R/Exam7.1.R

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

#' @title Example 7.1 from Generalized Linear Mixed Models: Modern Concepts, Methods and Applications by Walter W. Stroup (p-213)
#' @name   Exam7.1
#' @description Exam7.1 explains multifactor models with all factors qualitative
#' @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{DataSet7.1}}
#'
#' @import parameters
#' @import emmeans
#' @importFrom phia testInteractions
#' @importFrom car linearHypothesis
#'
#' @examples
#'
#' library(emmeans)
#' library(car)
#' data(DataSet7.1)
#'
#' DataSet7.1$a <- factor(x = DataSet7.1$a)
#' DataSet7.1$b <- factor(x = DataSet7.1$b)
#'
#' Exam7.1.lm1 <- lm(formula = y ~ a + b + a*b, data = DataSet7.1)
#' summary(Exam7.1.lm1)
#' library(parameters)
#' model_parameters(Exam7.1.lm1)
#' anova(Exam7.1.lm1)
#'
#' ##---Result obtained as in SLICE statement in SAS for a0 & a1
#' library(phia)
#' testInteractions(
#'     model  = Exam7.1.lm1
#'   , custom = list(a = c("0" = 1))
#'   , across = "b"
#'   )
#'
#' testInteractions(
#'     model  = Exam7.1.lm1
#'   , custom = list(a = c("1" = 1))
#'   , across = "b"
#'   )
#'
#'
#' ##---Interaction plot
#' emmip(
#'        object  = Exam7.1.lm1
#'      , formula = a~b
#'      , ylab    = "y Lsmeans"
#'      , main    = "Lsmeans for a*b"
#'       )
#'
#' #-------------------------------------------------------------
#' ## Individula least squares treatment means
#' #-------------------------------------------------------------
#' emmeans(object = Exam7.1.lm1, specs = ~a*b)
#'
#' ##---Simpe effects comparison of interaction by a
#' ##   (but it doesn't give the same p-value as in article 7.4.2 page#215)
#' emmeans(object = Exam7.1.lm1, specs = pairwise~b|a)$contrasts
#'
#' pairs(emmeans(object = Exam7.1.lm1, specs = ~b|a), simple = "each", combine = TRUE)
#' pairs(emmeans(object = Exam7.1.lm1, specs = ~b|a), simple = "a")
#' pairs(emmeans(object = Exam7.1.lm1, specs = ~b|a), simple = "b")
#' pairs(emmeans(object = Exam7.1.lm1, specs = ~b|a))
#' contrast(emmeans(object = Exam7.1.lm1, specs = ~b|a))
#' emmeans(object = Exam7.1.lm1, specs = pairwise~b|a)
#' emmeans(object = Exam7.1.lm1, specs = pairwise~b|a)$contrasts
#'
#' ##---Alternative method of pairwise comparisons by
#' ## applying contrast
#' ##   coefficient (gives the same p-value as in 7.4.2)
#' contrast(
#'           emmeans(object = Exam7.1.lm1, specs = ~a*b)
#'         , list (
#'                 c1 = c(1, 0, -1, 0, 0, 0)
#'               , c2 = c(1, 0, 0, 0, -1, 0)
#'               , c3 = c(0, 0, 1, 0, -1, 0)
#'               , c4 = c(0, 1, 0, -1, 0, 0)
#'               , c5 = c(0, 1, 0, 0, 0, -1)
#'               , c6 = c(0, 1, 0, 0, -1, 0)
#'               )
#'   )
#'
#'
#' ##---Nested Model (page 216)----
#' Exam7.1.lm2 <- lm(formula = y ~ a + a %in% b, data = DataSet7.1)
#'
#' summary(Exam7.1.lm2)
#' model_parameters(Exam7.1.lm2)
#' anova(Exam7.1.lm2)
#'
#' car::linearHypothesis(Exam7.1.lm2, c("a0:b1 = a0:b2"))
#' car::linearHypothesis(Exam7.1.lm2, c("a1:b1 = a1:b2"))
#'
#'  ##---Bonferroni's adjusted p-values
#' emmeans(object  = Exam7.1.lm2, specs = pairwise~b|a, adjust  = "bonferroni")$contrasts
#'
#' ##--- Alternative method of pairwise comparisons by
#' ##  applying contrast coefficient with Bonferroni adjustment
#' contrast(
#'           emmeans(object = Exam7.1.lm1, specs = ~a*b)
#'         , list (
#'                 c1 = c(1, 0, -1, 0, 0, 0)
#'               , c2 = c(1, 0, 0, 0, -1, 0)
#'               , c3 = c(0, 0, 1, 0, -1, 0)
#'               , c4 = c(0, 1, 0, -1, 0, 0)
#'               , c5 = c(0, 1, 0, 0, 0, -1)
#'               , c6 = c(0, 1, 0, 0, -1, 0)
#'               )
#'         , adjust = "bonferroni"
#'   )
#'
#'
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