diff --git a/man/ahs.Rd b/man/ahs.Rd
index 4569dd4eca3aaa17f45a2a28db2ebe070e5d7685..7cb32800493c4d577077f654dad50863d8004854 100644
--- a/man/ahs.Rd
+++ b/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{id} - Respondent's index.
+
+\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{id} - Respondent's index.
+
}
}
\keyword{datasets}
diff --git a/man/anova.mcglm.Rd b/man/anova.mcglm.Rd
index d367ebbf685bcb454cb9bf677f598f741b2458d2..5f4e4d9b241f5553306a2cbfa7728b513db9c0ee 100644
--- a/man/anova.mcglm.Rd
+++ b/man/anova.mcglm.Rd
@@ -1,5 +1,5 @@
% 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}
}
diff --git a/man/coef.mcglm.Rd b/man/coef.mcglm.Rd
index 741388b2237b81fe9ebe23671621ddc3c8ece256..127d214b5152113798f2404f7aafc658515a13d8 100644
--- a/man/coef.mcglm.Rd
+++ b/man/coef.mcglm.Rd
@@ -1,5 +1,5 @@
% 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}
}
diff --git a/man/confint.mcglm.Rd b/man/confint.mcglm.Rd
index efdb6bb31b69cae0964019622e95df923c4ffd36..677abb619e7afb01b4ed28cffcfec59cb32f5797 100644
--- a/man/confint.mcglm.Rd
+++ b/man/confint.mcglm.Rd
@@ -1,5 +1,5 @@
% 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}
}
diff --git a/man/fitted.mcglm.Rd b/man/fitted.mcglm.Rd
index 115d5810f201bc4391de693565a8e49413d55eb2..64bb7b17a4a68982952da97b25a98e1d863dbbd3 100644
--- a/man/fitted.mcglm.Rd
+++ b/man/fitted.mcglm.Rd
@@ -1,5 +1,5 @@
% 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}
}
diff --git a/man/mcglm.Rd b/man/mcglm.Rd
index 63c324fce7fbcaf6a8667b8cc84e3b626b68aa91..402d73c5cd3c00fe42f62ed64ae1c8e1006f5fd1 100644
--- a/man/mcglm.Rd
+++ b/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.
}
diff --git a/man/plot.mcglm.Rd b/man/plot.mcglm.Rd
index a1b852cc05cd1bff264060e921f0b7c96864cdb6..ebb64e8fd5d3dc830eeba23dd354d56390fe49d7 100644
--- a/man/plot.mcglm.Rd
+++ b/man/plot.mcglm.Rd
@@ -1,5 +1,5 @@
% 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}
}
diff --git a/man/print.mcglm.Rd b/man/print.mcglm.Rd
index 008141d86c9bb9cac15fb6e7b5427670d0d3eff6..c712e79bcad170d71bc11813a36011e95e1532cc 100644
--- a/man/print.mcglm.Rd
+++ b/man/print.mcglm.Rd
@@ -1,8 +1,9 @@
% 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}
}
diff --git a/man/qic.mcglm.Rd b/man/qic.mcglm.Rd
index a98434607d65cc254cbb68a96873b28c16760361..02235c1afd4b475b93b3badb8ff5f0aed4dd594f 100644
--- a/man/qic.mcglm.Rd
+++ b/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}
}
diff --git a/man/residuals.mcglm.Rd b/man/residuals.mcglm.Rd
index 0e5cc27de00e03907f2492c1e420db57674f0fa4..495705b9b5e2b99cff28a0cdb11a806cc4146bcc 100644
--- a/man/residuals.mcglm.Rd
+++ b/man/residuals.mcglm.Rd
@@ -1,25 +1,33 @@
% 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}
}
diff --git a/man/summary.mcglm.Rd b/man/summary.mcglm.Rd
index 8e94d1de27313318a23c0653e52c4da6ec0cbb7b..8061e7980152f9e306756a91f5d40889625ba597 100644
--- a/man/summary.mcglm.Rd
+++ b/man/summary.mcglm.Rd
@@ -1,21 +1,26 @@
% 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}
+}
diff --git a/man/vcov.mcglm.Rd b/man/vcov.mcglm.Rd
index 31f20be578f2a7d118ded6e55b24a24c585511c4..3ba9ffafda81d6fe7a5452222b20d5e94e83507d 100644
--- a/man/vcov.mcglm.Rd
+++ b/man/vcov.mcglm.Rd
@@ -1,21 +1,26 @@
% 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}
}