R/neg.pd.R

In negligible: A Collection of Functions for Negligible Effect/Equivalence Testing

#' Proportional Distance Function (post hoc function - not to be used independently)
#'
#' @param effect observed effect
#' @param PD proportional distance for effect
#' @param eil lower bound of the equivalence interval
#' @param eiu upper bound of the equivalence interval
#' @param PDcil lower bound of the CI for the proportional distance
#' @param PDciu upper bound of the CI for the proportional distance
#' @param cil lower bound of the CI for the effect
#' @param ciu upper bound of the CI for the effect
#' @param Elevel 1-2alpha CI for the effect
#' @param Plevel 1-alpha CI for the PD
#' @param save Whether to save the plot or not
#' @param oe Name of the original units of the effect of interest
#'
#' @return nothing is returned
#' @export
#'
#' @examples
#' \dontrun{
#' 1+1
#' }

neg.pd<-function(effect, PD, eil, eiu,
                 PDcil, PDciu,  cil, ciu, Elevel, Plevel, save, oe) {

  EIu<-c(eiu,0) #actual value
  EIl<-c(eil,0) #actual value
  if(oe=='CFI' | oe=="Shapiro-Wilk W"){PDp<-c(1-(abs(PD)/abs(PDcil)),1)} else {PDp<-c(effect,1)}
  effectp<-c(effect,0) #actual value
  if(oe=='CFI' | oe=="Shapiro-Wilk W"){start1<-c(1,1)} else{start1<-c(0,1)}
  if(oe=='CFI' | oe=="Shapiro-Wilk W"){start2<-c(1,0)} else{start2<-c(0,0)}

  #calculate 1/4 of the total 100*(1-x$alpha) distance to create the length of the scales (note that this is an arbitrary number)
  if(oe=='CFI' | oe=="Shapiro-Wilk W") {onefourth<- 1/4} else {onefourth<-(abs((cil/2)+ (PDcil*effect/PD)) + abs((ciu/2)+ (PDciu*effect/PD)))/4}
  a<- -3*onefourth
  if(a>eil)
  {a<-eil}
  if(eil==eiu){a<-0}
  b<- 3*onefourth
  if(b<eiu)
  {b<-eiu}
  extraL<-c(a,0)
  if(oe=='CFI' | oe=="Shapiro-Wilk W") {extraU<-c(1,0)} else{extraU<-c(b,0)}
  PDextraL<-c(a,1)
  if(oe=='CFI' | oe=="Shapiro-Wilk W") {PDextraU<-c(1,1)} else{PDextraU<-c(b,1)}

  #individual scale values after the (0,0) co-ordinate
  if (b==eiu & a==eil) {onefourth=eiu/3}
  first<-onefourth
  second <- first + onefourth
  third<-second + onefourth
  first<-c(first,0)
  second<-c(second,0)
  third<-c(third,0)
  PDfirst<-onefourth
  PDsecond <-PDfirst+onefourth
  PDthird<-PDsecond+onefourth
  PDfirst<-c(PDfirst,1)
  PDsecond<-c(PDsecond,1)
  PDthird<-c(PDthird,1)

  #individual scale values before the (0,0) co-ordinate
  Bfirst<-onefourth
  Bsecond <- Bfirst + onefourth
  Bthird<-Bsecond + onefourth

  if (eil==eiu)
  {  Bfirst<-0
  Bsecond <- 0
  Bthird<- 0 }

  Bfirst<-c(-Bfirst,0)
  Bsecond<-c(-Bsecond,0)
  Bthird<-c(-Bthird,0)

  BPDfirst<-onefourth
  BPDsecond <-BPDfirst+onefourth
  BPDthird<-BPDsecond+onefourth

  if (eil==eiu)
  {  BPDfirst<-0
  BPDsecond<- 0
  BPDthird<- 0 }

  BPDfirst<-c(-BPDfirst,1)
  BPDsecond<-c(-BPDsecond,1)
  BPDthird<-c(-BPDthird,1)

  #create a dataframe containing all the co-ordinates of interest
  X1<-NULL
  X2<-NULL
  dat<-rbind(BPDthird, BPDsecond, BPDfirst, start1, PDp, PDextraL, PDextraU, PDfirst, PDsecond, PDthird, Bthird, Bsecond, Bfirst, start2, effectp, EIl, EIu, extraL, extraU, first, second, third)
  dat<- data.frame(dat)
  p<-ggplot2::ggplot(data=dat, ggplot2::aes(x=X1,y=X2)) +
    ggplot2::geom_step(data=dat[6:7,], color = "black") +
    ggplot2::geom_step(data=dat[18:19,], color = "black") +
    ggplot2::geom_point(shape=c(3,3,3,3,23,3,3,3,3,3,3,3,3,3,21,8,8,16,16,3,3,3), fill=c("black" ,"black", "black","black", "darkred", "black", "black" ,"black", "black" ,"black", "black" ,"black", "black" ,"black" ,"purple","blue","blue", "black", "black","black", "black","black"), color=c("black" ,"black", "black","black", "darkred", "black", "black" ,"black", "black" ,"black", "black" ,"black", "black" ,"black" ,"purple","blue", "blue", "black", "black","black", "black","black"), size=c(3,3,3,3,2,3,3,3,3,3,3,3,3,3,2,2,2,0.1,0.1,3,3,3), stroke = 0.7) +
    ggplot2::annotate("text",x=extraU[1], y=-0.12, label=format(round(extraU[1], 2), nsmall = 2), size=3, colour = "black") +
    ggplot2::annotate("text",x=extraL[1], y=-0.12, label=format(round(extraL[1], 2), nsmall = 2), size=3, colour = "black") +
    ggplot2::annotate("text",x=a, y=0.4, label=(paste0(oe," (Original Units)")), size=3, hjust = 0) +
    ggplot2::annotate("text",x=a, y=2.6, label="    Equivalence Interval (EI) Boundary", size=3.5, colour = "blue4", hjust = 0) +
    ggplot2::geom_point(ggplot2::aes(x=a, y=2.6), shape = 8, colour="blue", size = 3) +
    ggplot2::annotate("text",x=a, y=3, label=(paste0("    Proportional Distance and its ",Plevel, "% CI")), size=3.5, colour = "darkred", hjust = 0) +
    ggplot2::geom_point(ggplot2::aes(x=a, y=3), shape = 22, colour="red", size = 4, fill = "grey") +
    ggplot2::geom_point(ggplot2::aes(x=a, y=3), shape = 18, colour="darkred", size = 3) +
    ggplot2::theme(panel.grid.major = ggplot2::element_blank(), panel.grid.minor = ggplot2::element_blank(), axis.title = ggplot2::element_blank(),
                   panel.background = ggplot2::element_blank(), axis.line = ggplot2::element_blank(), axis.ticks= ggplot2::element_blank(), axis.text = ggplot2::element_blank())

  if(oe=="Mean Difference" | oe=="Correlation Coefficients' Difference" | oe=="Regression Coefficient" | oe=="Interaction Coefficient" | oe=="Direct Effect" | oe=="Correlation (r)"){
    suppressWarnings(print(
    p+
      ggplot2::ylim(-0.5, 3) + ggplot2::annotate("rect", xmin = cil, xmax = ciu, ymin = -0.05, ymax = 0.05, alpha = .2,fill = "blue") +
      ggplot2::geom_step(data=dat[4:5,], color = "darkred") +
      ggplot2::geom_step(data=dat[14:15,], color = "blue") +
      ggplot2::annotate("text",x=a, y=2.2, label=(paste0("    ",oe," and its ",Elevel,"% CI")), size=3.5, colour = "purple", hjust=0) +
      ggplot2::annotate("rect", xmin = PDcil*effect/PD, xmax = PDciu*effect/PD, ymin = 0.95, ymax = 1.05, alpha = .2,fill = "red") +
      ggplot2::annotate("text",x=effect, y=1.12, label=format(round(PD, 2), nsmall = 2), size=3, colour = "darkred") +
      ggplot2::annotate("text",x=PDextraU[1], y=0.88, label=format(round((PDextraU[1]*PD)/effect, 2), nsmall = 2), size=3, colour = "black") +
      ggplot2::annotate("text",x=PDextraL[1], y=0.88, label=format(round((PDextraL[1]*PD)/effect, 2), nsmall = 2), size=3, colour = "black") +
      ggplot2::annotate("text",x=effect, y=0.12, label=format(round(effect, 2), nsmall = 2), size=3, colour = "purple") +
      ggplot2::annotate("text",x=cil, y=0.12, label=format(round(cil, 2), nsmall = 2), size=3, colour = "purple") +
      ggplot2::annotate("text",x=ciu, y=0.12, label=format(round(ciu, 2), nsmall = 2), size=3, colour = "purple") +
      ggplot2::annotate("text",x=PDcil*effect/PD, y=1.12, label=format(round(PDcil, 2), nsmall = 2), size=3, colour = "darkred") +
      ggplot2::annotate("text",x=PDciu*effect/PD, y=1.12, label=format(round(PDciu, 2), nsmall = 2), size=3, colour = "darkred") +
      ggplot2::annotate("text",x=onefourth, y=-0.12, label=format(round(onefourth, 2), nsmall = 2), size=3, colour = "black") +
      ggplot2::annotate("text",x=2*onefourth, y=-0.12, label=format(round(2*onefourth, 2), nsmall = 2), size=3, colour = "black") +
      ggplot2::annotate("text",x=3*onefourth, y=-0.12, label=format(round(3*onefourth, 2), nsmall = 2), size=3, colour = "black") +
      ggplot2::annotate("text",x=-onefourth, y=-0.12, label=format(round(-onefourth, 2), nsmall = 2), size=3, colour = "black") +
      ggplot2::annotate("text",x=-2*onefourth, y=-0.12, label=format(round(-2*onefourth, 2), nsmall = 2), size=3, colour = "black") +
      ggplot2::annotate("text",x=a, y=-0.12, label=format(round(a, 2), nsmall = 2), size=3, colour = "black") +
      ggplot2::annotate("text",x=0, y=-0.12, label=0, size=3, colour = "black") +
      ggplot2::annotate("text",x=0, y=0.88, label=0, size=3, colour = "black") +
      ggplot2::annotate("text",x=-onefourth, y=0.88, label=format(round((-onefourth*PD)/effect, 2), nsmall = 2), size=3, colour = "black") +
      ggplot2::annotate("text",x=-2*onefourth, y=0.88, label=format(round((-2*onefourth*PD)/effect, 2), nsmall = 2), size=3, colour = "black") +
      ggplot2::annotate("text",x=onefourth, y=0.88, label=format(round((onefourth*PD)/effect, 2), nsmall = 2), size=3, colour = "black") +
      ggplot2::annotate("text",x=2*onefourth, y=0.88, label=format(round((2*onefourth*PD)/effect, 2), nsmall = 2), size=3, colour = "black") +
      ggplot2::annotate("text",x=a, y=1.4, label=paste("The Proportional Distance from the Effect to the EI Bound of the Same Sign as the Effect"), size=3, hjust = 0) +
      ggplot2::geom_point(ggplot2::aes(x=a, y=2.2), shape = 22, colour="blue", size = 4, fill = "grey") +
      ggplot2::geom_point(ggplot2::aes(x=a, y=2.2), shape = 16, colour="purple", size = 3)
  ))}
  if(oe=="RMSEA" | oe=="Cramer's V" | oe=="SRMR"){
    suppressWarnings(print(
      p+
        ggplot2::ylim(-0.5, 3) + ggplot2::annotate("segment", x = ciu, xend = ciu, y = .08, yend = -.08, colour = "purple", size=2, alpha=0.6) +
        ggplot2::annotate("rect", xmin = PDcil*effect/PD, xmax = PDciu*effect/PD, ymin = 0.95, ymax = 1.05, alpha = .2,fill = "red") +
        ggplot2::annotate("text",x=effect, y=1.12, label=format(round(PD, 2), nsmall = 2), size=3, colour = "darkred") +
        ggplot2::annotate("text",x=PDextraU[1], y=0.88, label=format(round((PDextraU[1]*PD)/effect, 2), nsmall = 2), size=3, colour = "black") +
        ggplot2::annotate("text",x=PDextraL[1], y=0.88, label=format(round((PDextraL[1]*PD)/effect, 2), nsmall = 2), size=3, colour = "black") +
        ggplot2::annotate("text",x=effect, y=0.12, label=format(round(effect, 2), nsmall = 2), size=3, colour = "purple") +
        ggplot2::annotate("text",x=ciu, y=0.12, label=format(round(ciu, 2), nsmall = 2), size=3, colour = "purple") +
        ggplot2::annotate("text",x=onefourth, y=-0.12, label=format(round(onefourth, 2), nsmall = 2), size=3, colour = "black") +
        ggplot2::annotate("text",x=2*onefourth, y=-0.12, label=format(round(2*onefourth, 2), nsmall = 2), size=3, colour = "black") +
        ggplot2::annotate("text",x=3*onefourth, y=-0.12, label=format(round(3*onefourth, 2), nsmall = 2), size=3, colour = "black") +
        ggplot2::annotate("text",x=a, y=-0.12, label=format(round(a, 2), nsmall = 2), size=3, colour = "black") +
        ggplot2::annotate("text",x=onefourth, y=0.88, label=format(round((onefourth*PD)/effect, 2), nsmall = 2), size=3, colour = "black") +
        ggplot2::annotate("text",x=2*onefourth, y=0.88, label=format(round((2*onefourth*PD)/effect, 2), nsmall = 2), size=3, colour = "black") +
        ggplot2::annotate("text",x=a, y=2.2, label=(paste0("    ",oe)), size=3.5, colour = "purple", hjust=0) +
        ggplot2::annotate("text",x=a, y=1.4, label=(paste0("The Proportional Distance (",oe,"-0 / |EI-0|)")), size=3, hjust = 0) +
        ggplot2::annotate("text",x=a, y=1.8, label=(paste0("    The upper ",Elevel,"% CI boundary for the ",oe)), size=3.5, colour = "purple", hjust=0) +
        ggplot2::geom_point(ggplot2::aes(x=a, y=1.8), shape = 15, colour="purple", size = 3, alpha =1/50) +
        ggplot2::geom_point(ggplot2::aes(x=a, y=2.2), shape = 16, colour="purple", size = 3)
    ))}
  if(oe=='CFI' | oe=="Shapiro-Wilk W") {
    suppressWarnings(print(
      p+
        ggplot2::ylim(-0.5, 3) + ggplot2::annotate("segment", x = ciu, xend = ciu, y = .08, yend = -.08, colour = "purple", size=2, alpha=0.6) +
        ggplot2::annotate("rect", xmin = 0, xmax = 1-(PDciu/PDcil), ymin = 0.95, ymax = 1.05, alpha = .2,fill = "red") +
        ggplot2::annotate("text",x=1-(abs(PD)/abs(PDcil)), y=1.12, label=format(round(PD, 2), nsmall = 2), size=3, colour = "darkred") +
        ggplot2::annotate("text",x=PDextraU[1], y=0.88, label=0.00, size=3, colour = "black") +
        ggplot2::annotate("text",x=PDextraL[1], y=0.88, label=format(round(PDcil, 2), nsmall = 2), size=3, colour = "black") +
        ggplot2::annotate("text",x=0, y=1.12, label=format(round(PDcil, 2), nsmall = 2), size=3, colour = "darkred") +
        ggplot2::annotate("text",x=1-(PDciu/PDcil), y=1.12, label=format(round(PDciu, 2), nsmall = 2), size=3, colour = "darkred") +
        ggplot2::annotate("text",x=effect, y=0.12, label=format(round(effect, 2), nsmall = 2), size=3, colour = "purple") +
        ggplot2::annotate("text",x=cil, y=-0.12, label=format(round(cil, 2), nsmall = 2), size=3, colour = "purple") +
        ggplot2::annotate("text",x=onefourth, y=-0.12, label=format(round(onefourth, 2), nsmall = 2), size=3, colour = "black") +
        ggplot2::annotate("text",x=2*onefourth, y=-0.12, label=format(round(2*onefourth, 2), nsmall = 2), size=3, colour = "black") +
        ggplot2::annotate("text",x=3*onefourth, y=-0.12, label=format(round(3*onefourth, 2), nsmall = 2), size=3, colour = "black") +
        ggplot2::annotate("text",x=a, y=-0.12, label=format(round(a, 2), nsmall = 2), size=3, colour = "black") +
        ggplot2::annotate("text",x=onefourth, y=0.88, label=format(-round(abs(PDcil)-(abs(PDcil)/4), 2), nsmall = 2), size=3, colour = "black") +
        ggplot2::annotate("text",x=2*onefourth, y=0.88, label=format(-round((abs(PDcil)-(abs(PDcil)/4))-abs(PDcil)/4, 2), nsmall = 2), size=3, colour = "black") +
        ggplot2::annotate("text",x=3*onefourth, y=0.88, label=format(-round(((abs(PDcil)-(abs(PDcil)/4))-abs(PDcil)/4)-abs(PDcil)/4, 2), nsmall = 2), size=3, colour = "black") +
        ggplot2::annotate("text",x=a, y=2.2, label=(paste0("    ",oe)), size=3.5, colour = "purple", hjust=0) +
        ggplot2::annotate("text",x=a, y=1.4, label=(paste0("The Proportional Distance (",oe,"-1 / |EI-1|)")), size=3, hjust = 0) +
        ggplot2::annotate("text",x=a, y=1.8, label=(paste0("    The lower ",Elevel,"% CI boundary for the ",oe)), size=3.5, colour = "purple", hjust=0) +
        ggplot2::geom_point(ggplot2::aes(x=a, y=1.8), shape = 15, colour="purple", size = 3, alpha =1/50) +
        ggplot2::geom_point(ggplot2::aes(x=a, y=2.2), shape = 16, colour="purple", size = 3)
    ))
  }
  if (!(save == FALSE)) {
    if (save == "png") {
      ggplot2::ggsave(filename = "Proportional_Distance_Plot.png" ,width = 9, height = 4, device='png', dpi=700)
    }
    if (save == "jpeg") {
      ggplot2::ggsave(filename = "Proportional_Distance_Plot.jpeg" ,width = 9, height = 4, device='png', dpi=700)
    }
  }
}