Changelog

add TIMESAT global model function and cutoff function.
add the parameter na.rm in check_input. If na.rm = true, missing and spike values will be discarded; otherwise, they will be interpolated by valid neihbours.
change analytical to FALSE in PhenoDeriv.fFIT, PhenoGu.fFIT

fix minpeakheight error in PhenoKl, which leads to PhenoKl failed unexpectedly.
plateau line fitting in PhenoGu

Fix typo error in curvefits’ document.
Fix the error of plot.fFITs, due to fFIT renamed to model.
Rename function opt_season to season_input
In the case of none growing season division information, find_season.peaks will be error. Fixed now.
Fix the bug of init_param in the approximately monotonous time-sereis (e.g. fast harvest leads to a very short senescence period, and hence approximately monotonic in the whole growing season). In previous version, the parameter boundary of sos might exceed that of eos.
Improved the phenology extraction method PhenoTrs, PhenoDeriv and PhenoGu in the approximately monotonous time-sereis. In the previous version NA value will be return. In the current version, if the time series is monotonously increasing, EOS will be the mean value of t[n] and peak date of season (POP). But PhenoKlos has no method to avoid NA values, because it used the strict mathematical solution to find the extreme values in the curve of curvature’s change rate.

MAJOR updates to improve multi-GS phenology extraction

Fix the bug of findpeaks, which lead to sharp changed growing season failed to detect.
Fix the bug of PhenoKlos, where minpeakheight not work in previous version.
Fix the bug of check_season_dt, where peak might be able to greater than end.
Remove the parameter check_season_dt in removeClosedExtreme, which might eliminate good extreme values.
add get_pheno.rfit to extract vegetation phenology from rough fitting directly.

Parameters of season_mov and curvefits are wrapped into options. Scripts of phenofit v2.0 will not work anymore.
Add global options
Growing season division was improved. Rough fitting and growing season division are separated.
In the package dependency, plyr was replaced with dplyr.
Add doubleLog.AG2, which allows unbalanced background value in the first half and the second half.
Add lambda_vcurve and lambda_cv_jl to optimize Whittaker’s parameter lambda
Add pkgdown, http://phenofit.top/.
Growing season division was further tested on FLUXNET daily GPP estimations.
Julia interface is ready to go, https://github.com/eco-hydro/phenofit.jl.
phenofit script was separated into a another repository, https://github.com/eco-hydro/phenofit-scripts.

The rough fitting result returned by [season_mov()] and [season()] was renamed from whit to fit.
parameters of season_mov and curvefits are moved into options.

fix point shape error of plot_input
make_legend supports 4 quality categories (MOD13A1) and 6 quality categories (MOD09A1) now.
wWHIT only adjusts time series of growing season.

Melt parameters (i.e. nptperyear and south) into INPUT. check_input, season, season_mov and curvefits are impacted.
Add adj.param parameter to season, which determine whether to automatically adjust roughn curve fitting parameters.

fix Init_param
In previous version, parameters are only rely on “good” (w >= 0.5) values. But when “good” values in a relative low ratio, wield parameters will be generated.
In this version, when “good” values ratio is lower than 40%, all values will be used to generate initial parameters.
Export weigths of every iteration for growing season dividing function, (i.e. wHANT, sgfitw and whitsmw2). And unified their weights updating strategy.
doubleLog.zhang is still not as stable as others.
wTSM_cpp iter parameter is ignored now.

phenofit 0.3.8 (2023-02-15)2023-02-15