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R/ctStanFit.R
In ctsem: Continuous Time Structural Equation Modelling
Defines functions
ctFit
T0VARredundancies
ctFitUpdate
Documented in
ctFit
ctFitUpdate
#' Update a ctStanFit object
#'
#' Either to include different data, or because you have upgraded ctsem and the internal data structure has changed.
#'
#' @param oldfit fit object to be upgraded
#' @param data replacement long format data object
#' @param recompile whether to force a recompile -- safer but slower and usually unnecessary.
#' @param refit if TRUE, refits the model using the old estimates as a starting point. Only applicable for
#' optimized fits, not sampling.
#' @param ... extra arguments to pass to ctFit
#'
#' @return updated ctStanFit object.
#' @export
#'
#' @examples
#' newfit <- ctFitUpdate(ctstantestfit,refit=FALSE)
ctFitUpdate <- function(oldfit, data=NA, recompile=FALSE,refit=FALSE,...){
if(!refit) message('Trying to do a quick update -- if there are problems, try with refit=TRUE for more robustness')
dots <- list(...)
args <- as.list(oldfit$args)
for(n in names(dots)){
args[[n]] <- dots[[n]]
}
if(length(oldfit$stanfit$stanfit@sim) > 0) refit=FALSE
args$fit <- refit
args$inits <- oldfit$stanfit$rawest
args$model <- oldfit$ctstanmodelbase
args$ctstanmodel <- NULL
newargs <- as.list(args(ctFit))
for(argi in names(args)){
if(argi %in% names(args)) newargs[[argi]] <- args[[argi]] else message(argi, ' is no longer a valid argument, dropping...')
}
if(length(data==1)) args$datalong <- standatatolong(oldfit$standata,origstructure = TRUE,ctm=oldfit$ctstanmodelbase)
if(length(data) > 1) args$datalong <- data
newfit <- do.call(ctFit,args)
if(!refit){
oldfit$standata <- newfit$standata
if(oldfit$ctstanmodel$recompile || recompile) oldfit$stanmodel <- rstan::stan_model(model_code = newfit$stanmodeltext) else
oldfit$stanmodel <- stanmodels$ctsm
}
if(refit) oldfit <- newfit
return(oldfit)
}
#' Backward-compatible alias for \code{ctFitUpdate}.
#' @rdname ctFitUpdate
#' @export
ctStanFitUpdate <- ctFitUpdate
T0VARredundancies <- function(ctm) { #check for redundant T0VAR parameters (because indvarying t0means) and disable
whichT0VAR_T0MEANSindvarying <- ctm$pars$matrix %in% 'T0VAR' &
is.na(ctm$pars$value) &
(ctm$pars$row %in% ctm$pars$row[ctm$pars$matrix %in% 'T0MEANS' & ctm$pars$indvarying] |
ctm$pars$col %in% ctm$pars$row[ctm$pars$matrix %in% 'T0MEANS' & ctm$pars$indvarying])
if(any(whichT0VAR_T0MEANSindvarying)){
message('Free T0VAR parameters as well as indvarying T0MEANS -- fixing T0VAR pars to diag matrix of 1e-6')
ctm$pars$value[whichT0VAR_T0MEANSindvarying & ctm$pars$col == ctm$pars$row ] <- 1e-6
ctm$pars$value[whichT0VAR_T0MEANSindvarying & ctm$pars$col != ctm$pars$row ] <- 0
ctm$pars$param[whichT0VAR_T0MEANSindvarying] <- NA
ctm$pars$transform[whichT0VAR_T0MEANSindvarying] <- NA
ctm$pars$indvarying[whichT0VAR_T0MEANSindvarying] <- FALSE
}
return(ctm)
}
#' Fit a ctsem model
#'
#' Fits a ctsem model specified via \code{\link{ctModel}} with type either 'ct' or 'dt'.
#' \code{ctStanFit} is maintained as a backward-compatible alias.
#'
#' @param datalong long format data containing columns for subject id (numeric values, 1 to max subjects), manifest variables,
#' any time dependent (i.e. varying within subject) predictors,
#' and any time independent (not varying within subject) predictors.
#' @param model model object as generated by \code{\link{ctModel}} with type='ct' or 'dt', for continuous or discrete time
#' models respectively.
#' @param ctstanmodel Deprecated. Use \code{model}.
#' @param stanmodeltext already specified Stan model character string, generally leave NA unless modifying Stan model directly.
#' (Possible after modification of output from fitting with argument fit=FALSE)
#' @param intoverstates logical indicating whether or not to integrate over latent states using a Kalman filter.
#' Generally recommended to set TRUE unless using non-gaussian measurement model.
#' @param binomial Deprecated. Logical indicating the use of binary rather than Gaussian data, as with IRT analyses.
#' This now sets \code{intoverstates = FALSE} and the \code{manifesttype} of every indicator to 1, for binary.
#' @param fit If TRUE, fit specified model using Stan, if FALSE, return stan model object without fitting.
#' @param intoverpop if 'auto', set to TRUE if optimizing and FALSE if using hmc.
#' if TRUE, integrates over population distribution of parameters rather than full sampling.
#' Allows for optimization of non-linearities and random effects, via state expansion.
#' @param sameInitialTimes if TRUE, include an empty observation for every subject that has no observation
#' at the earliest observation time of the dataset. This ensures that the T0MEANS occurs for every subject at the same time,
#' rather than just at the earliest observation for that subject. Important when modelling trends over time, age, etc.
#' @param plot if TRUE, for sampling, a Shiny program is launched upon fitting to interactively plot samples.
#' May struggle with many (e.g., > 5000) parameters. For optimizing, various optimization details are plotted -- in development.
#' @param derrind deprecated, latents involved in dynamic error calculations are determined automatically now.
#' @param optimize if TRUE, use \code{\link{stanoptimis}} function for maximum a posteriori / importance sampling estimates,
#' otherwise use the HMC sampler from Stan, which is (much) slower, but generally more robust for complex individual differences.
#' @param optimcontrol list of parameters sent to \code{\link{stanoptimis}} governing optimization / importance sampling.
#' @param nopriors deprecated, use priors argument. logical. If TRUE, any priors are disabled -- sometimes desirable for optimization.
#' @param priors if TRUE, priors are included in computations, otherwise specified priors are ignored.
#' @param iter used when \code{optimize=FALSE}. number of iterations, half of which will be devoted to warmup by default when sampling.
#' @param inits either character string 'optimize, NULL, or vector of (unconstrained)
#' parameter start values, as returned by the rstan function \code{rstan::unconstrain_pars}, or the parameter values
#' found in a ctsem fit object \code{myfit$stanfit$rawest} (or \code{$rawposterior}) for instance.
#' @param chains used when \code{optimize=FALSE}. Number of chains to sample, during HMC or post-optimization importance sampling. Unless the cores
#' argument is also set, the number of chains determines the number of cpu cores used, up to
#' the maximum available minus one. Irrelevant when \code{optimize=TRUE}.
#' @param cores number of cpu cores to use. Either 'maxneeded' to use as many as available minus one,
#' up to the number of chains, or a positive integer. If \code{optimize=TRUE}, more cores are generally faster.
#' @param control Used when \code{optimize=FALSE}. List of arguments sent to \code{\link[rstan]{stan}} control argument,
#' regarding warmup / sampling behaviour. Unless specified, values used are:
#' list(adapt_delta = .8, adapt_window=2, max_treedepth=10, adapt_init_buffer=2, stepsize = .001)
#' @param nlcontrol List of non-linear control parameters.
#' \code{maxtimestep} must be a positive numeric, specifying the largest time
#' span covered by the numerical integration. The large default ensures that for each observation time interval,
#' only a single step of exponential integration is used. When \code{maxtimestep} is smaller than the observation time interval,
#' the integration is nested within an Euler like loop.
#' Smaller values may offer greater accuracy, but are slower and not always necessary. Given the exponential integration,
#' linear model elements are fit exactly with only a single step.
#' @param verbose Integer from 0 to 2. Higher values print more information during model fit -- for debugging.
#' @param stationary Logical. If TRUE, T0VAR and T0MEANS input matrices are ignored,
#' the parameters are instead fixed to long run expectations. More control over this can be achieved
#' by instead setting parameter names of T0MEANS and T0VAR matrices in the input model to 'stationary', for
#' elements that should be fixed to stationarity.
#' @param forcerecompile logical. For development purposes.
#' If TRUE, stan model is recompiled, regardless of apparent need for compilation.
#' @param saveCompile if TRUE and compilation is needed / requested, writes the stan model to
#' the parent frame as ctsem.compiled (unless that object already exists and is not from ctsem), to avoid unnecessary recompilation.
#' @param savescores Logical. If TRUE, output from the Kalman filter is saved in output. For datasets with many variables
#' or time points, will increase file size substantially.
#' @param savesubjectmatrices Logical. If TRUE, subject specific matrices are saved --
#' only relevant when either time dependent predictors or individual differences are
#' used. Can increase memory usage dramatically in large models, and can be computed after fitting using ctExtract
#' or ctSubjectPars .
#' @param saveComplexPars Logical. If TRUE, also save rowwise output of any complex parameters specified,
#' i.e. combinations of parameters, functions and states.
#' @param gendata Logical -- If TRUE, uses provided data for only covariates and a time and missingness structure, and
#' generates random data according to the specified model / priors.
#' Generated data is in the $Ygen subobject after running \code{extract} on the fit object.
#' For datasets with many manifest variables or time points, file size may be large.
#' To generate data based on the posterior of a fitted model, see \code{\link{ctGenerateFromFit}}.
#' @param vb Logical. Use variational Bayes algorithm from stan? Only kind of working, not recommended.
#' @param compileArgs List of arguments to pass to \code{\link[rstan]{stan_model}} for compilation of the Stan model.
#' @param ... additional arguments to pass to \code{\link[rstan]{stan}} function.
#' @export
#' @examples
#' \donttest{
#'
#' #generate a modern ctsem model relying heavily on defaults
#' model<-ctModel(type='ct',
#' latentNames=c('eta1','eta2'),
#' manifestNames=c('Y1','Y2'),
#' MANIFESTVAR=diag(.1,2),
#' TDpredNames='TD1',
#' TIpredNames=c('TI1','TI2','TI3'),
#' LAMBDA=diag(2))
#'
#' fit<-ctFit(ctstantestdat, model,priors=TRUE)
#'
#' summary(fit)
#'
#' plot(fit,wait=FALSE)
#'
#' #### extended examples
#'
#' library(ctsem)
#' set.seed(3)
#'
#' # Data generation (run this, but no need to understand!) -----------------
#'
#' Tpoints <- 20
#' nmanifest <- 4
#' nlatent <- 2
#' nsubjects<-20
#'
#' #random effects
#' age <- rnorm(nsubjects) #standardised
#' cint1<-rnorm(nsubjects,2,.3)+age*.5
#' cint2 <- cint1*.5+rnorm(nsubjects,1,.2)+age*.5
#' tdpredeffect <- rnorm(nsubjects,5,.3)+age*.5
#'
#' for(i in 1:nsubjects){
#' #generating model
#' gm<-ctModel(Tpoints=Tpoints,n.manifest = nmanifest,n.latent = nlatent,n.TDpred = 1,
#' type='omx',
#' LAMBDA = matrix(c(1,0,0,0, 0,1,.8,1.3),nrow=nmanifest,ncol=nlatent),
#' DRIFT=matrix(c(-.3, .2, 0, -.5),nlatent,nlatent),
#' TDPREDMEANS=matrix(c(rep(0,Tpoints-10),1,rep(0,9)),ncol=1),
#' TDPREDEFFECT=matrix(c(tdpredeffect[i],0),nrow=nlatent),
#' DIFFUSION = matrix(c(1, 0, 0, .5),2,2),
#' CINT = matrix(c(cint1[i],cint2[i]),ncol=1),
#' T0VAR=diag(2,nlatent,nlatent),
#' MANIFESTVAR = diag(.5, nmanifest))
#'
#' #generate data
#' newdat <- ctGenerate(ctmodelobj = gm,n.subjects = 1,burnin = 2,
#' dtmat<-rbind(c(rep(.5,8),3,rep(.5,Tpoints-9))))
#' newdat[,'id'] <- i #set id for each subject
#' newdat <- cbind(newdat,age[i]) #include time independent predictor
#' if(i ==1) {
#' dat <- newdat[1:(Tpoints-10),] #pre intervention data
#' dat2 <- newdat #including post intervention data
#' }
#' if(i > 1) {
#' dat <- rbind(dat, newdat[1:(Tpoints-10),])
#' dat2 <- rbind(dat2,newdat)
#' }
#' }
#' colnames(dat)[ncol(dat)] <- 'age'
#' colnames(dat2)[ncol(dat)] <- 'age'
#'
#'
#' #plot generated data for sanity
#' plot(age)
#' matplot(dat[,gm$manifestNames],type='l',pch=1)
#' plotvar <- 'Y1'
#' plot(dat[dat[,'id']==1,'time'],dat[dat[,'id']==1,plotvar],type='l',
#' ylim=range(dat[,plotvar],na.rm=TRUE))
#' for(i in 2:nsubjects){
#' points(dat[dat[,'id']==i,'time'],dat[dat[,'id']==i,plotvar],type='l',col=i)
#' }
#'
#'
#' dat2[,gm$manifestNames][sample(1:length(dat2[,gm$manifestNames]),size = 100)] <- NA
#'
#'
#' #data structure
#' head(dat2)
#'
#'
#' # Model fitting -----------------------------------------------------------
#'
#' ##simple univariate default model
#'
#' m <- ctModel(type = 'ct', manifestNames = c('Y1'), LAMBDA = diag(1))
#' ctModelLatex(m)
#'
#' #Specify univariate linear growth curve
#'
#' m1 <- ctModel(type = 'ct',
#' manifestNames = c('Y1'), latentNames=c('eta1'),
#' DRIFT=matrix(-.0001,nrow=1,ncol=1),
#' DIFFUSION=matrix(0,nrow=1,ncol=1),
#' T0VAR=matrix(0,nrow=1,ncol=1),
#' CINT=matrix(c('cint1'),ncol=1),
#' T0MEANS=matrix(c('t0m1'),ncol=1),
#' LAMBDA = diag(1),
#' MANIFESTMEANS=matrix(0,ncol=1),
#' MANIFESTVAR=matrix(c('merror'),nrow=1,ncol=1))
#'
#' ctModelLatex(m1)
#'
#' #fit
#' f1 <- ctFit(datalong = dat2, model = m1, optimize=TRUE, priors=FALSE)
#'
#' summary(f1)
#'
#' #plots of individual subject models v data
#' ctKalman(f1,plot=TRUE,subjects=1,kalmanvec=c('y','yprior'),timestep=.01)
#' ctKalman(f1,plot=TRUE,subjects=1:3,kalmanvec=c('y','ysmooth'),timestep=.01,errorvec=NA)
#'
#' ctPostPredict(f1, wait=FALSE) #compare randomly generated data from posterior to observed data
#'
#' cf<-ctCheckFit(f1) #compare mean and covariance of randomly generated data to observed cov
#' plot(cf,wait=FALSE)
#'
#' ### Further example models
#'
#' #Include intervention
#' m2 <- ctModel(type = 'ct',
#' manifestNames = c('Y1'), latentNames=c('eta1'),
#' n.TDpred=1,TDpredNames = 'TD1', #this line includes the intervention
#' TDPREDEFFECT=matrix(c('tdpredeffect'),nrow=1,ncol=1), #intervention effect
#' DRIFT=matrix(-1e-5,nrow=1,ncol=1),
#' DIFFUSION=matrix(0,nrow=1,ncol=1),
#' CINT=matrix(c('cint1'),ncol=1),
#' T0MEANS=matrix(c('t0m1'),ncol=1),
#' T0VAR=matrix(0,nrow=1,ncol=1),
#' LAMBDA = diag(1),
#' MANIFESTMEANS=matrix(0,ncol=1),
#' MANIFESTVAR=matrix(c('merror'),nrow=1,ncol=1))
#'
#'
#'
#' #Individual differences in intervention, Bayesian estimation, covariates
#' m2i <- ctModel(type = 'ct',
#' manifestNames = c('Y1'), latentNames=c('eta1'),
#' TIpredNames = 'age',
#' TDpredNames = 'TD1', #this line includes the intervention
#' TDPREDEFFECT=matrix(c('tdpredeffect||TRUE'),nrow=1,ncol=1), #intervention effect
#' DRIFT=matrix(-1e-5,nrow=1,ncol=1),
#' DIFFUSION=matrix(0,nrow=1,ncol=1),
#' CINT=matrix(c('cint1'),ncol=1),
#' T0MEANS=matrix(c('t0m1'),ncol=1),
#' T0VAR=matrix(0,nrow=1,ncol=1),
#' LAMBDA = diag(1),
#' MANIFESTMEANS=matrix(0,ncol=1),
#' MANIFESTVAR=matrix(c('merror'),nrow=1,ncol=1))
#'
#'
#' #Including covariate effects
#' m2ic <- ctModel(type = 'ct',
#' manifestNames = c('Y1'), latentNames=c('eta1'),
#' n.TIpred = 1, TIpredNames = 'age',
#' n.TDpred=1,TDpredNames = 'TD1', #this line includes the intervention
#' TDPREDEFFECT=matrix(c('tdpredeffect'),nrow=1,ncol=1), #intervention effect
#' DRIFT=matrix(-1e-5,nrow=1,ncol=1),
#' DIFFUSION=matrix(0,nrow=1,ncol=1),
#' CINT=matrix(c('cint1'),ncol=1),
#' T0MEANS=matrix(c('t0m1'),ncol=1),
#' T0VAR=matrix(0,nrow=1,ncol=1),
#' LAMBDA = diag(1),
#' MANIFESTMEANS=matrix(0,ncol=1),
#' MANIFESTVAR=matrix(c('merror'),nrow=1,ncol=1))
#'
#' m2ic$pars$indvarying[m2ic$pars$matrix %in% 'TDPREDEFFECT'] <- TRUE
#'
#'
#' #Include deterministic dynamics
#' m3 <- ctModel(type = 'ct',
#' manifestNames = c('Y1'), latentNames=c('eta1'),
#' n.TDpred=1,TDpredNames = 'TD1', #this line includes the intervention
#' TDPREDEFFECT=matrix(c('tdpredeffect'),nrow=1,ncol=1), #intervention effect
#' DRIFT=matrix('drift11',nrow=1,ncol=1),
#' DIFFUSION=matrix(0,nrow=1,ncol=1),
#' CINT=matrix(c('cint1'),ncol=1),
#' T0MEANS=matrix(c('t0m1'),ncol=1),
#' T0VAR=matrix('t0var11',nrow=1,ncol=1),
#' LAMBDA = diag(1),
#' MANIFESTMEANS=matrix(0,ncol=1),
#' MANIFESTVAR=matrix(c('merror1'),nrow=1,ncol=1))
#'
#'
#'
#'
#'
#' #Add system noise to allow for fluctuations that persist in time
#' m3n <- ctModel(type = 'ct',
#' manifestNames = c('Y1'), latentNames=c('eta1'),
#' n.TDpred=1,TDpredNames = 'TD1', #this line includes the intervention
#' TDPREDEFFECT=matrix(c('tdpredeffect'),nrow=1,ncol=1), #intervention effect
#' DRIFT=matrix('drift11',nrow=1,ncol=1),
#' DIFFUSION=matrix('diffusion',nrow=1,ncol=1),
#' CINT=matrix(c('cint1'),ncol=1),
#' T0MEANS=matrix(c('t0m1'),ncol=1),
#' T0VAR=matrix('t0var11',nrow=1,ncol=1),
#' LAMBDA = diag(1),
#' MANIFESTMEANS=matrix(0,ncol=1),
#' MANIFESTVAR=matrix(c(0),nrow=1,ncol=1))
#'
#'
#'
#' #include 2nd latent process
#'
#' m4 <- ctModel(n.manifest = 2,n.latent = 2, type = 'ct',
#' manifestNames = c('Y1','Y2'), latentNames=c('L1','L2'),
#' n.TDpred=1,TDpredNames = 'TD1',
#' TDPREDEFFECT=matrix(c('tdpredeffect1','tdpredeffect2'),nrow=2,ncol=1),
#' DRIFT=matrix(c('drift11','drift21','drift12','drift22'),nrow=2,ncol=2),
#' DIFFUSION=matrix(c('diffusion11','diffusion21',0,'diffusion22'),nrow=2,ncol=2),
#' CINT=matrix(c('cint1','cint2'),nrow=2,ncol=1),
#' T0MEANS=matrix(c('t0m1','t0m2'),nrow=2,ncol=1),
#' T0VAR=matrix(c('t0var11','t0var21',0,'t0var22'),nrow=2,ncol=2),
#' LAMBDA = matrix(c(1,0,0,1),nrow=2,ncol=2),
#' MANIFESTMEANS=matrix(c(0,0),nrow=2,ncol=1),
#' MANIFESTVAR=matrix(c('merror1',0,0,'merror2'),nrow=2,ncol=2))
#'
#' #dynamic factor model -- fixing CINT to 0 and freeing indicator level intercepts
#'
#' m3df <- ctModel(type = 'ct',
#' manifestNames = c('Y2','Y3'), latentNames=c('eta1'),
#' n.TDpred=1,TDpredNames = 'TD1', #this line includes the intervention
#' TDPREDEFFECT=matrix(c('tdpredeffect'),nrow=1,ncol=1), #intervention effect
#' DRIFT=matrix('drift11',nrow=1,ncol=1),
#' DIFFUSION=matrix('diffusion',nrow=1,ncol=1),
#' CINT=matrix(c(0),ncol=1),
#' T0MEANS=matrix(c('t0m1'),ncol=1),
#' T0VAR=matrix('t0var11',nrow=1,ncol=1),
#' LAMBDA = matrix(c(1,'Y3loading'),nrow=2,ncol=1),
#' MANIFESTMEANS=matrix(c('Y2_int','Y3_int'),nrow=2,ncol=1),
#' MANIFESTVAR=matrix(c('Y2residual',0,0,'Y3residual'),nrow=2,ncol=2))
#'
#' }
ctFit<-function(datalong, model, stanmodeltext=NA, iter=1000, intoverstates=TRUE, binomial=FALSE,
fit=TRUE, intoverpop='auto', sameInitialTimes=FALSE, stationary=FALSE,plot=FALSE, derrind=NA,
optimize=TRUE, optimcontrol=list(),
nlcontrol = list(), nopriors=NA, priors=FALSE, chains=2,
cores=ifelse(optimize,getOption("mc.cores", 2L),'maxneeded'),
inits=NULL,
compileArgs=list(),
forcerecompile=FALSE,saveCompile=TRUE,savescores=FALSE,
savesubjectmatrices=FALSE, saveComplexPars=FALSE,
gendata=FALSE,
control=list(),verbose=0,vb=FALSE,..., ctstanmodel){
if(missing(model)){
if(missing(ctstanmodel)) stop('model must be supplied')
warning('ctstanmodel argument is deprecated, use model instead')
model <- ctstanmodel
} else if(!missing(ctstanmodel)) {
stop('Use only one of model or deprecated ctstanmodel')
}
ctstanmodel <- model
if(!is.na(nopriors)){
warning('nopriors argument is deprecated, use priors argument in future')
priors <- !nopriors
}
if(any(!is.na(derrind))) warning('derrind argment is deprecated, computed automatically now')
datalong <- data.frame(datalong)
if(!ctstanmodel$timeName %in% colnames(datalong) && !ctstanmodel$continuoustime) {
dtable <- data.table(datalong)
dtable[,.ObsCount:=1:.N,by=ctstanmodel$id]
datalong[[ctstanmodel$timeName]] <- dtable[['.ObsCount']]
rm(dtable)
}
datalong <- datalong[order(datalong[[ctstanmodel$subjectIDname]],datalong[[ctstanmodel$timeName]]),] #sort by subject, time.
datavars <- c(ctstanmodel$timeName,ctstanmodel$subjectIDname, ctstanmodel$manifestNames,ctstanmodel$TDpredNames,ctstanmodel$TIpredNames)
sapply(datavars,function(x){
if(!x %in% colnames(datalong)) stop(paste0(x,' column not found in data!'))
if(!x %in% ctstanmodel$subjectIDname){ #if not an id column
if(any(!is.numeric(as.numeric(datalong[!is.na(datalong[,x]),x])))) stop(x ,' column contains non-numeric data!')
}
})
if(!'ctStanModel' %in% class(ctstanmodel)) stop('not a ctStanModel object')
#set nlcontrol defaults
if(is.null(nlcontrol$maxtimestep)) nlcontrol$maxtimestep = 999999
if(is.null(nlcontrol$Jstep)) nlcontrol$Jstep = 1e-6
args=c(as.list(environment()), list(...)) #as.list((match.call(expand.dots=FALSE)))
args$datalong <- NULL
args$model <- NULL
args$ctstanmodel <- NULL
ctm <- ctstanmodel
if(!is.null(ctm$TIpredAuto) && ctm$TIpredAuto %in% c(1L,TRUE)){ #if auto tipred, set all effects to true
for(tip in ctm$TIpredNames){
ctm$pars[[paste0(tip,'_effect')]] <- TRUE
}
}
if(optimize && !priors) message("Maximum likelihood estimation requested")
if(optimize && priors && (is.null(optimcontrol$is) || optimcontrol$is %in% FALSE)) message("Maximum a posteriori estimation requested")
if(optimize && priors && (!is.null(optimcontrol$is) && optimcontrol$is %in% TRUE)) message("Bayesian estimation via optimization and importance sampling requested")
if(!optimize) message("Bayesian estimation via Stan's NUTS sampler requested")
###stationarity
if(stationary) {
stop('Stationary option temporarily unavailable -- reductions needed to pass all CRAN checks')
ctm$pars$param[ctm$pars$matrix %in% c('T0VAR','T0MEANS')] <- 'stationary'
ctm$pars$value[ctm$pars$matrix %in% c('T0VAR','T0MEANS')] <- NA
ctm$pars$indvarying[ctm$pars$matrix %in% c('T0VAR','T0MEANS')] <- FALSE
}
#collect individual stationary elements and update ctm$pars
if(any(ctm$pars$param %in% 'stationary')) stop('Stationary option temporarily unavailable -- reductions needed to pass all CRAN checks')
ctm$t0varstationary <- as.matrix(rbind(ctm$pars[which(ctm$pars$param %in% 'stationary' & ctm$pars$matrix %in% 'T0VAR'),c('row','col')]))
if(nrow(ctm$t0varstationary) > 0){ #ensure upper tri is consistent with lower
for(i in 1:nrow(ctm$t0varstationary)){
if(ctm$t0varstationary[i,1] != ctm$t0varstationary[i,2]) ctm$t0varstationary <- rbind(ctm$t0varstationary,ctm$t0varstationary[i,c(2,1)])
}}
ctm$t0varstationary = unique(ctm$t0varstationary) #remove any duplicated rows
ctm$t0meansstationary <- as.matrix(rbind(ctm$pars[which(ctm$pars$param[ctm$pars$matrix %in% 'T0MEANS'] %in% 'stationary'),c('row','col')]))
ctm$pars$value[ctm$pars$param %in% 'stationary'] <- -99 #does this get inserted?
ctm$pars$indvarying[ctm$pars$param %in% 'stationary'] <- FALSE
ctm$pars$transform[ctm$pars$param %in% 'stationary'] <- NA
ctm$pars$param[ctm$pars$param %in% 'stationary'] <- NA
if(length(unique(datalong[,ctm$subjectIDname]))==1 && any(ctm$pars$indvarying[is.na(ctm$pars$value)]==TRUE)){
# is.null(ctm$fixedrawpopmeans) && is.null(ctm$fixedsubpars) & is.null(ctm$forcemultisubject)) {
ctm$pars$indvarying <- FALSE
message('Individual variation not possible as only 1 subject! indvarying set to FALSE on all parameters')
}
if(length(unique(datalong[,ctm$subjectIDname]))==1 & any(is.na(ctm$pars$value[ctm$pars$matrix %in% 'T0VAR']))){
# is.null(ctm$fixedrawpopmeans) & is.null(ctm$fixedsubpars) & is.null(ctm$forcemultisubject)) {
for(ri in 1:nrow(ctm$pars)){
if(is.na(ctm$pars$value[ri]) && ctm$pars$matrix[ri] %in% 'T0VAR'){
ctm$pars$value[ri] <- ifelse(ctm$pars$row[ri] == ctm$pars$col[ri], 1e-3, 0)
}
}
message('Free T0VAR parameters fixed to diagonal matrix of 0.001 as only 1 subject - consider appropriateness!')
}
if(binomial){
message('Binomial argument deprecated -- in future set manifesttype in the model object to 1 for binary indicators')
intoverstates <- FALSE
ctm$manifesttype[] <- 1
}
recompile <- FALSE
if(!optimize && !priors){
message('HMC sampling requested, but priors disabled -- are you sure? consider setting priors=TRUE')
# !priors <- FALSE
}
if(optimize && !intoverstates) warning('intoverstates=TRUE required for sensible optimization! Proceed onwards to weird output at own risk!')
if(intoverpop == 'auto') intoverpop <-
ifelse(optimize && any(ctm$pars$indvarying[is.na(ctm$pars$value)]),TRUE,FALSE)
# if(optimize && !intoverpop && any(ctm$pars$indvarying[is.na(ctm$pars$value)]) &&
# is.null(ctm$fixedrawpopchol) && is.null(ctm$fixedsubpars)){
# intoverpop <- TRUE
# message('Setting intoverpop=TRUE to enable optimization of random effects...')
# }
# if(intoverpop==TRUE && !any(ctm$pars$indvarying[is.na(ctm$pars$value)])) {
# # message('No individual variation -- disabling intoverpop switch');
# intoverpop <- FALSE
# }
ctm <- ctModel0DRIFT(ctm, ctm$continuoustime) #offset 0 drift
ctm$pars <- ctModelStatesAndPARS(ctm$pars,statenames = ctm$latentNames,tdprednames=ctm$TDpredNames) #replace latent states and PARS with state and PAR[] refs, need this early because we rely on [] detection
if(intoverpop) ctm <- ctStanModelIntOverPop(ctm) #extend system matrices for individual differences
# #check this *after* replacing PARS references as needed
# if(any(duplicated(ctm$pars$param[ctm$pars$matrix %in% 'T0MEANS' &
# !grepl('[',ctm$pars$param,fixed=TRUE) &
# !is.na(ctm$pars$param)]))) stop(paste0(
# 'Unfortunately, duplicate T0MEANS parameters must be specified via inclusion of additional PARS matrix in ctModel: e.g.,
# ctModel(... #regular model code
# PARS=c("t0mPar||TRUE"), #specify an additional parameter called t0mPar, with random effects
# T0MEANS=c("t0mPar","t0mPar"), #insert this parameter into the T0MEANS matrix as many times as needed.
# ... #regular model code)
# '))
#jacobian addition
ctm$jacobian <- try(ctJacobian(ctm))
if('try-error' %in% class(ctm$jacobian)) ctm$jacobian <- ctJacobian(ctm,simplify=FALSE)
# ctm$jacobian <- unfoldmats( #replaces matrix references with base parameter
# c(listOfMatrices(ctm$pars),ctm$jacobian))
ctm$jacobian <- ctm$jacobian[names(ctStanMatricesList()$jacobian)]
jl <- ctModelUnlist(ctm$jacobian,names(ctm$jacobian))
jl <- jl[apply(jl,1,function(x) any(!is.na(x))),] #clean up messy leftovers of NA's
jl2 <- as.data.frame(rbind(data.table(ctm$pars[1,]),data.table(jl),fill=TRUE))[-1,]
for(i in 1:nrow(jl2)){ #copy base parameter transforms etc to jacobian when needed
if(!is.na(jl2$param[i]) && jl2$param[i] %in% ctm$pars$param){
jl2[i, !colnames(jl2) %in% list('matrix','row','col')] <-
ctm$pars[which(ctm$pars$param %in% jl2$param[i])[1], !colnames(ctm$pars) %in% list('matrix','row','col')]
}
}
ctm$pars <- rbind(ctm$pars,jl2)
ctm$pars <- ctModelStatesAndPARS(ctm$pars,statenames = ctm$latentNames,tdprednames=ctm$TDpredNames) #replace any new state and par refs with square bracket refs
ctm <- ctModelTransformsToNum(ctm)
ctm$pars <- ctStanModelCleanctspec(ctm$pars)
ctm <- T0VARredundancies(ctm)
if(!all(ctm$pars$transform[!is.na(suppressWarnings(as.integer(ctm$pars$transform)))] %in% c(0,1,2,3,4))) stop('Unknown transform specified -- integers should be 0 to 4')
#fix binary manifestvariance
if(any(ctm$manifesttype > 0)){ #if any non continuous variables, (with free parameters)...
errfix <- which(ctm$pars$matrix %in% 'MANIFESTVAR' &
(ctm$pars$row %in% which(ctm$manifesttype==1) |
ctm$pars$col %in% which(ctm$manifesttype==1)) &
is.na(suppressWarnings(as.numeric(
ctm$pars$value))))
if(length(errfix) > 0){
message('Fixing any free MANIFESTVAR parameters for binary indicators to deterministic calculation')
ctm$pars$value[errfix] <- 1e-5
ctm$pars[errfix,c('param','transform','multiplier','offset','meanscale','inneroffset','sdscale')] <- NA
ctm$pars$indvarying[errfix] <- FALSE
}}
ctm$modelmats <- ctStanModelMatrices(ctm) #slow!
ctm <- ctStanCalcsList(ctm,save=saveComplexPars) #get extra calculations and adjust model spec as needed???
#store values in ctm
ctm$intoverpop <- as.integer(intoverpop)
ctm$nlatentpop <- as.integer(ifelse(ctm$intoverpop ==1, max(ctm$pars$row[ctm$pars$matrix %in% 'T0MEANS']), ctm$n.latent))
ctm$intoverstates <- as.integer(intoverstates)
ctm$priors <- as.integer(priors)
ctm$stationary <- as.integer(stationary)
ctm$nlcontrol <- nlcontrol
#recompile checks
if(forcerecompile) recompile <- TRUE
if(naf(!is.na(ctm$rawpopsdbaselowerbound))) recompile <- TRUE
if(ctm$rawpopsdbase != 'normal(0,1)') recompile <- TRUE
if(ctm$rawpopsdtransform != 'log1p_exp(2*rawpopsdbase-1) .* sdscale') ctm$recompile <- TRUE
if(any(ctm$modelmats$matsetup[,'transform'] < -10)) recompile <- TRUE #if custom transforms needed
ncalcsNoJ<- length(unlist(ctm$modelmats$calcs)[!grepl('JAx[',unlist(ctm$modelmats$calcs),fixed=TRUE)])
if(ncalcsNoJ > 0) recompile <- TRUE
if(!recompile &&
length(unlist(ctm$modelmats$calcs)[!grepl('JAx[',unlist(ctm$modelmats$calcs),fixed=TRUE)])>0)
message('Finite difference jacobian used to avoid recompiling -- use forcerecompile=TRUE for analytic jacobians')
#further model adjustments conditional on recompile
if(!recompile){ #then use finite diffs for some elements
#collect row and column of complicated jacobian elements into vector
ctm$JAxfinite <- array(as.integer(unique(
unlist(ctm$modelmats$matsetup[ctm$modelmats$matsetup$matrix %in% 52 &
ctm$modelmats$matsetup$when == -999, 'col']))))# &
# ctm$modelmats$matsetup$copyrow < 1,c('row','col')]))))
ctm$Jyfinite <- array(as.integer(unique(
unlist(ctm$modelmats$matsetup[ctm$modelmats$matsetup$matrix %in% 54 &
ctm$modelmats$matsetup$when == -999, 'col']))))
}
if(recompile) ctm$JAxfinite <- ctm$Jyfinite <- array(as.integer(c()))
ctm$recompile <- recompile
standata <- ctStanData(ctm,datalong,optimize=optimize, sameInitialTimes=sameInitialTimes) #bit slow
standata$verbose=as.integer(verbose)
standata$savesubjectmatrices=as.integer(savesubjectmatrices)
standata$gendata=as.integer(gendata)
if(standata$savesubjectmatrices==1L) savescores = TRUE
standata$savescores=as.integer(savescores)
# print(standata$savesubjectmatrices)
#####post model / data checks
if(cores=='maxneeded') cores=max(1,min(c(chains,parallel::detectCores()-1)))
if(is.logical(stanmodeltext)) {
stanmodeltext<- ctStanModelWriter(ctm, gendata, ctm$modelmats$extratforms,ctm$modelmats$matsetup)
}
if(fit){
# if(gendata && stanmodels$ctsmgen@model_code != stanmodeltext) recompile <- TRUE
# if(!gendata && paste0(stanmodels$ctsm@model_code) != paste0(stanmodeltext)) recompile <- TRUE
# STAN_NUM_THREADS <- Sys.getenv('STAN_NUM_THREADS',unset=NA)
# Sys.setenv(STAN_NUM_THREADS=cores)
if(recompile || forcerecompile) {
message('Compiling model...')
#r4.2 / windows / old rstan check
if(.Platform$OS.type=="windows" && R.version$major %in% 4 && as.numeric(R.version$minor) >= 2 &&
unlist(utils::packageVersion('rstan'))[2] < 25){
stop('
*****
Compiling not possible with R version 4.2+ on Windows with Rstan version < 2.26
To upgrade rstan, close and restart all R sessions then run:
install.packages("StanHeaders", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))
install.packages("rstan", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))
*****')
# a=readline('Attempt to upgrade Rstan from Stan repository? y/n')
# if(a %in% c('yes','y','Y','Yes','YES')){
# message(
# install.packages("StanHeaders", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))
# install.packages("rstan", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))
# }
}
compileArgs$model_name='ctsem'
compileArgs$model_code=stanmodeltext
compileArgs$auto_write=TRUE
sm <- do.call(stan_model,compileArgs)
# ,allow_undefined = TRUE,verbose=TRUE,
# includes = paste0(
# '\n#include "', file.path(getwd(), 'syl2.hpp'),'"',
# '\n')
if(saveCompile){
if(exists(x = 'ctsem.compiled',envir= parent.frame())
&& !'stanmodel' %in% class(get('ctsem.compiled',envir = parent.frame()))){
warning('ctsem.compiled object already exists, not saving compile')
} else assign(x = 'ctsem.compiled',sm,envir = parent.frame())
}
}
if(!recompile && !forcerecompile) {
if(!gendata) sm <- stanmodels$ctsm else sm <- stanmodels$ctsmgen
}
# configure inits ---------------------------------------------------------
initOptim <- (length(inits)==1 && (inits=='optimize' || inits=='Optimize' || inits=='optimise' || inits=='Optimise'))
if(optimize || initOptim){ #then set optimcontrol list
optimcontrol$cores <- cores
optimcontrol$verbose <- verbose
optimcontrol$priors <- as.logical(priors)
optimcontrol$standata=standata
optimcontrol$sm=sm
optimcontrol$init=inits
optimcontrol$plot=plot
optimcontrol$matsetup <- data.frame(ctm$modelmats$matsetup)
}
if(!optimize && !is.null(inits)){
if('list' %in% class(inits)){
staninits=inits
} else {
if(initOptim){ #then first optimize to get inits
if(!intoverpop && length(unique(datalong[[ctm$subjectIDname]]) > 1) && any(ctm$pars$indvarying)) stop('Cannot optimize to get inits unless intoverpop=TRUE')
optimcontrol$init <- NULL
optimcontrol$tol=1e-7
if(!intoverpop & ! intoverstates) stop('Cannot initialize with optimization unless intoverpop and intoverstates are set to TRUE')
inits <- do.call(stanoptimis,optimcontrol)$rawest
}
sf <- stan_reinitsf(sm,standata)
staninits <- list()
if(chains > 1){ #set all chains to same inits
for(i in 1:chains){
staninits[[i]]<-constrain_pars(sf,inits+rnorm(length(inits),0,.01))
}
}
}
}
if(!optimize){
#control arguments for rstan
# if(is.null(control$adapt_term_buffer)) control$adapt_term_buffer <- min(c(iter/10,max(iter-20,75)))
if(is.null(control$adapt_delta)) control$adapt_delta <- .8
if(is.null(control$adapt_window)) control$adapt_window <- 5
if(is.null(control$max_treedepth)) control$max_treedepth <- 10
if(is.null(control$adapt_init_buffer)) control$adapt_init_buffer=2
if(is.null(control$stepsize)) control$stepsize=.001
if(is.null(control$metric)) control$metric='diag_e'
message('Sampling...')
#
stanargs <- list(object = sm,
init_r=.03,
save_warmup=as.logical(plot),
refresh=20,
iter=iter,
data = standata, chains = chains, control=control,
cores=cores,
...)
if(!is.null(inits)) stanargs$init=staninits
if(vb){
if(!intoverpop && standata$nindvarying > 0) warning('Poor results are expected with variational inference and sampling individual differences! Suggest disabling vb or enabling intoverpop.')
stanfit <- list(stanfit=rstan::vb(object = sm,data=standata, importance_resampling=TRUE,tol_rel_obj=1e-3))
} else{ #if not vi
if(plot==TRUE) stanfit <- suppressWarnings(list(stanfit=do.call(stanWplot,stanargs))) else stanfit <- suppressWarnings(list(stanfit=do.call(sampling,stanargs)))
#find the median sample and compute kalman scores etc for this
# browser()
e=rstan::extract(stanfit$stanfit)
# middle <- which(abs(e$ll-quantile(e$ll,.5)) == min(abs(e$ll-quantile(e$ll,.5) )))
# middle <- which(e$ll==max(e$ll))
stanfit$rawposterior <- t(stan_unconstrainsamples(fit = stanfit$stanfit,standata = standata))
stanfit$rawest <- apply(stanfit$rawposterior,2,median)
}
}
if(optimize==TRUE) {
stanfit <- do.call(stanoptimis,optimcontrol) #eval(parse(text=opcall))
#update data that may have changed during optimization
for(ni in names(stanfit$standata)){
standata[[ni]] <- stanfit$standata[[ni]]
}
if(ctm$n.TIpred>0){
ctm$modelmats$TIPREDEFFECTsetup <- stanfit$standata$TIPREDEFFECTsetup
ms <- ctm$modelmats$matsetup
ms$tipred <- 0L
parswithtipreds <- sort(unique(ms$param[ms$param >0 & ms$when %in% c(0,-1) & ms$copyrow < 1]))
parswithtipreds<-parswithtipreds[apply(stanfit$standata$TIPREDEFFECTsetup,1,sum)>0]
ms$tipred[ms$param >0 & ms$when %in% c(0,-1) & ms$copyrow < 1 & ms$param %in% parswithtipreds] <- 1L
ctm$modelmats$matsetup <- ms
}
}
# if(is.na(STAN_NUM_THREADS)) Sys.unsetenv('STAN_NUM_THREADS') else Sys.setenv(STAN_NUM_THREADS = STAN_NUM_THREADS) #reset sys env
} # end if fit==TRUE
#convert missings back to NA's for data output
standataout<-standata
standataout$Y[standataout$Y==99999] <- NA
standataout$tipreds[standataout$tipreds==99999] <- NA
# standataout <- utils::relist((standataout),skeleton=standata)
setup=list(recompile=recompile,idmap=standata$idmap,matsetup=ctm$modelmats$matsetup,matvalues=ctm$modelmats$matvalues,
popsetup=ctm$modelmats$matsetup[ctm$modelmats$matsetup$when %in% c(0,-1) & ctm$modelmats$matsetup$param > 0,],
popvalues=ctm$modelmats$matvalues[ctm$modelmats$matsetup$when %in% c(0,-1) & ctm$modelmats$matsetup$param > 0,],
extratforms=ctm$modelmats$extratforms)
if(fit) {
stanfit$transformedparsfull <- suppressMessages(stan_constrainsamples(sm = sm,standata = standata,
savesubjectmatrices = TRUE, samples = matrix(stanfit$rawest,1),cores=1,savescores=TRUE,pcovn=5000))
out <- list(args=args,
setup=setup,
stanmodeltext=stanmodeltext, data=standataout, ctdatastruct=datalong[c(1,nrow(datalong)),],standata=standata,
ctstanmodelbase=ctstanmodel, ctstanmodel=ctm,stanmodel=sm, stanfit=stanfit)
class(out) <- 'ctStanFit'
out$stanfit$kalman<-suppressMessages(ctKalmanArray(out,pointest = TRUE))
}
if(!fit) out=list(args=args,setup=setup,
stanmodeltext=stanmodeltext,data=standataout, ctdatastruct=datalong[c(1,nrow(datalong)),],standata=standata,
ctstanmodelbase=ctstanmodel, ctstanmodel=ctm)
return(out)
}
#' Backward-compatible alias for \code{ctFit}.
#' @rdname ctFit
#' @export
ctStanFit <- ctFit
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Defines functions ctFit T0VARredundancies ctFitUpdate
Documented in ctFit ctFitUpdate
#' Update a ctStanFit object
#'
#' Either to include different data, or because you have upgraded ctsem and the internal data structure has changed.
#'
#' @param oldfit fit object to be upgraded
#' @param data replacement long format data object
#' @param recompile whether to force a recompile -- safer but slower and usually unnecessary.
#' @param refit if TRUE, refits the model using the old estimates as a starting point. Only applicable for
#' optimized fits, not sampling.
#' @param ... extra arguments to pass to ctFit
#'
#' @return updated ctStanFit object.
#' @export
#'
#' @examples
#' newfit <- ctFitUpdate(ctstantestfit,refit=FALSE)
ctFitUpdate <- function(oldfit, data=NA, recompile=FALSE,refit=FALSE,...){
if(!refit) message('Trying to do a quick update -- if there are problems, try with refit=TRUE for more robustness')
dots <- list(...)
args <- as.list(oldfit$args)
for(n in names(dots)){
args[[n]] <- dots[[n]]
}
if(length(oldfit$stanfit$stanfit@sim) > 0) refit=FALSE
args$fit <- refit
args$inits <- oldfit$stanfit$rawest
args$model <- oldfit$ctstanmodelbase
args$ctstanmodel <- NULL
newargs <- as.list(args(ctFit))
for(argi in names(args)){
if(argi %in% names(args)) newargs[[argi]] <- args[[argi]] else message(argi, ' is no longer a valid argument, dropping...')
}
if(length(data==1)) args$datalong <- standatatolong(oldfit$standata,origstructure = TRUE,ctm=oldfit$ctstanmodelbase)
if(length(data) > 1) args$datalong <- data
newfit <- do.call(ctFit,args)
if(!refit){
oldfit$standata <- newfit$standata
if(oldfit$ctstanmodel$recompile || recompile) oldfit$stanmodel <- rstan::stan_model(model_code = newfit$stanmodeltext) else
oldfit$stanmodel <- stanmodels$ctsm
}
if(refit) oldfit <- newfit
return(oldfit)
}
#' Backward-compatible alias for \code{ctFitUpdate}.
#' @rdname ctFitUpdate
#' @export
ctStanFitUpdate <- ctFitUpdate
T0VARredundancies <- function(ctm) { #check for redundant T0VAR parameters (because indvarying t0means) and disable
whichT0VAR_T0MEANSindvarying <- ctm$pars$matrix %in% 'T0VAR' &
is.na(ctm$pars$value) &
(ctm$pars$row %in% ctm$pars$row[ctm$pars$matrix %in% 'T0MEANS' & ctm$pars$indvarying] |
ctm$pars$col %in% ctm$pars$row[ctm$pars$matrix %in% 'T0MEANS' & ctm$pars$indvarying])
if(any(whichT0VAR_T0MEANSindvarying)){
message('Free T0VAR parameters as well as indvarying T0MEANS -- fixing T0VAR pars to diag matrix of 1e-6')
ctm$pars$value[whichT0VAR_T0MEANSindvarying & ctm$pars$col == ctm$pars$row ] <- 1e-6
ctm$pars$value[whichT0VAR_T0MEANSindvarying & ctm$pars$col != ctm$pars$row ] <- 0
ctm$pars$param[whichT0VAR_T0MEANSindvarying] <- NA
ctm$pars$transform[whichT0VAR_T0MEANSindvarying] <- NA
ctm$pars$indvarying[whichT0VAR_T0MEANSindvarying] <- FALSE
}
return(ctm)
}
#' Fit a ctsem model
#'
#' Fits a ctsem model specified via \code{\link{ctModel}} with type either 'ct' or 'dt'.
#' \code{ctStanFit} is maintained as a backward-compatible alias.
#'
#' @param datalong long format data containing columns for subject id (numeric values, 1 to max subjects), manifest variables,
#' any time dependent (i.e. varying within subject) predictors,
#' and any time independent (not varying within subject) predictors.
#' @param model model object as generated by \code{\link{ctModel}} with type='ct' or 'dt', for continuous or discrete time
#' models respectively.
#' @param ctstanmodel Deprecated. Use \code{model}.
#' @param stanmodeltext already specified Stan model character string, generally leave NA unless modifying Stan model directly.
#' (Possible after modification of output from fitting with argument fit=FALSE)
#' @param intoverstates logical indicating whether or not to integrate over latent states using a Kalman filter.
#' Generally recommended to set TRUE unless using non-gaussian measurement model.
#' @param binomial Deprecated. Logical indicating the use of binary rather than Gaussian data, as with IRT analyses.
#' This now sets \code{intoverstates = FALSE} and the \code{manifesttype} of every indicator to 1, for binary.
#' @param fit If TRUE, fit specified model using Stan, if FALSE, return stan model object without fitting.
#' @param intoverpop if 'auto', set to TRUE if optimizing and FALSE if using hmc.
#' if TRUE, integrates over population distribution of parameters rather than full sampling.
#' Allows for optimization of non-linearities and random effects, via state expansion.
#' @param sameInitialTimes if TRUE, include an empty observation for every subject that has no observation
#' at the earliest observation time of the dataset. This ensures that the T0MEANS occurs for every subject at the same time,
#' rather than just at the earliest observation for that subject. Important when modelling trends over time, age, etc.
#' @param plot if TRUE, for sampling, a Shiny program is launched upon fitting to interactively plot samples.
#' May struggle with many (e.g., > 5000) parameters. For optimizing, various optimization details are plotted -- in development.
#' @param derrind deprecated, latents involved in dynamic error calculations are determined automatically now.
#' @param optimize if TRUE, use \code{\link{stanoptimis}} function for maximum a posteriori / importance sampling estimates,
#' otherwise use the HMC sampler from Stan, which is (much) slower, but generally more robust for complex individual differences.
#' @param optimcontrol list of parameters sent to \code{\link{stanoptimis}} governing optimization / importance sampling.
#' @param nopriors deprecated, use priors argument. logical. If TRUE, any priors are disabled -- sometimes desirable for optimization.
#' @param priors if TRUE, priors are included in computations, otherwise specified priors are ignored.
#' @param iter used when \code{optimize=FALSE}. number of iterations, half of which will be devoted to warmup by default when sampling.
#' @param inits either character string 'optimize, NULL, or vector of (unconstrained)
#' parameter start values, as returned by the rstan function \code{rstan::unconstrain_pars}, or the parameter values
#' found in a ctsem fit object \code{myfit$stanfit$rawest} (or \code{$rawposterior}) for instance.
#' @param chains used when \code{optimize=FALSE}. Number of chains to sample, during HMC or post-optimization importance sampling. Unless the cores
#' argument is also set, the number of chains determines the number of cpu cores used, up to
#' the maximum available minus one. Irrelevant when \code{optimize=TRUE}.
#' @param cores number of cpu cores to use. Either 'maxneeded' to use as many as available minus one,
#' up to the number of chains, or a positive integer. If \code{optimize=TRUE}, more cores are generally faster.
#' @param control Used when \code{optimize=FALSE}. List of arguments sent to \code{\link[rstan]{stan}} control argument,
#' regarding warmup / sampling behaviour. Unless specified, values used are:
#' list(adapt_delta = .8, adapt_window=2, max_treedepth=10, adapt_init_buffer=2, stepsize = .001)
#' @param nlcontrol List of non-linear control parameters.
#' \code{maxtimestep} must be a positive numeric, specifying the largest time
#' span covered by the numerical integration. The large default ensures that for each observation time interval,
#' only a single step of exponential integration is used. When \code{maxtimestep} is smaller than the observation time interval,
#' the integration is nested within an Euler like loop.
#' Smaller values may offer greater accuracy, but are slower and not always necessary. Given the exponential integration,
#' linear model elements are fit exactly with only a single step.
#' @param verbose Integer from 0 to 2. Higher values print more information during model fit -- for debugging.
#' @param stationary Logical. If TRUE, T0VAR and T0MEANS input matrices are ignored,
#' the parameters are instead fixed to long run expectations. More control over this can be achieved
#' by instead setting parameter names of T0MEANS and T0VAR matrices in the input model to 'stationary', for
#' elements that should be fixed to stationarity.
#' @param forcerecompile logical. For development purposes.
#' If TRUE, stan model is recompiled, regardless of apparent need for compilation.
#' @param saveCompile if TRUE and compilation is needed / requested, writes the stan model to
#' the parent frame as ctsem.compiled (unless that object already exists and is not from ctsem), to avoid unnecessary recompilation.
#' @param savescores Logical. If TRUE, output from the Kalman filter is saved in output. For datasets with many variables
#' or time points, will increase file size substantially.
#' @param savesubjectmatrices Logical. If TRUE, subject specific matrices are saved --
#' only relevant when either time dependent predictors or individual differences are
#' used. Can increase memory usage dramatically in large models, and can be computed after fitting using ctExtract
#' or ctSubjectPars .
#' @param saveComplexPars Logical. If TRUE, also save rowwise output of any complex parameters specified,
#' i.e. combinations of parameters, functions and states.
#' @param gendata Logical -- If TRUE, uses provided data for only covariates and a time and missingness structure, and
#' generates random data according to the specified model / priors.
#' Generated data is in the $Ygen subobject after running \code{extract} on the fit object.
#' For datasets with many manifest variables or time points, file size may be large.
#' To generate data based on the posterior of a fitted model, see \code{\link{ctGenerateFromFit}}.
#' @param vb Logical. Use variational Bayes algorithm from stan? Only kind of working, not recommended.
#' @param compileArgs List of arguments to pass to \code{\link[rstan]{stan_model}} for compilation of the Stan model.
#' @param ... additional arguments to pass to \code{\link[rstan]{stan}} function.
#' @export
#' @examples
#' \donttest{
#'
#' #generate a modern ctsem model relying heavily on defaults
#' model<-ctModel(type='ct',
#' latentNames=c('eta1','eta2'),
#' manifestNames=c('Y1','Y2'),
#' MANIFESTVAR=diag(.1,2),
#' TDpredNames='TD1',
#' TIpredNames=c('TI1','TI2','TI3'),
#' LAMBDA=diag(2))
#'
#' fit<-ctFit(ctstantestdat, model,priors=TRUE)
#'
#' summary(fit)
#'
#' plot(fit,wait=FALSE)
#'
#' #### extended examples
#'
#' library(ctsem)
#' set.seed(3)
#'
#' # Data generation (run this, but no need to understand!) -----------------
#'
#' Tpoints <- 20
#' nmanifest <- 4
#' nlatent <- 2
#' nsubjects<-20
#'
#' #random effects
#' age <- rnorm(nsubjects) #standardised
#' cint1<-rnorm(nsubjects,2,.3)+age*.5
#' cint2 <- cint1*.5+rnorm(nsubjects,1,.2)+age*.5
#' tdpredeffect <- rnorm(nsubjects,5,.3)+age*.5
#'
#' for(i in 1:nsubjects){
#' #generating model
#' gm<-ctModel(Tpoints=Tpoints,n.manifest = nmanifest,n.latent = nlatent,n.TDpred = 1,
#' type='omx',
#' LAMBDA = matrix(c(1,0,0,0, 0,1,.8,1.3),nrow=nmanifest,ncol=nlatent),
#' DRIFT=matrix(c(-.3, .2, 0, -.5),nlatent,nlatent),
#' TDPREDMEANS=matrix(c(rep(0,Tpoints-10),1,rep(0,9)),ncol=1),
#' TDPREDEFFECT=matrix(c(tdpredeffect[i],0),nrow=nlatent),
#' DIFFUSION = matrix(c(1, 0, 0, .5),2,2),
#' CINT = matrix(c(cint1[i],cint2[i]),ncol=1),
#' T0VAR=diag(2,nlatent,nlatent),
#' MANIFESTVAR = diag(.5, nmanifest))
#'
#' #generate data
#' newdat <- ctGenerate(ctmodelobj = gm,n.subjects = 1,burnin = 2,
#' dtmat<-rbind(c(rep(.5,8),3,rep(.5,Tpoints-9))))
#' newdat[,'id'] <- i #set id for each subject
#' newdat <- cbind(newdat,age[i]) #include time independent predictor
#' if(i ==1) {
#' dat <- newdat[1:(Tpoints-10),] #pre intervention data
#' dat2 <- newdat #including post intervention data
#' }
#' if(i > 1) {
#' dat <- rbind(dat, newdat[1:(Tpoints-10),])
#' dat2 <- rbind(dat2,newdat)
#' }
#' }
#' colnames(dat)[ncol(dat)] <- 'age'
#' colnames(dat2)[ncol(dat)] <- 'age'
#'
#'
#' #plot generated data for sanity
#' plot(age)
#' matplot(dat[,gm$manifestNames],type='l',pch=1)
#' plotvar <- 'Y1'
#' plot(dat[dat[,'id']==1,'time'],dat[dat[,'id']==1,plotvar],type='l',
#' ylim=range(dat[,plotvar],na.rm=TRUE))
#' for(i in 2:nsubjects){
#' points(dat[dat[,'id']==i,'time'],dat[dat[,'id']==i,plotvar],type='l',col=i)
#' }
#'
#'
#' dat2[,gm$manifestNames][sample(1:length(dat2[,gm$manifestNames]),size = 100)] <- NA
#'
#'
#' #data structure
#' head(dat2)
#'
#'
#' # Model fitting -----------------------------------------------------------
#'
#' ##simple univariate default model
#'
#' m <- ctModel(type = 'ct', manifestNames = c('Y1'), LAMBDA = diag(1))
#' ctModelLatex(m)
#'
#' #Specify univariate linear growth curve
#'
#' m1 <- ctModel(type = 'ct',
#' manifestNames = c('Y1'), latentNames=c('eta1'),
#' DRIFT=matrix(-.0001,nrow=1,ncol=1),
#' DIFFUSION=matrix(0,nrow=1,ncol=1),
#' T0VAR=matrix(0,nrow=1,ncol=1),
#' CINT=matrix(c('cint1'),ncol=1),
#' T0MEANS=matrix(c('t0m1'),ncol=1),
#' LAMBDA = diag(1),
#' MANIFESTMEANS=matrix(0,ncol=1),
#' MANIFESTVAR=matrix(c('merror'),nrow=1,ncol=1))
#'
#' ctModelLatex(m1)
#'
#' #fit
#' f1 <- ctFit(datalong = dat2, model = m1, optimize=TRUE, priors=FALSE)
#'
#' summary(f1)
#'
#' #plots of individual subject models v data
#' ctKalman(f1,plot=TRUE,subjects=1,kalmanvec=c('y','yprior'),timestep=.01)
#' ctKalman(f1,plot=TRUE,subjects=1:3,kalmanvec=c('y','ysmooth'),timestep=.01,errorvec=NA)
#'
#' ctPostPredict(f1, wait=FALSE) #compare randomly generated data from posterior to observed data
#'
#' cf<-ctCheckFit(f1) #compare mean and covariance of randomly generated data to observed cov
#' plot(cf,wait=FALSE)
#'
#' ### Further example models
#'
#' #Include intervention
#' m2 <- ctModel(type = 'ct',
#' manifestNames = c('Y1'), latentNames=c('eta1'),
#' n.TDpred=1,TDpredNames = 'TD1', #this line includes the intervention
#' TDPREDEFFECT=matrix(c('tdpredeffect'),nrow=1,ncol=1), #intervention effect
#' DRIFT=matrix(-1e-5,nrow=1,ncol=1),
#' DIFFUSION=matrix(0,nrow=1,ncol=1),
#' CINT=matrix(c('cint1'),ncol=1),
#' T0MEANS=matrix(c('t0m1'),ncol=1),
#' T0VAR=matrix(0,nrow=1,ncol=1),
#' LAMBDA = diag(1),
#' MANIFESTMEANS=matrix(0,ncol=1),
#' MANIFESTVAR=matrix(c('merror'),nrow=1,ncol=1))
#'
#'
#'
#' #Individual differences in intervention, Bayesian estimation, covariates
#' m2i <- ctModel(type = 'ct',
#' manifestNames = c('Y1'), latentNames=c('eta1'),
#' TIpredNames = 'age',
#' TDpredNames = 'TD1', #this line includes the intervention
#' TDPREDEFFECT=matrix(c('tdpredeffect||TRUE'),nrow=1,ncol=1), #intervention effect
#' DRIFT=matrix(-1e-5,nrow=1,ncol=1),
#' DIFFUSION=matrix(0,nrow=1,ncol=1),
#' CINT=matrix(c('cint1'),ncol=1),
#' T0MEANS=matrix(c('t0m1'),ncol=1),
#' T0VAR=matrix(0,nrow=1,ncol=1),
#' LAMBDA = diag(1),
#' MANIFESTMEANS=matrix(0,ncol=1),
#' MANIFESTVAR=matrix(c('merror'),nrow=1,ncol=1))
#'
#'
#' #Including covariate effects
#' m2ic <- ctModel(type = 'ct',
#' manifestNames = c('Y1'), latentNames=c('eta1'),
#' n.TIpred = 1, TIpredNames = 'age',
#' n.TDpred=1,TDpredNames = 'TD1', #this line includes the intervention
#' TDPREDEFFECT=matrix(c('tdpredeffect'),nrow=1,ncol=1), #intervention effect
#' DRIFT=matrix(-1e-5,nrow=1,ncol=1),
#' DIFFUSION=matrix(0,nrow=1,ncol=1),
#' CINT=matrix(c('cint1'),ncol=1),
#' T0MEANS=matrix(c('t0m1'),ncol=1),
#' T0VAR=matrix(0,nrow=1,ncol=1),
#' LAMBDA = diag(1),
#' MANIFESTMEANS=matrix(0,ncol=1),
#' MANIFESTVAR=matrix(c('merror'),nrow=1,ncol=1))
#'
#' m2ic$pars$indvarying[m2ic$pars$matrix %in% 'TDPREDEFFECT'] <- TRUE
#'
#'
#' #Include deterministic dynamics
#' m3 <- ctModel(type = 'ct',
#' manifestNames = c('Y1'), latentNames=c('eta1'),
#' n.TDpred=1,TDpredNames = 'TD1', #this line includes the intervention
#' TDPREDEFFECT=matrix(c('tdpredeffect'),nrow=1,ncol=1), #intervention effect
#' DRIFT=matrix('drift11',nrow=1,ncol=1),
#' DIFFUSION=matrix(0,nrow=1,ncol=1),
#' CINT=matrix(c('cint1'),ncol=1),
#' T0MEANS=matrix(c('t0m1'),ncol=1),
#' T0VAR=matrix('t0var11',nrow=1,ncol=1),
#' LAMBDA = diag(1),
#' MANIFESTMEANS=matrix(0,ncol=1),
#' MANIFESTVAR=matrix(c('merror1'),nrow=1,ncol=1))
#'
#'
#'
#'
#'
#' #Add system noise to allow for fluctuations that persist in time
#' m3n <- ctModel(type = 'ct',
#' manifestNames = c('Y1'), latentNames=c('eta1'),
#' n.TDpred=1,TDpredNames = 'TD1', #this line includes the intervention
#' TDPREDEFFECT=matrix(c('tdpredeffect'),nrow=1,ncol=1), #intervention effect
#' DRIFT=matrix('drift11',nrow=1,ncol=1),
#' DIFFUSION=matrix('diffusion',nrow=1,ncol=1),
#' CINT=matrix(c('cint1'),ncol=1),
#' T0MEANS=matrix(c('t0m1'),ncol=1),
#' T0VAR=matrix('t0var11',nrow=1,ncol=1),
#' LAMBDA = diag(1),
#' MANIFESTMEANS=matrix(0,ncol=1),
#' MANIFESTVAR=matrix(c(0),nrow=1,ncol=1))
#'
#'
#'
#' #include 2nd latent process
#'
#' m4 <- ctModel(n.manifest = 2,n.latent = 2, type = 'ct',
#' manifestNames = c('Y1','Y2'), latentNames=c('L1','L2'),
#' n.TDpred=1,TDpredNames = 'TD1',
#' TDPREDEFFECT=matrix(c('tdpredeffect1','tdpredeffect2'),nrow=2,ncol=1),
#' DRIFT=matrix(c('drift11','drift21','drift12','drift22'),nrow=2,ncol=2),
#' DIFFUSION=matrix(c('diffusion11','diffusion21',0,'diffusion22'),nrow=2,ncol=2),
#' CINT=matrix(c('cint1','cint2'),nrow=2,ncol=1),
#' T0MEANS=matrix(c('t0m1','t0m2'),nrow=2,ncol=1),
#' T0VAR=matrix(c('t0var11','t0var21',0,'t0var22'),nrow=2,ncol=2),
#' LAMBDA = matrix(c(1,0,0,1),nrow=2,ncol=2),
#' MANIFESTMEANS=matrix(c(0,0),nrow=2,ncol=1),
#' MANIFESTVAR=matrix(c('merror1',0,0,'merror2'),nrow=2,ncol=2))
#'
#' #dynamic factor model -- fixing CINT to 0 and freeing indicator level intercepts
#'
#' m3df <- ctModel(type = 'ct',
#' manifestNames = c('Y2','Y3'), latentNames=c('eta1'),
#' n.TDpred=1,TDpredNames = 'TD1', #this line includes the intervention
#' TDPREDEFFECT=matrix(c('tdpredeffect'),nrow=1,ncol=1), #intervention effect
#' DRIFT=matrix('drift11',nrow=1,ncol=1),
#' DIFFUSION=matrix('diffusion',nrow=1,ncol=1),
#' CINT=matrix(c(0),ncol=1),
#' T0MEANS=matrix(c('t0m1'),ncol=1),
#' T0VAR=matrix('t0var11',nrow=1,ncol=1),
#' LAMBDA = matrix(c(1,'Y3loading'),nrow=2,ncol=1),
#' MANIFESTMEANS=matrix(c('Y2_int','Y3_int'),nrow=2,ncol=1),
#' MANIFESTVAR=matrix(c('Y2residual',0,0,'Y3residual'),nrow=2,ncol=2))
#'
#' }
ctFit<-function(datalong, model, stanmodeltext=NA, iter=1000, intoverstates=TRUE, binomial=FALSE,
fit=TRUE, intoverpop='auto', sameInitialTimes=FALSE, stationary=FALSE,plot=FALSE, derrind=NA,
optimize=TRUE, optimcontrol=list(),
nlcontrol = list(), nopriors=NA, priors=FALSE, chains=2,
cores=ifelse(optimize,getOption("mc.cores", 2L),'maxneeded'),
inits=NULL,
compileArgs=list(),
forcerecompile=FALSE,saveCompile=TRUE,savescores=FALSE,
savesubjectmatrices=FALSE, saveComplexPars=FALSE,
gendata=FALSE,
control=list(),verbose=0,vb=FALSE,..., ctstanmodel){
if(missing(model)){
if(missing(ctstanmodel)) stop('model must be supplied')
warning('ctstanmodel argument is deprecated, use model instead')
model <- ctstanmodel
} else if(!missing(ctstanmodel)) {
stop('Use only one of model or deprecated ctstanmodel')
}
ctstanmodel <- model
if(!is.na(nopriors)){
warning('nopriors argument is deprecated, use priors argument in future')
priors <- !nopriors
}
if(any(!is.na(derrind))) warning('derrind argment is deprecated, computed automatically now')
datalong <- data.frame(datalong)
if(!ctstanmodel$timeName %in% colnames(datalong) && !ctstanmodel$continuoustime) {
dtable <- data.table(datalong)
dtable[,.ObsCount:=1:.N,by=ctstanmodel$id]
datalong[[ctstanmodel$timeName]] <- dtable[['.ObsCount']]
rm(dtable)
}
datalong <- datalong[order(datalong[[ctstanmodel$subjectIDname]],datalong[[ctstanmodel$timeName]]),] #sort by subject, time.
datavars <- c(ctstanmodel$timeName,ctstanmodel$subjectIDname, ctstanmodel$manifestNames,ctstanmodel$TDpredNames,ctstanmodel$TIpredNames)
sapply(datavars,function(x){
if(!x %in% colnames(datalong)) stop(paste0(x,' column not found in data!'))
if(!x %in% ctstanmodel$subjectIDname){ #if not an id column
if(any(!is.numeric(as.numeric(datalong[!is.na(datalong[,x]),x])))) stop(x ,' column contains non-numeric data!')
}
})
if(!'ctStanModel' %in% class(ctstanmodel)) stop('not a ctStanModel object')
#set nlcontrol defaults
if(is.null(nlcontrol$maxtimestep)) nlcontrol$maxtimestep = 999999
if(is.null(nlcontrol$Jstep)) nlcontrol$Jstep = 1e-6
args=c(as.list(environment()), list(...)) #as.list((match.call(expand.dots=FALSE)))
args$datalong <- NULL
args$model <- NULL
args$ctstanmodel <- NULL
ctm <- ctstanmodel
if(!is.null(ctm$TIpredAuto) && ctm$TIpredAuto %in% c(1L,TRUE)){ #if auto tipred, set all effects to true
for(tip in ctm$TIpredNames){
ctm$pars[[paste0(tip,'_effect')]] <- TRUE
}
}
if(optimize && !priors) message("Maximum likelihood estimation requested")
if(optimize && priors && (is.null(optimcontrol$is) || optimcontrol$is %in% FALSE)) message("Maximum a posteriori estimation requested")
if(optimize && priors && (!is.null(optimcontrol$is) && optimcontrol$is %in% TRUE)) message("Bayesian estimation via optimization and importance sampling requested")
if(!optimize) message("Bayesian estimation via Stan's NUTS sampler requested")
###stationarity
if(stationary) {
stop('Stationary option temporarily unavailable -- reductions needed to pass all CRAN checks')
ctm$pars$param[ctm$pars$matrix %in% c('T0VAR','T0MEANS')] <- 'stationary'
ctm$pars$value[ctm$pars$matrix %in% c('T0VAR','T0MEANS')] <- NA
ctm$pars$indvarying[ctm$pars$matrix %in% c('T0VAR','T0MEANS')] <- FALSE
}
#collect individual stationary elements and update ctm$pars
if(any(ctm$pars$param %in% 'stationary')) stop('Stationary option temporarily unavailable -- reductions needed to pass all CRAN checks')
ctm$t0varstationary <- as.matrix(rbind(ctm$pars[which(ctm$pars$param %in% 'stationary' & ctm$pars$matrix %in% 'T0VAR'),c('row','col')]))
if(nrow(ctm$t0varstationary) > 0){ #ensure upper tri is consistent with lower
for(i in 1:nrow(ctm$t0varstationary)){
if(ctm$t0varstationary[i,1] != ctm$t0varstationary[i,2]) ctm$t0varstationary <- rbind(ctm$t0varstationary,ctm$t0varstationary[i,c(2,1)])
}}
ctm$t0varstationary = unique(ctm$t0varstationary) #remove any duplicated rows
ctm$t0meansstationary <- as.matrix(rbind(ctm$pars[which(ctm$pars$param[ctm$pars$matrix %in% 'T0MEANS'] %in% 'stationary'),c('row','col')]))
ctm$pars$value[ctm$pars$param %in% 'stationary'] <- -99 #does this get inserted?
ctm$pars$indvarying[ctm$pars$param %in% 'stationary'] <- FALSE
ctm$pars$transform[ctm$pars$param %in% 'stationary'] <- NA
ctm$pars$param[ctm$pars$param %in% 'stationary'] <- NA
if(length(unique(datalong[,ctm$subjectIDname]))==1 && any(ctm$pars$indvarying[is.na(ctm$pars$value)]==TRUE)){
# is.null(ctm$fixedrawpopmeans) && is.null(ctm$fixedsubpars) & is.null(ctm$forcemultisubject)) {
ctm$pars$indvarying <- FALSE
message('Individual variation not possible as only 1 subject! indvarying set to FALSE on all parameters')
}
if(length(unique(datalong[,ctm$subjectIDname]))==1 & any(is.na(ctm$pars$value[ctm$pars$matrix %in% 'T0VAR']))){
# is.null(ctm$fixedrawpopmeans) & is.null(ctm$fixedsubpars) & is.null(ctm$forcemultisubject)) {
for(ri in 1:nrow(ctm$pars)){
if(is.na(ctm$pars$value[ri]) && ctm$pars$matrix[ri] %in% 'T0VAR'){
ctm$pars$value[ri] <- ifelse(ctm$pars$row[ri] == ctm$pars$col[ri], 1e-3, 0)
}
}
message('Free T0VAR parameters fixed to diagonal matrix of 0.001 as only 1 subject - consider appropriateness!')
}
if(binomial){
message('Binomial argument deprecated -- in future set manifesttype in the model object to 1 for binary indicators')
intoverstates <- FALSE
ctm$manifesttype[] <- 1
}
recompile <- FALSE
if(!optimize && !priors){
message('HMC sampling requested, but priors disabled -- are you sure? consider setting priors=TRUE')
# !priors <- FALSE
}
if(optimize && !intoverstates) warning('intoverstates=TRUE required for sensible optimization! Proceed onwards to weird output at own risk!')
if(intoverpop == 'auto') intoverpop <-
ifelse(optimize && any(ctm$pars$indvarying[is.na(ctm$pars$value)]),TRUE,FALSE)
# if(optimize && !intoverpop && any(ctm$pars$indvarying[is.na(ctm$pars$value)]) &&
# is.null(ctm$fixedrawpopchol) && is.null(ctm$fixedsubpars)){
# intoverpop <- TRUE
# message('Setting intoverpop=TRUE to enable optimization of random effects...')
# }
# if(intoverpop==TRUE && !any(ctm$pars$indvarying[is.na(ctm$pars$value)])) {
# # message('No individual variation -- disabling intoverpop switch');
# intoverpop <- FALSE
# }
ctm <- ctModel0DRIFT(ctm, ctm$continuoustime) #offset 0 drift
ctm$pars <- ctModelStatesAndPARS(ctm$pars,statenames = ctm$latentNames,tdprednames=ctm$TDpredNames) #replace latent states and PARS with state and PAR[] refs, need this early because we rely on [] detection
if(intoverpop) ctm <- ctStanModelIntOverPop(ctm) #extend system matrices for individual differences
# #check this *after* replacing PARS references as needed
# if(any(duplicated(ctm$pars$param[ctm$pars$matrix %in% 'T0MEANS' &
# !grepl('[',ctm$pars$param,fixed=TRUE) &
# !is.na(ctm$pars$param)]))) stop(paste0(
# 'Unfortunately, duplicate T0MEANS parameters must be specified via inclusion of additional PARS matrix in ctModel: e.g.,
# ctModel(... #regular model code
# PARS=c("t0mPar||TRUE"), #specify an additional parameter called t0mPar, with random effects
# T0MEANS=c("t0mPar","t0mPar"), #insert this parameter into the T0MEANS matrix as many times as needed.
# ... #regular model code)
# '))
#jacobian addition
ctm$jacobian <- try(ctJacobian(ctm))
if('try-error' %in% class(ctm$jacobian)) ctm$jacobian <- ctJacobian(ctm,simplify=FALSE)
# ctm$jacobian <- unfoldmats( #replaces matrix references with base parameter
# c(listOfMatrices(ctm$pars),ctm$jacobian))
ctm$jacobian <- ctm$jacobian[names(ctStanMatricesList()$jacobian)]
jl <- ctModelUnlist(ctm$jacobian,names(ctm$jacobian))
jl <- jl[apply(jl,1,function(x) any(!is.na(x))),] #clean up messy leftovers of NA's
jl2 <- as.data.frame(rbind(data.table(ctm$pars[1,]),data.table(jl),fill=TRUE))[-1,]
for(i in 1:nrow(jl2)){ #copy base parameter transforms etc to jacobian when needed
if(!is.na(jl2$param[i]) && jl2$param[i] %in% ctm$pars$param){
jl2[i, !colnames(jl2) %in% list('matrix','row','col')] <-
ctm$pars[which(ctm$pars$param %in% jl2$param[i])[1], !colnames(ctm$pars) %in% list('matrix','row','col')]
}
}
ctm$pars <- rbind(ctm$pars,jl2)
ctm$pars <- ctModelStatesAndPARS(ctm$pars,statenames = ctm$latentNames,tdprednames=ctm$TDpredNames) #replace any new state and par refs with square bracket refs
ctm <- ctModelTransformsToNum(ctm)
ctm$pars <- ctStanModelCleanctspec(ctm$pars)
ctm <- T0VARredundancies(ctm)
if(!all(ctm$pars$transform[!is.na(suppressWarnings(as.integer(ctm$pars$transform)))] %in% c(0,1,2,3,4))) stop('Unknown transform specified -- integers should be 0 to 4')
#fix binary manifestvariance
if(any(ctm$manifesttype > 0)){ #if any non continuous variables, (with free parameters)...
errfix <- which(ctm$pars$matrix %in% 'MANIFESTVAR' &
(ctm$pars$row %in% which(ctm$manifesttype==1) |
ctm$pars$col %in% which(ctm$manifesttype==1)) &
is.na(suppressWarnings(as.numeric(
ctm$pars$value))))
if(length(errfix) > 0){
message('Fixing any free MANIFESTVAR parameters for binary indicators to deterministic calculation')
ctm$pars$value[errfix] <- 1e-5
ctm$pars[errfix,c('param','transform','multiplier','offset','meanscale','inneroffset','sdscale')] <- NA
ctm$pars$indvarying[errfix] <- FALSE
}}
ctm$modelmats <- ctStanModelMatrices(ctm) #slow!
ctm <- ctStanCalcsList(ctm,save=saveComplexPars) #get extra calculations and adjust model spec as needed???
#store values in ctm
ctm$intoverpop <- as.integer(intoverpop)
ctm$nlatentpop <- as.integer(ifelse(ctm$intoverpop ==1, max(ctm$pars$row[ctm$pars$matrix %in% 'T0MEANS']), ctm$n.latent))
ctm$intoverstates <- as.integer(intoverstates)
ctm$priors <- as.integer(priors)
ctm$stationary <- as.integer(stationary)
ctm$nlcontrol <- nlcontrol
#recompile checks
if(forcerecompile) recompile <- TRUE
if(naf(!is.na(ctm$rawpopsdbaselowerbound))) recompile <- TRUE
if(ctm$rawpopsdbase != 'normal(0,1)') recompile <- TRUE
if(ctm$rawpopsdtransform != 'log1p_exp(2*rawpopsdbase-1) .* sdscale') ctm$recompile <- TRUE
if(any(ctm$modelmats$matsetup[,'transform'] < -10)) recompile <- TRUE #if custom transforms needed
ncalcsNoJ<- length(unlist(ctm$modelmats$calcs)[!grepl('JAx[',unlist(ctm$modelmats$calcs),fixed=TRUE)])
if(ncalcsNoJ > 0) recompile <- TRUE
if(!recompile &&
length(unlist(ctm$modelmats$calcs)[!grepl('JAx[',unlist(ctm$modelmats$calcs),fixed=TRUE)])>0)
message('Finite difference jacobian used to avoid recompiling -- use forcerecompile=TRUE for analytic jacobians')
#further model adjustments conditional on recompile
if(!recompile){ #then use finite diffs for some elements
#collect row and column of complicated jacobian elements into vector
ctm$JAxfinite <- array(as.integer(unique(
unlist(ctm$modelmats$matsetup[ctm$modelmats$matsetup$matrix %in% 52 &
ctm$modelmats$matsetup$when == -999, 'col']))))# &
# ctm$modelmats$matsetup$copyrow < 1,c('row','col')]))))
ctm$Jyfinite <- array(as.integer(unique(
unlist(ctm$modelmats$matsetup[ctm$modelmats$matsetup$matrix %in% 54 &
ctm$modelmats$matsetup$when == -999, 'col']))))
}
if(recompile) ctm$JAxfinite <- ctm$Jyfinite <- array(as.integer(c()))
ctm$recompile <- recompile
standata <- ctStanData(ctm,datalong,optimize=optimize, sameInitialTimes=sameInitialTimes) #bit slow
standata$verbose=as.integer(verbose)
standata$savesubjectmatrices=as.integer(savesubjectmatrices)
standata$gendata=as.integer(gendata)
if(standata$savesubjectmatrices==1L) savescores = TRUE
standata$savescores=as.integer(savescores)
# print(standata$savesubjectmatrices)
#####post model / data checks
if(cores=='maxneeded') cores=max(1,min(c(chains,parallel::detectCores()-1)))
if(is.logical(stanmodeltext)) {
stanmodeltext<- ctStanModelWriter(ctm, gendata, ctm$modelmats$extratforms,ctm$modelmats$matsetup)
}
if(fit){
# if(gendata && stanmodels$ctsmgen@model_code != stanmodeltext) recompile <- TRUE
# if(!gendata && paste0(stanmodels$ctsm@model_code) != paste0(stanmodeltext)) recompile <- TRUE
# STAN_NUM_THREADS <- Sys.getenv('STAN_NUM_THREADS',unset=NA)
# Sys.setenv(STAN_NUM_THREADS=cores)
if(recompile || forcerecompile) {
message('Compiling model...')
#r4.2 / windows / old rstan check
if(.Platform$OS.type=="windows" && R.version$major %in% 4 && as.numeric(R.version$minor) >= 2 &&
unlist(utils::packageVersion('rstan'))[2] < 25){
stop('
*****
Compiling not possible with R version 4.2+ on Windows with Rstan version < 2.26
To upgrade rstan, close and restart all R sessions then run:
install.packages("StanHeaders", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))
install.packages("rstan", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))
*****')
# a=readline('Attempt to upgrade Rstan from Stan repository? y/n')
# if(a %in% c('yes','y','Y','Yes','YES')){
# message(
# install.packages("StanHeaders", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))
# install.packages("rstan", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))
# }
}
compileArgs$model_name='ctsem'
compileArgs$model_code=stanmodeltext
compileArgs$auto_write=TRUE
sm <- do.call(stan_model,compileArgs)
# ,allow_undefined = TRUE,verbose=TRUE,
# includes = paste0(
# '\n#include "', file.path(getwd(), 'syl2.hpp'),'"',
# '\n')
if(saveCompile){
if(exists(x = 'ctsem.compiled',envir= parent.frame())
&& !'stanmodel' %in% class(get('ctsem.compiled',envir = parent.frame()))){
warning('ctsem.compiled object already exists, not saving compile')
} else assign(x = 'ctsem.compiled',sm,envir = parent.frame())
}
}
if(!recompile && !forcerecompile) {
if(!gendata) sm <- stanmodels$ctsm else sm <- stanmodels$ctsmgen
}
# configure inits ---------------------------------------------------------
initOptim <- (length(inits)==1 && (inits=='optimize' || inits=='Optimize' || inits=='optimise' || inits=='Optimise'))
if(optimize || initOptim){ #then set optimcontrol list
optimcontrol$cores <- cores
optimcontrol$verbose <- verbose
optimcontrol$priors <- as.logical(priors)
optimcontrol$standata=standata
optimcontrol$sm=sm
optimcontrol$init=inits
optimcontrol$plot=plot
optimcontrol$matsetup <- data.frame(ctm$modelmats$matsetup)
}
if(!optimize && !is.null(inits)){
if('list' %in% class(inits)){
staninits=inits
} else {
if(initOptim){ #then first optimize to get inits
if(!intoverpop && length(unique(datalong[[ctm$subjectIDname]]) > 1) && any(ctm$pars$indvarying)) stop('Cannot optimize to get inits unless intoverpop=TRUE')
optimcontrol$init <- NULL
optimcontrol$tol=1e-7
if(!intoverpop & ! intoverstates) stop('Cannot initialize with optimization unless intoverpop and intoverstates are set to TRUE')
inits <- do.call(stanoptimis,optimcontrol)$rawest
}
sf <- stan_reinitsf(sm,standata)
staninits <- list()
if(chains > 1){ #set all chains to same inits
for(i in 1:chains){
staninits[[i]]<-constrain_pars(sf,inits+rnorm(length(inits),0,.01))
}
}
}
}
if(!optimize){
#control arguments for rstan
# if(is.null(control$adapt_term_buffer)) control$adapt_term_buffer <- min(c(iter/10,max(iter-20,75)))
if(is.null(control$adapt_delta)) control$adapt_delta <- .8
if(is.null(control$adapt_window)) control$adapt_window <- 5
if(is.null(control$max_treedepth)) control$max_treedepth <- 10
if(is.null(control$adapt_init_buffer)) control$adapt_init_buffer=2
if(is.null(control$stepsize)) control$stepsize=.001
if(is.null(control$metric)) control$metric='diag_e'
message('Sampling...')
#
stanargs <- list(object = sm,
init_r=.03,
save_warmup=as.logical(plot),
refresh=20,
iter=iter,
data = standata, chains = chains, control=control,
cores=cores,
...)
if(!is.null(inits)) stanargs$init=staninits
if(vb){
if(!intoverpop && standata$nindvarying > 0) warning('Poor results are expected with variational inference and sampling individual differences! Suggest disabling vb or enabling intoverpop.')
stanfit <- list(stanfit=rstan::vb(object = sm,data=standata, importance_resampling=TRUE,tol_rel_obj=1e-3))
} else{ #if not vi
if(plot==TRUE) stanfit <- suppressWarnings(list(stanfit=do.call(stanWplot,stanargs))) else stanfit <- suppressWarnings(list(stanfit=do.call(sampling,stanargs)))
#find the median sample and compute kalman scores etc for this
# browser()
e=rstan::extract(stanfit$stanfit)
# middle <- which(abs(e$ll-quantile(e$ll,.5)) == min(abs(e$ll-quantile(e$ll,.5) )))
# middle <- which(e$ll==max(e$ll))
stanfit$rawposterior <- t(stan_unconstrainsamples(fit = stanfit$stanfit,standata = standata))
stanfit$rawest <- apply(stanfit$rawposterior,2,median)
}
}
if(optimize==TRUE) {
stanfit <- do.call(stanoptimis,optimcontrol) #eval(parse(text=opcall))
#update data that may have changed during optimization
for(ni in names(stanfit$standata)){
standata[[ni]] <- stanfit$standata[[ni]]
}
if(ctm$n.TIpred>0){
ctm$modelmats$TIPREDEFFECTsetup <- stanfit$standata$TIPREDEFFECTsetup
ms <- ctm$modelmats$matsetup
ms$tipred <- 0L
parswithtipreds <- sort(unique(ms$param[ms$param >0 & ms$when %in% c(0,-1) & ms$copyrow < 1]))
parswithtipreds<-parswithtipreds[apply(stanfit$standata$TIPREDEFFECTsetup,1,sum)>0]
ms$tipred[ms$param >0 & ms$when %in% c(0,-1) & ms$copyrow < 1 & ms$param %in% parswithtipreds] <- 1L
ctm$modelmats$matsetup <- ms
}
}
# if(is.na(STAN_NUM_THREADS)) Sys.unsetenv('STAN_NUM_THREADS') else Sys.setenv(STAN_NUM_THREADS = STAN_NUM_THREADS) #reset sys env
} # end if fit==TRUE
#convert missings back to NA's for data output
standataout<-standata
standataout$Y[standataout$Y==99999] <- NA
standataout$tipreds[standataout$tipreds==99999] <- NA
# standataout <- utils::relist((standataout),skeleton=standata)
setup=list(recompile=recompile,idmap=standata$idmap,matsetup=ctm$modelmats$matsetup,matvalues=ctm$modelmats$matvalues,
popsetup=ctm$modelmats$matsetup[ctm$modelmats$matsetup$when %in% c(0,-1) & ctm$modelmats$matsetup$param > 0,],
popvalues=ctm$modelmats$matvalues[ctm$modelmats$matsetup$when %in% c(0,-1) & ctm$modelmats$matsetup$param > 0,],
extratforms=ctm$modelmats$extratforms)
if(fit) {
stanfit$transformedparsfull <- suppressMessages(stan_constrainsamples(sm = sm,standata = standata,
savesubjectmatrices = TRUE, samples = matrix(stanfit$rawest,1),cores=1,savescores=TRUE,pcovn=5000))
out <- list(args=args,
setup=setup,
stanmodeltext=stanmodeltext, data=standataout, ctdatastruct=datalong[c(1,nrow(datalong)),],standata=standata,
ctstanmodelbase=ctstanmodel, ctstanmodel=ctm,stanmodel=sm, stanfit=stanfit)
class(out) <- 'ctStanFit'
out$stanfit$kalman<-suppressMessages(ctKalmanArray(out,pointest = TRUE))
}
if(!fit) out=list(args=args,setup=setup,
stanmodeltext=stanmodeltext,data=standataout, ctdatastruct=datalong[c(1,nrow(datalong)),],standata=standata,
ctstanmodelbase=ctstanmodel, ctstanmodel=ctm)
return(out)
}
#' Backward-compatible alias for \code{ctFit}.
#' @rdname ctFit
#' @export
ctStanFit <- ctFit
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