fitGammaDist {MethylIT}R Documentation

Nonlinear fit of Gamma CDF (Gamma)


This function performs the nonlinear fit of GGamma CDF of a variable x


fitGammaDist(x, probability.x, parameter.values, location.par = FALSE,
  sample.size = 20, npoints = NULL, maxiter = 1024, ftol = 1e-12,
  ptol = 1e-12, maxfev = 1e+05, nlms = FALSE, verbose = TRUE)



numerical vector


probability vector of x. If not provided, the values are estimated using the empirical cumulative distribution function ('ecdf') from 'stats' R package.


initial parameter values for the nonlinear fit. If the locator paramter is included (mu != 0), this must be given as parameter.values = list(shape = 'value', scale = 'value', mu = 'value') or if mu = 0, as: parameter.values = list(shape = 'value', scale = 'value'). If not provided, then an initial guess is provided.


whether to consider the fitting to generalized gamma distribution (Gamma) including the location parameter, i.e., a Gamma with four parameters (GGamam3P).


size of the sample.


number of points used in the fit.


positive integer. Termination occurs when the number of iterations reaches maxiter. Default value: 1024.


non-negative numeric. Termination occurs when both the actual and predicted relative reductions in the sum of squares are at most ftol. Therefore, ftol measures the relative error desired in the sum of squares. Default value: 1e-12


non-negative numeric. Termination occurs when the relative error between two consecutive iterates is at most ptol. Therefore, ptol measures the relative error desired in the approximate solution. Default value: 1e-12.


integer; termination occurs when the number of calls to fn has reached maxfev. Note that nls.lm sets the value of maxfev to 100*(length(par) + 1) if maxfev = integer(), where par is the list or vector of parameters to be optimized.


Logical. Whether to return the nonlinear model object nls.lm. Default is FALSE.


if TRUE, prints the function log to stdout


The algorithm tries to fit the two-parameter Gamma CDF ("Gamma2P") or the three-parameter Gamma ("Gamma3P") using a modification of Levenberg-Marquardt algorithm implemented in function 'nls.lm' from 'minpack.lm' package that is used to perform the nonlinear fit. Cross-validations for the nonlinear regressions (R.Cross.val) were performed in each methylome as described in reference [1]. In addition, Stein's formula for adjusted R squared (rho) was used as an estimator of the average cross-validation predictive power [1].

If the number of values to fit is >10^6, the fitting to a GGamma CDF would be a time consuming task. To reduce the computational time, the data can be 'summarized' into 'npoints' (bins) and used as the new predictors.


Model table with coefficients and goodness-of-fit results: Adj.R.Square, deviance, AIC, R.Cross.val, and rho, as well as, the coefficient covariance matrix.


Robersy Sanchez - 06/03/2016


1. Stevens JP. Applied Multivariate Statistics for the Social Sciences. Fifth Edit. Routledge Academic; 2009.


x <- rgamma(1000, shape = 1.03, scale = 2.1)

[Package MethylIT version 0.3.1 ]