- fix clang15 warnings
- fix latex escape note
- fix version info from new.md note
- reset license from GPL-2 to the original GPL (>=2)
- fixed typo in C code causing i386 error in rmutil::int()
- 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
- Fixed call_R Issue https://github.com/swihart/rmutil/issues/11
- Updated links to https: where appropriate
- 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.
- 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.
- 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
- 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.
- 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))
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.
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 |
version 0.9
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(respy) 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 pred plot.profile:
accepts zindex
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