#—————————————————————————— #version 1.1.6
#——————————————————————————
- refined the previous version’s references to contemporary stable
distribution literature to help contextualize this package in the /man
files and README
- add example to bottom of README
#—————————————————————————— #version 1.1.5
#——————————————————————————
- http: –> https: where appropriate
- added references to contemporary stable distribution literature to
help contextualize this package to /man files and README
- Removed imports: stabledist from DESCRIPTION
#—————————————————————————— #version 1.1.4
#——————————————————————————
- FIXED NOTE: All declared Imports should be used.
#—————————————————————————— #version 1.1.3
#——————————————————————————
- Added functions
sd2s()
, s2sd()
,
pm1_to_pm0
, pm0_to_pm1
to help with switching
between parameterizations
- Updated README to detail how to use
sd2s()
,
s2sd()
, pm1_to_pm0
,
pm0_to_pm1
- Updated README to detail how to locate modes with
stable
and stabledist
equivalently
- FIXED NOTE: Found no calls to: ‘R_registerRoutines’,
‘R_useDynamicSymbols’.
#—————————————————————————— #version 1.1.2
#——————————————————————————
- Updated README to detail how to make
d/p/q/r stable()
calls from stable
the same as stabledist
- Fixed memtest / Valgrind error.
#—————————————————————————— #version 1.1.1
#——————————————————————————
- Fixed ASAN / UBSAN error.
#—————————————————————————— #version 1.1.0
#——————————————————————————
Major changes
Passed CRAN checks and is back on CRAN. Please see github page
https://github.com/swihart/stable to see the changes required to pass
CRAN checks. I’ll try to document the changes henceforth here and at
https://github.com/swihart/stable/issues.
- loc.g, loc.h, disp.g, disp.h, skew.g, skew.h, tail.g, tail.h are now
replaced with loc_g, loc_h, disp_g, disp_h, skew_g, skew_h, tail_g,
tail_h respectively.
Above this line will be News/Changes for stable
only
Below this line corresponds to changes.txt,
which was Jim Lindsey’s file for detailing changes across the v1.0
packages rmutil
, repeated
, gnlm
,
growth
, event
, stable
on his
homepage
#—————————————————————————— #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
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 packages)
- 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
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 $(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
#——————————————————————————