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=<dataframe> 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.