version 1.1.10 |

- fix clang15 warnings
- fix latex escape note
- fix version info from new.md note

version 1.1.9 |

- reset license from GPL-2 to the original GPL (>=2)

version 1.1.8 |

- fixed typo in C code causing i386 error in rmutil::int()

version 1.1.7 |

- added Author information of TOMS614/INTHP
- fixed void / SEXP registration issue (LTO / valgrind additional issues)
- fixed 0-sized array warning
- Fixed call_R Issue https://github.com/swihart/rmutil/issues/11
- Updated links to https: where appropriate

version 1.1.6 |

- Fixed call_R Issue https://github.com/swihart/rmutil/issues/11
- Updated links to https: where appropriate

version 1.1.5 |

- Fixed Issue https://github.com/swihart/rmutil/issues/10 – updated
BetaBinomial help documentation to relate
`m`

and`s`

to the standard/traditional`alpha`

and`beta`

parameterization. Thanks to @sjenkins20 on github for the suggestion! - Fixed Issue https://github.com/swihart/rmutil/issues/9 – Condition
has length > 1 and only the first element will be used warning in
`int`

. Thank you @ellessenne on github for chasing this one down.

version 1.1.4 |

- In response to K. Hornik email regarding the stringsAsFactors=FALSE default in upcoming R versions, I did the following 3 edits:
- add
`stringsAsFactors=TRUE`

to the v <- data.frame() call in the example of`tvctomat.Rd`

- add
`stringsAsFactors=TRUE`

to the data.frame() call in the function`tvctomat()`

(around line 1160 in`objectrm.r`

): (`oldtvcov$tvcov <- data.frame(oldtvcov$tvcov,tvcv, stringsAsFactors = TRUE)`

- turn
`tvcv <- as.data.frame(as.vector(t(as.matrix(tvcov))))`

into`tvcv <- data.frame(as.character(as.vector(t(as.matrix(tvcov)))),stringsAsFactors=TRUE)`

in the function`tvctomat()`

(around line 937 of`objectrm.r`

) - Issue https://github.com/swihart/rmutil/issues/8.

version 1.1.3 |

- Implemented better fixes for
https://github.com/swihart/rmutil/issues/5 (Thanks @hennerw!) where values
below the support will give 0 and values above support give 1 for
pbetabinom and dbetabinom as the last fix in 1.1.2 could give erroneous
results.

Let me know if other functions need this functionality – I’d be happy to update. - Removed local generic
`weights`

as per personal communication from K Hornik

version 1.1.2 |

- Implemented https://github.com/swihart/rmutil/issues/5 (Thanks @hennerw!) where values below the support will give 0 and values above support give 1 for pbetabinom and dbetabinom. Let me know if other functions need this functionality – I’d be happy to update.

version 1.1.1 |

- fixed an
`_R_CHECK_LENGTH_1_CONDITION_=true`

error - fixed
`_R_S3_METHOD_LOOKUP_BASEENV_AFTER_GLOBALENV_=true`

errors.

- changed Example in DataMethods.Rd to
`glm(y~x+z, data=as.data.frame(reps))`

version 1.1.0 |

Major changes

Passed CRAN checks and is back on CRAN. Please see github page https://github.com/swihart/rmutil to see the changes required to pass CRAN checks. I’ll try to document the changes henceforth here and at https://github.com/swihart/rmutil/issues.

version 1.0 |
---|

30.11.10 (growth) elliptic: twins option added for model using covfn with covariance matrix diagonal constant 28.11.10 elliptic: added an error check when covfn used 15.2.10 (rmutil) changed s<0 to s<=0 in qlaplace & rlaplace (thanks to Peter Ehlers) 18.11.09 (repeated) removed a redundant line in gausscop.r that now produced an error (thanks to Patrick Lindsey) 7.4.09 removed extra } in biv.binom.Rd (thanks to Christopher Marcum) 20.10.08 discrete q functions: changed trunc to round (thanks to Frederic Gosselin) 3.7.08 (gnlm) fit.dist: corrected check for negative values with Laplace, Cauchy, and Student t plus error in counts (f -> ni) for Laplace (thanks to Michael Anyadike-Danes) 24.10.07 fnenvir: changed way “=” is handled in gsub() because of error since R2.5.0 8.10.07 (event, gnlm, growth, repeated) changed typsiz to typsize in nlm() throughout 11.7.07 romberg.c: added missing R.h (thanks to Olivia Lau) 8.2.07 print out name of response variable in elliptic, bnlr, gnlr, gnlr3, gnlmm, gnlmm3, and fmr (thanks to Patrick Lindsey) qsimplex: corrected search interval updates 27.9.06 qhjorth, qinvgauss, qginvgauss, qboxcox: changed lower limit of search from 0.001 to .Machine$double.xmin (thanks to Franco Mendolia) 8.12.05 (rmutil, repeated, event) minor modifications to Fortran for F95 compatibility (thanks to Jan de Leeuw) 22.11.05 finterp, objectrm: added na.action=NULL in calls to model.frame (default is na.omit !!!!!) (thanks to Patrick Lindsey) 30.9.05 elliptic: corrected calculation of number of parameters for builtin logistic function (thanks to Tom Van Dooren) 1.8.05 qbetabinom: changed trunc() to round() (thanks to Elias Krainski) mprofile, iprofile: added check that times are available (thanks to Patrick Lindsey) 6.7.05 ksurvb, ksurvg, kcountb: added break; after default: in C code to satisfy some compilers (thanks to Patrick Lindsey) 30.6.05 finterp: correction for change in functioning of match() gnlm family: added coef.gnlm() and vcov.gnlm() (thanks to Bendix Carstensen) 25.4.05 (stable) rstable: eliminate production of NAs (thanks to Zhu Wang) 26.1.05 finterp: fixed a bug when >= or <= is used in a formula (thanks to Eliot McIntire) 1.11.04 gnlmm3: generalized nonlinear mixed models for three-parameter distributions 28.9.04 catmiss: removed codes() from example in help (thanks to Kjetil Brinchmann) 21.9.04 finterp: fixed if test to remove occasional warning (thanks to Ken Knoblauch) 17.9.04 gnlmix: removed erroneous printing that distribution is censored for binomial (thanks to Ken Knoblauch) 28.7.04 gnlmix, hnlmix: fixed printing of results when nonlinear function contains a linear part (thanks to Ken Knoblauch) 2.7.04 tvctomat: fixed warning message on removing tm (thanks to Patrick Lindsey) 1.6.04 glmm: changed print.summary.glmm to work under R1.9 (thanks to Spencer Graves) 5.4.04 fnenvir: fixed obscure error when linear used in a function (thanks to Ken Knoblauch) help: corrected truncation of usage formula for certain functions (thanks to Patrick Lindsey) 9.1.04 fitdist: fixed typo that stopped geometric distribution from working 6.1.04 ordglm: changed tapply to capply because of change to former (thanks to Andrew Criswell) 9.12.03 corgram: start abscissa at 0 for PACF fnenvir: fixed grep for checking redundant parameters bnlr, fmr, gnlmm, gnlr, gnlr3, int, nlr, nordr, read.list, stable.mode: fixed if() on vector 14.11.03 readdna, survkit, glmm, gnlmm, objectrm, readrm: removed obsolete codes() function (thanks to Ken Knoblauch) carma: give error when ccov=~1 used (thanks to Patrick Lindsey) 21.8.03 elliptic: corrected print function when the dispersion function depends on the location function (thanks to Gabrielle Kelly) 31.7.03 hnlmix: corrected options for dnbinom (thanks to Jagat Sheth) 30.6.03 dftorep: corrected check for ordered times to allow for two levels of nesting 25.5.03 ordglm: added a data argument (thanks to Kosuke Imai) 13.5.03 ordglm: corrected order of printing of standard errors (thanks to Kosuke Imai) 25.4.03 gnlr, gnlr3, gnlmm, fmr, nordr: changed test for environment because the value returned by parent.frame() has a class in R1.7 22.4.03 cphidden: a function to locate a changepoint in continuous time using a two-state hidden Markov model 9.4.03 biv.binom: corrected degrees of freedom printed (thanks to Goran Brostrom) 12.2.03 restovec: fixed handling of delta when the response is a list 16.1.03 kalsurv: fixed typo in print.kalsurv (thanks to Anthony Gichangi) 4.12.02 int: changed eps 2.12.02 fit.dist: added Laplace distribution 1.12.02 glmm: added error message if (codes of) nesting variable not consecutively numbered (thanks to Renaud Lancelot) 27.11.02 fit.dist: changed Weibull parametrisation so that mu refers to y and not to y^alpha 22.11.02 fit.dist: added Cauchy and Student t distributions use (log) density functions instead of writing formulae 18.11.02 fit.dist: added beta-binomial distribution 16.11.02 fit.dist: corrected error in calculation of log likelihood when censor=T 14.11.02 fit.dist: corrected error in calculation of fitted values for zeta distribution 31.10.02 int2: added default limits (thanks to Patrick Lindsey) 8.9.02 (repeated) gar: corrected recursive fitted values when binomial (thanks to Patrick Lindsey) 4.9.02 gausscop: exponential distribution now works (thanks to Patrick Lindsey) 30.8.02 restovec: modified checks for nesting in lists and allow nesting to be supplied separately when a list is given (thanks to Patrick Lindsey) gausscop: for positive-valued distributions, returned predicted values without transforming by log link function (thanks to Patrick Lindsey) 18.7.02 ehr: addition checks of data supplied to this suite of functions rs3: fixed typo marg.hom: added checks on data 16.7.02 chidden.r, hidden.r: corrected negative binomial check so that 0 responses are allowed (thanks to Ben Cooper) 10.7.02 modified man pages for changed arguments to rgamma function rmutil: created dist.h file 11.6.02 hnlmix: corrected AIC for penalty constraint (was too large by one) changed calculation of multiplicative random effects 23.5.02 rmutil: added [pdqr]twosidedpower distribution added log option to all density (d) functions gar, gnlr, gnlmix, gnlmm, hnlmix: added two-sided power distribution gnlr: user-supplied likelihood function works again (thanks to Martin Liermann) finterp, fnenvir: added option to allow any response to be a covariate 9.5.02 hnlmix: recursive fitted values available ordglm: fixed error that PearsRes not defined when individual data are supplied (thanks to Kamal Desai) 6.5.02 gnlmix, hnlmix: added inverse gamma mixture distribution gnlmix: handles censored data gnlmm: finds nesting variable when repeated environment is specified 5.5.02 finterp: modified so that as.factor(times) works 30.4.02 hnlmix: nonlinear random effects models using a modified Lee and Nelder h-likelihood gnlr: modified check on location parameters for Levy distribution added check that double Poisson, multiplicative Poisson, gamma count, and logarithmic data are not censored |

28.4.02 gnlmix: corrected typo in negative binomial distribution
23.4.02 carma, chidden, elliptic, hidden, kalseries: give error if
censored data supplied (thanks to Troels Ring) 22.4.02 elliptic: when
two levels of nesting, calculate correctly first recursive fitted value
in each cluster (was plotted correctly using iprofile) plus
corresponding simplification of plot.iprofile (thanks to Troels Ring)
17.4.02 (all libraries) gnlmix: corrected typo in inverse Gauss mixing
distribution print model methods: added option not to print correlations
15.3.02 restovec, tcctomat, tvctomat: added optional description slot to
response, tccov, and tvcov objects 13.3.02 glmm: convert repeated object
to dataframe if supplied as data tcctomat, tvctomat: corrected to detect
contrast options when dataframe=F 12.3.02 tvctomat: corrected problem
for list of factors when dataframe=F (thanks to Patrick Lindsey)
finterp.default: give error if members of dataframe named using $
(thanks to Christof Bigler) 28.2.02 chidden, hidden: added check for
correct number of initial estimates when list of functions supplied
(thanks to Patrick Lindsey) 22.2.02 corgram: added option for PACF
19.2.02 fmr: modified some discrete distributions to avoid overflow with
large counts 17.2.02 elliptic: added as.double for y in call to C code
because of change in read.table 12.2.02 finterp: give error if offset
used in W&R formula 31.1.02 %^%: power of a matrix elliptic:
corrected problem when common parameters in mean and variance functions
20.1.02 plot.repeated: added selection of profiles to be plotted by
using ccov 14.1.02 gar: added absolute value arch (names of others
changed: additive -> square, multiplicative -> exponential)
volatility method for extracting values of nonconstant dispersion
parameter Makefiles: removed . for SHLIB_EXT for R1.4.0 dist.c,
kcountb.c, romberg.c, stable.c: changed malloc to R_alloc 10.1.02
(dhpqr)ggamma, fmr, gausscop, gnlmix, gnlmm, gnlr, gnlr3, hgamma:
changed argument of (dpqr)gamma for compatibility with R1.4.0 modified
help to work with R1.4.0 18.12.01 contr.mean: provides correct labels on
mean constraints (corrects contr.sum) 4.12.01 chidden, hidden: corrected
printing out family parameter with AR when there is not one 28.11.01
qstable: corrected bug when tail<1 and skew=1 (thanks to Alec
Stephenson) 23.11.01 corgram: handles NAs in the series 19.11.01
cprocess: fixed error in checking for list of events (thanks to Troels
Ring) stablereg: changed alpha to allow parameter to be (0,2) instead of
(1,2) 18.11.01 chidden: added time-discretized Poisson process 17.11.01
chidden, hidden: added Student t distribution changed Cauchy shape
parameter to scale instead of scale^2 15.11.01 gar: added Student t
distribution added ARCH models elliptic: when AR, take log of
determinant returned by dpodi (thanks to Gabrielle Kelly) 13.11.01
elliptic: when series of independent observations, calculate covariance
determinant as sum of log variances instead of log of product (thanks to
Gabrielle Kelly) 8.11.01 cmcre: corrected problems when a covariate is
used (thanks to Anthony Gichangi) 6.11.01 print.response: do not print
mean if nominal (but not binary) or ordinal (thanks to Patrick Lindsey)
25.10.01 hidden.r: corrected check for fixed zeros in transition matrix
relaxed check for rows of transition matrix summing to one chidden.r:
relaxed check for rows of transition matrix summing to zero (all thanks
to Patrick Lindsey) 24.10.01 restovec: weights can be logical 14.10.01
gar: fixed output printing when shape is a function of location
parameter use dnbinom function changed negative binomial shape parameter
to be same as in gnlr 10.10.01 carma, chidden, gar, hidden, kalcount,
kalseries: check for two levels of nesting when serial dependence fitted
9.10.01 kalseries: corrected error when torder used with tvcov 8.10.01
hidden, chidden: added observed AR(1) gnlr, gnlmm, gnlmix: changed
parametrization of the shape parameter for the beta distribution (thanks
to Goran Arnoldsson) binnest: duplicate variables in Fortran call model
functions using envir: check that response specified is one in envir
when only one present 3.10.01 plevy, qlevy: use pnorm and qnorm instead
of integrating 26.9.01 elliptic: added second form of asymmetric
multivariate Laplace distribution with constant asymmetry parameter
25.9.01 elliptic: added asymmetric multivariate Laplace distribution
24.9.01 carma.r: removed unnecessary check that envir is a repeated
object (thanks to Troels Ring) 11.9.01 fit.dist: added checks that
grouped frequency data are supplied 10.9.01 kalsurv: corrected output
errors when environment is supplied gar: use log option in dbinom, dpois
kalcount: set first recursive prediction in series to marginal
prediction 6.9.01 gar: added loglog link for binomial data (corrected
cloglog which was, in fact, loglog) 20.8.01 gnlmix: set undefined sh3 to
NULL for one parameter distributions 1.8.01 chidden, gar, gnlr3, hidden:
added skew Laplace distribution 27.7.01 corgram: improved presentation
of correlogram 25.7.01 d,h,p,q,rskewlaplace: probability functions for
the skew Laplace distribution 24.7.01 autointensity.r: plots
autointensity function of a point process 12.7.01 plot.repeated: fixed
error of unknown type when plotted time-varying covariate (thanks to
Patrick Lindsey) carma: clearer error message when incorrect environment
supplied 10.7.01 carma: will handle data objects with (one of)
multivariate responses chidden, hidden: handle Jacobian correctly with
(one of) multivariate responses 6.7.01 cprocess.r: recognizes data
objects for events and not just for times 5.7.01 f2c.h included in
library for toms614.c (missing in R1.3.0) 27.6.01 iprofile, mprofile:
corrected links to other libraries for html help plot.cum.pergram:
corrected confidence interval pergram: changed calculation of length for
odd-lengthed series 22.6.01 gar.r: check that times are supplied and, if
not, create if possible 19.6.01 fmr.r, gnlmm.r, gnlr.r, gnlr3.r: linear
can be ~1 if mu not supplied 14.6.01 marg.hom.r: modified to handle
factor variables with non-numeric levels 8.6.01 ordglm.r: corrected
fitted values when weighted observations (thanks to Troels Ring) 31.5.01
elliptic: changed check on initial variance function estimates 16.5.01
print.response, print.tvcov, print.repeated: added option to print range
of numbers of observations per individual instead of vector of numbers
(thanks to Markus Jantti) dmultpois, etc: added additional check on
dependence parameter 9.5.01 gar.r: corrected printout for generalized
gamma parameter 26.4.01 changed F and T to FALSE and TRUE throughout
read.rep: removed col.names option because of changes in read.table
22.4.01 glmm: corrected typo when dataframe used with no offset 20.4.01
finterp: detects functions when given as arguments of other functions
19.4.01 finterp: formulae can be written on several lines, as several
instructions (e.g. to assign temporary variables) 11.4.01 dburr, pburr,
qburr, hidden, chidden, gnlr3: changed parametrization of Burr
distribution (thanks to Patrick Lindsey) 28.3.01 chidden, hidden:
corrected vector length problem in check for ordered intercepts in
ordinal models (thanks to Niko Speybroeck) several p and d functions:
changed check to y>=0 (thanks to Patrick Lindsey) 22.3.01 glmm: works
again with weights and/or offset (thanks to Luc Duchateau) gnlmix:
changed to log dispersion for mixing distribution 21.3.01 int.c:
corrected memory allocation problem GExtVal: changed man page to agree
with functions (both thanks to Patrick Lindsey) 20.3.01 use log option
in d and p functions for h functions 14.3.01 chidden, hidden: added
further checks on ordering of intercepts for ordinal data 13.3.01
gnlmix: changed dispersion parameter for normal mixing distribution from
standard deviation to variance delta: returns a vector instead of a
matrix if only for one variable 11.3.01 gnlmix: correction to work with
unbalanced data 9.3.01 gar, gnlr3: added power variance function Poisson
distribution 8.3.01 covariates: added expand option dpvfpois, ppvfpois,
qpvfpois, rpvfpois: functions for the overdispersed power variance
function Poisson distribution kalcount: corrected for power variance
function 7.3.01 plot.response: corrected indexing problem 1.3.01
kalcount, kalseries, kalsurv: removed constraints on family parameter
27.2.01 chidden, fmr, gar, gausscop, gnlmix, gnlmm, gnlr, gnlr3, hidden,
kalseries, kalsurv, nlr: relaxed type checks for continuous and duration
data 26.2.01 kalcount, kalseries, kalsurv: added two-parameter power
variance family mixture including gamma and inverse Gauss mixtures
(family) for serial dependence 23.2.01 response: if response is
univariate, returns a vector instead of a matrix covariates: if only one
covariate requested, return as a vector chidden, hidden: improved checks
for ordered intercepts with ordinal response improved calculation of
ordinal probabilities 22.2.01 plot(iprofile()): works for models from
kalsurv (thanks to Jacob Bowers) 19.2.01 chidden.r, hidden.r: corrected
error in calculating individual profiles when tvmu used (thanks to Jacob
Bowers) ordinal data can be used with multinomial option (thanks to
Patrick Lindsey) work with ordinal data with a list of different
formulae (thanks to Niko Speybroeck) 31.1.01 glmm.r: works if response
is a one-column matrix instead of a vector (thanks to Luc Duchateau)
restovec: corrected manual so that arguments section appears (thanks to
Patrick Lindsey) 30.1.01 finterp, fnenvir: further correction to handle
decimal numbers (including scientific notation) correctly finterp:
replaced gsub by all.vars 25.1.01 name of response can be a character
string when environment is supplied (thanks to Patrick Lindsey) hidden,
chidden: added description of pintercept to man page delta: works
properly when name is supplied plot functions: use 6 different line
types instead of 4 gausscop: corrected mean for gamma margin check that
only one initial estimate when no dispersion function 18.1.01
transform.response: works when units is NULL hidden, chidden: reversed
order of categories for proportional odds and continuation ratio
replaced dqrcf with dqrsl nordr: bug fix to work with data objects
8.1.01 cutil.c, romberg.c, toms614.c: changed include for call_R (thanks
to Dennis Murphy) 7.1.01 model fitting functions check for correct type
of response dftorep, read.rep: modified to handle new “types” of
responses dftorep: now handles two column binomial response ehr.r:
rewrote to conform to other functions 4.1.01 restovec: option to add
responses to an old response object and types of responses returned in
list instead of as a class resptype: new method to return types of
response variable(s) finterp.repeated: check that binomial and censored
responses are not used as covariates 21.12.00 gar.r: corrected error in
printing three-parameter distributions 19.12.00 finterp, fnenvir:
methods for dataframes gnlm functions: environment can be a dataframe
18.12.00 changed check for existence of response when environment
supplied bnlr, fmr, gnlmm, gnlr, gnlr3, nordr: fixed calculation of n
for null function 17.12.00 various changes because of new R1.2.0
handling of formulae finterp: check for + or - before ( (change to
R1.2.0) elliptic: removed check on tvcov, so can accept times and
individuals 15.12.00 bnlr, fmr, gnlr, gnlr3, gnlmm, nordr: nonlinear
formula need not contain covariates changes to cutil.c and coxre for
R1.2.0 14.12.00 restovec, tcctomat, tvctomat: added slot for units of
measurement dftorep, read.rep: id can be a factor variable carma,
elliptic, gar, gausscop, kalcount, kalseries, kalsurv: test if name of
response exists when envir contains multivariate responses stable:
corrected man pages 3.12.00 gnlmix: generalized nonlinear models with
one random parameter having arbitrary mixing distribution 30.11.00
fitdist.r: calculate log probabilities and likelihoods to avoid
underflow (thanks to Goran Brostrom) int2: vectorized two-dimensional
Romberg integration 28.11.00 added d, p, q, and r functions for Consul
generalized Poisson distribution added PACKAGE option to .C and .Fortran
calls bnlr.r: added cloglog and loglog links changed class of gnlr-type
functions from gnlr to gnlm gar.c: corrected calculation of censored
Burr, Pareto, power exponential distributions (thanks to Patrick
Lindsey) 24.11.00 q and r functions: improved calculations and checks
23.11.00 bnlr, fmr, gnlmm, gnlr, gnlr3, nordr: nonlinear formulae can
have a linear part qgweibull, qggamma, qgextval: corrected arguments to
functions and docs (thanks to Patrick Lindsey) 21.11.00 fmobj: find
objects referred to in a formula elliptic.r, fmr.r, gar.r, gausscop.r,
gnlmm.r, gnlr.r, gnlr3.r: models with common parameters in several
regression functions can be specified using formulae, not just functions
elliptic.r, gar.r, gausscop.r, gnlmm.r, gnlr.r: models with shape as a
function of location can be specified using formulae, not just functions
20.11.00 finterp.r: formulae can have common parameters and/or depend on
functions 16.11.00 hidden, chidden: added recursive predicted values
added q and r functions for distributions in rmutil 14.11.00 kalseries:
corrected error in inverse Gaussian distribution (thanks to Patrick
Lindsey) bnlr.r: added stable and mixture links gnlr, gnlmm, gar: added
beta and simplex distributions rmutil: added psimplex and dsimplex
9.11.00 improved checking for multivariate response and choosing one
response when several present in a data object 6.11.00 fmr.r, printrm.r:
corrected so that works with common parameters (thanks to Laura
Thompson) 29.10.00 gnlr3.r: corrected typo in normal and inverse Gauss
distributions 19.10.00 gausscop: multivariate Gaussian copula with
arbitrary marginals elliptic.r: several typing errors corrected
—————————————————————————— version 0.8 ——————————————————————————
17.10.00 carma, elliptic, kalseries: handles NULL delta correctly with
multivariate response in repeated object restovec: gives names correctly
to multivariate 3-dim array covariates.repeated: calculates number of
observations correctly when multivariate response 15.10.00 qstable:
corrected bug due to change in uniroot (thanks to Gabrielle Kelly)
dstable, pstable, qstable, rstable: added checks that parameter values
are correct 13.9.00 (growth, repeated, rmutil) restovec: check for NAs
in ordinal responses (thanks to Patrick Lindsey) elliptic, kalseries:
check that torder is not larger than number of time points (thanks to
Patrick Lindsey) elliptic: corrected undefined n (thanks to Patrick
Lindsey) 12.9.00 kalseries: constant shape parameter for (log) logistic,
Cauchy, and Laplace distributions previously had square root transform
kalseries: added inverse Gauss distribution 7.9.00 restovec: corrected
error (change in R) when censor is all ones (thanks to Troels Ring)
17.8.00 removed provide() rmutil: removed det() 14.8.00 rmna: corrected
typo in man page 17.7.00 nordr.r: corrected minor bugs for weights and
data object handling (thanks to Patrick Lindsey) 5.7.00 as.data.frame.x:
added options from default (thanks to Patrick Lindsey) rmna: removes NAs
in weights (thanks to Patrick Lindsey) restovec: handle correctly
option, times=T (thanks to Patrick Lindsey) covariates.repeated: handle
correctly non-repeated observations (thanks to Patrick Lindsey) 21.6.00
plotrm.r: plot.residuals corrected so ccov works (thanks to Patrick
Lindsey) 14.6.00 carma.r: correction for ccov as one-column matrix
(thanks to Patrick Lindsey) 7.6.00 elliptic.f: fixed crash with more
than one covariate in tvcov (thanks to Bruno Genicot) 1.6.00 elliptic.r:
corrected check to allow varfn=“identity” or “square” 30.5.00 bnlr.r:
binomial regression with various links 22.5.00 fnenvir.r: can handle
functions without parameters (thanks to Troels Ring) 11.5.00 fit.dist:
corrected exact fit for negative binomial and added default options for
main and xlab 6.4.00 runge.kutta, lin.diff.eqn: functions to solve
differential equations 5.4.00 gar.r: handles censored data correctly
when a data object contains more than one response 29.3.00
runge.kutta.r: solution of differential equations 20.3.00 nlr: corrected
undefined mu1 17.3.00 print.response: check for NAs in times 15.3.00
glmm: obtain nest vector from dataframe if supplied 14.3.00 nordr,
ordglm: clearer error message if the response is not a numeric vector
with integral values starting at 0 (thanks to Troels Ring) 15.2.00
ordglm: corrected bug when more than three categories 12.2.00 (repeated,
event) kalcount, kalseries, kalsurv: autoregression with frailty
dependence 9.2.00 kcountb.c, kserieb.c, ksurvb.c, ksurvg.c: changed
-log(1-pfn()) to -pfn(,,,0,1) and removed inthaz.c 8.2.00 all libraries:
corrected C code for R0.99 kalcount: corrected error in recursive
predicted values for gamma intensity 1.2.00 restovec: corrected handling
of weights when response is a list kalsurv.r: corrected plotting of
profiles for logged distributions cutil.c: changed Fortran.h to
Rconfig.h and moved to rmutil cgamma.c: replaced by cutil.c inthaz.c:
changed finite() to R_FINITE() 27.1.00 gar: three-parameter
distributions work with constant dispersion parameter kalcount,
kalseries, kalsurv: if mu contains time-varying covariates, initial
estimates must be in ptvc 24.1.00 finterp, fnenvir: changed name of .fn
to avoid conflicts most model functions: check that supplied function
was not produced by finterp already 20.1.00 as.data.frame: puts binomial
and censored responses as two-column matrices gnlr, fmr, gnlmm, gar:
binary response need only be one column for binomial 17.1.00 finterp,
fnenvir: handle decimal numbers correctly most model functions: print
out regression function correctly when envir supplied 16.1.00 gar: added
Consul generalized Poisson distribution transform: check for nonpositive
and infinite values in Jacobian carma, elliptic, gar, kalseries: sqrt
transformation checks for zero response values 14.1.00 most model
functions: check for NAs in data objects (because of lvna) gnlr, gnlr3,
fmr, gnlmm: possible to fit a model without optimizing any parameters in
the regressions if they are functions restovec, dftorep, read.rep: add
additional validity checks for responses times.default: replaces
times.repeated 11.1.00 hidden, chidden: handle multinomial count data
nlr: modified to handle data objects correctly most model functions:
changed way of detecting multivariate responses finterp: correct error
for length of response when multivariate 10.1.00 gettvc: works correctly
for first observation when ties=FALSE (thanks to Patrick Lindsey)
finterp: can find response variables of formula in repeated objects for
most model functions, one of multiple responses in a repeated data
object can be selected for the model 9.1.00 restovec: handles
multivariate matrices, arrays, and lists dftorep: transform a dataframe
to a repeated data object read.rep: read a rectangular data set from a
file and create a repeated data object directly 7.1.00 logitord.f:
reformatted to remove tabs for HP compilers (thanks to Osman Buyukisk)
restovec: responses can have more than one type class
—————————————————————————— version 0.7 ——————————————————————————
3.1.2000 residuals.elliptic: corrected error in calculation of raw
residuals 31.12.99 objectrm.r: can select certain individuals with
methods, covariates, delta, nesting, times, weights transform: handles
NAs in response correctly 28.12.99 restovec: added name of response
variable to list returned objectrm.r: added as.data.frame and as.matrix
methods for data objects wr: works with my data objects nordr: changed
sign of coefficients for continuation ratio and adjacent categories
models so comparable with proportional odds 27.12.99 finterp: with
W&R notation, design matrix no longer returned as attribute when ~1
and .envir supplied, returns a function yielding a vector of correct
length 26.12.99 fit.dist: corrected exact fit of negative binomial gnlr,
gnlr3, fmr, gnlmm: improved speed nordr, ordglm: ordinal categories
numbered from 0 instead of 1 hidden, chidden: multinomial categories
numbered from 0 instead of 1 handles ordinal models, thanks to Patrick
Lindsey gettvc: now handles NAs in response variable 25.12.99 improved
documentation for methods to access data objects and functions int: call
C instead of Fortran for TOMS614 23.12.99 restovec: added additional
checks that correct data are supplied (thanks to Troels Ring)
mprofile.carma: corrected bug when no covariates carma: corrected bug
when delta is a scalar carma, elliptic: added checks for incorrect
formulae 21.12.99 hidden, chidden: improved printout and corrected error
in checking number of parameters in lists of formulae 20.12.99 lvna:
creates a repeated object leaving NAs in hidden, chidden: interactions
between time-constant and time-varying covariates allowed 17.12.99
hidden, chidden: improved printout 16.12.99 tvctomat: handles lists of
factor variables correctly restovec: value returned has class of type of
response as well as “response” added checks hidden, chidden: can also
use formulae if multinomial 12.12.99 hidden, chidden: can use formulae
if not multinomial 7.12.99 cmcre: corrected memory leak 6.12.99 cmcre:
continuous-time two-state Markov process with random effects 5.12.99
coxre: corrected several errors 1.12.99 stable: fixed plot arguments in
help examples 29.11.99 finterp: fixed bug when multiple (’s or ^ before
( when detecting function names nobs: use method instead of direct
access in all functions provide default method covind: provide default
method 25.11.99 collapse: changed name to capply because of conflict in
nlme 23.11.99 profile: changed to mprofile because of conflict in R0.90
22.11.99 finterp: properly distinguishes unknown parameters from
functions finterp and fnenvir: when no variables found, changed stop to
warning nobs: corrected for independent observations when length is one
18.11.99 stablereg: corrected bug when some parameters are not optimized
check for NAs in the hessian 17.11.99 plot.repeated, plot.response:
added special call for ordinal responses corrected plot for independent
observations (thanks to Patrick Lindsey) 14.11.99 removed unneeded
aliases in man pages added aliases to plot.profile and plot.iprofile
11.11.99 added check for Inf (as well as NAs) in hessian to all
functions using nlm kalseries.r: added error message if times not
available for Markov dependence changed rep(1,n) to rep(1,nind) when mu
function returns scalar stable.r: moved call to C code into likelihood
function for speed int.r: limits can be specified as -Inf, Inf 4.11.99
kalcount.r, kalseries.r, kalsurv.r: with time-varying covariates in a
function or formula, initial estimates can be in preg or ptvc and
changed length(resp\(response\)y) to n
for speed 31.10.99 gar.r: fixed undefined npt3 for autoregression
parameter finterp.r: fixed bug for : in W&R formulae kalcount.r,
kalseries.r, kalsurv.r: added error message when time-varying covariates
22.10.99 covind: changed so that it works with carma, elliptic, gar,
hidden, kalcount, kalseries, and kalsurv objects 18.10.99 gar.r:
corrected printing of parameter values for three-parameter distributions
gar.c: corrected calculation of lambda in three-parameter distributions
17.10.99 gar.r: corrected fitted values (due to changes on 12.10.99)
14.10.99 gar.r: corrected undefined variable, tm (due to changes on
12.10.99) 12.10.99 stable: stablereg with nonlinear regression replaces
stableglm finterp, fnenvir: check for factor variables instead of not
being a numerical or logical vector gar: allow autoregression parameter
to depend on covariates dist.c, kcountb.c, kserieb.c, ksurvb.c,
ksurvg,c, stable.c: added #include “Rconfig.h” 4.10.99 ordglm.r: added
deviance and corrected for zeros in table nordr.r: corrected typo
potthoff.r: corrected erroneous calculation of standard errors (thanks
to Tim Auton)

1.10.99 finterp, fnenvir: fixed conflict of names by beginning all names
with a dot (thanks to Patrick Lindsey) elliptic.r: changed option and
title from elliptic to power exponential 30.9.99 ordglm.r: generalized
linear ordinal regression —————————————————————————— version 0.6
—————————————————————————— 21.9.99 pkpd.r: changed mu2.1o1cfp to ensure
ked>0 20.9.99 resid.f: correction to work with MS-Windows 7.9.99
binnest.r, survkit.r: changed NULLs for Fortran to work with R0.65
6.9.99 ehr.r, kalsurv.r, fmr.r, gnlr.r, gnlr3.r, nlr.r, nordr.r,
elliptic.r, gar.r, gnlmm.r, kalcount.r, kalseries.r: changed attributes
to work with R0.65 finterp, fnenvir: variables can be logical as well as
numeric 3.9.99 Makefiles: moved \((FLIBS) to
end of line 14.8.99 print.gnlr: corrected errors in printing fmr, gnlr3,
and gnlmm output fnenvir.tvcov: corrected error for undefined ex1a
(-> ex2a) Pareto, gnlmm, hstudent, kalcount, kalseries, pkpd,
read.list, read.surv, tvctomat: corrected examples 18.7.99 hidden.r,
chidden.r: corrected one error message added printout of degrees of
freedom 14.7.99 binnest.f: modified comments to compile with standard
Fortran (thanks to Martin Maechler)
------------------------------------------------------------------------------
version 0.5
------------------------------------------------------------------------------
29.6.99 plot.response: remove NAs when calculating default ylim 28.6.99
gnlr.r, gnlr3.r, fmr.r, nordr.r, gnlmm.r: check if user gives
a nonlinear formula in linear argument and correctly handle it 27.6.99
finterp: corrected error message when non-numeric vector supplied
restovec: corrected printing of total times when negative times present
added transform methods for response, tccov, and tvcov objects 24.6.99
gar.r: corrected error in printing shape functions 22.6.99 binnest.f:
modified to compile with g77 8.6.99 binnest: binary random effects model
with two levels of nesting 7.6.99 restovec: added an additional check
for nest variable in lists 6.6.99 logitord.f: corrected bug in
calculation of Hessian (and s.e.) 1.6.99 elliptic: added multivariate
Student t distribution 11.5.99 finterp.r: functions allowed in W&R
formulae carma.r, elliptic.r, kalseries.r, kalcount.r, kalsurv.r: allow
factor variables finterp: can locate and use indices for individuals and
nesting as factor covariates 10.5.99 tcctomat.r, tvctomat.r: allow
factor variables finterp, fnenvir: changed to check for factor variables
6.5.99 elliptic.r: allow variance to be a function of the mean function
4.5.99 gar.c: changed normal distribution shape parameter from sd to
variance 3.5.99 profile and iprofile: fixed to plot correctly with
nesting 1.5.99 tcctomat, tvctomat: allow dataframes 28.4.99 tvctomat:
time-varying covariates can be factors elliptic.r, gnlr.r, gnlr3.r,
fmr.r, gnlmm.r, gar.r: location and shape functions can have common
parameters 26.4.99 restovec: weights allowed for lists finterp, fnenvir:
can find the times when envir is a repeated object gar.r: allow shape to
be a function of the location function 23.4.99 gnlr.r, gnlr3.r, fmr.r,
nordr.r, nlr.r, elliptic.r, gnlmm.r, gar.r, kalseries.r, kalcount.r,
kalsurv.r, ehr.r: do not require envir if response has class, repeated
corrected bugs in restovec and plot.response (Lorenz Gygax) 22.4.99
generalized plot.residuals tvctomat: allow calculation of more than one
interaction with time-constant covariates at a time finterp and
fnenvir: allow variables in environment to have same name as a function
21.4.99 correction of 18.1.99 by Brian Ripley wrong: dist.c put back in
gnlm 20.4.99 ksurvb.c: corrected bug when time-varying covariates
elliptic.r: added option to ccov and tvcov to give covariate names when
response has class, repeated carma.r: added option to ccov to give
covariate names when response has class, repeated 19.4.99 changed
plot.profile to profile and plot.iprofile to iprofile 18.4.99
elliptic.r: added recursive predicted values when AR(1) and/or random
effect 16.4.99 gnlr.r, gnlr3.r, fmr.r, nordr.r, gnlmm.r, ehr.r: changed
order of parameters when function with linear part 15.9.99 ehr:
corrected two errors when lambda function with linear part nordr.r: n
changed to nrows 13.4.99 carma.r: corrected predicted values when
response is transformed gar.r, kalseries.r: changed handling of
transformed responses
------------------------------------------------------------------------------
version 0.4
------------------------------------------------------------------------------
12.4.99 added dependency on rmutil to DESCRIPTION 11.4.99 elliptic.f:
corrected handling of dose for PKPD model when time-varying covariates
are present 6.4.99 elliptic.r, gnlmm.r, gar.r, kalseries.r, kalcount.r,
kalsurv.r, ehr.r, nordr.r, nlr.r: modified to use fnenvir 5.4.99
gnlr.r, gnlr3.r, fmr.r: modified to use fnenvir 4.4.99 fnenvir: checks
functions for covariates and parameters and modifies them to read from
data objects 1.4.99 elliptic.r: modified to use model formulae with
unknowns finterp.r: added data objects as environment tvctomat,
tcctomat: can combine two data objects 31.3.99 gar.r: modified to use
model formulae with unknowns 30.3.99 rmna: check if a covariate only has
one value after NA removal fixed examples docs so that they work 29.3.99
kalcount.r, kalsurv.r, ehr.r: modified to use model formulae with
unknowns 28.3.99 gnlmm.r, kalseries: modified to use model formulae with
unknowns restovec: added coordinates to response class for spatial data
26.3.99 gnlr.r, gnlr3.r, fmr.r, nordr.r, nlr.r: modified to use model
formulae with unknowns 24.3.99 changed language check to inherits
formula in all functions added methods for extracting elements from data
objects finterp.r: transforms model formulae with unknowns into
functions 22.3.99 restovec: times no longer required for clustered
data type attribute added carma.r, elliptic.r, kalseries.r kalcount.r:
check to see if times available 15.3.99 rmaov.r: wrote documentation
pkpd.r : added two new models and corrected one other 13.3.99 restovec:
allow ties in times 23.2.99 gar.c: corrected Laplace cdf and allowed
negative values 11.2.99 ehr: corrected for ties kalsurv.r: prints out
"birth process" when applicable instead of renewal process
logitord.r: removed DUP=F from Fortran call 8.2.99 km.r: fixed bug in
plot.dist.km when several groups are plotted (Gareth Ridall) 7.2.99
improved handling of variable names in tcctomat, tvctomat,
and functions calling them rmaov.r: split-plot aov from Ralf Goertz
6.2.99 glmm.r: accepts transformed data if dataframe supplied 5.2.99
km.r: fixed bug for double lines with censored observations (Gareth
Ridall) ehr.r: modified handling of language 4.2.99 km.r: added print.km
to remove attributes restovec: accepts all response data, not just
repeated measurements tvctomat: added calculation of interactions 2.2.99
restovec: added adding several column matrices in lists with censoring
kalsurv.r: added delta option 1.2.99 glmm.r: binary response with
binomial handled correctly 30.1.99 plot.iprofile.carma: corrected nind
argument restovec, carma, elliptic, kalcount, kalseries: added how to
handle `times' for clustered data to docs 28.1.99 bivbinom.r,
marghom.r: minor corrections rs.r: improved printout 26.1.99 readrm.r:
corrected lty specification in plot.response added option to plot
points 24.1.99 gnlr.r, gnlr3.r, fmr.r, gnlmm.r: y can have classes,
response or repeated added DUP=F to all .C and .Fortran calls pbirth.r:
binomial data distributions 22.1.99 readrm.r: added ... for graphics
options in plot.response and plot.repeated 21.1.99 rmna: added checks
that ccov and tvcov have correct class 19.1.99 dist.c: changed static
romberg to romberg2 and added static interp carma.r, chidden.r,
elliptic.r, gar.r, hidden.r, kalcount.r, kalseries.r, kalsurv.r: allow
response to have class, repeated restovec: allow delta to be a dataframe
18.1.99 corrections by Brian Ripley gnlm: removed redundant dist.c
enclosed library.dynam in .First.lib potthoff.r: added matrix dimension
checks util.r: removed orth function potthoff.r: replaced orth by
contr.poly 17.1.99 carma.r, chidden.r, elliptic.r, gar.r, hidden.r,
kalcount.r, kalseries.r, kalsurv.r: copy response vector more
efficiently restovec: added total time for survival data coxre.r:
reorganized for efficiency, eliminating data.frame cprocess.r: times can
have class, response 16.1.99 gnlr.r, gnlr3.r, fmr.r, gnlmm.r: removed
-delta/2 in right censoring calculation dist.r, gnlr3.r, gar.c,
hidden.f: changed parametrization of Burr to agree with kalsurv.r
elliptic.r: use var(y) to get initial estimate of variance
------------------------------------------------------------------------------
version 0.3
------------------------------------------------------------------------------
14.1.99 kalsurv.r: corrected printing of number of subjects and
observations 2.1.99 cprocess.r: allow event counts with unequal times
added mode="double" to is.vector 29.12.98 corrected minor bugs
in fmr 28.12.98 corrected abs bug for Laplace in kalman C functions
27.12.98 restovec: corrected binary totals when given as a vector gar:
added Levy, Pareto, generalized inverse Gauss, and power exponential
distributions hidden and chidden: added various overdispersed and
continuous distributions 22.12.98 hidden and chidden: added filter
calculation and plots 21.12.98 moved Student t from gnlr to gnlr3
renamed beta as Pareto in kalcount, kalseries, and kalsurv corrected
various minor errors in fmr and gnlr3 20.12.98 dist.r, gnlr.r, fmr.r:
added gamma count and Pareto distributions 18.12.98 chidden:
continuous-time hidden Markov chain models 7.12.98 dist.r, gnlr.r,
fmr.r: added Levy distribution removed .so from Makefiles and
library.dynam 6.12.98 util.r: added spectral decomposition to mexp
5.12.98 rmutil: added several p and d functions gnlr3.r: added censored
generalized inverse Gaussian and power exponential distributions
2.12.98 int.r: vectorized Romberg integration 1.12.98 int.r: added
option for Romberg integration 30.11.98 updated libraries with Brian
Ripley's corrections 25.11.98 hidden: allow values in the transition
matrix to be fixed at 0 or 1 24.11.98 hidden: added independence model
23.11.98 inthaz.c: changed header include bessel: removed function
gnlr3.r: changed to internal bessel function 14.11.98 hidden: added
multinomial distribution 12.11.98 hidden.f: corrected Poisson and
binomial calculations 5.11.98 carmasub.f and survkit.f: changes for
compatibility with g77
------------------------------------------------------------------------------
version 0.2
------------------------------------------------------------------------------
2.11.98 ehr.r: corrected printing coefficients with linear and other
parameters 1.11.98 km.r: corrected NaNs in log 29.10.98 carma.r:
corrected printout of mean time km.r: corrected ylab for cdf 26.10.98
rmna: handles NAs in time-constant covariates properly carma.r and
elliptic.r: accept ccov of class, tccov cprocess.r: added plots from
counts of events 19.10.98 changed to inherits() throughout rationalized
printing of gnlr, gnlr3, fmr, gnlmm and moved to rmutil added delta
option to carma and elliptic 18.10.98 carma.r and elliptic.r: added
handling of delta when y has class, response 17.10.98 gar.r: added
cloglog link 12.10.98 gnlmm.r: corrected handling of delta when y has
class, response 11.10.98 replaced tapply() with collapse() in bivbinom,
catmiss, glmm, gnlmm, ehr, coxre 10.10.98 ehr.r check for singular
covariance matrix print names of variables for coefficients when
language 8.10.98 kcountb.c: corrected dplogis call gnlmm.r: corrected
calls to ddp, dmp, ddb, and dmb coxre.r: removed as.is=T in data.frame
corrected printing shape parameters when language used in gnlr,
gnlr3, fmr, gnlmm 7.10.98 rs.r: put in check that all covariates are
positive gnlmm.r: set censor to F for binomial data dist.c: changed ddp,
dmp, ddb, and dmb to log and introduced weights 6.10.98 kseries.c:
corrected error in serial update kalseries.r: correcting printing error
when there is an interaction kalsurv: added serial update inthaz.c: put
back ihlogis (disappeared with nmath) renamed wr.r as util.r moved det
and %**% from repeated and growth to rmutil/R/util.r 5.10.98 corrected
check in carma, elliptic, gar, and kalseries for
nonpositive transformed values 4.10.98 glmm.r: corrected two errors
1.10.98 extended residual plots to all of class recursive kalcount,
kalseries, kalsurv: return mean profiles in z\)pred plot.profile:
accepts z\(pred as well as a mean function
nbkal.r: corrections corrected and updated a lot of docs 30.9.98 moved
kalsurv to event library renamed rmtools as rmutil inthaz.c: corrected
error from change to nmath 29.8.98 kalsurv.r: added recursive fitted
values kalseries.r: added recursive fitted values updated plot.residuals
for recursive class 27.9.98 corrected docs for plot.profile,
plot.iprofile added covind.default plot.iprofile: corrected default
settings 24.9.98 gettvc.r: allow an option for ties bessel.r: only
calculate one kind of function 20.9.98 gettvc.r: allow NAs in
time-varying covariate corrected for ties between response and
covariate tvctomat: allow tvcov to already have class, "tvcov"
added as.double in all Fortran and C calls 18.9.98 plotrm.r: corrected
bug in plot.iprofile due to new covind() 16.9.98 pkpd.r: corrected
mu2.0o2c and added mu2.0o2cfp 15.9.98 replaced Bessel, Gauss-Hermite,
and integration routines bessel.r: added docs 14.9.98 moved wr to
rmtools and added docs added covind function to rmtools 12.9.98
kalserie.r: added delta option tcctomat.Rd: corrected alias created new
library, rmtools 11.9.98 dist.r: added beta binomial dist.c: simplified
calls to overdispersion functions autocor.r: corrected pergram
kalserie.r: corrected error in printing parameters with torder>0
kserieb.c: corrected error when mu function used 10.9.98 readlist.r:
corrected binomial totals for lists in restovec fmr.r: removed
unnecessary code gar.r: added overdispersed binomial data dist.r: allow
dispersion to be a scalar when mean is a vector created documentation
for p and d functions 9.9.98 nordr.r: corrected weights for adjacent
categories model test for p>1 in proportional odds gar.r: added
checks on times and mu arguments added binomial data corrected docs for
elliptic, gar, kalcount, kalseries, kalsurv, nbkal for z\)index
clarified docs for rmna, restovec, tcctomat, and tvctomat 8.9.98 removed
backslash at end of Makefiles for event, gnlm, growth moved integer
declarations to the beginning in carmasub.f, elliptic.f, gettvc.f,
survkit.f so that g77 should work 5.9.98 gar.r Corrected predictions for
transformed responses —————————————————————————— version 0.1