------------------- Version: 1.1-2 Date: 2012-09-18 * Now exporting accessor functions for 'msSurv' * Changed license from GPL-3 to GPL-2 * Added citation to JSS publication for msSurv (JSS 50:14, 2012) * Included modified JSS paper as package vignette * Changed all occurrences of 'sum.dNs' to 'sum_dNs' to avoid conflict with S3 generic 'sum' * Added package 'KMsurv' to the 'Suggests' field in the DESCRIPTION file ------------------- Version: 1.1-1 Date: 2012-06-25 * Modified output of 'print', 'show', and 'EntryExit' slightly ------------------- Version: 1.1-0 Date: 2012-04-18 * Changed name of function 'st.t' to 'SOPt' * Changed name of internal function 'stocc' to 'AJ.estimator' * Removed internal function 'Dist.BS.var' * Modified all functions to make more extensive use of vectorized calculations * Output now returned invisibly for functions Pst, SOPt, and EntryExit * Added accessor functions for ALL slots in msSurv objects. * Updated code throughout to use accessor functions rather than make explicit reference to slot names. * Updated functions throughout msSurv package so that the labels accessed the state names instead of column / array index locations. * Changed required names for data columns to 'id', 'start', 'stop', 'start.state', and 'end.state' ('start' is optional for right-censored only data) * Removed arguments 'start.states' and 'd.var' from function msSurv. * Added argument 'bs' to determine whether bootstrapping is used to calculate the variance. Bootstrapping is currently needed for the variance of the A-J estimators when there is dependent censoring, for the variance of the state entry / exit functions, and for the variance of the state occupation probabilities when there is > 1 possible starting state. * Starting proportions in each state (prior to the first observed transition time) are now calculated empirically based on the data * In class msSurv, changed names for the following slots: 'out' to 'cov.AJs', 'cov.p' to 'var.sop', 'all.ajs' to 'AJs', and 'all.I_dA' to 'I.dA'. * Added the computation and appropriate applications and output for non-normalized state entry and exit distributions (referred to as subdistributions). These are now calculated and stored in the 'Fsub' and 'Gsub' slots, respectively, in msSurv objects. Options for plotting subdistribution functions, and for calculating them using the EntryExit function, have been added, along with appropriately named accessor functions. * Changed notation for normalized state entry and exit distributions from 'Fs' and 'Gs' to 'Fnorm' and 'Gnorm'. Added accessor functions Fnorm and Gnorm. * Changed the normalization for the state exit distributions ('Gnorm') so that it matches that used for the state entry distributions. That is, the denominator consists of all individuals who will ever *enter*, not necessarily leave, a state. * Added the 'norm=TRUE' argument to the Dist.CIs function to allow users to specify whether they want normalized entry/exit distributions or if they prefer the non-normalized subdistributions. * Added "->" to output for print and show methods to clearly identify transitions between states. * Added a check and corresponding error message when users request 'bs=TRUE' with fewer than 10 subjects * Added a check to ensure that all start times are earlier than the stop times * Now requiring users to insert a " " between transitioning states they want to plot in the 'plot' function to clearly distinguish transitions, e.g. "1 12" instead of "112" * Modified argument "plot.type" in plot method for msSurv objects to include possibilities 'entry.sub', 'entry.norm', 'exit.sub', or 'exit.norm' for state entry and exit plots. * Created a "State Entry and Exit Distribution" section of the summary method and removed that information from the "State Occupation Probability" section. * Modified 'print' and 'show' methods to display sparse output concerning the msSurv object, and 'summary' to give more detailed information. Added arguments to the summary method to allow users to customize displayed output, including options for displaying / hiding the transition probabilities, state occupation probabilities, state entry / exit distributions, and Datta-Satten weighted estimates of the counting processes. Additionally, users can specify at which timepoints they want summary information. * Updated author contact information in the description file.