Includes all *.Rd files from building process.

man/ahs.Rd

@@ -6,42 +6,76 @@
 \title{Australian health survey}
 \format{a \code{data.frame} with 5190 records and 17 variables.}
 \source{
-Deb, P. and Trivedi, P. K. (1997). Demand for medical care by the elderly: A finite mixture approach,
-Journal of Applied Econometrics 12(3):313--336.
+Deb, P. and Trivedi, P. K. (1997). Demand for medical care by
+    the elderly: A finite mixture approach, Journal of Applied
+    Econometrics 12(3):313--336.
 }
 \usage{
 data(ahs)
 }
 \description{
-The Australian health survey was used by Bonat and Jorgensen (2015) as an example of multivariate
-count regression model. The data consists of five count response variables concerning health system access
-measures and nine covariates concerning  social conditions in Australian for 1987-88.
+The Australian health survey was used by Bonat and
+    Jorgensen (2015) as an example of multivariate count regression
+    model. The data consists of five count response variables
+    concerning health system access measures and nine covariates
+    concerning social conditions in Australian for 1987-88.
 
 \itemize{
+
 \item \code{sex} - Factor, two levels (0-Male; 1-Female).
+
 \item \code{age} - Respondent's age in years divided by 100.
-    \item \code{income} - Respondent's annual income in Australian dollars divided by 1000.
-    \item \code{levyplus} - Factor, two levels (1- if respondent is covered by private health
-    insurance fund for private patients in public hospital (with doctor of choice); 0 - otherwise).
-    \item \code{freepoor} - Factor, two levels (1 - if respondent is covered by government because low income,
-    recent immigrant, unemployed; 0 - otherwise).
-    \item \code{freerepa} - Factor, two levels (1 - if respondent is covered free by government because of
-    old-age or disability pension, or because invalid veteran or family of deceased veteran; 0 - otherwise).
-    \item \code{illnes} - Number of illnesses in past 2 weeks, with 5 or more weeks coded as 5.
-    \item \code{actdays} - Number of days of reduced activity in the past two weeks due to illness or injury.
-    \item \code{hscore} - Respondent's general health questionnaire score using Goldberg's method;
-    high score indicates poor health.
-    \item \code{chcond1} - Factor, two levels (1 - if respondent has chronic condition(s) but is not limited
-    in activity; 0 - otherwise).
-    \item \code{chcond2} - Factor, two levels (1 if respondent has chronic condition(s) and is limited in
-    activity; 0 - otherwise).
-    \item \code{Ndoc} - Number of consultations with a doctor or specialist (response variable).
-    \item \code{Nndoc} - Number of consultations with health professionals (response variable).
-    \item \code{Nadm} - Number of admissions to a hospital, psychiatric hospital, nursing or
-    convalescence home in the past 12 months (response variable).
-    \item \code{Nhosp} - Number of nights in a hospital during the most recent admission.
-    \item \code{Nmed} - Total number of prescribed and non prescribed medications used in the past two days.
+
+\item \code{income} - Respondent's annual income in Australian
+    dollars divided by 1000.
+
+\item \code{levyplus} - Factor, two levels (1- if respondent is
+    covered by private health insurance fund for private patients in
+    public hospital (with doctor of choice); 0 - otherwise).
+
+\item \code{freepoor} - Factor, two levels (1 - if respondent is
+    covered by government because low income, recent immigrant,
+    unemployed; 0 - otherwise).
+
+\item \code{freerepa} - Factor, two levels (1 - if respondent is
+    covered free by government because of old-age or disability
+    pension, or because invalid veteran or family of deceased
+    veteran; 0 - otherwise).
+
+\item \code{illnes} - Number of illnesses in past 2 weeks, with 5 or
+    more weeks coded as 5.
+
+\item \code{actdays} - Number of days of reduced activity in the past
+    two weeks due to illness or injury.
+
+\item \code{hscore} - Respondent's general health questionnaire score
+    using Goldberg's method; high score indicates poor health.
+
+\item \code{chcond1} - Factor, two levels (1 - if respondent has
+    chronic condition(s) but is not limited in activity; 0 -
+    otherwise).
+
+\item \code{chcond2} - Factor, two levels (1 if respondent has
+    chronic condition(s) and is limited in activity; 0 - otherwise).
+
+\item \code{Ndoc} - Number of consultations with a doctor or
+    specialist (response variable).
+
+\item \code{Nndoc} - Number of consultations with health
+    professionals (response variable).
+
+\item \code{Nadm} - Number of admissions to a hospital, psychiatric
+    hospital, nursing or convalescence home in the past 12 months
+    (response variable).
+
+\item \code{Nhosp} - Number of nights in a hospital during the most
+    recent admission.
+
+\item \code{Nmed} - Total number of prescribed and non prescribed
+    medications used in the past two days.
+
 \item \code{id} - Respondent's index.
+
 }
 }
 \keyword{datasets}

man/anova.mcglm.Rd

 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/mc_anova.R
+% Please edit documentation in R/mc_S3_methods.R
 \name{anova.mcglm}
 \alias{anova.mcglm}
 \title{ANOVA method for McGLMs.}
@@ -7,12 +7,22 @@
 \method{anova}{mcglm}(object, ...)
 }
 \arguments{
-\item{object}{an object of class mcglm, usually, a result of a call to \code{mcglm}.}
+\item{object}{an object of class \code{mcglm}, usually, a result of a
+call to \code{mcglm()}.}
 
-\item{...}{additional arguments affecting the summary produced. Note that there is no extra options for
-mcglm object class.}
+\item{...}{additional arguments affecting the summary produced. Note
+    that there is no extra options for mcglm object class.}
+}
+\value{
+A \code{data.frame} with Chi-square statistic to test the
+    null hypothesis of a parameter, or a set of parameters, be
+    zero. The Wald test based on the observed covariance matrix of
+    the parameters is used.
 }
 \description{
-ANOVA method for McGLMS.
+ANOVA method for object of class McGLMS.
+}
+\author{
+Wagner Hugo Bonat, \email{wbonat@ufpr.br}
 }
 

man/coef.mcglm.Rd

 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/mc_coef.R
+% Please edit documentation in R/mc_S3_methods.R
 \name{coef.mcglm}
 \alias{coef.mcglm}
 \title{Extract model coefficients for mcglm class}
@@ -9,23 +9,31 @@
   "correlation"), ...)
 }
 \arguments{
-\item{object}{An object of mcglm class.}
+\item{object}{An object of \code{mcglm} class.}
 
-\item{std.error}{Logical. Returns or not the standard errors.}
+\item{std.error}{Logical. If \code{TRUE} returns the standard errors
+of the estimates. Default is \code{FALSE}.}
 
-\item{response}{A numeric or vector specyfing for which response variables the coefficients
-should be returned.}
+\item{response}{A numeric vector specyfing for which response
+variables the coefficients should be returned.}
 
-\item{type}{A string or string vector specyfing which coefficients should be returned.
-Options are 'beta', 'tau', 'power', 'tau' and 'correlation'.}
+\item{type}{A string vector (can be 1 element length) specyfing which
+coefficients should be returned. Options are \code{"beta"},
+\code{"tau"}, \code{"power"}, \code{"tau"} and
+\code{"correlation"}.}
 
-\item{...}{additional arguments affecting the summary produced. Note that there is no extra options for
-mcglm object class.}
+\item{...}{additional arguments affecting the summary produced. Note
+    that there is no extra options for mcglm object class.}
 }
 \value{
-A data.frame with estimates, parameters names, response number and parameters type.
+A \code{data.frame} with parameters names, estimates,
+    response number and parameters type.
 }
 \description{
-coef.mcglm is a function which extracts model coefficients from objects of mcglm class.
+\code{coef.mcglm} is a function which extracts model
+    coefficients from objects of \code{mcglm} class.
+}
+\author{
+Wagner Hugo Bonat, \email{wbonat@ufpr.br}
 }
 

man/confint.mcglm.Rd

 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/mc_confint.mcglm.R
+% Please edit documentation in R/mc_S3_methods.R
 \name{confint.mcglm}
 \alias{confint.mcglm}
 \title{Confidence Intervals for mcglm}
@@ -7,22 +7,27 @@
 \method{confint}{mcglm}(object, parm, level = 0.95, ...)
 }
 \arguments{
-\item{object}{a fitted mcglm object.}
+\item{object}{a fitted \code{mcglm} object.}
 
-\item{parm}{a specification of which parameters are to be given confidence intervals, either a vector of
-number or a vector of names. If missing, all parameters are considered.}
+\item{parm}{a specification of which parameters are to be given
+confidence intervals, either a vector of number or a vector of
+strings. If missing, all parameters are considered.}
 
-\item{level}{the confidence level required.}
+\item{level}{the nominal confidence level.}
 
-\item{...}{additional arguments affecting the confidence interval produced.
-Note that there is no extra options for
-mcglm object class.}
+\item{...}{additional arguments affecting the confidence interval
+    produced. Note that there is no extra options for \code{mcglm}
+    object class.}
 }
 \value{
-A data.frame with confidence intervals, parameters names,
-response number and parameters type.
+A \code{data.frame} with confidence intervals, parameters
+    names, response number and parameters type.
 }
 \description{
-Computes confidence intervals for parameters in a fitted mcglm.
+Computes confidence intervals for parameters in a fitted
+    \code{mcglm} model.
+}
+\author{
+Wagner Hugo Bonat, \email{wbonat@ufpr.br}
 }
 

man/fitted.mcglm.Rd

 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/mc_fitted.mcglm.R
+% Please edit documentation in R/mc_S3_methods.R
 \name{fitted.mcglm}
 \alias{fitted.mcglm}
 \title{Extract Model Fitted Values of McGLM}
@@ -7,16 +7,20 @@
 \method{fitted}{mcglm}(object, ...)
 }
 \arguments{
-\item{object}{An object of mcglm class.}
+\item{object}{An object of \code{mcglm} class.}
 
-\item{...}{additional arguments affecting the summary produced. Note that there is no extra options for
-mcglm object class.}
+\item{...}{additional arguments affecting the summary produced. Note
+    that there is no extra options for \code{mcglm} object class.}
 }
 \value{
-Depending on the number of response variable the function \code{fitted.mcglm} returns
-a vector (univariate models) or a matrix (multivariate models) of fitted values.
+Depending on the number of response variable, the function
+    \code{fitted.mcglm} returns a vector (univariate models) or a
+    matrix (multivariate models) of fitted values.
 }
 \description{
-Extract fitted values for objects of mcglm class.
+Extract fitted values for objects of \code{mcglm} class.
+}
+\author{
+Wagner Hugo Bonat, \email{wbonat@ufpr.br}
 }
 

man/mcglm.Rd

@@ -52,16 +52,22 @@ fitted using an estimating function approach, combining quasi-score functions fo
 parameters and Pearson estimating function for covariance parameters. For details see Bonat and
 Jorgensen (2015).
 
-Fits a multivariate covariance generalized linear models (McGLMs) to data.
-McGLM is a general framework for non-normal multivariate data analysis, designed to handle
-multivariate response variables, along with a wide range of temporal and spatial correlation
-structures defined in terms of a covariance link function combined with a matrix linear predictor
-involving known matrices. The models take non-normality into account in the conventional way by means
-of a variance function, and the mean structure is modelled by means of a link function and a linear predictor.
-The models are fitted using an efficient Newton scoring algorithm based on quasi-likelihood and
-Pearson estimating functions, using only second-moment assumptions.
-This provides a unified approach to a wide variety of different types of response variables and
-covariance structures, including multivariate extensions of repeated measures, time series, longitudinal,
-spatial and spatio-temporal structures.
+Fits a multivariate covariance generalized linear
+    models (McGLMs) to data.  McGLM is a general framework for
+    non-normal multivariate data analysis, designed to handle
+    multivariate response variables, along with a wide range of
+    temporal and spatial correlation structures defined in terms of
+    a covariance link function combined with a matrix linear
+    predictor involving known matrices. The models take
+    non-normality into account in the conventional way by means of a
+    variance function, and the mean structure is modelled by means
+    of a link function and a linear predictor.  The models are
+    fitted using an efficient Newton scoring algorithm based on
+    quasi-likelihood and Pearson estimating functions, using only
+    second-moment assumptions.  This provides a unified approach to
+    a wide variety of different types of response variables and
+    covariance structures, including multivariate extensions of
+    repeated measures, time series, longitudinal, spatial and
+    spatio-temporal structures.
 }
 

man/plot.mcglm.Rd

 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/mc_plot.mcglm.R
+% Please edit documentation in R/mc_S3_methods.R
 \name{plot.mcglm}
 \alias{plot.mcglm}
 \title{Default Multivariate Covariance Generalized Linear models plotting}
@@ -7,16 +7,20 @@
 \method{plot}{mcglm}(x, type = "residuals", ...)
 }
 \arguments{
-\item{x}{a fitted mcglm object as produced by \code{mcglm()}.}
+\item{x}{a fitted \code{mcglm} object.}
 
-\item{type}{Specify which graphical analysis will be performed, options are: residuals, influence
-and algorithm.}
+\item{type}{Specify which graphical analysis will be performed.
+Options are: \code{"residuals"}, \code{"influence"} and
+\code{"algorithm"}.}
 
-\item{...}{additional arguments affecting the plot produced. Note that there is no extra options for
-mcglm object class.}
+\item{...}{additional arguments affecting the plot produced. Note
+that there is no extra options for mcglm object class.}
 }
 \description{
-takes a fitted mcglm object by \code{mcglm()} and plots, residuals,
-influence diagnostic measures and algorithm check.
+takes a fitted \code{mcglm} object and do plots based on
+    residuals, influence diagnostic measures and algorithm check.
+}
+\author{
+Wagner Hugo Bonat, \email{wbonat@ufpr.br}
 }
 

man/print.mcglm.Rd

 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/mc_print.mcglm.R
+% Please edit documentation in R/mc_S3_methods.R
 \name{print.mcglm}
 \alias{print.mcglm}
-\title{Print method for Multivariate Covariance Generalized Linear Model}
+\title{Print method for Multivariate Covariance Generalized Linear
+    Model}
 \usage{
 \method{print}{mcglm}(x, ...)
 }
@@ -12,6 +13,9 @@
 \item{...}{further arguments passed to or from other methods.}
 }
 \description{
-The default print method for a mcglm object.
+The default print method for a \code{mcglm} object.
+}
+\author{
+Wagner Hugo Bonat, \email{wbonat@ufpr.br}
 }
 

man/qic.mcglm.Rd

@@ -7,15 +7,19 @@
 qic.mcglm(object, object.iid)
 }
 \arguments{
-\item{object}{An object of mcglm class.}
+\item{object}{An object of \code{mcglm} class.}
 
-\item{object.iid}{An object of mcglm class contained the model fitted using independent
-covariance structure.}
+\item{object.iid}{An object of \code{mcglm} class contained the model
+    fitted using independent covariance structure.}
 }
 \value{
 The QIC value.
 }
 \description{
-qic.mcglm is a function which computes the QIC for McGLMs.
+\code{qic.mcglm} is a function which computes the QIC
+    for McGLMs.
+}
+\author{
+Wagner Hugo Bonat, \email{wbonat@ufpr.br}
 }
 

man/residuals.mcglm.Rd

 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/mc_residuals.mcglm.R
+% Please edit documentation in R/mc_S3_methods.R
 \name{residuals.mcglm}
 \alias{residuals.mcglm}
-\title{Residuals for Multivariate Covariance Generalized Linear Models (McGLM)}
+\title{Residuals for Multivariate Covariance Generalized Linear
+    Models (McGLM)}
 \usage{
 \method{residuals}{mcglm}(object, type = "raw", ...)
 }
 \arguments{
-\item{object}{An of class mcglm, typically the result of a call to \code{mcglm}.}
+\item{object}{An of class \code{mcglm}, typically the result of a
+call to \code{mcglm}.}
 
-\item{type}{the type of residuals which should be returned. The alternatives are: 'raw'
-(default), 'pearson' and 'standardized'.}
+\item{type}{the type of residuals which should be returned. The
+alternatives are: \code{"raw"} (default), \code{"pearson"} and
+\code{"standardized"}.}
 
-\item{...}{additional arguments affecting the residuals produced. Note that there is no extra options for
-mcglm object class.}
+\item{...}{additional arguments affecting the residuals
+    produced. Note that there is no extra options for mcglm object
+    class.}
 }
 \value{
-Depending on the number of response variable the function \code{residuals.mcglm} returns
-a vector (univariate models) or a matrix (multivariate models) of residuals values.
+Depending on the number of response variable the function
+    \code{residuals.mcglm} returns a vector (univariate models) or a
+    matrix (multivariate models) of residuals values.
 }
 \description{
-Compute residuals based on fitting mcglm models.
+Compute residuals based on fitting \code{mcglm} models.
+}
+\author{
+Wagner Hugo Bonat, \email{wbonat@ufpr.br}
 }
 

man/summary.mcglm.Rd

 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/mc_summary.mcglm.R
+% Please edit documentation in R/mc_S3_methods.R
 \name{summary.mcglm}
 \alias{summary.mcglm}
-\title{Summarizing Multivariate Covariance Generalized Linear Models fits.}
+\title{Summarizing Multivariate Covariance Generalized Linear Models
+    fits.}
 \usage{
 \method{summary}{mcglm}(object, ...)
 }
 \arguments{
-\item{object}{an object of class mcglm, usually, a result of a call to \code{mcglm}.}
+\item{object}{an object of class \code{mcglm}, usually, a result of a
+call to \code{mcglm}.}
 
-\item{...}{additional arguments affecting the summary produced. Note the there is no extra options for
-mcglm object class.}
+\item{...}{additional arguments affecting the summary produced. Note
+    the there is no extra options for mcglm object class.}
 }
 \value{
-Print an mcglm object.
+Print an \code{mcglm} object.
 }
 \description{
 Summary for McGLMs objects.
 }
+\author{
+Wagner Hugo Bonat, \email{wbonat@ufpr.br}
+}
 

man/vcov.mcglm.Rd

 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/mc_vcov.R
+% Please edit documentation in R/mc_S3_methods.R
 \name{vcov.mcglm}
 \alias{vcov.mcglm}
-\title{Calculate Variance-Covariance matrix for a fitted McGLM object.}
+\title{Calculate Variance-Covariance matrix for a fitted McGLM
+    object.}
 \usage{
 \method{vcov}{mcglm}(object, ...)
 }
 \arguments{
-\item{object}{a fitted model mcglm object.}
+\item{object}{a fitted model \code{mcglm} object.}
 
-\item{...}{additional arguments affecting the summary produced. Note that there is no extra options for
-mcglm object class.}
+\item{...}{additional arguments affecting the summary produced. Note
+    that there is no extra options for mcglm object class.}
 }
 \value{
 A variance-covariance matrix.
 }
 \description{
-Returns the variance-covariance matrix for all parameters of a mcglm fitted model object.
+Returns the variance-covariance matrix for all
+    parameters of a \code{mcglm} fitted model object.
+}
+\author{
+Wagner Hugo Bonat, \email{wbonat@ufpr.br}
 }