Package: phenofit 0.3.9

Dongdong Kong

phenofit: Extract Remote Sensing Vegetation Phenology

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>.

Authors:Dongdong Kong [aut, cre], Mingzhong Xiao [aut], Yongqiang Zhang [aut], Xihui Gu [aut], Jianjian Cui [aut]

phenofit_0.3.9.tar.gz
phenofit_0.3.9.tar.gz(r-4.5-noble)phenofit_0.3.9.tar.gz(r-4.4-noble)
phenofit_0.3.9.tgz(r-4.4-emscripten)phenofit_0.3.9.tgz(r-4.3-emscripten)
phenofit.pdf |phenofit.html
phenofit/json (API)
NEWS

# Install 'phenofit' in R:
install.packages('phenofit', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/eco-hydro/phenofit/issues

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library
Datasets:
  • CA_NS6 - MOD13A1 EVI observations at flux site CA-NS6
  • MOD13A1 - MOD13A1
  • input_single - Input object with one growing season per year

4.52 score 332 scripts 589 downloads 1 mentions 121 exports 48 dependencies

Last updated 11 months agofrom:efc2846baa. Checks:OK: 2. Indexed: no.

TargetResultDate
Doc / VignettesOKOct 31 2024
R-4.5-linux-x86_64OKOct 31 2024

Exports:%<-%%<>%%>%add_HeadTailbrks2rfitcheck_inputcheck_season_dtcheck_season_listcheck_ylucurvaturecurvefitcurvefit0curvefitscurvefits_LocalModelcv_coefD1D2date2doydoubleLog_AGdoubleLog_BeckdoubleLog_ElmoredoubleLog_GudoubleLog_KlosdoubleLog_ZhangdoubleLog.AGdoubleLog.AG2doubleLog.BeckdoubleLog.ElmoredoubleLog.GudoubleLog.KlosdoubleLog.Zhangdoy2datef_goalf_goal2find_season.defaultfind_season.peaksfindpeaksFitDL.AGFitDL.AG2FitDL.BeckFitDL.ElmoreFitDL.GuFitDL.KlosFitDL.Zhangget_fittingget_GOFget_optionsget_paramget_phenogetBitsgetRealDateGOFI_optimI_optimxinit_AGinit_AG2init_Beckinit_Elmoreinit_Guinit_Klosinit_lambdainit_paraminit_Zhangkurtosislambda_vcurvelogisticLogisticmake_datemelt_listmerge_LocalModelsmovmeanopt_nlmopt_nlminbopt_optimopt_ucminfoptim_phenoPhenoDerivPhenoGuPhenoKlPhenoTrsplot_curvefitsplot_inputplot_phenofitplot_seasonprocess_phenofitprocess_seasonqc_5lqc_colorsqc_FparLaiqc_levelsqc_NDVI3gqc_NDVIv4qc_sentinel2qc_shapesqc_SPOTqc_StateQAqc_summaryR2_signrcpp_season_filterrcpp_SGrcpp_wSGremoveClosedExtremeroughFitseasonseason_inputseason_movset_optionsskewnesssmooth_wHANTSsmooth_wSGsmooth_wWHITtidy_MOD13tidy_phenov_curvewBisquarewBisquare0wChenwhit2wKongwSELFwTSM

Dependencies:clicolorspacecpp11data.tabledplyrfansifarvergenericsggplot2gluegridExtragtableisobandlabelinglatticelifecyclelubridatemagrittrMASSMatrixmgcvmunsellnlmenloptrnumDerivoptimxpillarpkgconfigpracmapurrrR6RColorBrewerRcppRcppArmadillorlangscalesstringistringrtibbletidyselecttimechangeucminfutf8vctrsviridisLitewithrzeallotzoo

Extract vegetation phenology from MOD13A1 EVI

Rendered fromphenofit_CA-NS6.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2022-11-03
Started: 2021-10-15

Detailed procedures of phenofit

Rendered fromphenofit-procedures.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2022-11-03
Started: 2021-10-15

Readme and manuals

Help Manual

Help pageTopics
MOD13A1 EVI observations at flux site CA-NS6CA_NS6
check_inputcheck_input
check_ylucheck_ylu
Fine curve fittingcurvefit
Fine Curve fittingcurvefits
curvefits by local model functions of TIMESATcurvefits_LocalModel merge_LocalModels
Goal function of fine curve fitting methodsf_goal
findpeaksfindpeaks
Fine fittingFitDL FitDL.AG FitDL.AG2 FitDL.Beck FitDL.Elmore FitDL.Gu FitDL.Klos FitDL.Zhang
getFittingsget_fitting get_fitting.fFITs get_fitting.list
get_GOFget_GOF get_GOF.fFIT get_GOF.fFITs get_GOF.list
Get parameters from curve fitting resultget_param get_param.fFIT get_param.fFITs get_param.list
get_phenoget_pheno get_pheno.fFITs get_pheno.list get_pheno.rfit
GOFGOF
input object with one growing season per yearinput_single
Fine fitting functionsdoubleLog.AG doubleLog.AG2 doubleLog.Beck doubleLog.Elmore doubleLog.Gu doubleLog.Klos doubleLog.Zhang Logistic
MOD13A1MOD13A1
movmeanmovmean
Unified optimization functionopt_FUN opt_nlm opt_nlminb opt_optim opt_ucminf
optim_phenooptim_pheno
Phenology extraction in Derivative method (DER)PhenoDeriv PhenoDeriv.default PhenoDeriv.fFIT
Phenology extraction in GU method (GU)PhenoGu PhenoGu.default PhenoGu.fFIT
Phenology extraction in Inflection method (Zhang)PhenoKl
Phenology extraction in Threshold method (TRS)PhenoTrs PhenoTrs.default PhenoTrs.fFIT
plot_curvefitsplot_curvefits
Plot INPUT returned by check_inputplot_input
plot_seasonplot_season
Initial weights for sentinel2 according to SCL bandqc_sentinel2
Initial weights according to qcgetBits qcFUN qc_5l qc_FparLai qc_NDVI3g qc_NDVIv4 qc_SPOT qc_StateQA qc_summary
Weighted Savitzky-Golay written in RcppArmadillorcpp_SG rcpp_wSG
Moving growing season divisionseason_mov
set and get phenofit optionget_options set_options
Weighted HANTS SMOOTHsmooth_wHANTS
Weighted Savitzky-Golaysmooth_wSG
Weigthed Whittaker Smoothersmooth_wWHIT
Weighted Whittaker smoothing with a second order finite difference penaltywhit2
Weight updating functionswBisquare wBisquare0 wChen wKong wSELF wTSM