checkRd: (-1) additive_reg_mstep.Rd:20: Lost braces
    20 | \item \code{K}{ the degrees of freedom for the B-spline, default is \code{K=5}}
       |               ^
checkRd: (-1) additive_reg_mstep.Rd:21: Lost braces
    21 | \item \code{lambda0}{ the initial value of the smoothing parameter, default is \code{lambda0=0.01}}
       |                     ^
checkRd: (-1) additive_reg_mstep.Rd:22-24: Lost braces
    22 | \item \code{resp.ind}{ a vector of the column numbers of \code{x} which contain response variables. 
       |                      ^
checkRd: (-1) cov.miss.mix.wt.Rd:38: Lost braces
    38 | \item \code{"unbiased"}{ the unbiased estimator is given}
       |                        ^
checkRd: (-1) cov.miss.mix.wt.Rd:39: Lost braces
    39 | \item \code{"ML"}{ the maximum likelihood estimator is given}
       |                  ^
checkRd: (-1) cov.miss.mix.wt.Rd:45: Lost braces
    45 | \item \code{center}{ the weighted mean of \code{x}}
       |                    ^
checkRd: (-1) cov.miss.mix.wt.Rd:46: Lost braces
    46 | \item \code{cov}{ the weighted covariance of \code{x}}
       |                 ^
checkRd: (-1) cov.miss.mix.wt.Rd:47: Lost braces
    47 | \item \code{n.obs}{ the number of observations in \code{x}}
       |                   ^
checkRd: (-1) cov.miss.mix.wt.Rd:48-49: Lost braces
    48 | \item \code{cor}{ the weighted correlation of \code{x}, 
       |                 ^
checkRd: (-1) cov.miss.mix.wt.Rd:50: Lost braces
    50 | \item \code{wt1}{ the state weighs \code{wt1}}
       |                 ^
checkRd: (-1) cov.miss.mix.wt.Rd:51: Lost braces
    51 | \item \code{wt2}{ the mixture component weights \code{wt2}}
       |                 ^
checkRd: (-1) cov.miss.mix.wt.Rd:52: Lost braces
    52 | \item \code{pmix}{ the estimated mixture proportions}
       |                  ^
checkRd: (-1) cov.mix.wt.Rd:32: Lost braces
    32 | \item \code{"unbiased"}{ the unbiased estimator is given}
       |                        ^
checkRd: (-1) cov.mix.wt.Rd:33: Lost braces
    33 | \item \code{"ML"}{ the maximum likelihood estimator is given}
       |                  ^
checkRd: (-1) cov.mix.wt.Rd:39: Lost braces
    39 | \item \code{center}{ the weighted mean of \code{x}}
       |                    ^
checkRd: (-1) cov.mix.wt.Rd:40: Lost braces
    40 | \item \code{cov}{ the weighted covariance of \code{x}}
       |                 ^
checkRd: (-1) cov.mix.wt.Rd:41: Lost braces
    41 | \item \code{n.obs}{ the number of observations in \code{x}}
       |                   ^
checkRd: (-1) cov.mix.wt.Rd:42-43: Lost braces
    42 | \item \code{cor}{ the weighted correlation of \code{x}, 
       |                 ^
checkRd: (-1) cov.mix.wt.Rd:44: Lost braces
    44 | \item \code{wt1}{ the state weighs \code{wt1}}
       |                 ^
checkRd: (-1) cov.mix.wt.Rd:45: Lost braces
    45 | \item \code{wt2}{ the mixture component weights \code{wt2}}
       |                 ^
checkRd: (-1) cov.mix.wt.Rd:46: Lost braces
    46 | \item \code{pmix}{ the estimated mixture proportions}
       |                  ^
checkRd: (-1) dnorm_additive_reg.Rd:21: Lost braces
    21 | \item \code{K}{ the degrees of freedom for the B-spline, default is \code{K=5}}
       |               ^
checkRd: (-1) dnorm_additive_reg.Rd:22-24: Lost braces
    22 | \item \code{resp.ind}{ a vector of the column numbers of \code{x} which contain response variables. 
       |                      ^
checkRd: (-1) hhsmmfit.Rd:31: Lost braces
    31 | \item \code{maxit}{ the maximum number of iterations for the EM algorithm}
       |                   ^
checkRd: (-1) hhsmmfit.Rd:32: Lost braces
    32 | \item \code{lock.transition}{ logical. if TRUE the transition matrix will not be updated through the EM algorithm}
       |                             ^
checkRd: (-1) hhsmmfit.Rd:33: Lost braces
    33 | \item \code{lock.d}{ logical. if TRUE the sojourn probability matrix d will not be updated through the EM algorithm}
       |                    ^
checkRd: (-1) hhsmmfit.Rd:34: Lost braces
    34 | \item \code{lock.init}{ logical. if TRUE the initial probability vector will not be updated through the EM algorithm}
       |                       ^
checkRd: (-1) hhsmmfit.Rd:35: Lost braces
    35 | \item \code{graphical}{ logical. if TRUE a plot of the sojourn probabilities will be plotted through the EM algorithm}
       |                       ^
checkRd: (-1) hhsmmfit.Rd:36: Lost braces
    36 | \item \code{verbose}{ logical. if TRUE the outputs will be printed}
       |                     ^
checkRd: (-1) hhsmmfit.Rd:42: Lost braces
    42 | \item \code{loglike}{ the log-likelihood of the fitted model}
       |                     ^
checkRd: (-1) hhsmmfit.Rd:43: Lost braces
    43 | \item \code{AIC}{ the Akaike information criterion of the fitted model}
       |                 ^
checkRd: (-1) hhsmmfit.Rd:44: Lost braces
    44 | \item \code{BIC}{ the Bayesian information criterion of the fitted model}
       |                 ^
checkRd: (-1) hhsmmfit.Rd:45: Lost braces
    45 | \item \code{model}{ the fitted model}
       |                   ^
checkRd: (-1) hhsmmfit.Rd:46: Lost braces
    46 | \item \code{estep_variables}{ the E step (forward-backward) probabilities of the final iteration of the EM algorithm}
       |                             ^
checkRd: (-1) hhsmmfit.Rd:47: Lost braces
    47 | \item \code{M}{ the maximum duration in each state}
       |               ^
checkRd: (-1) hhsmmfit.Rd:48: Lost braces
    48 | \item \code{J}{ the number of states}
       |               ^
checkRd: (-1) hhsmmfit.Rd:49: Lost braces
    49 | \item \code{NN}{ the vector of sequence lengths}
       |                ^
checkRd: (-1) hhsmmfit.Rd:50: Lost braces
    50 | \item \code{f}{ the emission probability density function}
       |               ^
checkRd: (-1) hhsmmfit.Rd:51: Lost braces
    51 | \item \code{mstep}{ the M step function of the EM algorithm}
       |                   ^
checkRd: (-1) hhsmmfit.Rd:52: Lost braces
    52 | \item \code{yhat}{ the estimated sequence of states}
       |                  ^
checkRd: (-1) initial_cluster.Rd:52: Lost braces
    52 | \item \code{clust.X}{ a list of clustered observations for each sequence and state}
       |                     ^
checkRd: (-1) initial_cluster.Rd:53: Lost braces
    53 | \item \code{mix.clus}{ a list of the clusters for the mixtures for each state}
       |                      ^
checkRd: (-1) initial_cluster.Rd:54: Lost braces
    54 | \item \code{state.clus}{ the exact state clusters of each observation (available if \code{ltr}=FALSE)}
       |                        ^
checkRd: (-1) initial_cluster.Rd:55: Lost braces
    55 | \item \code{nmix}{ the number of mixture components (a vector of positive (non-zero) integers of length \code{nstate})}
       |                  ^
checkRd: (-1) initial_cluster.Rd:56: Lost braces
    56 | \item \code{ltr}{ logical. if TRUE a left to right hidden hybrid Markov/semi-Markov model is assumed}
       |                 ^
checkRd: (-1) initial_cluster.Rd:57: Lost braces
    57 | \item \code{final.absorb}{ logical. if TRUE the final state of the sequence is assumed to be the absorbance state}
       |                          ^
checkRd: (-1) initial_cluster.Rd:58-59: Lost braces
    58 | \item \code{miss}{ logical. if TRUE the \code{train$x} matrix contains missing 
       |                  ^
checkRd: (-1) initial_estimate.Rd:21: Lost braces
    21 | \item \code{emission}{ list the estimated parameterers of the emission distribution}
       |                      ^
checkRd: (-1) initial_estimate.Rd:22: Lost braces
    22 | \item \code{leng}{ list of waiting times in each state for each sequence}
       |                  ^
checkRd: (-1) initial_estimate.Rd:23: Lost braces
    23 | \item \code{clusters}{ the exact clusters of each observation (available if \code{ltr}=FALSE)}
       |                      ^
checkRd: (-1) initial_estimate.Rd:24: Lost braces
    24 | \item \code{nmix}{ the number of mixture components (a vector of positive (non-zero) integers of length \code{nstate})}
       |                  ^
checkRd: (-1) initial_estimate.Rd:25: Lost braces
    25 | \item \code{ltr}{ logical. if TRUE a left to right hidden hybrid Markovian/semi-Markovianmodel is assumed}
       |                 ^
checkRd: (-1) initialize_model.Rd:31: Lost braces
    31 | \item \code{"nonparametric"}{ non-parametric sojourn distribution}
       |                             ^
checkRd: (-1) initialize_model.Rd:32: Lost braces
    32 | \item \code{"nbinom"}{ negative binomial sojourn distribution}
       |                      ^
checkRd: (-1) initialize_model.Rd:33: Lost braces
    33 | \item \code{"logarithmic"}{ logarithmic sojourn distribution}
       |                           ^
checkRd: (-1) initialize_model.Rd:34: Lost braces
    34 | \item \code{"poisson"}{ poisson sojourn distribution}
       |                       ^
checkRd: (-1) initialize_model.Rd:35: Lost braces
    35 | \item \code{"gamma"}{ gamma sojourn distribution}
       |                     ^
checkRd: (-1) initialize_model.Rd:36: Lost braces
    36 | \item \code{"weibull"}{ weibull sojourn distribution}
       |                       ^
checkRd: (-1) initialize_model.Rd:37: Lost braces
    37 | \item \code{"lnorm"}{ log-normal sojourn distribution}
       |                     ^
checkRd: (-1) initialize_model.Rd:38: Lost braces
    38 | \item \code{"auto"}{automatic determination of the sojourn distribution using the chi-square test}
       |                    ^
checkRd: (-1) initialize_model.Rd:46-47: Lost braces
    46 | \item \code{NULL}{ if \code{ltr}=TRUE then \code{semi = c(rep(TRUE,nstate-1),FALSE)}, else 
       |                  ^
checkRd: (-1) initialize_model.Rd:60: Lost braces
    60 | \item \code{init}{ initial probabilities of states}
       |                  ^
checkRd: (-1) initialize_model.Rd:61: Lost braces
    61 | \item \code{transition}{ transition matrix}
       |                        ^
checkRd: (-1) initialize_model.Rd:62: Lost braces
    62 | \item \code{parms.emission}{ parameters of the mixture normal emission (\code{mu}, \code{sigma}, \code{mix.p})}
       |                            ^
checkRd: (-1) initialize_model.Rd:63: Lost braces
    63 | \item \code{sojourn}{ list of sojourn time distribution parameters and its \code{type}}
       |                     ^
checkRd: (-1) initialize_model.Rd:64: Lost braces
    64 | \item \code{dens.emission}{ the emission probability density function}
       |                           ^
checkRd: (-1) initialize_model.Rd:65: Lost braces
    65 | \item \code{mstep}{ the M step function of the EM algorithm}
       |                   ^
checkRd: (-1) initialize_model.Rd:66: Lost braces
    66 | \item \code{semi}{ a logical vector of length nstate with the TRUE associated states are considered as semi-Markovian}
       |                  ^
checkRd: (-1) make_model.Rd:28-29: Lost braces
    28 | \item \code{NULL}{ if \code{ltr}=TRUE then \code{semi = c(rep(TRUE,nstate-1),FALSE)}, else 
       |                  ^
checkRd: (-1) make_model.Rd:36: Lost braces
    36 | \item \code{"nonparametric"}{ non-parametric sojourn distribution}
       |                             ^
checkRd: (-1) make_model.Rd:37: Lost braces
    37 | \item \code{"nbinom"}{ negative binomial sojourn distribution}
       |                      ^
checkRd: (-1) make_model.Rd:38: Lost braces
    38 | \item \code{"logarithmic"}{ logarithmic sojourn distribution}
       |                           ^
checkRd: (-1) make_model.Rd:39: Lost braces
    39 | \item \code{"poisson"}{ poisson sojourn distribution}
       |                       ^
checkRd: (-1) make_model.Rd:40: Lost braces
    40 | \item \code{"gamma"}{ gamma sojourn distribution}
       |                     ^
checkRd: (-1) make_model.Rd:41: Lost braces
    41 | \item \code{"weibull"}{ weibull sojourn distribution}
       |                       ^
checkRd: (-1) make_model.Rd:42: Lost braces
    42 | \item \code{"lnorm"}{ log-normal sojourn distribution}
       |                     ^
checkRd: (-1) make_model.Rd:43: Lost braces
    43 | \item \code{"auto"}{ automatic determination of the sojourn distribution using the chi-square test}
       |                    ^
checkRd: (-1) make_model.Rd:49: Lost braces
    49 | \item \code{init}{ initial probabilities of states}
       |                  ^
checkRd: (-1) make_model.Rd:50: Lost braces
    50 | \item \code{transition}{ transition matrix}
       |                        ^
checkRd: (-1) make_model.Rd:51: Lost braces
    51 | \item \code{parms.emission}{ parameters of the mixture normal emission (\code{mu}, \code{sigma}, \code{mix.p})}
       |                            ^
checkRd: (-1) make_model.Rd:52: Lost braces
    52 | \item \code{sojourn}{ list of sojourn distribution parameters and its \code{type}}
       |                     ^
checkRd: (-1) make_model.Rd:53: Lost braces
    53 | \item \code{dens.emission}{ the emission probability density function}
       |                           ^
checkRd: (-1) make_model.Rd:54: Lost braces
    54 | \item \code{mstep}{ the M step function of the EM algorithm}
       |                   ^
checkRd: (-1) make_model.Rd:55: Lost braces
    55 | \item \code{semi}{ a logical vector of length nstate with the TRUE associated states are considered as semi-Markovian}
       |                  ^
checkRd: (-1) nonpar_mstep.Rd:20: Lost braces
    20 | \item \code{K}{ the degrees of freedom for the B-spline, default is \code{K=5}}
       |               ^
checkRd: (-1) nonpar_mstep.Rd:21: Lost braces
    21 | \item \code{lambda0}{ the initial value of the smoothing parameter, default is \code{lambda0=0.5}}
       |                     ^
checkRd: (-1) predict.hhsmm.Rd:28: Lost braces
    28 | \item \code{"viterbi"}{ (default) uses the Viterbi algorithm for prediction}
       |                       ^
checkRd: (-1) predict.hhsmm.Rd:29: Lost braces
    29 | \item \code{"smoothing"}{ uses the smoothing algorithm for prediction}
       |                         ^
checkRd: (-1) predict.hhsmm.Rd:37-38: Lost braces
    37 | \item \code{"max"}{ (default) the maximum probability as the point predict and the high probability critical
       |                   ^
checkRd: (-1) predict.hhsmm.Rd:39-40: Lost braces
    39 | \item \code{"mean"}{ the mean value as the point predict and the normal confidence lower and upper bounds as the 
       |                    ^
checkRd: (-1) predict.hhsmm.Rd:50: Lost braces
    50 | \item \code{x}{ the observation sequence}
       |               ^
checkRd: (-1) predict.hhsmm.Rd:51: Lost braces
    51 | \item \code{s}{ the predicted state sequence}
       |               ^
checkRd: (-1) predict.hhsmm.Rd:52: Lost braces
    52 | \item \code{N}{ the vector of sequence lengths}
       |               ^
checkRd: (-1) predict.hhsmm.Rd:53: Lost braces
    53 | \item \code{p}{ the state probabilities }
       |               ^
checkRd: (-1) predict.hhsmm.Rd:54: Lost braces
    54 | \item \code{RUL}{ the point predicts of the RUL}
       |                 ^
checkRd: (-1) predict.hhsmm.Rd:55: Lost braces
    55 | \item \code{RUL.low}{ the lower bounds for the prediction intervals of the RUL}
       |                     ^
checkRd: (-1) predict.hhsmm.Rd:56: Lost braces
    56 | \item \code{RUL.up}{ the upper bounds for the prediction intervals of the RUL}
       |                    ^
checkRd: (-1) predict.hhsmmspec.Rd:16: Lost braces
    16 | \item \code{"viterbi"}{ (default) uses the Viterbi algorithm for prediction}
       |                       ^
checkRd: (-1) predict.hhsmmspec.Rd:17: Lost braces
    17 | \item \code{"smoothing"}{ uses the smoothing algorithm for prediction}
       |                         ^
checkRd: (-1) predict.hhsmmspec.Rd:27: Lost braces
    27 | \item \code{x}{ the observation sequence}
       |               ^
checkRd: (-1) predict.hhsmmspec.Rd:28: Lost braces
    28 | \item \code{s}{ the predicted state sequence}
       |               ^
checkRd: (-1) predict.hhsmmspec.Rd:29: Lost braces
    29 | \item \code{N}{ the vector of sequence lengths}
       |               ^
checkRd: (-1) predict.hhsmmspec.Rd:30: Lost braces
    30 | \item \code{p}{ the state probabilities }
       |               ^
checkRd: (-1) predict.hhsmmspec.Rd:31: Lost braces
    31 | \item \code{RUL}{ the point predicts of the RUL}
       |                 ^
checkRd: (-1) predict.hhsmmspec.Rd:32: Lost braces
    32 | \item \code{RUL.low}{ the lower bounds for the prediction intervals of the RUL}
       |                     ^
checkRd: (-1) predict.hhsmmspec.Rd:33: Lost braces
    33 | \item \code{RUL.up}{ the upper bounds for the prediction intervals of the RUL}
       |                    ^
checkRd: (-1) raddreg.Rd:16: Lost braces
    16 | \item \code{mean}{ the mean vector of covariates (to be generated from multivariate normal distribution)}
       |                  ^
checkRd: (-1) raddreg.Rd:17: Lost braces
    17 | \item \code{cov}{ the variance-covariance matrix of covariates (to be generated from multivariate normal distribution)}
       |                 ^
checkRd: (-1) rmixlm.Rd:16: Lost braces
    16 | \item \code{mean}{ the mean vector of covariates (to be generated from multivariate normal distribution)}
       |                  ^
checkRd: (-1) rmixlm.Rd:17: Lost braces
    17 | \item \code{cov}{ the variance-covariance matrix of covariates (to be generated from multivariate normal distribution)}
       |                 ^
checkRd: (-1) simulate.hhsmmspec.Rd:31-32: Lost braces
    31 | \item \code{autoregress}{ logical. if TRUE the auto-regressive data generation will be considered with 
       |                         ^
checkRd: (-1) simulate.hhsmmspec.Rd:33-34: Lost braces
    33 | \item \code{lags}{ a positive integer which is the number of lags to be considered for the 
       |                  ^
checkRd: (-1) simulate.hhsmmspec.Rd:35-39: Lost braces
    35 | \item \code{start}{ a list containing the items \code{mean} which is the mean vector 
       |                   ^
checkRd: (-1) simulate.hhsmmspec.Rd:45: Lost braces
    45 | \item \code{s}{ the vector of states}
       |               ^
checkRd: (-1) simulate.hhsmmspec.Rd:46: Lost braces
    46 | \item \code{x}{ observation matrix}
       |               ^
checkRd: (-1) simulate.hhsmmspec.Rd:47: Lost braces
    47 | \item\code{N}{ vector of sequence lengths}
       |              ^
checkRd: (-1) train_test_split.Rd:25: Lost braces
    25 | \item\code{train}{ the randomly selected subset of train data of class \code{"hhsmmdata"}}
       |                  ^
checkRd: (-1) train_test_split.Rd:26: Lost braces
    26 | \item\code{test}{ the randomly selected subset of test data of class \code{"hhsmmdata"}}
       |                 ^
checkRd: (-1) train_test_split.Rd:27: Lost braces
    27 | \item\code{trimmed}{ right trimmed test subset, if \code{trim}=TRUE, with trim ratios equal to \code{trim.ratio} }
       |                    ^
checkRd: (-1) train_test_split.Rd:28: Lost braces
    28 | \item\code{trimmed.count}{ the number of right trimmed individuals in each sequence of the test subset, if \code{trim}=TRUE }
       |                          ^