Help to Fit of a Parametric Distribution to Non-Censored or Censored Data

Extends the fitdistr() function (of the MASS package) with several functions to help the fit of a parametric distribution to non-censored or censored data. Censored data may contain left censored, right censored and interval censored values, with several lower and upper bounds. In addition to maximum likelihood estimation (MLE), the package provides moment matching (MME), quantile matching (QME) and maximum goodness-of-fit estimation (MGE) methods (available only for non-censored data). Weighted versions of MLE, MME and QME are available.


News

=== fitdistrplus : Help to fit of a parametric distribution ===

Version 1.0-7

NEW FEATURES

  • keep the JSS vignette as a pdf.
  • start the FAQ vignette and add datasets (?dataFAQ) for it.
  • provide likelihood plot/surface/curve: llplot, llcurve, llsurface.
  • provide parallelization of bootstrap in bootdist and bootdistcens.
  • provide graphic of (e)cdf with bootstraped confidence interval/area: CIcdfplot.
  • allow the use of constrOptim() in mledist, mmedist, mgedist, qmedist functions.
  • add a possible pre-fitting procedure: prefit.

BUG FIXES

  • add invisible() for all graphical functions.
  • bug fixed concerning the use of weights on censored data

Version 1.0-6

BUG FIXES

  • automatic definition of starting values for distributions "llogis" and "invweibull" is now working.

Version 1.0-5

NEW FEATURES

  • update starting/fixing values in mledist, mmedist, mgedist, qmedist functions.
  • update graphics for bootstrap procedure.
  • add argument do.points in cdfcomp.
  • add argument weights in mledist, qmedist, mmedist, fitdist, fitdistcens.
  • add argument keepdata in fitdist, fitdistcens.
  • suppress warnings/errors in fitdist(cens), bootdist(cens).

BUG FIXES

  • defensive programming in plotdist, cdfcomp,...
  • simplify plotting curves in cdfcomp where seq(xmin, xmax, by=1) was used.

Version 1.0-4

  • release for the JSS publication.

Version 1.0-3

NEW FEATURES

  • new generic functions for fitdist(cens): loglik, vcov and coef.
  • vignette updated to the version of a paper accepted by the Journal of Statistical Software.
  • add of an argument discrete in fitdist in order to be able to take into account non classical discrete distributions while plotting the fit with plot.fitdist or cdfcomp and while calculating goodness-of-fit statistics with gofstat (add of an example : fit of a zero inflate Poisson distribution).
  • add of an S3 class for descdist and a print method.

BUG FIXES

  • fitdist can handle non invertible Hessian matrices.

Version 1.0-2

NEW FEATURES

  • plotdist can plot empirical density as an histogram, a density plot or both superimposed.
  • a strong warning was added to the documentation of function descdist about the problematic high variance of skewness and kurtosis.

BUG FIXES

  • bug fixed in bootdistcens : argument fix.arg is now correctly passed to mle

Version 1.0-1

NEW FEATURES

  • gofstat can handle multiple 'fitdist' objects.
  • plotdist for discrete data is slightly enhanced.

Version 1.0-0

NEW FEATURES

  • update cdfcomp and add denscomp, ppcomp and qqcomp functions.
  • add of an argument Turnbull.confint to functions plotdistcens and cdfcompcens in order to draw confidence intervals on the empirical distribution only if requested.
  • ppoints now used in "fitdist" for QQ plot, PP plot and cdf plot for continuous data (was used only for QQ plot in previous versions) to enable Blom type plotting position (using by default Hazen plotting position than can be chanfge using arguments use.ppoints and a.ppoints)
  • many changes in the examples given in the reference manual.
  • the vignette was removed, to be transformed in a paper that we will soon submit to a journal.
  • add of four data sets : fluazinam, salinity, danishuni and danishmulti.
  • add of functions to calculate quantiles of the fitted distribution, with 95 percent CI calculated by bootstrap : quantile generic function is available both for "fitdist" and "bootdist" objects and quantile generic function is available both for "fitdistcens" and "bootdistcens" objects.

BUG FIXES

  • correction the formula for the CvM test for Weibull distribution
  • elimination of CvM and AD tests for normal, lognormal and logistic distributions : formulas previously used (given by Stephens 1986) do not use exactly MLE estimates and thus results were only approximates.
  • make arguments xlim and ylim functional in cdfcompcens
  • bug fix in the closed formula in mmedist for lognormal distributions.

Version 0.3-4

NEW FEATURES

  • posibility to fix xlegend to a keyword (e.g. "bottomright") in "cdfcomp" and "cdfcompdens"
  • improvement of the new vignette

BUG FIXES

  • correction of the NAMESPACE file in order to enable the correct print of a summary of a fitdistcens object (with the correlation matrix, the loglikelihood and AIC and BIC statistics)

Version 0.3-3

NEW FEATURES

  • a new function ("cdfcompcens") to plot cumulative distributions corresponding to various fits using a same censored data set.
  • add an example with scaling problem in man pages.

Version 0.3-2

NEW FEATURES

  • new plot of the empirical cdf curve in plotdistcens, using the Turnbull algorithm by a call to function survfit{survival}
  • new arguments to function "cdfcomp" : verticals, horizontals and xlim

Version 0.3-1

NEW FEATURES

  • add of a draft of a new version of the vignette

Version 0.3-0

NEW FEATURES

  • a new function ("cdfcomp") to plot cumulative distributions corresponding to various fits using a same non censored data set.
  • add of two data sets : "endosulfan" and "toxocara".

Version 0.2-2

BUG FIXES

  • elimination of NON-ASCII characters in the vignette.

Version 0.2-1

NEW FEATURES

  • a new fitting method was implemented for continuous distributions : the maximum goodness-of-fit estimation (function "mgedist") (for the moment only available for non censored data).

Version 0.1-5

NEW FEATURES

  • a new goodness-of-fit statistic was added in gofstat, with corresponding test : the Cramer-von Mises distance
  • a new fitting method has been implemented : the quantile matching estimation (function "qmedist"). For the moment, only available for non censored data.
  • the moment matching estimation has been extended (in function mmedist) to enable numerical matching when closed formula are not available.

BUG FIXES

  • correction of a bug inserted while adding the argument "fix.arg" which prevent the print of the results of goodness-of-fit tests .

Version 0.1-4

NEW FEATURES

  • a component named dots added to the list returned by fitdist and fitdistcens in order to pass optional arguments for the control of optimization in mledist to bootdist and bootdistcens. bootdist and bootdistcens changed to take into account these optional arguments if they are defined in the call to fitdist or fitdistcens.
  • an argument added to fitdist, fitdistcens and mledist, named fix.arg, and giving the possibility to fix some of the distribution parameters while maximizing the likelihood. Functions bootdist, bootdistcens and gofstat were also changed in order to take this new argument into account.
  • a new data file of bacterial contamination censored data extracted from Busschaert et al. 2000 and examples corresponding to analysis of this dataset.

BUG FIXES

  • correction of a bug in the print and the plot of bootstraped samples using bootdist or bootdistcens when there was only one parameter estimated by maximum likelihood.

Version 0.1-3

NEW FEATURES

  • new data file "groundbeef" (groundbeef.rda and groundbeef.Rd) and new use of this dataset in some examples.
  • new function gofstat. Goodness-of-fit statistics are no more computed by fitdist but may computed and printed by the use of the function gofstat. In this new function, the whole results computed are not printed : results of tests are printed only if the argument print.test==TRUE and for continuous distributions only Anderson-Darling and Kolomogorov-Smirnov statistics are printed by default (but complete results are returned by gofstat).
  • modifications in descdist : three arguments were added in descdist 1/ method, to choose between unbiased estimations of standard deviation, skewness and kurtosis (default choice) and sample values. 2/ obs.col to choose the color used to plot the observed point on the graph. 3/ boot.col to choose the color used to plot the bootstrap sample of points on the graph.
  • modifications in plotfit : minor changes were performed in order to facilitate the use of the argument ... to personnalize the plots (see examples in plotdist.Rd)
  • modication of the vignette

BUG FIXES

  • correction of a bug in plotdist due to the redefinition in the previous version of the parameter "ylim" for the plot of a histogram with theoretical density function (there was a problem with infinite values of theoretical density function)

Version 0.1-2

NEW FEATURES

  • deletion of mledistcens and modification of mledist in order to maximize likelihood for both censored and non censored data.
  • possibility to choose the optimization method used for maximum likelihood estimation (MLE) of distribution parameters using the new argument "optim.method" of mledist.
  • possibility to specify contraints on distribution parameters using the new arguments "lower" and "upper" of mledist.
  • possibility to use a custom optimization function for MLE using the new argument "custom.optim".
  • moment matching estimation is no longer done with argument method set to "mom" but set to "mme" in fitdist.
  • renaming of momdist in mmedist.
  • calculation of AIC and BIC criterion after maximum likelihood estimation of distribution parameters
  • change of the default number of iterations from 999 to 1001 for bootstrap in order to avoid interpolation using the quantile function
  • use of the argument "log" and (resp. "log.p") of density (resp. distribution) when available to compute the loglikelihood.

BUG FIXES

  • omitting the name of the first argument in calls to the density function during maximization of the likelihood in order to enable the use of a density function defined with a first parameter (the vector of quantiles) with a name differing from "x" (classical name for density distributions defined in R), such as the density function dexGAUS from the package gamlss.dist.

Version 0.1-1

  • Initial release.

Reference manual

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install.packages("fitdistrplus")

1.0-9 by Aurélie Siberchicot, 6 months ago


MailingList: http://listes.univ-lyon1.fr/wws/info/fitdist-users; https://lbbe.univ-lyon1.fr/fitdistrplus.html, http://riskassessment.r-forge.r-project.org


Browse source code at https://github.com/cran/fitdistrplus


Authors: Marie-Laure Delignette-Muller [aut], Christophe Dutang [aut], Regis Pouillot [ctb], Jean-Baptiste Denis [ctb], Aurélie Siberchicot [aut, cre]


Documentation:   PDF Manual  


Task views: Probability Distributions, Survival Analysis


GPL (>= 2) license


Imports stats

Depends on MASS, grDevices, survival, methods

Suggests actuar, rgenoud, mc2d, gamlss.dist, knitr, knitcitations, ggplot2, GeneralizedHyperbolic


Imported by Dpit, EnviroPRA, SCORPIUS, STI, bayou, fitur, myTAI, simPop.

Depended on by BMT, SCI, enveomics.R, genasis, goft, mbbefd, qmap.

Suggested by AICcmodavg, LindleyR, mc2d, mle.tools, raw.


See at CRAN