R Observatory: Metrics for phenofit version 0.3.11

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

phenofit

0.3.11Package record

Extract Remote Sensing Vegetation Phenology

0packages depend

7Kdownloads / year

77.3%test coverage

12/13flavors OK

Overview

About

Maintained by Dongdong KongCRAN page ↗GitHub ↗Issues ↗

The merits of 'TIMESAT' and 'phenopix' are adopted. Besides, a simple and growing season dividing method and a practical snow elimination method based on Whittaker were proposed. 7 curve fitting methods and 4 phenology extraction methods were provided. Parameters boundary are considered for every curve fitting methods according to their ecological meaning. And 'optimx' is used to select best optimization method for different curve fitting methods. Reference: Kong, D., (2020). R package: A state-of-the-art Vegetation Phenology extraction package, phenofit version 0.3.1, doi:10.5281/zenodo.5150204; 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. doi:10.1029/2020JG005636; 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; 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. doi:10.1016/j.agrformet.2017.10.026.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("phenofit", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("eco-hydro/phenofit")

Development version from eco-hydro/phenofit. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-phenofit

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-phenofit

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-phenofit

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

1ERROR12OK

Check messages

ERRORtestsr-devel-windows-x86_64

Running 'testthat.R' [55s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(phenofit)
  > 
  > test_check("phenofit")
  
  Attaching package: 'data.table'
  
  The following object is masked from 'package:base':
  
      %notin%
  
  Saving _problems/test-PhenoExtract-25.R
  List of 5
   $ AG    : tibble [6 × 8] (S3: tbl_df/tbl/data.frame)
   $ Beck  : tibble [6 × 7] (S3: tbl_df/tbl/data.frame)
   $ Elmore: tibble [6 × 8] (S3: tbl_df/tbl/data.frame)
   $ Gu    : tibble [6 × 10] (S3: tbl_df/tbl/data.frame)
   $ Zhang : tibble [6 × 8] (S3: tbl_df/tbl/data.frame)
  NULL
  # A tibble: 6 × 8
    flag      t0    mn    mx     rsp    a3     rau    a5
    <chr>  <dbl> <dbl> <dbl>   <dbl> <dbl>   <dbl> <dbl>
  1 1999_1 -135. 0.201 0.636 0.00932  2.85 0.00852  2   
  2 2000_1  189. 0.238 0.635 0.0126   2.47 0.00801  3.21
  3 2001_1  569. 0.252 0.626 0.0108   2.96 0.00950  2.96
  4 2002_1  892. 0.253 0.614 0.0159   2    0.00724  3.08
  5 2003_1 126
...[truncated]...
is singular; attempting approx solution
  
  warning: solve(): system is singular; attempting approx solution
  
  warning: solve(): system is singular; attempting approx solution
  
  warning: solve(): system is singular; attempting approx solution
  
  warning: solve(): system is singular; attempting approx solution
  
  warning: solve(): system is singular; attempting approx solution
  
  warning: solve(): system is close to singular; rcond: 3.31005e-17; attempting approx solution
  [ FAIL 2 | WARN 2 | SKIP 0 | PASS 68 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-PhenoExtract.R:23:1'): (code run outside of `test_that()`) ───
  Expected `{ ... }` to run silently.
  Actual noise: warnings.
  ── Failure ('test-PhenoExtract.R:50:5'): get_pheno.fFIT works ──────────────────
  Expected `{ ... }` to run silently.
  Actual noise: warnings.
  
  [ FAIL 2 | WARN 2 | SKIP 0 | PASS 68 ]
  Error:
  ! Test failures.
  Execution halted

CRAN check page ↗

Slowest check: 7.4 min · r-oldrel-windows-x86_64

Status changes

ERROR12 OK, 1 ERROR2026-09-18
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK12 OK, 1 FAILURE2026-06-08
NOTE12 OK, 1 NOTE2026-06-07

Show 3 earlier changesHide 3 earlier changes

OK14 OK2026-04-22
ERROR13 OK, 1 ERROR2026-04-18
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.3.11

READMEYes · 557 wordsVignettesYes · 2 · dynamicNEWSYes · 100% structured · does not mention 0.3.11Citation fileNo

Help pages: 71 (34 internal)includes a package overview page
Examples that run: 96%45 run in a plain check · 1 never run · 1 hold no code
Exported functions with examples: 73%
Documented parameters: 86%
Return-value docs: 49%
Help pages citing references: 25%

Vignettes (2)

How these are measured

Downloads

7K

CRAN downloads in the past year

Rank #7,190 · ~19/day · ~584/mo

Releases R versions

Daily download trend is not available in this view yet.

45730 days

1.2K90 days

7K1 year

Compare downloads with other packages →

Also on796 r2u4 autocran

How downloads are counted

Repository

eco-hydro/phenofit ↗Organization: eco-hydro

94Stars

36Forks

3Open issues

0Open PRs

6Releases

225Commits

5Commit identities

phenologyremote-sensing

License file reads as GPL-2.0 · 225 commits · Last activity 2026-07-09 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 1
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2026-07-14 · 882026-09-11 · 94

How these are measured

PracticesBeta

12 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/eco-hydro/phenofit on 2026-10-22.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-07-09 · The repository has a site deploy workflow

Coverage (2)

Coverage reporting.covrignore

Reproducibility and dev environment (1)

data-raw/

Show all practicesHide 2 practices

Lint, format, editor (2)

VS CodeRStudio project

Git structural (1)

Submodules

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

19 external dependencies (excludes base and recommended)

Installing phenofit adds 41 packages (22 with compiled code, 42 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (1)

R >= 3.1

Imports (15)

Rcpp purrr dplyr stringr magrittr lubridate data.table zoo gridExtra ggplot2 optimx ucminf numDerivmethodszeallot

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (3)

knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (5)

Dongdong Kong

Author, Maintainer since 0.2.0 (2019)

Author

Author

Author

Author

Releases (12)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
unarchivedReturned to CRAN
2026-01-23
0.3.11Latest
record
2026-01-23 · current release · diff ↗
archivedRemoved from CRAN
2025-12-13
issues were not corrected despite reminders
0.3.10
record
2025-05-25 · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
0.3.9
record
2024-01-23 · diff ↗
R
R 4.3.0 released · 2023-04-21
0.3.8
record
2023-02-15 · diff ↗
0.3.7
record
2022-11-07 · diff ↗
0.3.6
record
2022-11-03 · diff ↗ ·
removed 13 exports
.Greenup, backval, cheak_season_list, get_GOF.fFITs, get_fitting.fFITs, get_param.fFITs, get_pheno.fFITs, julia_setup, lambda_cv_jl, lambda_vcurve_jl, opt_nlminb_julia, opt_season, rough_fitting

added 17 exports
brks2rfit, check_season_list, curvefit0, curvefits_LocalModel, date2doy, doy2date, init_AG, init_AG2, init_Beck, init_Elmore, init_Gu, init_Klos, init_Zhang, merge_LocalModels, qc_sentinel2, roughFit, season_input
R
R 4.2.0 released · 2022-04-22
0.3.2
record
2021-10-15 · diff ↗ ·
removed 5 exports
check_season, julia_init, phenofit_plot, tidyFitPheno, tidy_MOD13.gee

added 27 exports
%<-%, %<>%, %>%, FitDL.AG2, doubleLog.AG2, find_season.default, find_season.peaks, get_options, julia_setup, lambda_cv_jl, lambda_vcurve, lambda_vcurve_jl, make_date, melt_list, opt_season, plot_curvefits, process_phenofit, process_season, qc_colors, qc_levels, qc_shapes, rcpp_season_filter, removeClosedExtreme, rough_fitting, set_options, tidy_MOD13, tidy_pheno
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24

Show 11 earlier eventsHide 11 earlier events

unarchivedReturned to CRAN
2020-04-02
0.2.7
record
2020-04-02 · diff ↗ ·
removed 8 exports
FitAG, doubleAG, phenofit_loaddata, phenofit_shiny, smooth_SG, wHANTS, wSG, wWHIT

added 22 exports
FitDL.AG, cheak_season_list, check_season, check_season_dt, doubleLog.AG, doubleLog_AG, doubleLog_Beck, doubleLog_Elmore, doubleLog_Gu, doubleLog_Klos, doubleLog_Zhang, f_goal2, julia_init, logistic, opt_nlminb_julia, qc_FparLai, qc_SPOT, rcpp_SG, rcpp_wSG, smooth_wHANTS, smooth_wWHIT, wBisquare0
archivedRemoved from CRAN
2020-03-30
check problems were not corrected in time Misuse of 'strptime' causing array overruns in 3.x
unarchivedReturned to CRAN
2019-06-07
0.2.5-2
record
2019-06-07 · diff ↗
archivedRemoved from CRAN
2019-06-05
check issues not corrected despite reminders
0.2.4
record
2019-05-24 · diff ↗
0.2.3
record
2019-05-23 · diff ↗ ·
removed 14 exports
add_dn, check_fit, contain, fprintf, ifelse2, list.cbind, list.rbind, listk, melt_list, merge_pdf, obj.size, reorder_name, rm_empty, runningId

added 9 exports
check_ylu, movmean, phenofit_loaddata, phenofit_plot, phenofit_shiny, qc_NDVI3g, smooth_SG, smooth_wSG, wKong
R
R 3.6.0 released · 2019-04-26
0.2.0
record
2019-02-18
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2019-02-18
Total releases: 12 / 7 yrs
License: GPL-2 | file LICENSE OSI
Minimum R: ≥ 3.1
Bundled data: 86 KB / 3 files
Download size: 415 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("phenofit")

Format

Kong, D., Cui, J., Gu, X., Xiao, M., & Zhang, Y. (2026). phenofit: Extract Remote Sensing Vegetation Phenology (Version 0.3.11) [Computer software]. https://doi.org/10.32614/CRAN.package.phenofit

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for phenofit version 0.3.11 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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