phenofit
R package: A state-of-the-art Vegetation Phenology extraction package, phenofit
Science Score: 36.0%
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
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✓DOI references
Found 11 DOI reference(s) in README -
✓Academic publication links
Links to: zenodo.org -
○Committers with academic emails
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○Scientific vocabulary similarity
Low similarity (17.6%) to scientific vocabulary
Keywords
phenology
remote-sensing
Last synced: 6 months ago
·
JSON representation
Repository
R package: A state-of-the-art Vegetation Phenology extraction package, phenofit
Basic Info
- Host: GitHub
- Owner: eco-hydro
- License: gpl-2.0
- Language: R
- Default Branch: master
- Homepage: http://phenofit.top
- Size: 93.9 MB
Statistics
- Stars: 79
- Watchers: 6
- Forks: 36
- Open Issues: 3
- Releases: 6
Topics
phenology
remote-sensing
Created almost 8 years ago
· Last pushed about 1 year ago
Metadata Files
Readme
Changelog
License
README.Rmd
---
output: github_document
---
```{r, echo = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#",
fig.width = 10, fig.height = 5,
fig.align = "center",
fig.path = "man/Figure/",
dev = 'svg'
)
```
# phenofit
[](https://github.com/eco-hydro/phenofit/actions)
[](https://app.codecov.io/gh/eco-hydro/phenofit)
[](http://www.gnu.org/licenses/gpl-2.0.html)
[](https://cran.r-project.org/package=phenofit)
[](https://cran.r-project.org/package=phenofit)
[](https://cran.r-project.org/package=phenofit)
[](https://doi.org/10.5281/zenodo.5150204)
A state-of-the-art **remote sensing vegetation phenology** extraction package: `phenofit`
- `phenofit` combine merits of TIMESAT and phenopix
- A simple and stable growing season dividing methods was proposed
- Provide a practical snow elimination method, based on Whittaker
- 7 curve fitting methods and 4 phenology extraction methods
- We add parameters boundary for every curve fitting methods according to their ecological meaning.
- `optimx` is used to select best optimization method for different curve fitting methods.
***Task lists***
- [x] Test the performance of `phenofit` in multiple growing season regions (e.g. the North China Plain);
- [ ] Uncertainty analysis of curve fitting and phenological metrics;
- [x] shiny app has been moved to [phenofit.shiny](https://github.com/eco-hydro/phenofit.shiny);
- [x] Complete script automatic generating module in shinyapp;
- [x] `Rcpp` improve double logistics optimization efficiency by 60%;
- [x] Support spatial analysis;
- [x] Support annual season in curve fitting;
- [x] flexible fine fitting input ( original time-series or smoothed time-series by rough fitting).
- [x] Asymmetric of Threshold method
# Installation
You can install phenofit from github with:
```{r gh-installation, eval = FALSE}
# install.packages("remotes")
remotes::install_github("eco-hydro/phenofit")
```
# Note
Users can through the following options to improve the performance of phenofit in multiple growing
season regions:
- Users can decrease those three parameters `nextend`, `minExtendMonth` and
`maxExtendMonth` to a relative low value, by setting option
`set_options(fitting = list(nextend = 1, minExtendMonth = 0, maxExtendMonth = 0.5))`.
- Use `wHANTS` as the rough fitting function. Due to nature of fourier functions,
`wHANTS` is more stable for multiple growing seasons, but it is less flexible
than `wWHIT.` `wHANTS` is suitable for regions with the static growing season
pattern accoss multiple years, `wWHIT` is more suitable for regions with the
dynamic growing season pattern.
Dynamic growing season pattern is the most challenging task, which also means
that large uncertainty might be exists.
- Use only one iteration in fine fitting procedure.
# **References**
> [1] Kong, D., McVicar, T. R., Xiao, M., Zhang, Y., Peña-Arancibia, J. L., Filippa, G., Xie, Y., Gu, X. (2022). phenofit: An R package for extracting vegetation phenology from time series remote sensing. *Methods in Ecology and Evolution*, 13, 1508-1527. https://doi.org/10.1111/2041-210X.13870
> [2] Kong, D., Zhang, Y., Wang, D., Chen, J., & Gu, X. (2020). Photoperiod Explains the Asynchronization Between Vegetation Carbon Phenology and Vegetation Greenness Phenology. *Journal of Geophysical Research: Biogeosciences*, 125(8), e2020JG005636. https://doi.org/10.1029/2020JG005636
>
> [3] Kong, D., Zhang, Y., Gu, X., & Wang, D. (2019). A robust method for reconstructing global MODIS EVI time series on the Google Earth Engine. *ISPRS Journal of Photogrammetry and Remote Sensing*, 155, 13–24.
>
> [4] Kong, D., (2020). R package: A state-of-the-art Vegetation Phenology extraction package, `phenofit` version 0.3.1,
>
> [5] Zhang, Q., Kong, D., Shi, P., Singh, V.P., Sun, P., 2018. Vegetation phenology on the Qinghai-Tibetan Plateau and its response to climate change (1982–2013). Agric. For. Meteorol. 248, 408–417.
# Acknowledgements
Keep in mind that this repository is released under a GPL2 license, which permits commercial use but requires that the source code (of derivatives) is always open even if hosted as a web service.
Owner
- Name: Eco-Hydrological Researches in China University of Geosciences (Wuhan)
- Login: eco-hydro
- Kind: organization
- Location: China
- Website: http://www.phenofit.top/
- Repositories: 5
- Profile: https://github.com/eco-hydro
GitHub Events
Total
- Issues event: 3
- Watch event: 4
- Issue comment event: 3
- Push event: 6
- Pull request event: 3
- Fork event: 4
Last Year
- Issues event: 3
- Watch event: 4
- Issue comment event: 3
- Push event: 6
- Pull request event: 3
- Fork event: 4
Committers
Last synced: 7 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Dongdong Kong | k****d | 219 |
| Dirk Eddelbuettel | e****d@d****g | 2 |
Committer Domains (Top 20 + Academic)
debian.org: 1
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 9
- Total pull requests: 14
- Average time to close issues: 1 day
- Average time to close pull requests: about 24 hours
- Total issue authors: 9
- Total pull request authors: 3
- Average comments per issue: 1.44
- Average comments per pull request: 0.5
- Merged pull requests: 13
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 3
- Pull requests: 4
- Average time to close issues: N/A
- Average time to close pull requests: 10 minutes
- Issue authors: 3
- Pull request authors: 1
- Average comments per issue: 0.67
- Average comments per pull request: 0.75
- Merged pull requests: 3
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- suffenjoy (1)
- Hisschao (1)
- weichow12318 (1)
- andreattad (1)
- liuh1995 (1)
- kalibera (1)
- dkwang1017 (1)
- SveBuch (1)
- Gaohq123 (1)
Pull Request Authors
- kongdd (9)
- eddelbuettel (4)
- lionel- (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- cran 1,005 last-month
- Total dependent packages: 0
- Total dependent repositories: 2
- Total versions: 11
- Total maintainers: 1
cran.r-project.org: phenofit
Extract Remote Sensing Vegetation Phenology
- Homepage: https://github.com/eco-hydro/phenofit
- Documentation: http://cran.r-project.org/web/packages/phenofit/phenofit.pdf
- License: GPL-2 | file LICENSE
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Latest release: 0.3.10
published 9 months ago
Rankings
Forks count: 2.7%
Stargazers count: 5.6%
Average: 14.3%
Downloads: 16.1%
Dependent repos count: 19.5%
Dependent packages count: 27.9%
Maintainers (1)
Last synced:
6 months ago
Dependencies
DESCRIPTION
cran
- R >= 3.1 depends
- JuliaCall * imports
- Rcpp * imports
- data.table * imports
- dplyr * imports
- ggplot2 * imports
- gridExtra * imports
- lubridate * imports
- magrittr * imports
- methods * imports
- numDeriv * imports
- optimx * imports
- purrr * imports
- stringr * imports
- ucminf * imports
- zeallot * imports
- zoo * imports
- knitr * suggests
- reshape2 * suggests
- rmarkdown * suggests
- spam * suggests
- testthat >= 2.1.0 suggests
.github/workflows/R-CMD-check.yaml
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- actions/checkout v3 composite
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- r-lib/actions/setup-pandoc v2 composite
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.github/workflows/pkgdown.yaml
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- actions/cache v3 composite
- actions/checkout v3 composite
- r-lib/actions/setup-pandoc v2 composite
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.github/workflows/test-coverage.yaml
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- actions/checkout v3 composite
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- r-lib/actions/setup-r v2 composite
- r-lib/actions/setup-r-dependencies v2 composite