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phenocamr

Facilitates the retrieval and post-processing of PhenoCam time series.
https://github.com/bluegreen-labs/phenocamr

Category: Biosphere
Sub Category: Terrestrial Wildlife

Keywords

phenocam phenocam-data phenology-modelling remote-sensing

Keywords from Contributors

camera phenocam-installation phenocam-network climate-data data-retrieval daymet gridded-data ornl-daac model-calibration phenology-models

Last synced: about 23 hours ago
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Repository metadata

An R Interface and Post-Processing Framework for PhenoCam Web Services

README.md

phenocamr

R-CMD-check
codecov
CRAN_Status_Badge
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Facilitates the retrieval and post-processing of PhenoCam time series. The post-processing of PhenoCam data includes outlier removal and the generation of data products such as phenological transition dates. If requested complementary Daymet climate data will be downloaded and merged with the PhenoCam data for modelling purposes. For a detailed overview of the assumptions made during post-processing I refer publications by Hufkens et al. (2018) and Richardson et al. (2018).

How to cite this package

Hufkens K., Basler J. D., Milliman T. Melaas E., Richardson A.D. 2018
An integrated phenology modelling framework in R: Phenology modelling
with phenor. Methods in Ecology &
Evolution, 9: 1-10. https://doi.org/10.1111/2041-210X.12970

Installation

stable release

To install the current stable release use a CRAN repository:

install.packages("phenocamr")
library(phenocamr)

development release

To install the development releases of the package run the following commands:

if(!require(devtools)){install.package(devtools)}
devtools::install_github("bluegreen-labs/phenocamr")
library(phenocamr)

Vignettes are not rendered by default, if you want to include additional documentation please use:

if(!require(devtools)){install.package("devtools")}
devtools::install_github("bluegreen-labs/phenocamr", build_vignettes = TRUE)
library(phenocamr)

Use

To download data for a single deciduous broadleaf forest site (harvard) use the following syntax:

download_phenocam(site = "harvard",
                  veg_type = "DB",
                  frequency = 3,
                  phenophase = TRUE,
                  out_dir = "~")

This will download all deciduous broadleaf (DB) PhenoCam time series for the "harvard" site at a 3-day time step into your home directory. In addition, the data is processed to estimate phenological transition dates (phenophases) and written to file. For detailed overview of all functions and worked example we reference to the R help documentation and the manuscripts below.

References

Hufkens K., Basler J. D., Milliman T. Melaas E., Richardson A.D. 2018 An integrated phenology modelling framework in R: Phenology modelling with phenor. Methods in Ecology & Evolution, 9: 1-10.

Richardson, A.D., Hufkens, K., Milliman, T., Aubrecht, D.M., Chen, M., Gray, J.M., Johnston, M.R., Keenan, T.F., Klosterman, S.T., Kosmala, M., Melaas, E.K., Friedl, M.A., Frolking, S. 2017. Tracking vegetation phenology across diverse North American biomes using PhenoCam imagery. Scientific Data, 5, 180028.

Acknowledgements

This project was is supported by the National Science Foundation’s Macro-system Biology Program (awards EF-1065029 and EF-1702697). Logo design elements are taken from the FontAwesome library according to these terms.

Owner metadata

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Committers metadata

Last synced: 7 days ago

Total Commits: 279
Total Committers: 5
Avg Commits per committer: 55.8
Development Distribution Score (DDS): 0.097

Commits in past year: 6
Committers in past year: 1
Avg Commits per committer in past year: 6.0
Development Distribution Score (DDS) in past year: 0.0

Name Email Commits
Koen Hufkens k****s@g****m 252
Koen Hufkens k****s@P****l 12
bnasr b****r@g****m 7
Koen Hufkens k****s@P****l 6
Tom Milliman t****n 2

Committer domains:

Issue and Pull Request metadata

Last synced: 2 days ago

Total issues: 19
Total pull requests: 13
Average time to close issues: 12 months
Average time to close pull requests: about 1 hour
Total issue authors: 6
Total pull request authors: 3
Average comments per issue: 1.21
Average comments per pull request: 0.69
Merged pull request: 9
Bot issues: 0
Bot pull requests: 0

Past year issues: 0
Past year pull requests: 0
Past year average time to close issues: N/A
Past year average time to close pull requests: N/A
Past year issue authors: 0
Past year pull request authors: 0
Past year average comments per issue: 0
Past year average comments per pull request: 0
Past year merged pull request: 0
Past year bot issues: 0
Past year bot pull requests: 0

More stats: https://issues.ecosyste.ms/repositories/lookup?url=https://github.com/bluegreen-labs/phenocamr

Top Issue Authors

  • khufkens (12)
  • tmilliman (3)
  • benjaminrobinson (1)
  • atkinsjeff (1)
  • jmertic (1)
  • kongdd (1)

Top Pull Request Authors

  • bnasr (10)
  • tmilliman (2)
  • khufkens (1)

Top Issue Labels

  • enhancement (5)

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Package metadata

proxy.golang.org: github.com/bluegreen-labs/phenocamr

cran.r-project.org: phenocamr

Facilitates 'PhenoCam' Data Access and Time Series Post-Processing

  • Homepage: https://github.com/bluegreen-labs/phenocamr
  • Documentation: http://cran.r-project.org/web/packages/phenocamr/phenocamr.pdf
  • Licenses: AGPL-3
  • Latest release: 1.1.5 (published almost 3 years ago)
  • Last Synced: 2025-04-25T13:01:04.714Z (2 days ago)
  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 2
  • Downloads: 327 Last month
  • Rankings:
    • Forks count: 7.383%
    • Stargazers count: 11.875%
    • Average: 17.871%
    • Dependent repos count: 19.546%
    • Downloads: 22.697%
    • Dependent packages count: 27.852%
  • Maintainers (1)

Dependencies

.github/workflows/R-CMD-check.yaml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/upload-artifact main composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
.github/workflows/deploy_docs.yaml actions
  • JamesIves/github-pages-deploy-action v4.4.1 composite
  • actions/checkout v3 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/test-coverage.yaml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • r-lib/actions/setup-pandoc v1 composite
  • r-lib/actions/setup-r v1 composite
DESCRIPTION cran
  • R >= 3.6 depends
  • MODISTools * imports
  • changepoint * imports
  • daymetr * imports
  • graphics * imports
  • httr * imports
  • jsonlite * imports
  • memoise * imports
  • stats * imports
  • utils * imports
  • zoo * imports
  • DT * suggests
  • covr * suggests
  • knitr * suggests
  • leaflet * suggests
  • plotly * suggests
  • rmarkdown * suggests
  • shiny * suggests
  • shinydashboard * suggests
  • testthat * suggests

Score: 10.704367432898955