% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/RcppExports.R
\name{createSequenceMatrix}
\alias{createSequenceMatrix}
\alias{markovchainFit}
\title{Function to fit a discrete Markov chain}
\usage{
createSequenceMatrix(
  stringchar,
  toRowProbs = FALSE,
  sanitize = FALSE,
  possibleStates = character()
)

markovchainFit(
  data,
  method = "mle",
  byrow = TRUE,
  nboot = 10L,
  laplacian = 0,
  name = "",
  parallel = FALSE,
  confidencelevel = 0.95,
  confint = TRUE,
  hyperparam = matrix(),
  sanitize = FALSE,
  possibleStates = character()
)
}
\arguments{
\item{stringchar}{It can be a {n x n} matrix or a character vector or a list}

\item{toRowProbs}{converts a sequence matrix into a probability matrix}

\item{sanitize}{put 1 in all rows having rowSum equal to zero}

\item{possibleStates}{Possible states which are not present in the given sequence}

\item{data}{It can be a character vector or a {n x n} matrix or a {n x n} data frame or a list}

\item{method}{Method used to estimate the Markov chain. Either "mle", "map", "bootstrap" or "laplace"}

\item{byrow}{it tells whether the output Markov chain should show the transition probabilities by row.}

\item{nboot}{Number of bootstrap replicates in case "bootstrap" is used.}

\item{laplacian}{Laplacian smoothing parameter, default zero. It is only used when "laplace" method 
is chosen.}

\item{name}{Optional character for name slot.}

\item{parallel}{Use parallel processing when performing Boostrap estimates.}

\item{confidencelevel}{\deqn{\alpha} level for conficence intervals width. 
Used only when \code{method} equal to "mle".}

\item{confint}{a boolean to decide whether to compute Confidence Interval or not.}

\item{hyperparam}{Hyperparameter matrix for the a priori distribution. If none is provided, 
default value of 1 is assigned to each parameter. This must be of size
{k x k} where k is the number of states in the chain and the values
should typically be non-negative integers.}
}
\value{
A list containing an estimate, log-likelihood, and, when "bootstrap" method is used, a matrix 
        of standards deviations and the bootstrap samples. When the "mle", "bootstrap" or "map" method 
        is used, the lower and upper confidence bounds are returned along with the standard error. 
        The "map" method also returns the expected value of the parameters with respect to the 
        posterior distribution.
}
\description{
Given a sequence of states arising from a stationary state, 
 it fits the underlying Markov chain distribution using either MLE (also using a 
 Laplacian smoother), bootstrap or by MAP (Bayesian) inference.
}
\details{
Disabling confint would lower the computation time on large datasets. If \code{data} or \code{stringchar} 
contain \code{NAs}, the related \code{NA} containing transitions will be ignored.
}
\note{
This function has been rewritten in Rcpp. Bootstrap algorithm has been defined "heuristically". 
      In addition, parallel facility is not complete, involving only a part of the bootstrap process.
      When \code{data} is either a \code{data.frame} or a \code{matrix} object, only MLE fit is 
      currently available.
}
\examples{
sequence <- c("a", "b", "a", "a", "a", "a", "b", "a", "b", "a", "b", "a", "a", 
              "b", "b", "b", "a")        
sequenceMatr <- createSequenceMatrix(sequence, sanitize = FALSE)
mcFitMLE <- markovchainFit(data = sequence)
mcFitBSP <- markovchainFit(data = sequence, method = "bootstrap", nboot = 5, name = "Bootstrap Mc")

na.sequence <- c("a", NA, "a", "b")
# There will be only a (a,b) transition        
na.sequenceMatr <- createSequenceMatrix(na.sequence, sanitize = FALSE)
mcFitMLE <- markovchainFit(data = na.sequence)

# data can be a list of character vectors
sequences <- list(x = c("a", "b", "a"), y = c("b", "a", "b", "a", "c"))
mcFitMap <- markovchainFit(sequences, method = "map")
mcFitMle <- markovchainFit(sequences, method = "mle")
}
\references{
A First Course in Probability (8th Edition), Sheldon Ross, Prentice Hall 2010
            
            Inferring Markov Chains: Bayesian Estimation, Model Comparison, Entropy Rate, 
            and Out-of-Class Modeling, Christopher C. Strelioff, James P. Crutchfield, 
            Alfred Hubler, Santa Fe Institute

            Yalamanchi SB, Spedicato GA (2015). Bayesian Inference of First Order Markov Chains. R
            package version 0.2.5
}
\seealso{
\code{\link{markovchainSequence}}, \code{\link{markovchainListFit}}
}
\author{
Giorgio Spedicato, Tae Seung Kang, Sai Bhargav Yalamanchi
}
