n0\n0\n\n\nSYCA\nSycamore Creek NEON\n0\n1\n0\n0\n0\n\n\nTALL\nTalladega National Forest NEON\n1\n0\n1\n1\n1\n\n\nTEAK\nLower Teakettle NEON\n1\n0\n1\n0\n1\n\n\nTECR\nTeakettle Creek - Watershed 2 NEON\n0\n1\n0\n0\n0\n\n\nTOMB\nLower Tombigbee River NEON\n0\n1\n0\n0\n0\n\n\nTOOK\nToolik Lake NEON\n0\n1\n0\n0\n0\n\n\nTOOL\nToolik Field Station NEON\n1\n0\n1\n0\n1\n\n\nTREE\nTreehaven NEON\n1\n0\n1\n0\n1\n\n\nUKFS\nUniversity of Kansas Field Station NEON\n1\n0\n1\n1\n1\n\n\nUNDE\nUniversity of Notre Dame Environmental Research Center NEON\n1\n0\n1\n0\n1\n\n\nWALK\nWalker Branch NEON\n0\n1\n0\n0\n0\n\n\nWLOU\nWest St Louis Creek NEON\n0\n1\n0\n0\n0\n\n\nWOOD\nChase Lake National Wildlife Refuge NEON\n1\n0\n1\n0\n1\n\n\nWREF\nWind River Experimental Forest NEON\n1\n0\n1\n0\n1\n\n\nYELL\nYellowstone National Park NEON\n1\n0\n1\n0\n1" + "objectID": "performance.html#aggregated-scores", + "href": "performance.html#aggregated-scores", + "title": "Forecast performance", + "section": "Aggregated scores", + "text": "Aggregated scores\nAverage skill scores of each model across all sites.\n\nScores are shown by reference date and forecast horizon (in days).\n\nScores are averaged across all submissions of the model with a given horizon or a given reference_datetime using submissions made since in the last 30 days for the daily or sub-daily variables and the past year for the weekly variables\n\nLearn about the continuous ranked probability score here\n\nTerrestrial: Net Ecosystem ExchangeTerrestrial: Latent Heat FluxPhenology: GreenessPhenology: RednessAquatics: water temperatureAquatics: dissolved oxygenAquatics: chrophyll-aBeetle community richnessBeetle community abundanceTicks: Amblyomma americanum" } ] \ No newline at end of file diff --git a/sitemap.xml b/sitemap.xml index a5ee2007c0..36882e22ef 100644 --- a/sitemap.xml +++ b/sitemap.xml @@ -2,1462 +2,1470 @@ https://projects.ecoforecast.org/neon4cast-ci/catalog.html - 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2024-02-23 + 2024-03-07 https://radiantearth.github.io/stac-browser/#/external/raw.githubusercontent.com/eco4cast/neon4cast-ci/main/catalog/summaries/models/model_items/tg_temp_lm.json - 2024-02-23 + 2024-03-07 https://radiantearth.github.io/stac-browser/#/external/raw.githubusercontent.com/eco4cast/neon4cast-ci/main/catalog/summaries/models/model_items/tg_temp_lm_all_sites.json - 2024-02-23 + 2024-03-07 https://radiantearth.github.io/stac-browser/#/external/raw.githubusercontent.com/eco4cast/neon4cast-ci/main/catalog/summaries/models/model_items/tidymodels_ML.json - 2024-02-23 + 2024-03-07 https://radiantearth.github.io/stac-browser/#/external/raw.githubusercontent.com/eco4cast/neon4cast-ci/main/catalog/summaries/models/model_items/tidymodels_lm.json - 2024-02-23 + 2024-03-07 https://radiantearth.github.io/stac-browser/#/external/raw.githubusercontent.com/eco4cast/neon4cast-ci/main/catalog/summaries/models/model_items/zimmerman_proj1.json - 2024-02-23 + 2024-03-07 https://radiantearth.github.io/stac-browser/#/external/raw.githubusercontent.com/eco4cast/neon4cast-ci/main/catalog/targets/collection.json - 2024-02-23 + 2024-03-07 diff --git a/targets.html b/targets.html index 0b7700383a..3b282b0d77 100644 --- a/targets.html +++ b/targets.html @@ -689,7 +689,7 @@

30 minute

facet_grid(variable~site_id, scales = "free_y") + theme_bw()
-
Warning: Removed 8174 rows containing missing values or values outside the scale range
+
Warning: Removed 8178 rows containing missing values or values outside the scale range
 (`geom_point()`).
@@ -971,8 +971,8 @@

30 minute

Explore the sites

-
- +
+



The following table lists all the sites in the NEON Ecological Forecasting Challenge. The columns with “theme” names incidate whether that site is included in that theme’s target file.

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