diff --git a/man/anonymise.Rd b/man/anonymise.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..d6ed8946f289aa4f9254943c3fd45223055605fb
--- /dev/null
+++ b/man/anonymise.Rd
@@ -0,0 +1,37 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/markov.R
+\name{anonymise}
+\alias{anonymise}
+\alias{anonymise.vocaldia}
+\alias{anonymise.default}
+\title{anonymise: anonymise a vocalisation diagram}
+\usage{
+anonymise(vd)
+
+\method{anonymise}{vocaldia}(vd)
+
+\method{anonymise}{default}(vd)
+}
+\arguments{
+\item{vd}{a vocalisation diagram (vocaldia object)}
+}
+\value{
+a new vocaldia with speaker names replaced by variables
+    \eqn{s_1,...,s_n} s.t. \eqn{s_1} is the speaker who spoke the least
+    and \eqn{s_n} the one who did the most talking.
+}
+\description{
+Anonymise a vocalisation diagram
+}
+\details{
+"anonymise" a \code{vocaldia} turn taking probability matrix by
+replacing speaker names by variables \eqn{s_1,...,s_n$ s.t. $s_1} is
+the speaker who spoke the least and \eqn{s_n} the one who did the most
+talking.
+}
+\examples{
+data(vocdia)
+x2 <- getSampledVocalMatrix(subset(atddia, id=='Abbott_Maddock_01'),
+                            individual=TRUE, nodecolumn='speaker')
+anonymise(x2)
+}
diff --git a/man/atddia.Rd b/man/atddia.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..9f192476998c978aa55ee241926984ce599a25ae
--- /dev/null
+++ b/man/atddia.Rd
@@ -0,0 +1,33 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/vocalgraphs.R
+\docType{data}
+\name{atddia}
+\alias{atddia}
+\title{A sample Medical Team Meeting dialogue encoded as a vocaldia}
+\format{A data frame with 7869 rows and 7 variables:
+\describe{
+  \item{id}{The dialogue indentifier}
+  \item{begin}{The start time of a speech turn or silence interval}
+  \item{end}{The end time of a speech turn or silence interval}
+  \item{speaker}{An identifier for the speaker of the turn, or Floor for silence.}
+  \item{role}{The speaker's role (patient, interviewer, other, or Floor}
+  \item{trans}{The transcription of the turn (blanked out for anonymity)}
+  \item{dx}{The diagnosis (ad or nonad}
+ }}
+\source{
+This dataset was generated from the Carolina Conversations
+    Collection, and used in the work described in De La Fuente,
+    Albert and Luz:
+    "Detecting cognitive decline through dialogue processing",
+    2017. For the full data set, please contact the Medical
+    University of South Carolina (MUSC)
+    http://carolinaconversations.musc.edu/
+}
+\usage{
+atddia
+}
+\description{
+A dataset containing 38 dialogues (17 control patients, and 21 AD
+patients) and 7869 vocalisation events.
+}
+\keyword{datasets}
diff --git a/man/getEntropy.Rd b/man/getEntropy.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..98a0f450f185500870131a331327427d5f61432d
--- /dev/null
+++ b/man/getEntropy.Rd
@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/markov.R
+\name{getEntropy}
+\alias{getEntropy}
+\title{getEntropy: safely return the Shannon entropy of a distribution.}
+\usage{
+getEntropy(distribution)
+}
+\arguments{
+\item{distribution}{a probability distribution.}
+}
+\value{
+a numeric value.
+}
+\description{
+Compute the entropy of a distribution.
+}
+\details{
+Compute the entropy of a distribution.
+}
diff --git a/man/getPauseType.Rd b/man/getPauseType.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..b7345f38964f7051fcc777eff95d10b3bf17a883
--- /dev/null
+++ b/man/getPauseType.Rd
@@ -0,0 +1,39 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/vocalgraphs.R
+\name{getPauseType}
+\alias{getPauseType}
+\title{getPauseType: name pause type between two vocalisation events.}
+\usage{
+getPauseType(prevspeaker, nextspeaker)
+}
+\arguments{
+\item{prevspeaker}{speaker of the vocalisation immediately before Floor}
+
+\item{nextspeaker}{speaker of the vocalisation immediately after Floor}
+}
+\value{
+the pause type.
+}
+\description{
+Identify the type of pause between vocalisations.
+}
+\details{
+The type of pause a 'Floor' (silence) event represents can be:
+'Pause', 'SwitchingPause', 'GrpPause', or 'GrpSwitchingPause'. See
+(Luz, 2013) for details.
+}
+\examples{
+getPauseType('a', 'b')
+ ## [1]  "SwitchingPause"
+getPauseType('a', 'Grp')
+ ## [1]  "SwitchingPause"
+getPauseType('Grp', 'Grp')
+ ## [1]  "GrpPause"
+getPauseType('Grp', 'a')
+ ## [1]  "GrpSwitchingPause"
+getPauseType('a', 'a')
+ ##[1] "Pause"
+}
+\seealso{
+\code{\link{namePauses}}
+}
diff --git a/man/getPofAgivenB.Rd b/man/getPofAgivenB.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..9b39356462880becae780743ac88b21ada8ec7cd
--- /dev/null
+++ b/man/getPofAgivenB.Rd
@@ -0,0 +1,25 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/markov.R
+\name{getPofAgivenB}
+\alias{getPofAgivenB}
+\title{getPofAgivenB: transtion probability.}
+\usage{
+getPofAgivenB(a, b, ttarray)
+}
+\arguments{
+\item{a}{target node}
+
+\item{b}{source node}
+
+\item{ttarray}{adjacency matrix}
+}
+\value{
+a transition probability.
+}
+\description{
+Conditional (transition ) probability
+}
+\details{
+Retrieve \eqn{p(a|b)}, probability of a transition from b to a in an
+adjacency matrix
+}
diff --git a/man/getSampledVocalCountMatrix.Rd b/man/getSampledVocalCountMatrix.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..6ac13d20b763511120694475eb0aea5c6c64064e
--- /dev/null
+++ b/man/getSampledVocalCountMatrix.Rd
@@ -0,0 +1,60 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/vocalgraphs.R
+\name{getSampledVocalCountMatrix}
+\alias{getSampledVocalCountMatrix}
+\title{getSampledVocalCountMatrix: generate vocalisation diagrams}
+\usage{
+getSampledVocalCountMatrix(cdf, rate = 1, individual = FALSE,
+  noPauseTypes = FALSE, begin = "begin", end = "end",
+  nodecolumn = "role")
+}
+\arguments{
+\item{cdf}{a data frame consisting, minimally, of a column for
+vocalisation/pause start times, a column for end times, and a
+column identifying the speaker, speaker role or 'Floor' (for
+silences).}
+
+\item{rate}{the rate at which to sample the vocalisation events
+(in seconds)}
+
+\item{individual}{whether to include individual speakers or group
+them into a single Vocalisation node}
+
+\item{noPauseTypes}{if TRUE, ignore distinctions between pauses
+(SwitchingPause, GrpSwitchingPause, etc)}
+
+\item{begin}{the name of the column containing the start time of
+the vocalisation event in a row.}
+
+\item{end}{the name of the column containing the end time of the
+vocalisation event in the same row.}
+
+\item{nodecolumn}{the name of the column containing the node
+(speaker) name (e.g. 'speaker', 'role').}
+}
+\value{
+a vocaldia object, consisting of a vocalisation matrix
+    (vocmatrix) where cell <m,n> contains the counts of
+    transitions from node n to node m, and a table of prior
+    probabilities (stationary distribution) per node.
+}
+\description{
+Generate a count vocalisation diagram through 'sampling'.
+}
+\details{
+A vocalisation diagram (vocaldia) is a representation of a
+dialogue as a Markov process whose cell <m,n> contains the
+transition probability from node n to node m). This function for
+'cases' (an identifier for a case or a vector of identifiers
+identifying a set of cases) in data frame 'df', obtained by
+sampling the timeline every 'rate'-th second (see
+getSampledVocalCountMatrix).
+}
+\examples{
+data(vocdia) 
+getSampledVocalCountMatrix(subset(atddia,
+     id=='Abbott_Maddock_01'), nodecolumn='role')
+}
+\seealso{
+(Luz, 2013)
+}
diff --git a/man/getSampledVocalMatrix.Rd b/man/getSampledVocalMatrix.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..441d4b385b4969cc79be87809e1f60fdbd62dcd3
--- /dev/null
+++ b/man/getSampledVocalMatrix.Rd
@@ -0,0 +1,49 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/vocalgraphs.R
+\name{getSampledVocalMatrix}
+\alias{getSampledVocalMatrix}
+\title{getSampledVocalCountMatrix: generate vocalisation diagrams}
+\usage{
+getSampledVocalMatrix(df, ...)
+}
+\arguments{
+\item{df}{a data frame consisting, minimally, of a column for
+vocalisation/pause start times, a column for end times, and a
+column identifying the speaker, speaker role or 'Floor' (for
+silences).}
+
+\item{...}{general parameter to be passed to
+\code{\link{getSampledVocalCountMatrix}}}
+}
+\value{
+a vocaldia object, consisting of a vocalisation matrix
+    (vocmatrix) where cell <m,n> contains the transition
+    probability from node n to node m, and a table of prior
+    probabilities (stationary distribution) per node.
+}
+\description{
+Generate a probabilistic vocalisation diagram through 'sampling'.
+}
+\details{
+A vocalisation diagram (vocaldia) is a representation of a
+dialogue as a Markov process whose cell <m,n> contains the
+transition probability from node n to node m).
+}
+\examples{
+data(vocdia) 
+getSampledVocalMatrix(subset(atddia,
+         id=='Abbott_Maddock_01'),nodecolumn='speaker', individual=TRUE)
+}
+\references{
+S. Luz. Automatic identification of experts and performance
+  prediction in the multimodal math data corpus through analysis
+  of speech interaction. In \emph{Proceedings of the 15th ACM on
+  International Conference on Multimodal Interaction, ICMI'13},
+  pages 575--582, New York, NY, USA, 2013. ACM.
+}
+\seealso{
+\code{\link{getSampledVocalCountMatrix}}
+}
+\author{
+Saturnino Luz  \email{luzs@acm.org}
+}
diff --git a/man/getTurnTakingMatrix.Rd b/man/getTurnTakingMatrix.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..d19ff2175acb140e662fca119341d9d04b8d4da0
--- /dev/null
+++ b/man/getTurnTakingMatrix.Rd
@@ -0,0 +1,62 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/vocalgraphs.R
+\name{getTurnTakingMatrix}
+\alias{getTurnTakingMatrix}
+\title{getSampledVocalCountMatrix: generate vocalisation diagrams}
+\usage{
+getTurnTakingMatrix(df, begin = "begin", end = "end", nodecolumn = "role",
+  individual = FALSE, noPauseTypes = FALSE)
+}
+\arguments{
+\item{df}{a data frame consisting, minimally, of a column for
+vocalisation/pause start times, a column for end times, and a
+column identifying the speaker, speaker role or 'Floor' (for
+silences).}
+
+\item{begin}{the name of the column containing the start time of
+the vocalisation event in a row.}
+
+\item{end}{the name of the column containing the end time of the
+vocalisation event in the same row.}
+
+\item{nodecolumn}{the name of the column containing the node
+(speaker) name (e.g. 'speaker', 'role').}
+
+\item{individual}{whether to include individual speakers or group
+them into a single Vocalisation node}
+
+\item{noPauseTypes}{if TRUE, ignore distinctions between pauses
+(SwitchingPause, GrpSwitchingPause, etc)}
+}
+\value{
+a vocaldia object, consisting of a vocalisation matrix
+    (vocmatrix) where cell <m,n> contains the counts of
+    transitions from node n to node m, and a table of absolute
+    durations of vocalisation events.
+}
+\description{
+Generate a vocalisation diagram with absolute vocalisation durations.
+}
+\details{
+A vocalisation diagram (vocaldia) is a representation of a
+dialogue as a Markov process whose cell <m,n> contains the
+transition probability from node n to node m). Unlike
+\code{\link{getSampledVocalCountMatrix}} this function
+accummulates event durations directly, therefore resulting in no
+self-transitions (in general).
+}
+\examples{
+x <- subset(atddia, id=='Abbott_Maddock_01')
+getTurnTakingMatrix(x)
+getTurnTakingMatrix(x, individual=TRUE)
+}
+\references{
+S. Luz. Automatic identification of experts and performance
+    prediction in the multimodal math data corpus through analysis
+    of speech interaction. In \emph{Proceedings of the 15th ACM on
+    International Conference on Multimodal Interaction, ICMI'13},
+    pages 575--582, New York, NY, USA, 2013. ACM.
+}
+\seealso{
+(Luz, 2013) and \code{\link{getTurnTakingMatrix}}.
+}
diff --git a/man/getTurnTakingProbMatrix.Rd b/man/getTurnTakingProbMatrix.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..005660af3b811ff95fbf1f1eea9784f9139633fe
--- /dev/null
+++ b/man/getTurnTakingProbMatrix.Rd
@@ -0,0 +1,54 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/vocalgraphs.R
+\name{getTurnTakingProbMatrix}
+\alias{getTurnTakingProbMatrix}
+\title{getTurnTakingProbMatrix: create a vocaldia from a
+    data.frame.}
+\usage{
+getTurnTakingProbMatrix(df, individual = FALSE, ...)
+}
+\arguments{
+\item{df}{a data frame consisting, minimally, of a column for
+vocalisation/pause start times, a column for end times, and a
+column identifying the speaker, speaker role or 'Floor' (for
+silences).}
+
+\item{individual}{whether to include individual speakers or group
+them into a single Vocalisation node}
+
+\item{...}{other parameters to be passed to
+\code{\link{getTurnTakingMatrix}}.}
+}
+\value{
+a vocaldia object, consisting of a vocalisation matrix
+    (vocmatrix) where cell \eqn{(m,n)} contains the probabilities \eqn{P(n|m)}
+    transitions to node \eqn{n} from node \eqn{m}, and a table of prior
+    probabilities (stationary distribution) per node.
+}
+\description{
+Convert a data frame into a vocalisation diagram using counts rather than sampling.
+}
+\details{
+Unlike \code{\link{getSampledVocalMatrix}}, this function is based
+on transition counts rather than sampled intervals. As a result,
+where in this version self transitions will always be set to 0
+(since a vocalisation by a speaker is never followed by another
+vocalisation by the same speaker) in the sampled version self
+transitons will usually dominate the distribution, since the
+speaker who is speaking now is very likely to be the one who were
+speaking one second ago.
+}
+\examples{
+x <- subset(atddia, id=='Abbott_Maddock_01')
+getTurnTakingProbMatrix(x)
+getTurnTakingProbMatrix(x, individual=TRUE)
+}
+\seealso{
+(Luz, 2013) and  \code{\link{getTurnTakingMatrix}}.
+
+  S. Luz. Automatic identification of experts and performance
+  prediction in the multimodal math data corpus through analysis
+  of speech interaction. In \emph{Proceedings of the 15th ACM on
+  International Conference on Multimodal Interaction, ICMI'13},
+  pages 575--582, New York, NY, USA, 2013. ACM.
+}
diff --git a/man/getTurnType.Rd b/man/getTurnType.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..77d8c3d288f347216c4f663c7a76212979130a64
--- /dev/null
+++ b/man/getTurnType.Rd
@@ -0,0 +1,40 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/vocalgraphs.R
+\name{getTurnType}
+\alias{getTurnType}
+\title{getTurnType: return type of turn}
+\usage{
+getTurnType(df, i, individual = FALSE, nodecolumn = "speaker",
+  noPauseTypes = F)
+}
+\arguments{
+\item{df}{a data frame consisting, minimally, of a column for
+vocalisation/pause start times, a column for end times, and a
+column identifying the speaker, speaker role or 'Floor' (for
+silences).}
+
+\item{i}{the identifier (index number) whose type will be returned}
+
+\item{individual}{if TRUE, return the identifier, a Pause or Grp}
+
+\item{nodecolumn}{the name of the column containing the node
+(speaker) name (e.g. 'speaker', 'role').}
+
+\item{noPauseTypes}{if TRUE, ignore distinctions between pauses
+(SwitchingPause, GrpSwitchingPause, etc)}
+}
+\value{
+a string containing the turn type or identifier.
+}
+\description{
+Identify turn types
+}
+\details{
+Return one of {Vocalisation, GrpVocalisation, ...} or identifier.
+}
+\examples{
+data(vocdia)
+atddia[1:10,]
+getTurnType(atddia, 3, nodecolumn='role') ## a vocalisation
+getTurnType(atddia, 4, nodecolumn='role') ## a pause
+}
diff --git a/man/identifyGrpVocalisations.Rd b/man/identifyGrpVocalisations.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..2cf27567886b78442d3f484fc5934353bad2b129
--- /dev/null
+++ b/man/identifyGrpVocalisations.Rd
@@ -0,0 +1,27 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/markov.R
+\name{identifyGrpVocalisations}
+\alias{identifyGrpVocalisations}
+\title{identifyGrpVocalisations: replace appropriate vocalisation
+    types}
+\usage{
+identifyGrpVocalisations(vocvector)
+}
+\arguments{
+\item{vocvector}{a character vector containing a sequence of
+vocalisation events}
+}
+\value{
+A vector with all events replaced by the appropriate type
+    identifier.
+}
+\description{
+Identify group vocalisations
+}
+\details{
+Standardise identifier for group vocalisations
+}
+\examples{
+data(vocdia)
+identifyGrpVocalisations(atddia$speaker[1:60])
+}
diff --git a/man/identifyPauses.Rd b/man/identifyPauses.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..1dc1ab94bfc0c2556b51adcf84d183d9db00742d
--- /dev/null
+++ b/man/identifyPauses.Rd
@@ -0,0 +1,27 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/markov.R
+\name{identifyPauses}
+\alias{identifyPauses}
+\title{identifyPauses: label pauses according to type.}
+\usage{
+identifyPauses(vocvector)
+}
+\arguments{
+\item{vocvector}{a character vector containing a sequence of
+vocalisation events}
+}
+\value{
+A vector with all Floor events replaced by the appropriate
+    pause type identifier.
+}
+\description{
+Assign types to the pauses (Floor events) in a sequence
+}
+\details{
+Identify the pauses in a vector as one of the pauses in
+\code{pauseTypes}
+}
+\examples{
+data(vocdia)
+identifyPauses(atddia$speaker[1:60])
+}
diff --git a/man/identifyVocalisations.Rd b/man/identifyVocalisations.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..87e303876f42d1ecb7aa5953018f6d1d1e0c588c
--- /dev/null
+++ b/man/identifyVocalisations.Rd
@@ -0,0 +1,42 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/markov.R
+\name{identifyVocalisations}
+\alias{identifyVocalisations}
+\title{identifyVocalisations: replace appropriate vocalisation
+    types}
+\usage{
+identifyVocalisations(vocvector, idswitchvoc = T)
+}
+\arguments{
+\item{vocvector}{a character vector containing a sequence of
+vocalisation events}
+
+\item{idswitchvoc}{if TRUE distinguise between
+SwitchingVocalisation and Vocalisation.}
+}
+\value{
+A vector with all events replaced by the appropriate type
+    identifier.
+}
+\description{
+Identify switching vocalisations
+}
+\details{
+SwitchingVocalisation is a vocalisation that signals a immediate
+speaker transition; that is, a transition from speaker to
+speaker (as opposed to speaker to Grp or speaker to Pause).
+
+E.g (speakers A, B, C):
+\preformatted{
+AAAAAAAABBBBBBBCCCCCBBBBBPauseBBBBSwitchingPauseAAAAAGrpVocalisation
+       ^      ^    ^    ^        ^                  ^
+       |      |    |    |        |                  |
+       |      |    |    ---------------- Non-SwitchingVocalisation's
+       |      |    |
+       ---------------------> SwitchingVocalisation's
+}
+}
+\examples{
+data(vocdia)
+identifyVocalisations(atddia$speaker[1:60])
+}
diff --git a/man/igraph.vocaldia.Rd b/man/igraph.vocaldia.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..0f31590f450429ad8ae3dfffb456d41ac3be2260
--- /dev/null
+++ b/man/igraph.vocaldia.Rd
@@ -0,0 +1,27 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/markov.R
+\name{igraph.vocaldia}
+\alias{igraph.vocaldia}
+\title{igraph.vocaldia: Create an igraph vocalisation diagram}
+\usage{
+igraph.vocaldia(vd, ...)
+}
+\arguments{
+\item{vd}{a vocalisation diagram}
+
+\item{...}{arguments for the layout algorithm}
+}
+\value{
+an igraph
+}
+\description{
+Create an igraph vocalisation diagram
+}
+\details{
+Create a vocalisation diagram
+}
+\examples{
+data(vocdia)
+igraph.vocaldia(getSampledVocalMatrix(subset(atddia, id=='Abbott_Maddock_01'),
+                  individual=TRUE, nodecolumn='speaker'))
+}
diff --git a/man/matrixExp.Rd b/man/matrixExp.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..6bb8171e5e6d6aa7b12184da5069a158aab41a55
--- /dev/null
+++ b/man/matrixExp.Rd
@@ -0,0 +1,29 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/markov.R
+\name{matrixExp}
+\alias{matrixExp}
+\title{matrixExp: raise matrix to exp.}
+\usage{
+matrixExp(matrix, exp, mmatrix = matrix)
+}
+\arguments{
+\item{matrix}{a matrix}
+
+\item{exp}{the power to which matrix will be raised}
+
+\item{mmatrix}{a placeholder.}
+}
+\value{
+matrix^exp
+}
+\description{
+Matrix exponentials
+}
+\details{
+A (sort of) exponential function for matrix multiplication (to be
+used with \code{\link{staticMatrix}}).
+}
+\examples{
+data(vocdia)
+matrixExp(vocmatrix$ttarray, 3)
+}
diff --git a/man/namePauses.Rd b/man/namePauses.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..cc0b38489a6326939487b74d1d5e1f7e14c23e2e
--- /dev/null
+++ b/man/namePauses.Rd
@@ -0,0 +1,38 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/vocalgraphs.R
+\name{namePauses}
+\alias{namePauses}
+\title{namePauses: name pause types.}
+\usage{
+namePauses(df, nodecolumn = "role")
+}
+\arguments{
+\item{df}{a data frame consisting, minimally, of a column for
+vocalisation/pause start times, a column for end times, and a
+column identifying the speaker, speaker role or 'Floor' (for
+silences).}
+
+\item{nodecolumn}{the name of the column containing the node
+(speaker) name (e.g. 'speaker', 'role').}
+}
+\value{
+a data.frame with pauses in nodecolumn replaced by different pause types.
+}
+\description{
+Replace identified pause pause types in data frame.
+}
+\details{
+replace all 'Floor' speakers in df by 'Pause', 'SwitchingPause'
+etc, and return a new data fame containing pause types in place of
+'Floor' (see markov.R, identifyPauses() for a better
+implementation)
+}
+\examples{
+data(vocdia)
+x <- subset(atddia, id=='Abbott_Maddock_01')
+x[1:15,1:6]
+namePauses(x)[1:15,1:6]
+}
+\seealso{
+\code{\link{identifyPauses}} for a better implementation
+}
diff --git a/man/plot.matrixseries.Rd b/man/plot.matrixseries.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..b4e0b481279b8632f5e30fc591022db679d3c0fa
--- /dev/null
+++ b/man/plot.matrixseries.Rd
@@ -0,0 +1,34 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/markov.R
+\name{plot.matrixseries}
+\alias{plot.matrixseries}
+\title{plotConvergence: plots Markov diagram convergence.}
+\usage{
+\method{plot}{matrixseries}(x, ..., par = list(), interact = F)
+}
+\arguments{
+\item{x}{an object of class matrixseries; a list where the
+\eqn{i^{th}} element corresponds to \eqn{M^i}.}
+
+\item{...}{extra graphics parameters for plot.}
+
+\item{par}{graphic parameters alist}
+
+\item{interact}{if TRUE, pauses the drawing after each node.}
+}
+\value{
+the matrixseries
+}
+\description{
+Visualise  convergence properties of vocalisation graphs
+}
+\details{
+A 'toy' for visualisation of convergence properties of
+vocalisation graphs. Plot the convergence paths of each
+Vocalisation event (i.e. each row-column transition probability,
+grouped by colour according to the inciding node)
+}
+\examples{
+data(vocdia)
+plot(staticMatrix(vocmatrix$ttarray, digits=4, history=TRUE))
+}
diff --git a/man/plot.vocaldia.Rd b/man/plot.vocaldia.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..ad47186af254c7f1b1ce829e50c005964a6093ad
--- /dev/null
+++ b/man/plot.vocaldia.Rd
@@ -0,0 +1,31 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/markov.R
+\name{plot.vocaldia}
+\alias{plot.vocaldia}
+\title{plot.vocaldia}
+\usage{
+\method{plot}{vocaldia}(x, ..., package = "igraph")
+}
+\arguments{
+\item{x}{a vocalisation diagram}
+
+\item{...}{arguments for the layout algorithm}
+
+\item{package}{the package to be used for ploting (igraph
+(default) or Rgraphviz)}
+}
+\value{
+\code{NULL}
+}
+\description{
+Plot a vocalisation diagram
+}
+\details{
+Plot a vocalisation diagram
+}
+\examples{
+data(vocdia)
+require('igraph')
+plot(getSampledVocalMatrix(subset(atddia, id=='Abbott_Maddock_01'),
+                          individual=TRUE, nodecolumn='speaker'))
+}
diff --git a/man/printARFFfile.Rd b/man/printARFFfile.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..56ca8f211da6b9900020f5e490d8863f90920827
--- /dev/null
+++ b/man/printARFFfile.Rd
@@ -0,0 +1,62 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/vocalgraphs.R
+\name{printARFFfile}
+\alias{printARFFfile}
+\title{printARFFfile: Create arff files by creating and flattening vocaldias}
+\usage{
+printARFFfile(df, ids = c(), idcolumn = "id", noPauseTypes = F,
+  sampled = 0, individual = TRUE, nodecolumn = "role",
+  classcolumn = "dx", file = "/tmp/ccc.arff")
+}
+\arguments{
+\item{df}{df a data frame consisting, minimally, of a column for
+vocalisation/pause start times, a column for end times, and a
+column identifying the speaker, speaker role or 'Floor' (for
+silences).}
+
+\item{ids}{Ids of dialogues to generate (as defined in column named idcolumn)}
+
+\item{idcolumn}{the name of the column containing the dialogue id}
+
+\item{noPauseTypes}{if TRUE, ignore distinctions between pauses
+(SwitchingPause, GrpSwitchingPause, etc)}
+
+\item{sampled}{if >0 use \code{\link{getSampledVocalMatrix}} with rate=sampled}
+
+\item{individual}{whether to include individual speakers or group
+them into a single Vocalisation node}
+
+\item{nodecolumn}{the name of the column containing the node
+(speaker) name (e.g. 'speaker', 'role').}
+
+\item{classcolumn}{the name of the column containing the target class (or value).}
+
+\item{file}{name of ARFF file to be generated.}
+}
+\description{
+Generate ARFF files from vocalisation diagrams
+}
+\details{
+Use this function to generate turn-taking diragrams in ARFF format for
+}
+\examples{
+data(vocdia)
+printARFFfile(atddia, individual=TRUE, classcolumn='dx',
+              file='/tmp/test.arff', noPauseTypes=FALSE)
+library("foreign")
+x1 <- read.arff('/tmp/test.arff')
+x1[1:3,]
+## remove empty columns
+x1[,c(unlist(apply(x1[1:(ncol(x1)-1)],2,sum)!=0), TRUE)]
+}
+\references{
+S. Luz. Automatic identification of experts and performance
+  prediction in the multimodal math data corpus through analysis
+  of speech interaction. In \emph{Proceedings of the 15th ACM on
+  International Conference on Multimodal Interaction, ICMI'13},
+  pages 575--582, New York, NY, USA, 2013. ACM.
+}
+\seealso{
+\code{\link{getSampledVocalCountMatrix}},
+    \code{\link{getTurnTakingProbMatrix}}.
+}
diff --git a/man/startmatrix.Rd b/man/startmatrix.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..8fec5f1a724612b4432c73598718cde4c4a54a59
--- /dev/null
+++ b/man/startmatrix.Rd
@@ -0,0 +1,32 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/markov.R
+\name{startmatrix}
+\alias{startmatrix}
+\alias{startmatrix.default}
+\alias{startmatrix.matrixseries}
+\title{startmatrix: return the first matrix of a converging series.}
+\usage{
+startmatrix(mseries)
+
+\method{startmatrix}{default}(mseries)
+
+\method{startmatrix}{matrixseries}(mseries)
+}
+\arguments{
+\item{mseries}{a matrixseries object}
+}
+\value{
+the initial matrix.
+}
+\description{
+Access initital matrix in a \code{matrixseries}
+}
+\details{
+Access initital matrix in a \code{matrixseries}
+}
+\examples{
+data(vocdia)
+x2 <- staticMatrix(vocmatrix$ttarray, digits=4, history=TRUE)
+## original matrix
+ startmatrix(x2)
+}
diff --git a/man/staticMatrix.Rd b/man/staticMatrix.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..d53d0e8ba317eb5a34e08a7016831b7c4bae3a11
--- /dev/null
+++ b/man/staticMatrix.Rd
@@ -0,0 +1,54 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/markov.R
+\name{staticMatrix}
+\alias{staticMatrix}
+\title{staticMatrix Iterate until transition probabilities converge (or give up).}
+\usage{
+staticMatrix(matrix, limit = 1000, digits = 4, history = F)
+}
+\arguments{
+\item{matrix}{an adjecency matrix of trnasition probabilities}
+
+\item{limit}{maximum number of iterations until we give up on
+convergence}
+
+\item{digits}{the number of decimal places to compare}
+
+\item{history}{if TRUE, keep track of all matrix products}
+}
+\value{
+a matrixseries object; that is, a list where each element
+    is either the initial matrix or the product of the two
+    preceding matrices
+}
+\description{
+Compute the stationary distribution for a Markov diagram
+}
+\details{
+Return static matrix (i.e. the stationary distribution) for the
+Markov process represented by the given adjacency matrix. In the
+particular case of vocaldia's, each column should roughly
+correspond to the amount of time a speaker held the floor for).
+Of course, not all Markov chains converge, an example being:
+\preformatted{
+           1
+     /----->-------\
+    A               B
+     \----<--------/
+           1
+
+which gives
+
+.      | 0  1 |             | 0x0+1x1  0x1+1x0|   | 1  0 |
+.  M = | 1  0 |  and  M^2 = | 1x0+0x1  1x1+1x0| = | 0  1 |
+
+}
+}
+\examples{
+data(vocdia)
+x2 <- staticMatrix(vocmatrix$ttarray, digits=4, history=TRUE)
+## original matrix
+round(x2[[1]],3)
+## stationary matrix (M^139)
+round(x2[[length(x2)]],3)
+}
diff --git a/man/toDotNotation.Rd b/man/toDotNotation.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..c21731e1dc569cd9d49b8333e88440ed4ade38cd
--- /dev/null
+++ b/man/toDotNotation.Rd
@@ -0,0 +1,44 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/markov.R
+\name{toDotNotation}
+\alias{toDotNotation}
+\title{toDotNotation: conver vocaldia to graphviz dot notation}
+\usage{
+toDotNotation(vd, individual = T, varsizenode = T, shape = "circle",
+  fontsize = 16, rankdir = "LR", nodeattribs = "fixedsize=true;",
+  comment = "")
+}
+\arguments{
+\item{vd}{a vocalisation diagram}
+
+\item{individual}{if TRUE write individual node names}
+
+\item{varsizenode}{if true set varsizenode in dot}
+
+\item{shape}{node shape}
+
+\item{fontsize}{font size}
+
+\item{rankdir}{direction of ranking (LR, RF etc)}
+
+\item{nodeattribs}{attributes for node}
+
+\item{comment}{comments}
+}
+\value{
+character data containing the diagram in dot format.
+}
+\description{
+Create vocalisation diagram to file in dot (graphviz) notation
+}
+\details{
+Create a vocalisation diagram in dot notation
+}
+\examples{
+data(vocdia)
+toDotNotation(getSampledVocalMatrix(subset(atddia, id=='Abbott_Maddock_01'),
+                                    individual=TRUE, nodecolumn='speaker'))
+}
+\seealso{
+graphviz manual
+}
diff --git a/man/vocmatrix.Rd b/man/vocmatrix.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..f76611d2d19563b408322846ba4d90ff02c67166
--- /dev/null
+++ b/man/vocmatrix.Rd
@@ -0,0 +1,32 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/vocalgraphs.R
+\docType{data}
+\name{vocmatrix}
+\alias{vocmatrix}
+\title{A sample vocalisation matrix}
+\format{A list containing 2 arrayes
+\describe{
+  \item{ttarray}{The vocaldia adjacency matrix}
+  \item{tdarray}{The proportional durations (stationary probabilities) of each event (node)}
+}}
+\source{
+This dataset was generated from the Multomodal Leatrning
+    Analytics dataset, for the eponymous ICMI'13 Grand
+    Challenge. The use these vocaldias were put to is described in
+    Luz (2013). The full dataset and code is available
+    at https://gitlab.scss.tcd.ie/saturnino.luz/icmi-mla-challenge
+}
+\usage{
+vocmatrix
+}
+\description{
+A \code{vocaldia} object containing a 3-speaker dialogue
+}
+\references{
+S. Luz. Automatic identification of experts and performance
+  prediction in the multimodal math data corpus through analysis
+  of speech interaction. In \emph{Proceedings of the 15th ACM on
+  International Conference on Multimodal Interaction, ICMI'13},
+  pages 575--582, New York, NY, USA, 2013. ACM.
+}
+\keyword{datasets}
diff --git a/man/write.vocaldia.Rd b/man/write.vocaldia.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..131875eb487aeb63206a6ac69dbab2ee9dc1f0ef
--- /dev/null
+++ b/man/write.vocaldia.Rd
@@ -0,0 +1,30 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/markov.R
+\name{write.vocaldia}
+\alias{write.vocaldia}
+\title{write.vocaldia}
+\usage{
+write.vocaldia(vd, file = "", ...)
+}
+\arguments{
+\item{vd}{a vocalisation diagram}
+
+\item{file}{name of file to which dot diagram will be written.}
+
+\item{...}{arguments passed on to toDotNotation. If "", write to STDOUT.}
+}
+\value{
+\code{NULL}
+}
+\description{
+Write vocalisation diagram to file in dot (graphviz) notation
+}
+\details{
+Write a vocalisation diagram
+}
+\examples{
+data(vocdia)
+write.vocaldia(getSampledVocalMatrix(subset(atddia, id=='Abbott_Maddock_01'),
+                            individual=TRUE, nodecolumn='speaker'),
+                            file='/tmp/vocdia.dot')
+}