minor documentation updates

27 files changed, 136 insertions, 116 deletions

diff --git a/man/armax.Rd b/man/armax.Rd
index fc2388a..a7c92e4 100644
--- a/man/armax.Rd
+++ b/man/armax.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/estpoly.R
 \name{armax}
 \alias{armax}
@@ -11,15 +11,15 @@ armax(x, order = c(0, 1, 1, 0), options = optimOptions())
 
 \item{options}{Estimation Options, setup using \code{\link{optimOptions}}}
 
-\item{order:}{Specification of the orders: the four integer components
-(na,nb,nc,nk) are the order of polynolnomial A, order of polynomial B
+\item{order:}{Specification of the orders: the four integer components 
+(na,nb,nc,nk) are the order of polynolnomial A, order of polynomial B 
 + 1, order of the polynomial C,and the input-output delay respectively}
 }
 \value{
 An object of class \code{estpoly} containing the following elements:
 
 \tabular{ll}{
-   \code{sys} \tab an \code{idpoly} object containing the
+   \code{sys} \tab an \code{idpoly} object containing the 
    fitted ARMAX coefficients \cr
    \code{fitted.values} \tab the predicted response \cr
    \code{residuals} \tab the residuals  \cr
@@ -30,31 +30,31 @@ An object of class \code{estpoly} containing the following elements:
      \code{vcov} \tab the covariance matrix of the fitted coefficients\cr
      \code{sigma} \tab the standard deviation of the innovations
    } \cr
-   \code{options} \tab Option set used for estimation. If no
+   \code{options} \tab Option set used for estimation. If no 
    custom options were configured, this is a set of default options. \cr
    \code{termination} \tab Termination conditions for the iterative
     search used for prediction error minimization.
    \tabular{ll}{
      \code{WhyStop} \tab Reason for termination \cr
      \code{iter} \tab Number of Iterations \cr
-     \code{iter} \tab Number of Function Evaluations
-   }
+     \code{iter} \tab Number of Function Evaluations 
+   }  
  }
 }
 \description{
 Fit an ARMAX model of the specified order given the input-output data
 }
 \details{
-SISO ARMAX models are of the form
+SISO ARMAX models are of the form 
 \deqn{
-   y[k] + a_1 y[k-1] + \ldots + a_{na} y[k-na] = b_{nk} u[k-nk] +
+   y[k] + a_1 y[k-1] + \ldots + a_{na} y[k-na] = b_{nk} u[k-nk] + 
    \ldots + b_{nk+nb} u[k-nk-nb] + c_{1} e[k-1] + \ldots c_{nc} e[k-nc]
-   + e[k]
+   + e[k] 
 }
-The function estimates the coefficients using non-linear least squares
+The function estimates the coefficients using non-linear least squares 
 (Levenberg-Marquardt Algorithm)
 \\
-The data is expected to have no offsets or trends. They can be removed
+The data is expected to have no offsets or trends. They can be removed 
 using the \code{\link{detrend}} function.
 }
 \examples{
@@ -63,9 +63,10 @@ z <- dataSlice(data,end=1533) # training set
 mod_armax <- armax(z,c(1,2,1,2))
 summary(mod_armax) # obtain estimates and their covariances
 plot(mod_armax) # plot the predicted and actual responses
+
 }
 \references{
-Arun K. Tangirala (2015), \emph{Principles of System Identification:
+Arun K. Tangirala (2015), \emph{Principles of System Identification: 
 Theory and Practice}, CRC Press, Boca Raton. Sections 14.4.1, 21.6.2
 }
 
diff --git a/man/arx.Rd b/man/arx.Rd
index bae6f0b..4c15af3 100644
--- a/man/arx.Rd
+++ b/man/arx.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/estpoly.R
 \name{arx}
 \alias{arx}
@@ -9,15 +9,15 @@ arx(x, order = c(0, 1, 0))
 \arguments{
 \item{x}{an object of class \code{idframe}}
 
-\item{order:}{Specification of the orders: the three integer components
-(na,nb,nk) are the order of polynolnomial A, (order of polynomial B + 1) and
+\item{order:}{Specification of the orders: the three integer components 
+(na,nb,nk) are the order of polynolnomial A, (order of polynomial B + 1) and 
 the input-output delay}
 }
 \value{
 An object of class \code{estpoly} containing the following elements:
 
 \tabular{ll}{
-   \code{sys} \tab an \code{idpoly} object containing the
+   \code{sys} \tab an \code{idpoly} object containing the 
    fitted ARX coefficients \cr
    \code{fitted.values} \tab the predicted response \cr
    \code{residuals} \tab the residuals  \cr
@@ -27,7 +27,7 @@ An object of class \code{estpoly} containing the following elements:
    \tabular{ll}{
      \code{vcov} \tab the covariance matrix of the fitted coefficients\cr
      \code{sigma} \tab the standard deviation of the innovations\cr
-     \code{df} \tab the residual degrees of freedom
+     \code{df} \tab the residual degrees of freedom 
    }
  }
 }
@@ -35,16 +35,16 @@ An object of class \code{estpoly} containing the following elements:
 Fit an ARX model of the specified order given the input-output data
 }
 \details{
-SISO ARX models are of the form
+SISO ARX models are of the form 
 \deqn{
-   y[k] + a_1 y[k-1] + \ldots + a_{na} y[k-na] = b_{nk} u[k-nk] +
-   \ldots + b_{nk+nb} u[k-nk-nb] + e[k]
+   y[k] + a_1 y[k-1] + \ldots + a_{na} y[k-na] = b_{nk} u[k-nk] + 
+   \ldots + b_{nk+nb} u[k-nk-nb] + e[k] 
 }
 The function estimates the coefficients using linear least squares (with
-no regularization). Future versions may include regularization
+no regularization). Future versions may include regularization 
 parameters as well
 \\
-The data is expected to have no offsets or trends. They can be removed
+The data is expected to have no offsets or trends. They can be removed 
 using the \code{\link{detrend}} function.
 }
 \examples{
@@ -52,12 +52,13 @@ data(arxsim)
 model <- arx(data,c(2,1,1))
 model
 plot(model) # plot the predicted and actual responses
+
 }
 \references{
-Arun K. Tangirala (2015), \emph{Principles of System Identification:
+Arun K. Tangirala (2015), \emph{Principles of System Identification: 
 Theory and Practice}, CRC Press, Boca Raton. Section 21.6.1
 
-Lennart Ljung (1999), \emph{System Identification: Theory for the User},
+Lennart Ljung (1999), \emph{System Identification: Theory for the User}, 
 2nd Edition, Prentice Hall, New York. Section 10.1
 }
 
diff --git a/man/dataSlice.Rd b/man/dataSlice.Rd
index 5ff6f00..f0c1cd6 100644
--- a/man/dataSlice.Rd
+++ b/man/dataSlice.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/preprocess.R
 \name{dataSlice}
 \alias{dataSlice}
@@ -20,13 +20,13 @@ to be sampled.}
 an idframe object
 }
 \description{
-\code{dataSlice} is a subsetting method for objects of class \code{idframe}. It
+\code{dataSlice} is a subsetting method for objects of class \code{idframe}. It 
 extracts the subset of the object \code{data} observed between indices \code{start}
-and \code{end}.  If a frequency is specified, the series is then re-sampled at the
+and \code{end}.  If a frequency is specified, the series is then re-sampled at the 
 new frequency.
 }
 \details{
-The dataSlice function extends the \code{\link[stats]{window}}
+The dataSlice function extends the \code{\link[stats]{window}} 
 function for idframe objects
 }
 \examples{
@@ -34,7 +34,8 @@ data(cstr)
 cstrsub <- dataSlice(cstr,start=200,end=400) # extract between indices 200 and 400
 cstrTrain <- dataSlice(cstr,end=4500) # extract upto index 4500
 cstrTest <- dataSlice(cstr,start=6501) # extract from index 6501 till the end
-cstr_new <- dataSlice(cstr,freq=0.5) # resample data at half the original frequency
+cstr_new <- dataSlice(cstr,freq=0.5) # resample data at half the original frequency  
+
 }
 \seealso{
 \code{\link[stats]{window}}
diff --git a/man/detrend.Rd b/man/detrend.Rd
index 3f4faa4..b10565d 100644
--- a/man/detrend.Rd
+++ b/man/detrend.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/preprocess.R
 \name{detrend}
 \alias{detrend}
@@ -16,9 +16,9 @@ A list containing the following elements
 
 \tabular{ll}{
    \code{fitted.values} \tab \code{idframe} object with detrended variables \cr
-   \code{output_trend} \tab \code{list} containing trend fits for each output
+   \code{output_trend} \tab \code{list} containing trend fits for each output 
    variable \cr
-   \code{input_trend} \tab \code{list} containing trend fits for each input
+   \code{input_trend} \tab \code{list} containing trend fits for each input 
    variable
  }
 }
@@ -27,11 +27,12 @@ Removes the offsets or linear trends in each of the input and output matrices.
 }
 \examples{
 data(cstr)
-fit <- detrend(cstr,type="linear") # remove linear trends
+fit <- detrend(cstr,type="linear") # remove linear trends 
 Zdetrend <- predict(fit) # get the detrended data
 
 demean <- detrend(cstr) # remove offsets
 Zcent <- predict(demean) # get the centered data
+
 }
 \seealso{
 \code{\link{predict.detrend}}, \code{\link[stats]{lm}}
diff --git a/man/etfe.Rd b/man/etfe.Rd
index b0bd836..0990ea0 100644
--- a/man/etfe.Rd
+++ b/man/etfe.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/nonparam.R
 \name{etfe}
 \alias{etfe}
@@ -13,15 +13,16 @@ etfe(data)
 an \code{idfrd} object containing the estimated frequency response
 }
 \description{
-Estimates the emperical transfer function from the data by taking the
+Estimates the emperical transfer function from the data by taking the 
 ratio of the fourier transforms of the output and the input variables
 }
 \examples{
 data(frf)
 frf <- etfe(data)
+
 }
 \references{
-Arun K. Tangirala (2015), \emph{Principles of System Identification:
+Arun K. Tangirala (2015), \emph{Principles of System Identification: 
 Theory and Practice}, CRC Press, Boca Raton. Sections 5.3 and 20.4.2
 }
 \seealso{
diff --git a/man/getcov.Rd b/man/getcov.Rd
index b5f0369..8ee2537 100644
--- a/man/getcov.Rd
+++ b/man/getcov.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/estUtil.R
 \name{getcov}
 \alias{getcov}
@@ -10,7 +10,7 @@ getcov(sys)
 \item{sys}{a linear, identified parametric model}
 }
 \description{
-Obtain the parameter covariance matrix of the linear, identified
+Obtain the parameter covariance matrix of the linear, identified 
 parametric model
 }
 
diff --git a/man/idframe.Rd b/man/idframe.Rd
index b44694a..3ec50e7 100644
--- a/man/idframe.Rd
+++ b/man/idframe.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/idframe.R
 \name{idframe}
 \alias{idframe}
@@ -27,11 +27,13 @@ an idframe object
 \code{idframe} is an S3 class for storing and manipulating input-ouput data. It supports discrete time and frequency domain data.
 }
 \examples{
-dataMatrix <- matrix(rnorm(1000),ncol=5)
+
+dataMatrix <- matrix(rnorm(1000),ncol=5) 
 data <- idframe(output=dataMatrix[,3:5],input=dataMatrix[,1:2],Ts=1)
+
 }
 \seealso{
-\code{\link{plot.idframe}}, the plot method for idframe objects,
+\code{\link{plot.idframe}}, the plot method for idframe objects, 
 \code{\link{summary.idframe}}, the summary method for idrame objects
 }
 
diff --git a/man/idfrd.Rd b/man/idfrd.Rd
index 1a0b72e..6cbabb5 100644
--- a/man/idfrd.Rd
+++ b/man/idfrd.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/idframe.R
 \name{idfrd}
 \alias{idfrd}
@@ -20,7 +20,7 @@ an idfrd object
 S3 class for storing frequency response data
 }
 \note{
-The class can currently store only SISO Responses. Future versions will
+The class can currently store only SISO Responses. Future versions will 
 have support for multivariate data
 }
 \seealso{
diff --git a/man/idinput.Rd b/man/idinput.Rd
index 3f64f4b..01f0b7c 100644
--- a/man/idinput.Rd
+++ b/man/idinput.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/idinput.R
 \name{idinput}
 \alias{idinput}
@@ -9,7 +9,7 @@ idinput(n, type = "rgs", band = c(0, 1), levels = c(-1, 1))
 \arguments{
 \item{n}{integer length of the input singal to be generated}
 
-\item{type}{the type of input signal to be generated.
+\item{type}{the type of input signal to be generated. 
 'rgs' - generates random gaussian signal
 'rbs' - generates random binary signal
 'prbs' - generates pseudorandom binary signal
@@ -17,13 +17,13 @@ idinput(n, type = "rgs", band = c(0, 1), levels = c(-1, 1))
 
 Default value is type='rgs'}
 
-\item{band}{determines the frequency content of the signal.
+\item{band}{determines the frequency content of the signal. 
 For type='rbs'/'sine'/,  band = [wlow,whigh]
 which specifies the lower and the upper bound of the passband frequencies(expressed as fractions of Nyquist frequency). Default is c(0,1)
 For type='prbs', band=[0,B]
 where B is such that the singal is constant over 1/B (clock period). Default is c(0,1)}
 
-\item{levels}{row vector defining the input level. It is of the form
+\item{levels}{row vector defining the input level. It is of the form 
 levels=c(minu, maxu)
 For 'rbs','prbs', 'sine', the generated signal always between minu and maxu.
 For 'rgs', minu=mean value of signal minus one standard deviation and maxu=mean value of signal plus one standard deviation
diff --git a/man/idpoly.Rd b/man/idpoly.Rd
index 98f0036..3f82594 100644
--- a/man/idpoly.Rd
+++ b/man/idpoly.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/poly.R
 \name{idpoly}
 \alias{idpoly}
@@ -9,10 +9,10 @@ idpoly(A = 1, B = 1, C = 1, D = 1, F1 = 1, ioDelay = 0, Ts = 1)
 \arguments{
 \item{A}{Autoregressive coefficients}
 
-\item{B,F1}{Coefficients of the numerator and denominator respectively
+\item{B, F1}{Coefficients of the numerator and denominator respectively
 of the deterministic model between the input and output}
 
-\item{C,D}{Coefficients of the numerator and denominator respectively
+\item{C, D}{Coefficients of the numerator and denominator respectively
 of the stochastic model}
 
 \item{ioDelay}{the delay in the input-output channel}
@@ -25,8 +25,8 @@ Creates a polynomial model with identifiable coefficients
 \details{
 Discrete-time polynomials are of the form
 \deqn{
- A(q^{-1}) y[k] = \frac{B(q^{-1})}{F1(q^{-1})} u[k] +
- \frac{C(q^{-1})}{D(q^{-1})} e[k]
+ A(q^{-1}) y[k] = \frac{B(q^{-1})}{F1(q^{-1})} u[k] + 
+ \frac{C(q^{-1})}{D(q^{-1})} e[k] 
 }
 }
 \examples{
@@ -39,5 +39,6 @@ C <- c(1,-0.3)
 D <- c(1,1.5,0.7)
 F1 <- c(1,-0.5)
 mod_bj <- idpoly(1,B,C,D,F1,ioDelay=1)
+
 }
 
diff --git a/man/impulseest.Rd b/man/impulseest.Rd
index 0eddac7..4852d2c 100644
--- a/man/impulseest.Rd
+++ b/man/impulseest.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/nonparam.R
 \name{impulseest}
 \alias{impulseest}
@@ -11,21 +11,21 @@ impulseest(x, M = 30, K = NULL, regul = F, lambda = 1)
 
 \item{M}{Order of the FIR Model (Default:\code{30})}
 
-\item{K}{Transport delay in the estimated impulse response
+\item{K}{Transport delay in the estimated impulse response 
 (Default:NULL)}
 
-\item{regul}{Parameter indicating whether regularization should be
+\item{regul}{Parameter indicating whether regularization should be 
 used. (Default:\code{FALSE})}
 
 \item{lambda}{The value of the regularization parameter. Valid only if
 \code{regul=TRUE}. (Default:\code{1})}
 }
 \description{
-\code{impulseest} is used to estimate impulse response coefficients from
+\code{impulseest} is used to estimate impulse response coefficients from 
 the data
 }
 \details{
-The IR Coefficients are estimated using linear least squares. Future
+The IR Coefficients are estimated using linear least squares. Future 
 Versions will provide support for multivariate data.
 }
 \examples{
@@ -34,9 +34,10 @@ yk <- filter (uk,c(0.9,-0.4),method="recursive") + rnorm(1000,1)
 data <- idframe(output=data.frame(yk),input=data.frame(uk))
 fit <- impulseest(data)
 plot(fit)
+
 }
 \references{
-Arun K. Tangirala (2015), \emph{Principles of System Identification:
+Arun K. Tangirala (2015), \emph{Principles of System Identification: 
 Theory and Practice}, CRC Press, Boca Raton. Sections 17.4.11 and 20.2
 }
 \seealso{
diff --git a/man/misdata.Rd b/man/misdata.Rd
index 45ec512..a6d4df8 100644
--- a/man/misdata.Rd
+++ b/man/misdata.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/preprocess.R
 \name{misdata}
 \alias{misdata}
@@ -21,6 +21,7 @@ The missing data is indicated using the value \emph{NA}.
 data(cstr_mis)
 summary(cstr_mis) # finding out the number of NAs
 cstr <- misdata(cstr_mis)
+
 }
 \seealso{
 \code{\link[zoo]{na.approx}}
diff --git a/man/oe.Rd b/man/oe.Rd
index eee4839..42f6aec 100644
--- a/man/oe.Rd
+++ b/man/oe.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/estpoly.R
 \name{oe}
 \alias{oe}
@@ -9,18 +9,18 @@ oe(x, order = c(1, 1, 0), options = optimOptions())
 \arguments{
 \item{x}{an object of class \code{idframe}}
 
-\item{options}{Estimation Options, setup using
-\code{\link{optimOptions}}}
-
-\item{order:}{Specification of the orders: the four integer components
+\item{order}{Specification of the orders: the four integer components 
 (nb,nf,nk) are order of polynomial B + 1, order of the polynomial F,
 and the input-output delay respectively}
+
+\item{options}{Estimation Options, setup using 
+\code{\link{optimOptions}}}
 }
 \value{
 An object of class \code{estpoly} containing the following elements:
 
 \tabular{ll}{
-   \code{sys} \tab an \code{idpoly} object containing the
+   \code{sys} \tab an \code{idpoly} object containing the 
    fitted OE coefficients \cr
    \code{fitted.values} \tab the predicted response \cr
    \code{residuals} \tab the residuals  \cr
@@ -31,43 +31,44 @@ An object of class \code{estpoly} containing the following elements:
      \code{vcov} \tab the covariance matrix of the fitted coefficients\cr
      \code{sigma} \tab the standard deviation of the innovations
    } \cr
-   \code{options} \tab Option set used for estimation. If no
+   \code{options} \tab Option set used for estimation. If no 
    custom options were configured, this is a set of default options. \cr
    \code{termination} \tab Termination conditions for the iterative
     search used for prediction error minimization.
    \tabular{ll}{
      \code{WhyStop} \tab Reason for termination \cr
      \code{iter} \tab Number of Iterations \cr
-     \code{iter} \tab Number of Function Evaluations
-   }
+     \code{iter} \tab Number of Function Evaluations 
+   }  
  }
 }
 \description{
 Fit an output-error model of the specified order given the input-output data
 }
 \details{
-SISO OE models are of the form
+SISO OE models are of the form 
 \deqn{
-   y[k] + f_1 y[k-1] + \ldots + f_{nf} y[k-nf] = b_{nk} u[k-nk] +
+   y[k] + f_1 y[k-1] + \ldots + f_{nf} y[k-nf] = b_{nk} u[k-nk] + 
    \ldots + b_{nk+nb} u[k-nk-nb] + f_{1} e[k-1] + \ldots f_{nf} e[k-nf]
-   + e[k]
+   + e[k] 
 }
-The function estimates the coefficients using non-linear least squares
+The function estimates the coefficients using non-linear least squares 
 (Levenberg-Marquardt Algorithm)
 \\
-The data is expected to have no offsets or trends. They can be removed
+The data is expected to have no offsets or trends. They can be removed 
 using the \code{\link{detrend}} function.
 }
 \examples{
 data(oesim)
 z <- dataSlice(data,end=1533) # training set
 mod_oe <- oe(z,c(2,1,2),optimOptions(tol=1e-04,LMinit=0.01))
-mod_oe
+mod_oe 
 plot(mod_oe) # plot the predicted and actual responses
+
 }
 \references{
-Arun K. Tangirala (2015), \emph{Principles of System Identification:
-Theory and Practice}, CRC Press, Boca Raton. Sections 14.4.1, 17.5.2,
+Arun K. Tangirala (2015), \emph{Principles of System Identification: 
+Theory and Practice}, CRC Press, Boca Raton. Sections 14.4.1, 17.5.2, 
 21.6.3
 }
 
diff --git a/man/optimOptions.Rd b/man/optimOptions.Rd
index a0b4ef6..801f9be 100644
--- a/man/optimOptions.Rd
+++ b/man/optimOptions.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/estUtil.R
 \name{optimOptions}
 \alias{optimOptions}
@@ -7,19 +7,19 @@
 optimOptions(tol = 1e-05, maxIter = 20, LMinit = 2, LMstep = 2)
 }
 \arguments{
-\item{tol}{Minimum ratio of the improvement to the current loss
+\item{tol}{Minimum ratio of the improvement to the current loss 
 function. Iterations stop if this ratio goes below the tolerance
 limit (Default: \code{1e-5})}
 
 \item{maxIter}{Maximum number of iterations to be performed}
 
-\item{LMinit}{Starting value of search-direction length
+\item{LMinit}{Starting value of search-direction length 
 in the Levenberg-Marquardt method.}
 
 \item{LMstep}{Size of the Levenberg-Marquardt step}
 }
 \description{
-Specify optimization options that are to be passed to the
+Specify optimization options that are to be passed to the 
 numerical estimation routines
 }
 
diff --git a/man/plot.idframe.Rd b/man/plot.idframe.Rd
index 22653d4..3c90cf9 100644
--- a/man/plot.idframe.Rd
+++ b/man/plot.idframe.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/idframe.R
 \name{plot.idframe}
 \alias{plot.idframe}
@@ -22,6 +22,7 @@ Plotting method for objects inherting from class \code{idframe}
 \examples{
 data(cstr)
 plot(cstr,col="blue")
+
 }
 \seealso{
 \code{\link[tfplot]{tfplot}}
diff --git a/man/plot.idfrd.Rd b/man/plot.idfrd.Rd
index 7c1b008..b2459f4 100644
--- a/man/plot.idfrd.Rd
+++ b/man/plot.idfrd.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/idframe.R
 \name{plot.idfrd}
 \alias{plot.idfrd}
@@ -17,6 +17,7 @@ ggplot2 plotting engine
 data(frf)
 frf <- spa(data) # Estimates the frequency response from data
 plot(frf)
+
 }
 \seealso{
 \code{\link[ggplot2]{ggplot}}
diff --git a/man/plot.impulseest.Rd b/man/plot.impulseest.Rd
index bb273f5..7a0d963 100644
--- a/man/plot.impulseest.Rd
+++ b/man/plot.impulseest.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/nonparam.R
 \name{plot.impulseest}
 \alias{plot.impulseest}
diff --git a/man/predict.detrend.Rd b/man/predict.detrend.Rd
index e969de9..e91fb7e 100644
--- a/man/predict.detrend.Rd
+++ b/man/predict.detrend.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/preprocess.R
 \name{predict.detrend}
 \alias{predict.detrend}
@@ -9,7 +9,7 @@
 \arguments{
 \item{model}{an object of class \code{detrend}}
 
-\item{newdata}{An optional idframe object in which to look for variables with
+\item{newdata}{An optional idframe object in which to look for variables with 
 which to predict. If ommited, the original detrended idframe object is used}
 }
 \value{
@@ -25,5 +25,6 @@ test <- dataSlice(cstr,start=6001)
 fit <- detrend(train)
 Ztrain <- predict(fit)
 Ztest <- predict(fit,test)
+
 }
 
diff --git a/man/read.idframe.Rd b/man/read.idframe.Rd
index dd60160..fd546d7 100644
--- a/man/read.idframe.Rd
+++ b/man/read.idframe.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/readData.R
 \name{read.idframe}
 \alias{read.idframe}
@@ -25,5 +25,6 @@ Read the contents of a data.frame/matrix into a \code{idframe} object.
 \examples{
 data(cstr)
 data <- read.idframe(cstrData,ninputs=1,Ts= 1,unit="minutes")
+
 }
 
diff --git a/man/read.odf.idframe.Rd b/man/read.odf.idframe.Rd
index f7a797a..fcf4c40 100644
--- a/man/read.odf.idframe.Rd
+++ b/man/read.odf.idframe.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/readData.R
 \name{read.odf.idframe}
 \alias{read.odf.idframe}
@@ -12,7 +12,7 @@ read.odf.idframe(file, sheetName, header = TRUE, ninputs = 0, Ts = 1,
 
 \item{sheetName}{a character string with the sheet name}
 
-\item{header}{a logical value indicating whether the first row corresponding to
+\item{header}{a logical value indicating whether the first row corresponding to 
 the first element of the rowIndex vector contains the names of the variables.}
 
 \item{ninputs}{the number of input columns. (Default: 0)}
@@ -30,8 +30,8 @@ an idframe object
 Read the contents of an a .odf document into a \code{idframe} object.
 }
 \details{
-The \code{read.odf.idframe} function uses the \code{\link[gnumeric]{read.gnumeric.sheet}} function,
-provided by the \pkg{xlsx} package, to read data from a .odf file and then calls the
+The \code{read.odf.idframe} function uses the \code{\link[gnumeric]{read.gnumeric.sheet}} function, 
+provided by the \pkg{xlsx} package, to read data from a .odf file and then calls the 
 \code{\link{read.idframe}} function to read the data into a idframe object
 }
 \seealso{
diff --git a/man/read.table.idframe.Rd b/man/read.table.idframe.Rd
index 5065317..ca80a4c 100644
--- a/man/read.table.idframe.Rd
+++ b/man/read.table.idframe.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/readData.R
 \name{read.table.idframe}
 \alias{read.table.idframe}
@@ -10,11 +10,11 @@ read.table.idframe(file, header = TRUE, sep = ",", ninputs = 0, Ts = 1,
 \arguments{
 \item{file}{the path to the file to read}
 
-\item{header}{a logical value indicating whether the first row corresponding to
-the first element of the rowIndex vector contains the names of the variables.
+\item{header}{a logical value indicating whether the first row corresponding to 
+the first element of the rowIndex vector contains the names of the variables. 
 (Default: \code{TRUE})}
 
-\item{sep}{the field separator character. Values on each line of the file are
+\item{sep}{the field separator character. Values on each line of the file are 
 separated by this character. (Default: \code{","})}
 
 \item{ninputs}{the number of input columns. (Default: 0)}
@@ -32,16 +32,17 @@ an idframe object
 Read the contents of an file in table format into a \code{idframe} object.
 }
 \details{
-The \code{read.table.idframe} function uses the \code{\link[utils]{read.table}} function,
-provided by the \pkg{utils} package, to read data from a table-formatted file and then calls the
+The \code{read.table.idframe} function uses the \code{\link[utils]{read.table}} function, 
+provided by the \pkg{utils} package, to read data from a table-formatted file and then calls the 
 \code{\link{read.idframe}} function to read the data into a idframe object
 }
 \examples{
 dataMatrix <- data.frame(matrix(rnorm(1000),ncol=5))
 colnames(dataMatrix) <- c("u1","u2","y1","y2","y3")
 write.csv(dataMatrix,file="test.csv",row.names=FALSE)
-
+ 
 data <- read.table.idframe("test.csv",ninputs=2,unit="minutes")
+
 }
 \seealso{
 \code{\link[utils]{read.table}}
diff --git a/man/read.xls.idframe.Rd b/man/read.xls.idframe.Rd
index 449ccf9..a7123bb 100644
--- a/man/read.xls.idframe.Rd
+++ b/man/read.xls.idframe.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/readData.R
 \name{read.xls.idframe}
 \alias{read.xls.idframe}
@@ -12,7 +12,7 @@ read.xls.idframe(file, sheetName, header = TRUE, ninputs = 0, Ts = 1,
 
 \item{sheetName}{a character string with the sheet name}
 
-\item{header}{a logical value indicating whether the first row corresponding to
+\item{header}{a logical value indicating whether the first row corresponding to 
 the first element of the rowIndex vector contains the names of the variables.}
 
 \item{ninputs}{the number of input columns. (Default: 0)}
@@ -30,11 +30,11 @@ an idframe object
 Read the contents of an excel worksheet into a \code{idframe} object.
 }
 \details{
-The \code{read.xlsx.idframe} function uses the \code{\link[xlsx]{read.xlsx2}} function,
-provided by the \pkg{xlsx} package, to read data from an excel file and then calls the
+The \code{read.xlsx.idframe} function uses the \code{\link[xlsx]{read.xlsx2}} function, 
+provided by the \pkg{xlsx} package, to read data from an excel file and then calls the 
 \code{\link{read.idframe}} function to read the data into a idframe object
 
-The function requires the java runtime to be installed on the system (Requirement of
+The function requires the java runtime to be installed on the system (Requirement of 
 the \pkg{xlsx} package).
 }
 \examples{
@@ -42,8 +42,9 @@ library(xlsx)
 dataMatrix <- data.frame(matrix(rnorm(1000),ncol=5))
 colnames(dataMatrix) <- c("u1","u2","y1","y2","y3")
 write.xlsx2(dataMatrix,file="test.xlsx",row.names=FALSE)
-
+ 
 data <- read.xls.idframe("test.xlsx","Sheet1",ninputs=2,unit="minutes")
+
 }
 \seealso{
 \code{\link[xlsx]{read.xlsx2}}
diff --git a/man/sim.Rd b/man/sim.Rd
index 562b656..5ed27ea 100644
--- a/man/sim.Rd
+++ b/man/sim.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/sim.R
 \name{sim}
 \alias{sim}
diff --git a/man/sim.idpoly.Rd b/man/sim.idpoly.Rd
index d206017..eae901e 100644
--- a/man/sim.idpoly.Rd
+++ b/man/sim.idpoly.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/sim.R
 \name{sim.idpoly}
 \alias{sim.idpoly}
@@ -31,6 +31,7 @@ include support for MIMO systems
 u <- rnorm(200,sd=1)
 model <- idpoly(A=c(1,-1.5,0.7),B=c(0.8,-0.25),ioDelay=1)
 y <- sim(model,u,sigma=0.1)
+
 }
 \seealso{
 \code{\link{idpoly}} for defining polynomial models
diff --git a/man/spa.Rd b/man/spa.Rd
index 13778ea..3979b7a 100644
--- a/man/spa.Rd
+++ b/man/spa.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/nonparam.R
 \name{spa}
 \alias{spa}
@@ -9,30 +9,31 @@ spa(data, npad = 255)
 \arguments{
 \item{data}{an \code{idframe} object}
 
-\item{npad}{an integer representing the total length of each time series
-to analyze after padding with zeros. This argument allows the user to
-control the spectral resolution of the SDF estimates: the normalized
+\item{npad}{an integer representing the total length of each time series 
+to analyze after padding with zeros. This argument allows the user to 
+control the spectral resolution of the SDF estimates: the normalized 
 frequency interval is deltaf=1/npad. (Default: 255)}
 }
 \value{
 an \code{idfrd} object containing the estimated frequency response
 }
 \description{
-Estimates Frequency Response with fixed frequency resolution using
+Estimates Frequency Response with fixed frequency resolution using 
 spectral analysis
 }
 \details{
 The function calls the \code{SDF} function in the \code{sapa} package to
-compute the cross-spectral densities. The method used is \strong{Welch's
+compute the cross-spectral densities. The method used is \strong{Welch's 
 Overlapped Segment Averaging} with a normalized \strong{Hanning} window.
 The overlap used is 50%.
 }
 \examples{
 data(frf)
 frf <- spa(data)
+
 }
 \references{
-Arun K. Tangirala (2015), \emph{Principles of System Identification:
+Arun K. Tangirala (2015), \emph{Principles of System Identification: 
 Theory and Practice}, CRC Press, Boca Raton. Sections 16.5 and 20.4
 }
 \seealso{
diff --git a/man/step.Rd b/man/step.Rd
index b6aa624..a4c547d 100644
--- a/man/step.Rd
+++ b/man/step.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/nonparam.R
 \name{step}
 \alias{step}
@@ -17,7 +17,8 @@ uk <- rnorm(1000,1)
 yk <- filter (uk,c(0.9,-0.4),method="recursive") + rnorm(1000,1)
 data <- idframe(output=data.frame(yk),input=data.frame(uk))
 fit <- impulseest(data)
-step(fit)
+step(fit) 
+
 }
 \seealso{
 \code{\link{impulseest}}
diff --git a/man/tf.Rd b/man/tf.Rd
index 3cfc35c..9d0b60e 100644
--- a/man/tf.Rd
+++ b/man/tf.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/tf.R
 \name{tf}
 \alias{tf}