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ChangeLog
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2016-11-02 THIS FILE IS NO LONGER MAINTAINED. Detailed changes are visible through the commits on https://github.com/chjackson/msm
2016-10-19 Chris Jackson <[email protected]>
* Bug fix to prevalence.msm with factor subject IDs
2016-10-02 Chris Jackson <[email protected]>
* Vignette sources moved from "src/doc" to "vignettes" on CRAN
request.
* DESCRIPTION: Version 1.6.4 released to CRAN and r-forge
2016-06-03 Chris Jackson <[email protected]>
* R/utils.R: Bug fix for qtnorm with vectorised arguments. Thanks
to James Gibbons for the report.
* DESCRIPTION: Version 1.6.3 released to r-forge.
2016-03-09 Chris Jackson <[email protected]>
* R/pearson.R: Bug fix for dropping censored states. Thanks to
Casimir Sofeu for the report.
* DESCRIPTION: Version 1.6.2 released to r-forge.
2016-03-09 Chris Jackson <[email protected]>
* DESCRIPTION: Version 1.6.1 released to CRAN.
2016-03-07 Chris Jackson <[email protected]>
* tests: tests updated to work with the development version of
testthat.
2016-02-18 Chris Jackson <[email protected]>
* src/lik.c,R/msm.R: Bug fix and documentation clarification for
models with "obstrue" and "ematrix".
* R/draic.R: Bug fix for initprobs, and only allow expected
information if all panel data.
* R/msm.R: Bug fix for printing CIs with pci and all fixedpars.
* DESCRIPTION: Version 1.6.1 released to r-forge.
2015-11-17 Chris Jackson <[email protected]>
* DESCRIPTION: Version 1.6 released to r-forge and CRAN.
2015-11-10 Chris Jackson <[email protected]>
* src/lik.c: Several bug fixes in calculation of the derivatives
for multivariate HMMs.
* R/msm.R(msm.form.obstrue): Better detection of when obstrue is
supplied as an indicator or a true state + NA.
2015-10-07 Chris Jackson <[email protected]>
* R/outputs.R(msm.form.qoutput): Bug fix for printing model output
when only one transition rate is affected by covariates. Thanks
to Jordi Blanch for the report.
2015-09-14 Chris Jackson <[email protected]>
* src/lik.c: More underflow correction for probabilities of hidden
states in viterbi.msm. Thanks to Hannah Linder for the report.
* R/msm.R: "death" argument in msm() is deprecated and renamed to
"deathexact".
* R/msm.R: censor.states now defaults to all transient states if
not supplied, instead of complaining, even if there is no
absorbing state. Thanks to Jonathan Williams for the report.
* DESCRIPTION: Version 1.5.3 released to r-forge.
2015-04-10 Chris Jackson <[email protected]>
* R/msm.R(statetable.msm): Code simplified, now row names work
with factor states.
2015-02-17 Chris Jackson <[email protected]>
* DESCRIPTION: Version 1.5.2 released to r-forge.
2015-02-10 Chris Jackson <[email protected]>
* R/msm.R, src/lik.c: obstrue can now contain the actual true
state, instead of an indicator. This allows the information from
HMM outcomes generated conditionally on this state to be included
in the model.
* R/msm.R(na.find.msmdata): Fix of bug in na.find.msmdata that
could lead to NAs being passed through to C and causing a crash.
Triggered when state or time were NA and there were covariates.
2015-02-09 Chris Jackson <[email protected]>
* R/hmm-dists.R(hmmDIST): Fix of bug when HMM parameters come from
named vectors.
2015-01-29 Chris Jackson <[email protected]>
* R/outputs.R(msm.form.qoutput) Bug fix in printing fitted model
objects.
2015-01-16 Chris Jackson <[email protected]>
* hmm.R: "links" component dropped from hmodel objects, as it is
no longer used.
* simul.R: "keep" component added to simmulti.msm result.
* R/hmm.R and others: Multivariate observations in HMMs with
different models for each variable. Limited testing so far.
2015-01-15 Chris Jackson <[email protected]>
* Correct version of the built vignette restored to the package
(1.5 instead of 1.3.2).
* Experimental feature: multivariate observations in HMMs. Start
by supporting multiple outcomes from the same distribution at the
same time, with the data supplied as a matrix.
* DESCRIPTION: Version 1.5.1 released to r-forge.
2015-01-05 Chris Jackson <[email protected]>
* DESCRIPTION: Version 1.5 released to CRAN.
2014-12-12 Chris Jackson <[email protected]>
* R/msm.R,R/phase.R. Phase type models now allow HMM on top. Bug
fixes to these models.
* DESCRIPTION: Version 1.4.3 released to r-forge.
2014-12-11 Chris Jackson <[email protected]>
* Posterior probability of the hidden state at each time in the
Viterbi algorithm now conditions on all the data.
* R/msm.R,R/outputs.R(various): Bug fixes to misclassification
models where some states were misclassified as other states with
probability 1, for both ematrix and hmmCat specifications. Thanks
to Li Su for the report.
* DESCRIPTION: Version 1.4.2 released to r-forge.
2014-12-10 Chris Jackson <[email protected]>
* src/lik.c, R/outputs.R: Viterbi algorithm now also returns the
probability of each hidden state at each time given the data up to
that point.
* data/msmdata.rda: statemax added to CAV data.
* man: Document that generic AIC function AIC() works for msm
models.
* DESCRIPTION: Version 1.4.1 released to r-forge.
2014-12-08 Chris Jackson <[email protected]>
* R/phase.R,R/msm.R,Rd/2phase.Rd: New features for phase-type
models.
2014-12-04 Chris Jackson <[email protected]>
* R/draic.R: Bug fixes in drlcv.msm (likelihood of big model on
left-one-out subject was using the original instead of the
refitted model, and used covariate centering
inconsistently). Thanks to Howard Thom.
2014-12-02 Chris Jackson <[email protected]>
* R/msm.R(msm.initprobs2mat,msm.form.houtput): Bug fixes for
covariates on initial state occupancy probabilities with
structural zeros in. Thanks to Jeffrey Eaton and Tara Mangal.
* R/msm.R(msm.form.output): Clean up code, also ensure models
fitted with 1.4 can be printed with 1.4.1.
2014-11-27 Chris Jackson <[email protected]>
* R/draic.R: Bug fix in "prob > 0" in drlcv.msm. Thanks to Howard
Thom.
* R/msm.R: colSums efficiency improvement in msm.add.qcovs,
msm.form.dq. Thanks to Jeffrey Eaton.
2014-11-19 Chris Jackson <[email protected]>
* R/outputs.R: Allow qmatrix to be passed to pmatrix.msm, and a
list of qmatrices to pmatrix.piecewise.msm, instead of a fitted
model.
2014-11-18 Chris Jackson <[email protected]>
* R/outputs.R: qmatrix.msm and related functions tidied up.
* R/outputs.R,R/msm.R: Don't print CIs for fixed parameters in
output formatting functions.
* R/msm.R: Warn that polynomial contrasts aren't supported.
2014-11-11 Chris Jackson <[email protected]>
* src/pijt.c(MatrixExpEXPM): give error if optimiser has chosen
overflowing parameter values. Stops infinite loops seen on
Windows.
2014-11-10 Chris Jackson <[email protected]>
* R/msm.R: Documentation and error message for factor states.
2014-10-31 Chris Jackson <[email protected]>
* R/outputs.R(efpt.msm): Support tostate as character.
* man/plot.survfit.msm: Reference Turnbull method.
* src/lik.c(GetCensored): Fixed valgrind uninitialized value warning.
2014-09-22 Chris Jackson <[email protected]>
* R/optim.R(deriv.test): require namespace instead of loading
numDeriv
2014-07-04 Chris Jackson <[email protected]>
* src/analyticp.c: memory leaks removed.
2014-07-04 Chris Jackson <[email protected]>
* DESCRIPTION: Version 1.4 released to CRAN.
2014-07-02 Chris Jackson <[email protected]>
* R/outputs.R: Default CI method for pnext.msm changed to
"normal", since delta method may not respect probability <1
constraint.
2014-06-23 Chris Jackson <[email protected]>
* C interface changed from .C to .Call.
* Added ppass.msm for passage probabilites.
* DESCRIPTION: Version 1.3.3 released to r-forge.
2014-06 Chris Jackson <[email protected]>
* src/lik.c: Bug fix in infosimple: info was not being initialized
at zero, leading to occasional random output.
* DESCRIPTION: Version 1.3.2 released to r-forge.
2014-06 Chris Jackson <[email protected]>
* tests: Test suite tidied up and converted to use "testthat" package.
* R/boot.R(efpt.ci.msm): Bug fix for bootstrap and efpt.msm.
* src/lik.c(likhidden): Give informative warning for initial
outcomes in HMMs which are impossible for given initial state
probabilites and outcome models. Makes use of a global variable
in a private environment called msm.globals.
* draic.msm, drlcv.msm added.
2014-06 Chris Jackson <[email protected]>
* If msm is called with hessian=FALSE, then the Fisher (expected)
information is used to obtain standard errors and CIs, which may
be preferable if the observed Hessian is very intensive to
approximate or its estimate is nonsingular / nonpositive-definite.
2014-05 Chris Jackson <[email protected]>
* Analytic derivatives available for most hidden Markov models and
models with censored states (excluding unknown initial state
probabilities, constraints on misclassification / categorical
outcome probabilities and their covariates, and truncated or
measurement error distributions). This should speed up
optimisation with the BFGS or CG methods. The corresponding
Fisher information matrix is also available for misclassification
(categorical/identity outcome) models.
* The BFGS optimisation method is now the default, rather than
Nelder-Mead.
2014-05 Chris Jackson <[email protected]>
* msm.optim.fixed, msm.rep.constraints: Bug fix for constraints on
misclassification probabilities and fixed parameters.
2014-05 Chris Jackson <[email protected]>
* msm.R(msm.mnlogit.transform): Bug fix: reapply sum to 1
constraint after applying constraints to baseline probabilities in
HMMs. May affect results.
2014-05 Chris Jackson <[email protected]>
* hmm.R(msm.econstr2hconstr): internal constraints in
misclassification models mapped to 1,2,... using match(constr,
unique(constr))
2014-05 Chris Jackson <[email protected]>
* msm.R(msm.unfixallparams): Don't unconstrain constraints, so
derivatives of fully fixed models refer to constrained pars.
2014-05 Chris Jackson <[email protected]>
* Various help pages now document the objects and data structures
used internally and returned by msm() in the fitted model object.
2014-04 Chris Jackson <[email protected]>
* msm.R and others: major rewrite of much of the internal code
that deals with reading the data and passing it to models. This
uses model frames and model formulae more efficiently. As a
result the "data" component of the msm has a different structure:
a list with one component "mf", the model frame, containing all
original variables required for the model fit. This and related
data structures can can be extracted with the new
"model.frame.msm" and "model.matrix.msm" methods.
* outputs.R: new print method now the default, and new functions
msm.form.qoutput and msm.form.eoutput to produce the printed
numbers in the same arrangement.
* msm.R: Centering of "timeperiod" covariates in "pci" models is
now done consistently with other covariates, i.e. with last
observation omitted.
* outputs.R(factorcov2numeric.msm): bug fix for misclassification
covariates.
* msm.R(crudeinits.msm): Times consistency check added.
* msm.R(msm.check.model): Model consistency check error messages
now report row numbers before missing data are omitted.
* hmm.R(msm.form.hcmodel): Bug fix for when initial values for HMM
covariate effects of wrong length, this should ignore and carry
on.
* pearson.R: Bug fix for when integral for accurate p-value
doesn't converge.
* lik.c: Don't recalculate P matrices for timelag / obstype /
covariate combinations that occur more than once. This may speed
up some hidden Markov or censoring models.
2014-04-11 Chris Jackson <[email protected]>
* msm.R(msm.form.params): Fix of bug which broke models with
covariates on initial state occupancy.
2014-04-10 Chris Jackson <[email protected]>
* R/boot.R,R/outputs.R: Parallel processing using "doParallel"
added for bootstrapping and bootstrap CIs.
2014-04-09 Chris Jackson <[email protected]>
* R/optim.R: Optimisation methods abstracted into their own
functions.
2014-04-04 Chris Jackson <[email protected]>
* DESCRIPTION: Version 1.3.1 released to r-forge.
2014-04-03 Chris Jackson <[email protected]>
* R/msm.R(msm.add.qcovs,msm.add.dqcovs): Fix of drop=FALSE bug for
data with only one transition.
2014-04-02 Chris Jackson <[email protected]>
* R/msm.R: Fix of obscure bug that broke some subject-specific
likelihoods, caused by omitting obstype.obs from data object.
2014-04-01 Chris Jackson <[email protected]>
* R/outputs.R: Time-dependent covariates supported in totlos.msm.
* R/outputs.R(envisits.msm, totlos.msm): New facility for expected
number of visits.
2014-02-26 Chris Jackson <[email protected]>
* R/mstate.R,man/msm2Surv.Rd: New function for exporting data in
counting process format for use with survival and mstate.
2014-02-25 Chris Jackson <[email protected]>
* R/msm.R: Handle convergence failure codes from optim().
2014-02-20 Chris Jackson <[email protected]>
* R/outputs.R(mattotrans): printnew.msm fixed for 2-state
models. Thanks to Martyn Plummer.
2014-01-15 Chris Jackson <[email protected]>
* DESCRIPTION: Version 1.3 released to CRAN.
2014-01-09 Chris Jackson <[email protected]>
* inst/doc/msm-manual.Rnw: Fixed error in analytic p13(t) in
section 1.4.
2013-12-04 Chris Jackson <[email protected]>
* R/outputs.R: Experimental new print method available as
printnew.msm.
* srcR/pijt.c(MatrixExpPade): Fix for int coercion from special
values, to pass CRAN UBSanitizer check.
* src/analyticp.c: Some algebra rearranged to fix potential
division by zeros.
* src/analyticp.c, R/msm.R(msm.form.qmodel): Corrected permutation
for Q matrix, fixing bug from 1.2.3 which broke models with
non-standard state ordering.
* R/outputs.R: New "start" argument to efpt.msm, allowing
averaging over a set of starting states.
* DESCRIPTION: Datasets now lazy loaded so data() not required.
2013-10-07 Chris Jackson <[email protected]>
* DESCRIPTION: Version 1.2.7 released to r-forge.
2013-10-04 Chris Jackson <[email protected]>
* R/outputs.R(observed.msm): Don't use Viterbi imputed states at
change points when computing observed prevalences in "pci" models
with piecewise-constant intensities.
2013-10-01 Chris Jackson <[email protected]>
* R/msm.R(msm.mninvlogit.transform): Fix for bug with
misclassification models with only one misclassification
probability.
* src/lik.c: Match Q matrices with covariates from start of
transition, not end, in likelihoods and derivatives by subject.
2013-09-13 Chris Jackson <[email protected]>
* R/msm.R: "missing" for some null default arguments in msm()
changed to is.null.
* DESCRIPTION: Version 1.2.6 released to r-forge.
2013-08-30 Chris Jackson <[email protected]>
* R/msm.R(msm.R): Give an informative error if trying to use
gen.inits with a HMM, and document that this is not supported.
2013-08-20 Chris Jackson <[email protected]>
* R/msm.R(msm.check.times): Row numbers reported in error message
about different states at the same time corrected to account for
missing data. Thanks to Lucy Leigh for the report.
2013-07-30 Chris Jackson <[email protected]>
* R/outputs.R: formula for totlos.msm implemented, which is vastly
more efficient than the numerical integration used previously.
Debugging outputs left in 1.2.3 also removed.
* R/msm.R, src/*.c: Likelihood calculations use expm from the expm
package by default where matrix exponentiation is required. As a
result msm now depends on the expm package.
* R/utils.R: MatrixExp now uses expm from the expm package by
default.
* R/various: some fixes for bugs introduced by the range facility.
* DESCRIPTION: Version 1.2.5 released to r-forge.
2013-07-22 Chris Jackson <[email protected]>
* R/(various): Range constraints can now be given for HMM outcome
parameters, through a new argument "hranges" to msm(). This may
improve HMM identifiability. Thanks to Soon-Ee Cheah for the
suggestion.
* R/constants.R: Scale parameters of Weibull and t HMM outcome
distributions now restricted properly to be positive in estimation.
* DESCRIPTION: Version 1.2.4 released to r-forge.
2013-07-04 Chris Jackson <[email protected]>
* R/utils.R: MatrixExp rewritten to use C code for series method
and analytic solutions for Markov models, avoiding code
duplication.
2013-07-02 Chris Jackson <[email protected]>
* R/msm.R: If available, loglikelihood derivatives, expected and
(if requested) observed information are returned in paramdata
component for all models. If all parameters fixed, these are over
all parameters. If some are fixed, than these are just over the
parameters that are optimised.
* R/outputs.R: surface.msm fixed for models fitted with Fisher
scoring.
2013-06-06 Chris Jackson <[email protected]>
* R/outputs.R: totlos.msm was calculating the wrong thing for
fromt > 0.
* DESCRIPTION: Version 1.2.3 released to r-forge.
2013-06-04 Chris Jackson <[email protected]>
* R/pearson.R: Corrected data rows mismatch in bootstrapping with
imputed sampling times after deaths in Pearson statistic.
* src/lik.c: Memory crash bug in Viterbi fixed.
2013-06-03 Chris Jackson <[email protected]>
* (Most R and C files): Major restructuring of the internals.
Main change is to adjust all parameters for covariates in R rather
than C, making for much tidier code. New R functions for applying
transformations and inverse transformations.
* src/pijt.c: Derivatives of the likelihood for non-hidden models
now work properly with negative constraints.
* R/msm.R: Initial state occupancy probabilities are estimated on
the multivariate logit scale, rather than univariate logit, and
confidence intervals are calculated using the normal simulation
method. Probability for the baseline category "initpbase" is now
a labelled parameter.
* R/msm.R: When centering covariates around their means for the
default likelihood calculation, the means used are now after
dropping missing values and subjects with one observation, not
before. Thanks to Howard Thom for the report.
* Relatedly, the covariate values for subjects' last observations
are not included in this mean, since they don't contribute to the
likelihood, so interpretation of initial values for the qmatrix,
and outputs for covariates="mean", will now be very slightly
different.
2013-05-28 Chris Jackson <[email protected]>
* inst/doc/msm-manual.Rnw: Likelihood for exact times still had
wrong sign for qii (see version 1.1.2).
2013-05-25 Chris Jackson <[email protected]>
* inst/doc/msm-manual.Rnw: Added advice about "function cannot be
evaluated at initial parameters".
2013-05-24 Chris Jackson <[email protected]>
* R/msm.R: New interface for supplying different covariates on
different transition intensities.
* R/msm.R: Redundant constraint check and factor warning fixed and
cleaned.
2013-05-23 Chris Jackson <[email protected]>
* R/msm.R(msm.form.covdata): checks on constraints and covinits
separated into new functions.
* R/msm.R(msm.form.covmodel): wrong names in error message for
constraint length checking.
2013-05-21 Chris Jackson <[email protected]>
* R/msm.R(msm.form.data): Handle factor states (with levels
1:nstates) by converting to numeric.
* R/msm.R, src/lik.c: Can now print subject-specific
log-likelihoods at the MLE via logLik.msm().
* DESCRIPTION: Version 1.2.2 released to r-forge.
2013-05-19 Chris Jackson <[email protected]>
* R/utils.R: qtnorm, qmenorm, qmeunif and qpexp changed to use
qgeneric. Their results should be the same.
* R/utils.R: long-redundant identity function finally removed.
2013-05-18 Chris Jackson <[email protected]>
* R/utils.R: qgeneric function copied from flexsurv
package and modified to handle argument clashes.
* R/utils.R: Return NaN for all dpqr(tnorm,menorm,meunif) if lower
bound greater than upper bound.
2013-05-17 Chris Jackson <[email protected]>
* R/msm.R: Don't warn if not all states observed in data for
misclassification models (typo bugfix in msm.form.data).
2013-05-16 Chris Jackson <[email protected]>
* R/msm.R,R/hmm.R,src/lik.c: Allow matrix by patient to be
supplied for the initial state occupancy probabilities.
* DESCRIPTION: Version 1.2.1 released to r-forge.
2013-05-15 Chris Jackson <[email protected]>
* R/msm.R: move gen.inits from msm.form.qmodel to main function.
2013-05-14 Chris Jackson <[email protected]>
* DESCRIPTION: Version 1.2 released
2013-05-08 Chris Jackson <[email protected]>
* R/msm.R,R/outputs.R: Misclassification models where some
off-diagonal misclassification probabilities are 1 are now handled
properly. Thanks to Howard Thom for uncovering this.
2013-04-19 Chris Jackson <[email protected]>
* R/outputs.R: prevalence.msm can now produce expected values by
integrating model predictions over the covariate histories
observed in the data.
* R/msm.R(msm.form.data): Drop subjects with only one observation
remaining after dropping missing data (e.g. psor data). This gives
a more appropriate measure of the numbers at risk in prevalence.msm.
2013-04-18 Chris Jackson <[email protected]>
* R/outputs.R(summary.msm): Allow arguments to be passed through
summary.msm to prevalence.msm.
* R/outputs.R(pmatrix.piecewise.msm): Allow this to be used for
time-homogeneous models with change point vector "times" of length
0.
2013-04-15 Chris Jackson <[email protected]>
* R/outputs.R: New function efpt.msm for expected first passage
times for time-homogeneous models. Thanks to Howard Thom for the
research.
* R/outputs.R: totlos.msm now passes options to integrate() to
bootstrapping functions.
2013-04-10 Chris Jackson <[email protected]>
* R/msm.form.data: firstobs was wrong with missing data.
2013-04-08 Chris Jackson <[email protected]>
* R/simul.R, R/pearson.R: Function boot.param.msm renamed to
simfitted.msm and made user-accessible.
2013-04-05 Chris Jackson <[email protected]>
* R/pearson.R: Accurate p-values from Titman (Lifetime Data
Analysis, 2009).
* R/pearson.R: Degrees of freedom were being calculated
incorrectly (via "n.zerofrom" variable) when user-defined groups
included from-states.
* R/simul.R: Include an option to simmulti.msm (and getobs.msm) to
not drop absorbing-absorbing transitions.
2013-03-22 Chris Jackson <[email protected]>
* R/pearson.R: Fix of bug in Pearson test introduced in version
0.9.5, which affected the expected transitions to the final state
(and resulting test statistics) for panel data without exact death
times.
* src/lik.c, src/pijt.c: Implement the Fisher information for
non-hidden models without censored states.
* R/msm.R: Implement a Fisher scoring algorithm which uses this
expected information.
2013-02-02 Chris Jackson <[email protected]>
* R/outputs.R(observed.msm): Add a censoring time facility to
optionally remove subjects from the risk set a certain time after
they have reached an absorbing state. Thanks to Andrew Titman.
2013-02-02 Chris Jackson <[email protected]>
* src/lik.c: Bug fix for Viterbi with obstrue. Thanks to Linda
Sharples.
* R/outputs.R(print.msm): Don't print message about baseline
covariate values in misclassification model outputs if there are
no covariates.
2013-01-14 Chris Jackson <[email protected]>
* R/outputs.R(observed.msm): Bug fix for interp="midpoint" method
in observed prevalence calculation. Thanks to Erica Liu.
2012-12-10 Chris Jackson <[email protected]>
* tests/simple.R: Modified pmatrix.msm normal bootstrap test
output to work with new seeding behaviour of rmvnorm.
* DESCRIPTION: Version 1.1.4 released
2012-09-28 Chris Jackson <[email protected]>
* src/doc: Remember to copy the up-to-date manual source into src
for new releases, as required by Linux distribution package
builders.
* DESCRIPTION: Version 1.1.3 released
2012-09-27 Chris Jackson <[email protected]>
* inst/doc/msm-manual.Rnw: Work around texi2dvi problem where
non-breaking spaces appear as tildes.
2012-09-25 Chris Jackson <[email protected]>
* R/outputs.R(qematrix.msm): Bug fix for user-supplied covariate
values when center=FALSE. Thanks to Vikki O'Neill for the report.
2012-09-24 Chris Jackson <[email protected]>
* man/boot.msm.Rd: Documented failure of boot.msm to handle
user-defined objects that clash with built-in objects.
2012-09-21 Chris Jackson <[email protected]>
* R/msm.R: Use BFGS method for one-parameter optimisation unless
method supplied explicitly, avoiding warning about unreliability
of Nelder-Mead.
2012-07-31 Chris Jackson <[email protected]>
* R/pearson.R: Browser was still on for pearson.msm. Thanks to
Chyi-Hung Hsu.
* DESCRIPTION: Version 1.1.2 released
2012-05-28 Chris Jackson <[email protected]>
* (various files): New Student t distribution for hidden Markov
model outcomes. Thanks to Darren Gillis.
2012-05-11 Chris Jackson <[email protected]>
* R/msm.R(msm.check.times): Bug fix in data consistency checks
with unsorted subject IDs. Thanks to Kelly Williams-Sieg for the
report.
* DESCRIPTION: Version 1.1.1 released
2012-05-01 Chris Jackson <[email protected]>
* R/utils.R: Corner cases in qtnorm fixed. Thanks to Art Owen for
the report.
* R/boot.R: Multicore functionality removed from this release
since doSMP was removed from CRAN. Will restore when a stable
preferred cross-platform solution emerges.
2012-01-31 Chris Jackson <[email protected]>
* R/pearson.R: Bug fix for models where transitions are only
allowed from one state. Thanks to Gavin Chan for the report.
2012-01-31 Chris Jackson <[email protected]>
* R/msm.R: If user supplies an ematrix with all misclassification
probabilities zero, the non-misclassification model is fitted.
Thanks to Sharareh Taghipour for the report.
* R/msm.R(msm.check.model): Bug fix for error messages when model
inconsistent with data.
2011-11-28 Chris Jackson <[email protected]>
* R/boot.R: boot.msm and functions which use this can now use
doSMP to parallelise calculations.
2011-11-25 Chris Jackson <[email protected]>
* R/boot.R: Fix of bug which affected calculation of confidence
intervals by the "normal" method when there were fixed parameters
or HMMs.
2011-10-27 Chris Jackson <[email protected]>
* R/outputs.R: Bug fix: Subset function "[.msm.est" was labelling
columns wrong for objects with no SE component (pmatrix.msm,
pnext.msm).
2011-09-09 Chris Jackson <[email protected]>
* DESCRIPTION: Version 1.1 released
2011-07-25 Chris Jackson <[email protected]>
* R/outputs.R: New function "[.msm.est" to extract specific rows
and columns of the output from, e.g., qmatrix.msm() in a more
intuitive way.
2011-07-24 Chris Jackson <[email protected]>
* R/outputs.R: New function "pnext.msm" to compute a matrix of
probabilities for the next state of the process.
2011-07-07 Chris Jackson <[email protected]>
* man/msm.Rd: Doc clarifies that "death" is overridden by
"obstype" and "exacttimes", and "exacttimes" is overridden
by "obstype".
2011-06-09 Chris Jackson <[email protected]>
* man/msm.Rd: Correct documentation for factor levels of
"timeperiod".
* R/outputs.R(qematrix.msm): Fix CIs for diagonal entries when
first state is absorbing.
* R/msm.R(msm.check.model): Refer to observation numbers, not
transition numbers, in "data inconsistent with model" error
message.
2011-05-26 Chris Jackson <[email protected]>
* DESCRIPTION: Version 1.0.1 released
2011-05-20 Chris Jackson <[email protected]>
* R/outputs.R(msm.fill.pci.covs): Bug fix, pmatrix.msm would break
for models with non-integer time change points "pci". Thanks to
Christos Argyropoulos for the report.
* man/prevalence.msm.Rd: Clarify that "piecewise.times" is not
needed for models fitted with "pci". Thanks to Christos
Argyropoulos.
* R/msm.R(msm): Warning if initcovariates is supplied but the
model is not hidden Markov. Thanks to Christos Argyropoulos.
2011-05-05 Chris Jackson <[email protected]>
* R/utils.R(dtnorm): Return -Inf when log=TRUE and x outside
truncation bounds. Thanks to William Leeds for the report.
2011-02-08 Chris Jackson <[email protected]>
* man/msm.Rd: Help page clarified to say that "state" is also used
for the observed outcome in a HMM. Thanks to Ricardo Antunes.
2010-11-24 Chris Jackson <[email protected]>
* R/outputs.R: Line types, colours and widths can be configured in
plotprog.msm, plot.survfit.msm and plot.prevalence.msm.
* DESCRIPTION: Version 1.0 finally released to accompany the
forthcoming paper on msm in Journal of Statistical Software.
2010-11-12 Chris Jackson <[email protected]>
* man/msm.Rd: Documentation for the return value of msm corrected
to state that the "logbaseline" components of result matrices are
evaluated with covariates set to zero if center=FALSE, and at
their means if center=TRUE. Previously it stated that
"logbaseline" was evaluated at the mean covariate values.
* R/msm.R(msm), R/outputs.R(print.msm): Return the "baseline" and
"sojourn" components of result matrices at covariate values of 0
if center=0. Thanks to Kenneth Gundersen for the report.
2010-11-01 Chris Jackson <[email protected]>
* R/boot.R(bootdata.trans.msm): Fix for bootstrapping when some
levels of a factor do not appear in a bootstrapped dataset.
Thanks to Gale Bravener for the report.
2010-10-29 Chris Jackson <[email protected]>
* R/msm.R(msm.check.times): Fixed a bug in comparing small floating
point numbers to zero, and added "may be" to warning about data
inconsistent with transition matrix, due to uncertainty about
these comparisons.
2010-09-22 Chris Jackson <[email protected]>
* R/msm.R(msm.check.times): Added warning for multiple observations
at the same time on the same person with different states, which
leads to zero likelihood and "cannot be evaluated at initial
values" message.
2010-05-18 Chris Jackson <[email protected]>
* DESCRIPTION: Version 0.9.7 released
2010-05-07 Chris Jackson <[email protected]>
* R/msm.R: Ematrices and ematrix.msm for models with all
"fixedpars" returned correctly.
2010-05-04 Chris Jackson <[email protected]>
* R/boot.R: Bug fixes. "end" argument wasn't included in
totlos.ci.msm and totlos.normci.msm, bootstrapping broke with
covariates on HMM outcomes, and "fixedpars" weren't accounted for
in normboot.msm. Thanks to Li Su for these reports.
2010-02-09 Chris Jackson <[email protected]>
* R/pearson.R: Fix for "NA in probability vector" error caused by
floating point comparisons in empiricaldists(), which were still
happening. Thanks to Wen-Wen Yang for the report.
* DESCRIPTION: Version 0.9.6 released
2010-01-29 Chris Jackson <[email protected]>
* src/pijt.c(Pmat): Don't round extreme likelihood contributions
to 0 and 1 for models with "exacttimes", since they are not
probabilities. Fixes occasional wrong likelihood calculations.
2010-01-14 Chris Jackson <[email protected]>
* R/msm.R: The "pci" element of fitted model objects now excludes
values which are outside the time range of the data. Allows
pmatrix.msm to be used on such models without error. Also give a
warning when any "pci" cut points equal the min/max time point in
the data. Thanks to Matt Cowperthwaite.
2009-11-25 Chris Jackson <[email protected]>
* R/pearson.R: Fix for problem revealed by different handling of
factors in R-2.10.0, which caused all expected values to be
returned as zero. Thanks to Brian Tom for the report.
* DESCRIPTION: Version 0.9.5 released.
2009-11-13 Chris Jackson <[email protected]>
* R/msm.R(msm.form.data): Bug fix for handling missing subject ID.
* DESCRIPTION: Version 0.9.4 released.
2009-11-05 Chris Jackson <[email protected]>
* R/outputs.R(pmatrix.msm, pmatrix.piecewise.msm): Allow options
to MatrixExp to be passed through.
* R/msm.R(crudeinits.msm): Don't break with missing values.
2009-09-15 Chris Jackson <[email protected]>
* R/likderiv.msm: Bug fix: Use obstype.obs when calculating score
residuals, not obstype. Also fixed misplaced for loop initialising
patient derivatives to zero in src/lik.c(derivsimple_subj). Thanks
to Aidan O'Keeffe for the report.
2009-08-26 Chris Jackson <[email protected]>
* R/pearson.R: Fix for "replacement has 0 rows" error - don't add
covariates column to internal data when there are no covariates.
* R/pearson.R: timeinterval rounded in empiricaldists to avoid "NA
in probability vector" errors in R-devel arising from floating
point fuzz.
2009-08-20 Chris Jackson <[email protected]>
* R/msm.R: fix of previous bug fix from 06-24 for derivatives with
respect to fixed parameters. Thanks to Aidan O'Keeffe for the