https://github.com/cran/Epi
Tip revision: 648a51644b2e4d7f422d53db2c6c754408cf4c9b authored by Bendix Carstensen on 27 April 2008, 00:00:00 UTC
version 1.0.8
version 1.0.8
Tip revision: 648a516
CHANGES
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.