R/betapower_plot.R
In CastleLi/BetaPSS: Calculate Power and Sample Size with Beta Regression.
plot.unit1 = function(input.data){
input.data$`sample size` <- as.factor(input.data$`sample size`)
levels(input.data$`sample size`) <- paste0("sample size = ",levels(input.data$`sample size`))
Labels <- as.factor(input.data$`sample size`)
input.data$subj <- as.factor(input.data$subj)
base_size <- 12
ggplot2::ggplot(data=input.data,ggplot2::aes_string(x = "mu1",y= "power",colour = "Labels"))+
ggplot2::geom_line(ggplot2::aes(linetype = Labels)) +
ggplot2::geom_point(ggplot2::aes(shape = Labels)) +
ggplot2::ylab("Power") +
ggplot2::xlab("mu1")+
ggplot2::facet_grid(~ input.data$subj)+
ggplot2::theme(
axis.line = ggplot2::element_blank(),
axis.text.x = ggplot2::element_text(size = base_size * 0.8 , lineheight = 0.9, vjust = 1),
axis.text.y = ggplot2::element_text(size = base_size * 0.8, lineheight = 0.9, hjust = 1),
axis.ticks = ggplot2::element_line(colour = "black", size = 0.2),
axis.title.x = ggplot2::element_text(size = base_size, vjust = 1),
axis.title.y = ggplot2::element_text(size = base_size, angle = 90, vjust = 0.5),
axis.ticks.length = ggplot2::unit(0.3, "lines"),
legend.justification=c(1,0),
legend.background = ggplot2::element_rect(colour=NA),
legend.key = ggplot2::element_rect(colour = "grey80"),
legend.key.size = ggplot2::unit(1.2, "lines"),
legend.text = ggplot2::element_text(size = base_size * 0.8),
legend.title = ggplot2::element_text(size = base_size * 0.8, face = "bold", hjust = 0),
legend.position = "right",
panel.background = ggplot2::element_rect(fill = "white", colour = NA),
panel.border = ggplot2::element_rect(fill = NA, colour="grey50"),
panel.grid.major = ggplot2::element_line(colour = "grey90", size = 0.2),
panel.grid.minor = ggplot2::element_line(colour = "grey98", size = 0.5),
panel.spacing = ggplot2::unit(1, "lines"),
aspect.ratio = 2,
plot.background = ggplot2::element_rect(colour = NA),
plot.title = ggplot2::element_text(size = base_size * 1.2),
plot.margin = ggplot2::unit(c(1, 1, 0.5, 0.5), "lines"),
strip.background = ggplot2::element_rect(fill = "grey",size = 1)
) +
ggplot2::scale_y_continuous(breaks=seq(0,1,0.1))
}
plot.unit2 = function(input.data){
Labels <- as.factor(input.data$subj)
input.data$`sample size` <- as.factor(input.data$`sample size`)
levels(input.data$`sample size`) <- paste0("sample size = ",levels(input.data$`sample size`))
base_size <- 12
ggplot2::ggplot(data=input.data,ggplot2::aes_string(x = "mu1",y= "power",colour = "Labels"))+
ggplot2::geom_line(ggplot2::aes(linetype = Labels)) +
ggplot2::geom_point(ggplot2::aes(shape = Labels)) +
ggplot2::ylab("Power") +
ggplot2::xlab("mu1")+
ggplot2::facet_grid(~ input.data$`sample size`)+
ggplot2::theme(
axis.line = ggplot2::element_blank(),
axis.text.x = ggplot2::element_text(size = base_size * 0.8 , lineheight = 0.9, vjust = 1),
axis.text.y = ggplot2::element_text(size = base_size * 0.8, lineheight = 0.9, hjust = 1),
axis.ticks = ggplot2::element_line(colour = "black", size = 0.2),
axis.title.x = ggplot2::element_text(size = base_size, vjust = 1),
axis.title.y = ggplot2::element_text(size = base_size, angle = 90, vjust = 0.5),
axis.ticks.length = ggplot2::unit(0.3, "lines"),
legend.justification=c(1,0),
legend.background = ggplot2::element_rect(colour=NA),
legend.key = ggplot2::element_rect(colour = "grey80"),
legend.key.size = ggplot2::unit(1.2, "lines"),
legend.text = ggplot2::element_text(size = base_size * 0.8),
legend.title = ggplot2::element_text(size = base_size * 0.8, face = "bold", hjust = 0),
legend.position = "right",
panel.background = ggplot2::element_rect(fill = "white", colour = NA),
panel.border = ggplot2::element_rect(fill = NA, colour="grey50"),
panel.grid.major = ggplot2::element_line(colour = "grey90", size = 0.2),
panel.grid.minor = ggplot2::element_line(colour = "grey98", size = 0.5),
panel.spacing = ggplot2::unit(1, "lines"),
aspect.ratio = 2,
plot.background = ggplot2::element_rect(colour = NA),
plot.title = ggplot2::element_text(size = base_size * 1.2),
plot.margin = ggplot2::unit(c(1, 1, 0.5, 0.5), "lines"),
strip.background = ggplot2::element_rect(fill = "grey",size = 1)
) +
ggplot2::scale_y_continuous(breaks=seq(0,1,0.1))
}
plot.unit3 = function(input.data){
Labels <- as.factor(input.data$subj)
input.data$mu1 <- as.factor(input.data$mu1)
levels(input.data$mu1) <- paste0("mu1 = ",levels(input.data$mu1))
base_size <- 12
ggplot2::ggplot(data=input.data,ggplot2::aes_string(x = input.data[,"sample size"],y= "power",colour = "Labels"))+
ggplot2::geom_line(ggplot2::aes(linetype = Labels)) +
ggplot2::geom_point(ggplot2::aes(shape = Labels)) +
ggplot2::ylab("Power") +
ggplot2::xlab("Sample Size")+
ggplot2::facet_grid(~ input.data$mu1)+
ggplot2::theme(
axis.line = ggplot2::element_blank(),
axis.text.x = ggplot2::element_text(size = base_size * 0.8 , lineheight = 0.9, vjust = 1),
axis.text.y = ggplot2::element_text(size = base_size * 0.8, lineheight = 0.9, hjust = 1),
axis.ticks = ggplot2::element_line(colour = "black", size = 0.2),
axis.title.x = ggplot2::element_text(size = base_size, vjust = 1),
axis.title.y = ggplot2::element_text(size = base_size, angle = 90, vjust = 0.5),
axis.ticks.length = ggplot2::unit(0.3, "lines"),
legend.justification=c(1,0),
legend.background = ggplot2::element_rect(colour=NA),
legend.key = ggplot2::element_rect(colour = "grey80"),
legend.key.size = ggplot2::unit(1.2, "lines"),
legend.text = ggplot2::element_text(size = base_size * 0.8),
legend.title = ggplot2::element_text(size = base_size * 0.8, face = "bold", hjust = 0),
legend.position = "right",
panel.background = ggplot2::element_rect(fill = "white", colour = NA),
panel.border = ggplot2::element_rect(fill = NA, colour="grey50"),
panel.grid.major = ggplot2::element_line(colour = "grey90", size = 0.2),
panel.grid.minor = ggplot2::element_line(colour = "grey98", size = 0.5),
panel.spacing = ggplot2::unit(1, "lines"),
aspect.ratio = 2,
plot.background = ggplot2::element_rect(colour = NA),
plot.title = ggplot2::element_text(size = base_size * 1.2),
plot.margin = ggplot2::unit(c(1, 1, 0.5, 0.5), "lines"),
strip.background = ggplot2::element_rect(fill = "grey",size = 1)
) +
ggplot2::scale_y_continuous(breaks=seq(0,1,0.1))
}
#' @title Plots of Beta power
#' @description Generate several comparison plots of power.
#' @usage betapower.plot(betapower.matrix,link.type,by)
#' @param betapower.matrix a matrix obtained by the function betapower.(the formula was described as the output formula in the function betapower)
#' @param link.type the type of link used in the beta regression. You can choose one or more of the following: "logit", "probit", "cloglog", "cauchit", "log", "loglog", "all"
#' @param by the type of plot. see details.
#' @details betapower.plot() returns different plots depends on by\cr
#' by = "linktype": betapower.plot() returns graphs that plot power against mu1,
#' where mu1 is the mean for the treatment group under the alternative.
#' The number of plots will vary depending on the number of link types selected with the last plot showing power based on Wilcoxon Rank Sum Test.
#' The first one or several plots show comparisons of power with different sample size, using GLM method with one or several link types.
#' The last plot shows a comparison of the power with different sample size using Wilcoxon Rank Sum Test.
#' Y-axis denotes power and X-axis denotes mu1, the mean for the treatment group under the alternative.\cr
#' by = "samplesize": betapower.plot() returns a number of plots equal to the number of sample sizes tested.
#' Each plot compares power calculated with different link types and the Wilcoxon Rank Sum Test.
#' Y-axis denotes power and X-axis denotes mu1, the mean for the treatment group under the alternative.\cr
#' by = "mu1": betapower.plot() returns a number of plots equal to the number of mu1 used in the procedure.
#' Each plot compares power calculated with different link types and the Wilcoxon Rank Sum Test.
#' Y-axis denotes power and X-axis denotes sample size.\cr
#' @examples
#' BPmat <- betapower(0.56,0.255,.70,.75,.05,30,50, 20,40,610201501,"all")
#' betapower.plot(BPmat,link.type = "all",by="linktype")
#' betapower.plot(BPmat,link.type = "all",by="samplesize")
#' betapower.plot(BPmat,link.type = "all",by="mu1")
#' BPmat2 <- betapower(0.56,0.255,.560,.76,.05,30,45, 5,200,610201511,c("logit","loglog","log"))
#' betapower.plot(BPmat2,link.type = c("logit","loglog","log"),by="linktype")
#' betapower.plot(BPmat2,link.type = c("logit","loglog","log"),by="samplesize")
#' betapower.plot(BPmat2,link.type = c("logit","loglog","log"),by="mu1")
#' @export
betapower.plot <- function(Tmp.matrix,link.type,by){
if(link.type[1]=="all"){
link.type <- c("logit", "probit", "cloglog", "log", "loglog")
}
if(by!="linktype"&by!="samplesize"&by!="mu1"){
step("Wrong plot type")
}
name.plot <- c(paste("power of GLM:",link.type),"power of Wilcoxon test")
output.name.plot <- c(paste0("Power: GLM (",link.type,")"), "Power: Wilcoxon")
input.data <- reshape(Tmp.matrix,varying = name.plot,
v.names = "power",
timevar = "subj",
times = output.name.plot,
direction = "long",
new.row.names = c(1:(length(name.plot)*nrow(Tmp.matrix))))
if(by == "linktype"){
plot.unit1(input.data = input.data)
}
else if(by == "samplesize"){
plot.unit2(input.data = input.data)
}
else if(by == "mu1"){
plot.unit3(input.data = input.data)
}
}
CastleLi/BetaPSS documentation built on May 15, 2019, 10:34 p.m.
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
plot.unit1 = function(input.data){
input.data$`sample size` <- as.factor(input.data$`sample size`)
levels(input.data$`sample size`) <- paste0("sample size = ",levels(input.data$`sample size`))
Labels <- as.factor(input.data$`sample size`)
input.data$subj <- as.factor(input.data$subj)
base_size <- 12
ggplot2::ggplot(data=input.data,ggplot2::aes_string(x = "mu1",y= "power",colour = "Labels"))+
ggplot2::geom_line(ggplot2::aes(linetype = Labels)) +
ggplot2::geom_point(ggplot2::aes(shape = Labels)) +
ggplot2::ylab("Power") +
ggplot2::xlab("mu1")+
ggplot2::facet_grid(~ input.data$subj)+
ggplot2::theme(
axis.line = ggplot2::element_blank(),
axis.text.x = ggplot2::element_text(size = base_size * 0.8 , lineheight = 0.9, vjust = 1),
axis.text.y = ggplot2::element_text(size = base_size * 0.8, lineheight = 0.9, hjust = 1),
axis.ticks = ggplot2::element_line(colour = "black", size = 0.2),
axis.title.x = ggplot2::element_text(size = base_size, vjust = 1),
axis.title.y = ggplot2::element_text(size = base_size, angle = 90, vjust = 0.5),
axis.ticks.length = ggplot2::unit(0.3, "lines"),
legend.justification=c(1,0),
legend.background = ggplot2::element_rect(colour=NA),
legend.key = ggplot2::element_rect(colour = "grey80"),
legend.key.size = ggplot2::unit(1.2, "lines"),
legend.text = ggplot2::element_text(size = base_size * 0.8),
legend.title = ggplot2::element_text(size = base_size * 0.8, face = "bold", hjust = 0),
legend.position = "right",
panel.background = ggplot2::element_rect(fill = "white", colour = NA),
panel.border = ggplot2::element_rect(fill = NA, colour="grey50"),
panel.grid.major = ggplot2::element_line(colour = "grey90", size = 0.2),
panel.grid.minor = ggplot2::element_line(colour = "grey98", size = 0.5),
panel.spacing = ggplot2::unit(1, "lines"),
aspect.ratio = 2,
plot.background = ggplot2::element_rect(colour = NA),
plot.title = ggplot2::element_text(size = base_size * 1.2),
plot.margin = ggplot2::unit(c(1, 1, 0.5, 0.5), "lines"),
strip.background = ggplot2::element_rect(fill = "grey",size = 1)
) +
ggplot2::scale_y_continuous(breaks=seq(0,1,0.1))
}
plot.unit2 = function(input.data){
Labels <- as.factor(input.data$subj)
input.data$`sample size` <- as.factor(input.data$`sample size`)
levels(input.data$`sample size`) <- paste0("sample size = ",levels(input.data$`sample size`))
base_size <- 12
ggplot2::ggplot(data=input.data,ggplot2::aes_string(x = "mu1",y= "power",colour = "Labels"))+
ggplot2::geom_line(ggplot2::aes(linetype = Labels)) +
ggplot2::geom_point(ggplot2::aes(shape = Labels)) +
ggplot2::ylab("Power") +
ggplot2::xlab("mu1")+
ggplot2::facet_grid(~ input.data$`sample size`)+
ggplot2::theme(
axis.line = ggplot2::element_blank(),
axis.text.x = ggplot2::element_text(size = base_size * 0.8 , lineheight = 0.9, vjust = 1),
axis.text.y = ggplot2::element_text(size = base_size * 0.8, lineheight = 0.9, hjust = 1),
axis.ticks = ggplot2::element_line(colour = "black", size = 0.2),
axis.title.x = ggplot2::element_text(size = base_size, vjust = 1),
axis.title.y = ggplot2::element_text(size = base_size, angle = 90, vjust = 0.5),
axis.ticks.length = ggplot2::unit(0.3, "lines"),
legend.justification=c(1,0),
legend.background = ggplot2::element_rect(colour=NA),
legend.key = ggplot2::element_rect(colour = "grey80"),
legend.key.size = ggplot2::unit(1.2, "lines"),
legend.text = ggplot2::element_text(size = base_size * 0.8),
legend.title = ggplot2::element_text(size = base_size * 0.8, face = "bold", hjust = 0),
legend.position = "right",
panel.background = ggplot2::element_rect(fill = "white", colour = NA),
panel.border = ggplot2::element_rect(fill = NA, colour="grey50"),
panel.grid.major = ggplot2::element_line(colour = "grey90", size = 0.2),
panel.grid.minor = ggplot2::element_line(colour = "grey98", size = 0.5),
panel.spacing = ggplot2::unit(1, "lines"),
aspect.ratio = 2,
plot.background = ggplot2::element_rect(colour = NA),
plot.title = ggplot2::element_text(size = base_size * 1.2),
plot.margin = ggplot2::unit(c(1, 1, 0.5, 0.5), "lines"),
strip.background = ggplot2::element_rect(fill = "grey",size = 1)
) +
ggplot2::scale_y_continuous(breaks=seq(0,1,0.1))
}
plot.unit3 = function(input.data){
Labels <- as.factor(input.data$subj)
input.data$mu1 <- as.factor(input.data$mu1)
levels(input.data$mu1) <- paste0("mu1 = ",levels(input.data$mu1))
base_size <- 12
ggplot2::ggplot(data=input.data,ggplot2::aes_string(x = input.data[,"sample size"],y= "power",colour = "Labels"))+
ggplot2::geom_line(ggplot2::aes(linetype = Labels)) +
ggplot2::geom_point(ggplot2::aes(shape = Labels)) +
ggplot2::ylab("Power") +
ggplot2::xlab("Sample Size")+
ggplot2::facet_grid(~ input.data$mu1)+
ggplot2::theme(
axis.line = ggplot2::element_blank(),
axis.text.x = ggplot2::element_text(size = base_size * 0.8 , lineheight = 0.9, vjust = 1),
axis.text.y = ggplot2::element_text(size = base_size * 0.8, lineheight = 0.9, hjust = 1),
axis.ticks = ggplot2::element_line(colour = "black", size = 0.2),
axis.title.x = ggplot2::element_text(size = base_size, vjust = 1),
axis.title.y = ggplot2::element_text(size = base_size, angle = 90, vjust = 0.5),
axis.ticks.length = ggplot2::unit(0.3, "lines"),
legend.justification=c(1,0),
legend.background = ggplot2::element_rect(colour=NA),
legend.key = ggplot2::element_rect(colour = "grey80"),
legend.key.size = ggplot2::unit(1.2, "lines"),
legend.text = ggplot2::element_text(size = base_size * 0.8),
legend.title = ggplot2::element_text(size = base_size * 0.8, face = "bold", hjust = 0),
legend.position = "right",
panel.background = ggplot2::element_rect(fill = "white", colour = NA),
panel.border = ggplot2::element_rect(fill = NA, colour="grey50"),
panel.grid.major = ggplot2::element_line(colour = "grey90", size = 0.2),
panel.grid.minor = ggplot2::element_line(colour = "grey98", size = 0.5),
panel.spacing = ggplot2::unit(1, "lines"),
aspect.ratio = 2,
plot.background = ggplot2::element_rect(colour = NA),
plot.title = ggplot2::element_text(size = base_size * 1.2),
plot.margin = ggplot2::unit(c(1, 1, 0.5, 0.5), "lines"),
strip.background = ggplot2::element_rect(fill = "grey",size = 1)
) +
ggplot2::scale_y_continuous(breaks=seq(0,1,0.1))
}
#' @title Plots of Beta power
#' @description Generate several comparison plots of power.
#' @usage betapower.plot(betapower.matrix,link.type,by)
#' @param betapower.matrix a matrix obtained by the function betapower.(the formula was described as the output formula in the function betapower)
#' @param link.type the type of link used in the beta regression. You can choose one or more of the following: "logit", "probit", "cloglog", "cauchit", "log", "loglog", "all"
#' @param by the type of plot. see details.
#' @details betapower.plot() returns different plots depends on by\cr
#' by = "linktype": betapower.plot() returns graphs that plot power against mu1,
#' where mu1 is the mean for the treatment group under the alternative.
#' The number of plots will vary depending on the number of link types selected with the last plot showing power based on Wilcoxon Rank Sum Test.
#' The first one or several plots show comparisons of power with different sample size, using GLM method with one or several link types.
#' The last plot shows a comparison of the power with different sample size using Wilcoxon Rank Sum Test.
#' Y-axis denotes power and X-axis denotes mu1, the mean for the treatment group under the alternative.\cr
#' by = "samplesize": betapower.plot() returns a number of plots equal to the number of sample sizes tested.
#' Each plot compares power calculated with different link types and the Wilcoxon Rank Sum Test.
#' Y-axis denotes power and X-axis denotes mu1, the mean for the treatment group under the alternative.\cr
#' by = "mu1": betapower.plot() returns a number of plots equal to the number of mu1 used in the procedure.
#' Each plot compares power calculated with different link types and the Wilcoxon Rank Sum Test.
#' Y-axis denotes power and X-axis denotes sample size.\cr
#' @examples
#' BPmat <- betapower(0.56,0.255,.70,.75,.05,30,50, 20,40,610201501,"all")
#' betapower.plot(BPmat,link.type = "all",by="linktype")
#' betapower.plot(BPmat,link.type = "all",by="samplesize")
#' betapower.plot(BPmat,link.type = "all",by="mu1")
#' BPmat2 <- betapower(0.56,0.255,.560,.76,.05,30,45, 5,200,610201511,c("logit","loglog","log"))
#' betapower.plot(BPmat2,link.type = c("logit","loglog","log"),by="linktype")
#' betapower.plot(BPmat2,link.type = c("logit","loglog","log"),by="samplesize")
#' betapower.plot(BPmat2,link.type = c("logit","loglog","log"),by="mu1")
#' @export
betapower.plot <- function(Tmp.matrix,link.type,by){
if(link.type[1]=="all"){
link.type <- c("logit", "probit", "cloglog", "log", "loglog")
}
if(by!="linktype"&by!="samplesize"&by!="mu1"){
step("Wrong plot type")
}
name.plot <- c(paste("power of GLM:",link.type),"power of Wilcoxon test")
output.name.plot <- c(paste0("Power: GLM (",link.type,")"), "Power: Wilcoxon")
input.data <- reshape(Tmp.matrix,varying = name.plot,
v.names = "power",
timevar = "subj",
times = output.name.plot,
direction = "long",
new.row.names = c(1:(length(name.plot)*nrow(Tmp.matrix))))
if(by == "linktype"){
plot.unit1(input.data = input.data)
}
else if(by == "samplesize"){
plot.unit2(input.data = input.data)
}
else if(by == "mu1"){
plot.unit3(input.data = input.data)
}
}
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