CRAN Package Check Results for Package hhsmm

Last updated on 2024-05-02 01:57:01 CEST.

Flavor	Version	Tinstall	Tcheck	Ttotal	Status	Flags
r-devel-linux-x86_64-debian-clang	0.3.6	21.04	194.48	215.52	NOTE
r-devel-linux-x86_64-debian-gcc	0.3.6	16.26	137.12	153.38	NOTE
r-devel-linux-x86_64-fedora-clang	0.3.7			262.09	OK
r-devel-linux-x86_64-fedora-gcc	0.3.7			251.12	OK
r-devel-windows-x86_64	0.3.6	21.00	155.00	176.00	NOTE
r-patched-linux-x86_64	0.3.6	13.95	182.29	196.24	NOTE
r-release-linux-x86_64	0.3.6	16.72	180.69	197.41	NOTE
r-release-macos-arm64	0.3.7			59.00	OK
r-release-macos-x86_64	0.3.7			111.00	OK
r-release-windows-x86_64	0.3.6	21.00	158.00	179.00	NOTE
r-oldrel-macos-arm64	0.3.7			72.00	OK
r-oldrel-macos-x86_64	0.3.7			115.00	OK
r-oldrel-windows-x86_64	0.3.6	28.00	194.00	222.00	OK

Check Details

Version: 0.3.6
Check: Rd files
Result: NOTE 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 } | ^ Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-windows-x86_64