R/Examp3.1.R

In MYaseen208/VetResearchLMM: Linear Mixed Models - An Introduction with Applications in Veterinary Research

#' @title    Examp3.1 from Duchateau, L. and Janssen, P. and Rowlands, G. J. (1998).\emph{Linear Mixed Models. An Introduction with applications in Veterinary Research}. International Livestock Research Institute.
#' @name     Examp3.1
#' @docType  data
#' @keywords datasets
#' @description Examp3.1 is.
#' @author \enumerate{
#'          \item  Muhammad Yaseen (\email{myaseen208@@gmail.com})
#'          }
#' @references \enumerate{
#' \item Duchateau, L. and Janssen, P. and Rowlands, G. J. (1998).\emph{Linear Mixed Models. An Introduction with applications in Veterinary Research}.
#'              International Livestock Research Institute.
#'  }
#' @seealso
#'    \code{\link{ex124}}
#' @importFrom ggplot2 ggplot
#' @importFrom lme4 lmer
#' @importFrom lmerTest lsmeansLT
#' @examples
#' #-------------------------------------------------------------
#' ## Example 3.1 Model 1 p-80
#' #-------------------------------------------------------------
#' # PROC MIXED DATA=ex31;
#' # CLASS drug dose herd;
#' # MODEL PCV2=drug dose(drug)/solution ddfm=satterth;
#' # RANDOM herd(drug);
#' # ESTIMATE 'Mean Samorin' intercept 1 drug 0 1 dose(drug) 0 0 1;
#' # ESTIMATE 'Berenil 2 doses' dose(drug) 1 -1 0;
#' # ESTIMATE 'Ber vs Sam at dose 1' drug 1 -1 dose(drug) 1 0 -1;
#' # CONTRAST 'Mean Samorin' intercept 1 drug 0 1 dose(drug) 0 0 1;
#' # CONTRAST 'Berenil dif 2 doses' dose(drug) 1 -1 0;
#' # CONTRAST 'Ber vs Sam at dose 1' drug 1 -1 dose(drug) 1 0 -l;
#' # CONTRAST 'some difference' drug 1 -1 dose(drug) 0.5 0.5 -1,
#' #           drug 0 0 dose(drug) 1 -1 0;
#' # LSMEANS dose(drug);
#' # RUN;
#'
#'  library(lmerTest)
#'  str(ex31)
#'  ex31$drug1 <- factor(ex31$drug)
#'  ex31$dose1 <- factor(ex31$dose)
#'  ex31$herd1 <- factor(ex31$herd)
#'
#'  fm3.1 <-
#'   lmerTest::lmer(
#'          formula    = PCV2 ~ drug1 + dose1:drug1 + (1|herd1:drug1)
#'        , data       = ex31
#'        , REML       = TRUE
#'        , control    = lmerControl()
#'        , start      = NULL
#'        , verbose    = 0L
#'     #  , subset
#'     #  , weights
#'     #  , na.action
#'     #  , offset
#'        , contrasts  = list(dose1 = "contr.SAS", drug1 = "contr.SAS")
#'        , devFunOnly = FALSE
#'     #  , ...
#'        )
#'  summary(fm3.1)
#'  anova(object = fm3.1, ddf = "Satterthwaite")
#'  lsmeansLT(model = fm3.1, test.effs = "dose1:drug1")
#'
#' #-------------------------------------------------------------
#' ## Example 3.1 Model 2 p-84
#' #-------------------------------------------------------------
#' # PROC MIXED DATA=ex31;
#' # CLASS drug dose herd;
#' # MODEL PCV2=PCV1 drug dose(drug)/solution ddfm=satterth;
#' # RANDOM herd(drug);
#' # RUN;
#'
#'  library(lmerTest)
#'  str(ex31)
#'  ex31$drug1 <- factor(ex31$drug)
#'  ex31$dose1 <- factor(ex31$dose)
#'  ex31$herd1 <- factor(ex31$herd)
#'
#'  fm3.2 <-
#'   lmerTest::lmer(
#'          formula    = PCV2 ~ PCV1 + drug1 + dose1:drug1 + (1|herd1:drug1)
#'        , data       = ex31
#'        , REML       = TRUE
#'        , control    = lmerControl()
#'        , start      = NULL
#'        , verbose    = 0L
#'     #  , subset
#'     #  , weights
#'     #  , na.action
#'     #  , offset
#'        , contrasts  = list(dose1 = "contr.SAS", drug1 = "contr.SAS")
#'        , devFunOnly = FALSE
#'     #  , ...
#'        )
#'  summary(fm3.2)
#'  anova(object = fm3.2, ddf = "Satterthwaite")
#'  lsmeansLT(model = fm3.2, test.effs = "herd1:drug1")
#'
#' #-------------------------------------------------------------
#' ## Example 3.1 Model 3 p-86
#' #-------------------------------------------------------------
#' # PROC MIXED DATA=ex31;
#' # CLASS drug dose herd;
#' # MODEL PCV2=drug dose(drug) PCV1*dose(drug)/solution ddfm=satterth;
#' # RANDOM herd(drug);
#' # RUN;
#'
#'  library(lmerTest)
#'  str(ex31)
#'  ex31$drug1 <- factor(ex31$drug)
#'  ex31$dose1 <- factor(ex31$dose)
#'  ex31$herd1 <- factor(ex31$herd)
#'
#'  fm3.3 <-
#'   lmerTest::lmer(
#'          formula    = PCV2 ~ drug1 + PCV1*dose1:drug1 + (1|herd1:drug1)
#'        , data       = ex31
#'        , REML       = TRUE
#'        , control    = lmerControl()
#'        , start      = NULL
#'        , verbose    = 0L
#'     #  , subset
#'     #  , weights
#'     #  , na.action
#'     #  , offset
#'        , contrasts  = list(dose1 = "contr.SAS", drug1 = "contr.SAS")
#'        , devFunOnly = FALSE
#'     #  , ...
#'        )
#'  summary(fm3.3)
#'  anova(object = fm3.3, ddf = "Satterthwaite")
#'  lsmeansLT(model = fm3.3, test.effs = "dose1:drug1")
NULL