Utilities for Nonlinear Regression and Repeated Measurements Models

A toolkit of functions for nonlinear regression and repeated measurements not to be used by itself but called by other Lindsey packages such as 'gnlm', 'stable', 'growth', 'repeated', and 'event' (available at < http://www.commanster.eu/rcode.html>).


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
  • 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

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(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

Reference manual

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1.1.3 by Bruce Swihart, 21 days ago


Report a bug at https://github.com/swihart/rmutil/issues

Browse source code at https://github.com/cran/rmutil

Authors: Bruce Swihart [cre, aut] , Jim Lindsey [aut] (Jim created this package , Bruce is maintaining the CRAN version)

Documentation:   PDF Manual  

GPL-2 license

Imported by CompDist, ZOIP, basad, gnFit, powdist.

Depended on by event, gnlm, growth, repeated, stable.

Suggested by cnbdistr, greta, mixdir.

See at CRAN