R/Exam3.2.R

In myaseen208/StroupGLMM: R Codes and Datasets for Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup

#' @title Example 3.2 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup(p-73)
#' @name   Exam3.2
#' @docType data
#' @keywords datasets
#' @description Exam3.2 used binomial data, two treatment samples
#' @author \enumerate{
#'          \item  Muhammad Yaseen (\email{myaseen208@@gmail.com})
#'          \item Adeela Munawar (\email{adeela.uaf@@gmail.com})
#'          }
#' @references \enumerate{
#' \item Stroup, W. W. (2012).
#'      \emph{Generalized Linear Mixed Models: Modern Concepts, Methods and Applications}.
#'        CRC Press.
#'  }
#' @seealso
#'    \code{\link{DataSet3.1}}
#'    
#' @importFrom lsmeans lsmeans contrast
#' @importFrom phia testFactors
#' @importFrom stats glm summary.glm
#'    
#' @examples
#' #-------------------------------------------------------------
#' ## Linear Model and results discussed in Article 1.2.1 after Table1.1
#' #-------------------------------------------------------------
#' data(DataSet3.1)
#' DataSet3.1$trt <- factor(x =  DataSet3.1$trt)
#' Exam3.2.glm <-
#'   glm(
#'          formula    =  F/N~trt
#'        , family     =  quasibinomial(link = "logit")
#'        , data       =  DataSet3.1
#'        , weights    =  NULL
#'     #  , subset
#'     #  , na.action
#'        , start      =  NULL
#'     #  , etastart
#'     #  , mustart
#'     #  , offset
#'     #  , control    =  list(...)
#'     #  , model      =  TRUE
#'        , method     =  "glm.fit"
#'     #  , x          =  FALSE
#'     #  , y          =  TRUE
#'        , contrasts  =  NULL
#'     #  , ...
#'   )
#' summary(Exam3.2.glm)
#' 
#' #-------------------------------------------------------------
#' ## Individula least squares treatment means
#' #-------------------------------------------------------------
#' library(lsmeans)
#' (Lsm3.2    <-
#'   lsmeans::lsmeans(
#'     object  = Exam3.2.glm
#'     , specs   = "trt"
#'     # , ...
#'   )
#' )
#' OddsRatioMean3.2 <-  1/(1 + exp(-summary(Lsm3.2)[c("lsmean")] ) )
#' #---------------------------------------------------
#' ## Over all mean
#' #---------------------------------------------------
#' library(phia)
#' list3.2<-   list(trt=c("0" = 0.5,"1" = 0.5 ))
#' (Test3.2 <-
#'   testFactors(
#'       model  =  Exam3.2.glm
#'     , levels =  list3.2 )
#' )
#' #---------------------------------------------------
#' ## Pairwise treatment means estimate
#' #---------------------------------------------------
#' contrast(object = Lsm3.2 , method = "pairwise")
#' #---------------------------------------------------
#' ## Repairwise treatment means estimate
#' #---------------------------------------------------
#' ## contrast( object = Lsm3.2 , method = "repairwise")
NULL