Changes in 1.1.17 o A comma was missing in the code-output from boxes.Lexis o mstate.Lexis function changed name to msdata.Lexis, according to the change in convention in the mstate package. Code simplified as it is now using the functionality in stack.Lexis. o A factorize.Lexis function has been added, it basically changes the variables lex.Cst and lex.Xst to factors with same set of levels. A useful facility when we want boxes.Lexis to work. Changes in 1.1.16 o boxes.Lexis now resets the graphical parameters (par()) on exit. o plot.Lexis now has a default Lexis object as argument, allowing use of the function to plot empty Lexis diagrams without setting up a Lexis object first. The bogus object has timescales c("Date","Age") but 0 follwo-up time. Changes in 1.1.14 o ci.lin now has an argument df to allow for t-quantiles in ci calculations. o lls() function revised to give nicer (left justified) output. Changes in 1.1.13 o ci.lin now supports objects of class clogistic. o utility function ci.mat() added --- earlier defined inside ci.lin and ci.cum, but also useful on its own. o lls() and clear() added, to ease overview and clearing of workspace (and attachements!) o apc.frame now sets the option "apc.frame.par" with the offset and scaling of calendar time part of the apc frame. This is recognised now by apc.lines automatically. o Function pc.points, pc.lines, pc.matlines, pc.matpoints added to ease plotting the calendar time region of an apc frame; live off the option "apc.frame.par". Changes in 1.1.12 o Added function clogistic for conditional logistic regression. Changes in 1.1.9 o A function PY.ann.Lexis is added. It writes the length of (pieces of) lifelines in a Lexis digram produced by plot.Lexis. o plot.Lexis now sets an option "Lexis.time.scale" which is queried by lines.Lexis and points.Lexis, so that time.scale is only needed in plot.Lexis. Changes in 1.1.8 o apc.fit had a bug in the specification of knots when using the argument model="bs". Fixed. Changes in 1.1.7 o boxes.Lexis has been furter enhanced with the facility to plot rates instead of no. transitions on the arrows if required. The code has been tidied a bit too. o The man file for boxes.Lexis and subsidiaries have been renamed to MS.boxes.Rd Changes in 1.1.5 o boxes.Lexis have been enhanced to accomodate two-way transitions between states. Annotation by number of transitions has been improved to accomodate this too by always putting the number on the left side of the arrow. Changes in 1.1.3 o ci.lin() and ci.cum() have been expanded to accept objects of class "MIresult" from the mitools package (Esa Läärä). o The boxes.Lexis() now gives a more versatile piece of code, which computes the text widths and heights. Changes in 1.1.2 o cutLexis crashed if new.state=TRUE and new.scale=FALSE were specified. Fixed. Changes in 1.1.1 o Functions stack.Lexis, tmat.Lexis and mstate.Lexis have been added to facilitate practical multistate modelling. The two latter provides an interface to the mstate package. o Functions tbox, dbox, fillarr, boxarr and boxes.Lexis added to facilitate drawing of multistate box diagrams. Changes in 1.1.0 o Two new datasets DMrand and DMlate with random samples from the Danish National diabetes register. The examples from these illustrate most of the recently added multistate stuff. o Minor bug in check.time.scale was fixed (misplaced parentheses in the argument to any(), causing a warning). o cutLexis introduces a new timescale "time since event", which has missing values for any follow-up time prior to event. Hence requires that the Lexis plotting functions explicitly discards the units with missing on timescales in use. Accomplished by the new function valid.times. o cutLexis now places the new states after the precursor states and before the other ones in the factors lex.Cst and lex.Xst. o splitLexis uses the first timescale by default. Which in particular means that in the case of only one time scale it is not necessary to specify it, so this has become acceptable now. o Vignettes has been updated. o Example for ci.cum has been fixed to be compatible with the new survival package as of 2.9.0 as announced. o apc.fit fitted the wrong model when using parm="AC-P". Fixed o The axis scaling of apc.plot has been improved. o apc.frame now by default plots a reference line for RR=1, this may be switched off by the (newly introduced) parameter "ref.line=FALSE". Changes in 1.0.10 o Fixed parse errors in documentation. Changes in 1.0.9 o Thanks to Mike Murphy, Professor of Demography, Department of Social Policy, London School of Economics, a bug causing a crash of apc.fit if only one row in the model matrix correponds to the reference level was fixed. o Also thanks to Mike Murphy, a much more efficient calculation of median period and cohort is now used. o apc.fit expanded with an argument allowing logistic regression model instead of a Poisson model only. Changes in 1.0.8 o tab.Lexis removed and replaced by summary.Lexis which gives a better summary of the transitions and transition rates. o A bug in ci.pd (confidence interval for probability difference) has been fixed. Changes in 1.0.7 o Stat.table data= argument fixed. Changes in 1.0.6 o Lexis now converts character values of entry/exit.status to factors for lex.Cst and lex.Xst. And produces a warning if the entry.state is defaulted to the first level of exit.state (i.e. when exit.state is given as charcter or factor). o splitLexis gave wrong results for factor states. cutLexis gave wrong results for character states. Fixed by letting Lexis coerce character mode entry.status and exit.status to factors for lex.Cst and lex.Xst. In split.lexis.1D was the problem with the factor states, they were coerced to numeric when stuffed into the new.Xst matrix. Now states are turned to numeric before the call to split.lexis.1D and the factor attributes reinstituted after the split. o Added transform method for Lexis objects. Changes in 1.0.5 o Typos in documentation of APC functions corrected. o cutLexis updated to handle various instances by MP. A few BxC additions to MP's code: - cutLexis2 is renamed cutLexis. BxC's old cutLexis killed. - count=FALSE as argument to cutLexis, just calls countLexis if TRUE. - cutLexis no longer returns the working column lex.cut - cutLexis was missing the attributes "time.scales" and "breaks". Added. - cut= is allowed, simplifying cut of split Lexis objects. - documentation accordingly altered. o splitLexis amended so that lex.Xst is returned as a factor if lex.Cst is a factor. splitLexis crashed if lex.Cst and lex.Xst were factors. o Lexis now allows omission of entry.status --- if exit.status is numeric/logical/factor, entry.status (and hence lex.Cst) will be set to 0/FALSE/first level. o Lexis made sure that lex.Cst and lex.Xst have the same class. If they are factors, the set of levels is taken to be the union. Changes in 1.0.1 o cutLexis now works properly - no it did not! o cutLexis now accepts a (smaller) dataframe with cutpoints and states as input. Changes in 0.9.6 o Bugfix in timeBand, crashed when type="factor" was chosen. levels was given as 0:(lengh(breaks)+1), changed to 0:lengh(breaks) Changes in 0.9.5 o The Lexis definition now assumes that entry is 0 if only one of exit or duration are given as a one-component list. o tab.Lexis is now properly working as a method for Lexis objects. Changes in 0.9.4 o The lex.-variables in Lexis objects are now called lex.dur, lex.Cst, lex.Xst, lex.id (duration, Current state, eXit state and identification) o An extra option states= added to Lexis. If used the state variables are returned as factors. o The utility function deltat.Lexis() has been renamed to dur(). o state() now returns a dataframe of both (entry,exit) states a default. The reason for this is that lex.Cst and lex.Xst may be factors (which actually would be the logical thing to have by default, but it is not enforced only allowed). o entry() and exit() now by default returns matrices with entry and exit times on all timescales. If only one timescale is requested, they return a 1-column matrix. o A minor typo in stat.table corrected: in the definition of the quantile function prob=probs changed to probs=probs. o cutLexis() bugs corrected. Now works with split data too, but requires specification of censoring states --- i.e. states that will be replaced by the new state obtained at the cut date. Changes in 0.9.3 (since 0.9.0) o New function cutLexis() to allow cutting of follow-up time at a specific date for each person, where a new state is assumed. o New function tab.Lexis() which tabulates records as well as events and person-years from a Lexis object. o splitLexis got state information wrong if breaks were not unique. Fixed. Changes in 0.9.0 o effx and effx.match updated following Tartu 2007 to avoid attaching the data, and to correct the parsing of the list of control variables. Changes in 0.8.0 o A new function Lexis() to define follow-up on multiple timescales has been added. An object of class Lexis is defined and a number of utilities for the class are available. Time-splititng is now done by splitLexis(). o The old Lexis function for time-splitting has been renamed to W.Lexis for backward compatibility. o The function epi.eff() has been replaced by effx() and effx.match(). Changes 0.7.2 to 0.7.3 o Icens is now able to handle a constant underlying rate. (A bug in expand.data was fixed). Changes 0.7.0 to 0.7.2 o Bugs in ROC fixed, and the functionality of the grid option slightly chnaged. Changes 0.6.1 to 0.7.0 o Function Icens() for estimation of rates from intervalcensored follow-up data by Martyn Plummer added. o Function epi.eff by Michael Hills is added. Estimates effects in various epidemiological study types. Changes 0.6.0 to 0.6.1 o Coding errors in thoro dataset corrected. Only concerning dates and status for livercancer diagnosis. o Lexis.lines now allows col.life, lwd.life, pch.fail, col.fail and cex.fail to have the same length as the data, i.e. to produce individualized lines and points. As Lexis.diagram calls Lexis.lines, this facility is also available through Lexis.diagram. Changes from 0.4 to 0.6 o ci.pd() amended to support the Agresti-Caffo method for confidence intervals for difference between proportions. Newcombes method 10 is still used in twoby2. o apc.fit() added. Fits age-period-cohort models with a range of possibilities for parametrizations. o Functions for time-splitting at arbitrary times and at recurrent failures have been added: isec(), icut(), fcut1(), fcut() and ex1(). Eventually they will be superseded by new facilities in Lexis. o Function apc.plot() to make a plot of an apc fit is added. It is just a wrapper for apc.frame() and apc.lines(), with suitable computation of the paramters supplied to apc.frame. o Lexis.lines(): pch.fail and col.fail expandS to vectors of length two if only one value is given. o ci.cum() aimed at computing cumulative hazard functions from parametric functions for hazards. o Problem in print.floated() with printing of objects of class "floated" fixed. o Problem in ci.lin when subset did not match any factor names and diff=T was given the function crashed. Fixed, and documentation updated. o cal.yr produces objects of class c("cal.yr","numeric"). Functions as.Date.numeric and as.Date.cal.yr added.