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phenocamr

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

https://github.com/bluegreen-labs/phenocamr

Science Score: 23.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: wiley.com, nature.com
  • ○
    Committers with academic emails
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    Institutional organization owner
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (15.6%) to scientific vocabulary

Keywords

phenocam phenocam-data phenology-modelling remote-sensing

Keywords from Contributors

model-calibration phenology-models vegetation-phenology climate-data daymet gridded-data ornl-daac
Last synced: 6 months ago · JSON representation

Repository

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

Basic Info
Statistics
  • Stars: 24
  • Watchers: 2
  • Forks: 9
  • Open Issues: 4
  • Releases: 2
Topics
phenocam phenocam-data phenology-modelling remote-sensing
Created about 10 years ago · Last pushed about 2 years ago
Metadata Files
Readme License

README.md

phenocamr

R-CMD-check codecov CRAN\_Status\_Badge CRAN\_Downloads

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:

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

development release

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

R 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:

R 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:

R 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

  • Name: BlueGreen Labs
  • Login: bluegreen-labs
  • Kind: organization
  • Email: info@bluegreenlabs.org
  • Location: Melsele, Belgium

BlueGreen open science labs & consulting, providing environmental research infrastructure and editorial solutions.

GitHub Events

Total
  • Watch event: 3
  • Fork event: 1
Last Year
  • Watch event: 3
  • Fork event: 1

Committers

Last synced: 6 months ago

All Time
  • Total Commits: 279
  • Total Committers: 5
  • Avg Commits per committer: 55.8
  • Development Distribution Score (DDS): 0.097
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
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@u****m 2

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • 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 requests: 9
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • khufkens (12)
  • tmilliman (3)
  • jmertic (1)
  • benjaminrobinson (1)
  • kongdd (1)
  • atkinsjeff (1)
Pull Request Authors
  • bnasr (10)
  • tmilliman (2)
  • khufkens (1)
Top Labels
Issue Labels
enhancement (5)
Pull Request Labels

Packages

  • Total packages: 2
  • Total downloads:
    • cran 443 last-month
  • Total dependent packages: 0
    (may contain duplicates)
  • Total dependent repositories: 2
    (may contain duplicates)
  • Total versions: 6
  • Total maintainers: 1
proxy.golang.org: github.com/bluegreen-labs/phenocamr
  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 7.0%
Average: 8.2%
Dependent repos count: 9.3%
Last synced: 6 months ago
cran.r-project.org: phenocamr

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

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 2
  • Downloads: 443 Last month
Rankings
Forks count: 7.4%
Stargazers count: 11.9%
Average: 17.9%
Dependent repos count: 19.5%
Downloads: 22.7%
Dependent packages count: 27.9%
Maintainers (1)
koen.hufkens@gmail.com
Last synced: 6 months ago

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