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Question

我想拍这样的照片：

在图中，参数（三角形分布的a，b和c），它们的分布和参数的置信区间基于原始数据集，模拟的参数由参数和非参数自举产生。如何在R中画出这样的图片？你能给出一个这样的简单例子吗？非常感谢你！

这是我的代码。

x1<-c(1300,541,441,35,278,167,276,159,126,170,251.3,155.84,187.01,850)
x2<-c(694,901,25,500,42,2.2,7.86,50)
x3<-c(2800,66.5,420,260,50,370,17)
x4<-c(12,3.9,10,28,84,138,6.65)
y1<-log10(x1)
y2<-log10(x2)
y3<-log10(x3)
y4<-log10(x4)
#Part 1 (Input the data) In this part, I have calculated the parameters (a and b) and  the confidence interval (a and b ) by MLE and PB-MLE with different data sets(x1 to x4)
#To calculate the parameters (a and b) with data sets x1
y.n<-length(y1)
y.location<-mean(y1)
y.var<-(y.n-1)/y.n*var(y1)
y.scale<-sqrt(3*y.var)/pi
library(stats4)
ll.logis<-function(location=y.location,scale=y.scale){-sum(dlogis(y1,location,scale,log=TRUE))}
fit.mle<-mle(ll.logis,method="Nelder-Mead")
a1_mle<-coef(fit.mle)[1]
b1_mle<-coef(fit.mle)[2]
summary(a1_mle)# To calculate the parameters (a)
summary(b1_mle)# To calculate the parameters (b)
confint(fit.mle)#  To  calculate  the confidence interval (a and b ) by MLE
# load fitdistrplus package for using fitdist function
library(fitdistrplus)
# fit logistic distribution using MLE method
x1.logis <- fitdist(y1, "logis", method="mle")
A<- bootdist(x1.logis, bootmethod="param", niter=1001)
summary(A)      #  To calculate the parameters (a and b ) and the confidence interval (a and b ) by parametric bootstrap
a <- A$estim
a1<-c(a$location)
b1<-c(a$scale)

#To calculate the parameters (a and b) with data sets x2
y.n<-length(y2)
y.location<-mean(y2)
y.var<-(y.n-1)/y.n*var(y2)
y.scale<-sqrt(3*y.var)/pi
library(stats4)
ll.logis<-function(location=y.location,scale=y.scale){-sum(dlogis(y2,location,scale,log=TRUE))}
fit.mle<-mle(ll.logis,method="Nelder-Mead")
a2_mle<-coef(fit.mle)[1]
b2_mle<-coef(fit.mle)[2]
summary(a2_mle)# To calculate the parameters (a)
summary(b2_mle)# To calculate the parameters (b)
confint(fit.mle)#  To  calculate  the confidence interval (a and b ) by MLE
x2.logis <- fitdist(y2, "logis", method="mle")
B<- bootdist(x2.logis, bootmethod="param", niter=1001)
summary(B)
b <- B$estim
a2<-c(b$location)
b2<-c(b$scale)

#To calculate the parameters (a and b) with data sets x3
y.n<-length(y3)
y.location<-mean(y3)
y.var<-(y.n-1)/y.n*var(y3)
y.scale<-sqrt(3*y.var)/pi
library(stats4)
ll.logis<-function(location=y.location,scale=y.scale){-sum(dlogis(y3,location,scale,log=TRUE))}
fit.mle<-mle(ll.logis,method="Nelder-Mead")
a3_mle<-coef(fit.mle)[1]
b3_mle<-coef(fit.mle)[2]
summary(a3_mle)# To calculate the parameters (a)
summary(b3_mle)# To calculate the parameters (b)
confint(fit.mle)#  To  calculate  the confidence interval (a and b ) by MLE
x3.logis <- fitdist(y3, "logis", method="mle")
C <- bootdist(x3.logis, bootmethod="param", niter=1001)
summary(C)
c<- C$estim
a3<-c(c$location)
b3<-c(c$scale)

#To calculate the parameters (a and b) with data sets x4
y.n<-length(y4)
y.location<-mean(y4)
y.var<-(y.n-1)/y.n*var(y4)
y.scale<-sqrt(3*y.var)/pi
library(stats4)
ll.logis<-function(location=y.location,scale=y.scale){-sum(dlogis(y4,location,scale,log=TRUE))}
fit.mle<-mle(ll.logis,method="Nelder-Mead")
a4_mle<-coef(fit.mle)[1]
b4_mle<-coef(fit.mle)[2]
summary(a4_mle)# To calculate the parameters (a)
summary(b4_mle)# To calculate the parameters (b)
confint(fit.mle)#  To  calculate  the confidence interval (a and b ) by MLE
x4.logis <- fitdist(y4, "logis", method="mle")
D <- bootdist(x4.logis, bootmethod="param", niter=1001)
summary(D)
d <- D$estim
a4<-c(d$location)
b4<-c(d$scale)

Answer 1

更新

这是我的尝试。这很草率，但我认为它做你想做的事。如果其他人可以提供更好的解决方案或提出建议/意见，那就太好了。

x1<-c(1300,541,441,35,278,167,276,159,126,170,251.3,155.84,187.01,850)
x2<-c(694,901,25,500,42,2.2,7.86,50)
x3<-c(2800,66.5,420,260,50,370,17)
x4<-c(12,3.9,10,28,84,138,6.65)
y1<-log10(x1)
y2<-log10(x2)
y3<-log10(x3)
y4<-log10(x4)

library(stats4)
library(fitdistrplus)
library(reshape2)
library(ggplot2)
library(gridExtra)

首先，将所有内容都放在一个函数中，这样您就不必重复自己了：

tmp <- function(y){
    y.n <-length(y)
    y.location <-mean(y)
    y.var<-(y.n-1)/y.n*var(y)
    y.scale<-sqrt(3*y.var)/pi
    ll.logis<-function(location, scale){-sum(dlogis(y, location, scale,log=TRUE))}

    fit.mle<-mle(ll.logis,
                 start = list(location = y.location, scale = y.scale),
                 method="Nelder-Mead")

    a_mle <-coef(fit.mle)[1] # mean a
    b_mle <-coef(fit.mle)[2] # mean b
    mle <- confint(fit.mle)

    mle_df <- as.data.frame(cbind(c("a", "b"), c(a_mle, b_mle), mle))
    mle_df <- setNames(mle_df, c("par","mean", "lower", "upper"))
    mle_df$method <- "MLE"

    x.logis <- fitdist(y, "logis", method="mle")
    A <- bootdist(x.logis, bootmethod="param", niter=1001)
    a <- A$estim
    a_pbmle <-c(a$location)
    b_pbmle <-c(a$scale)

    pbmle_df <- data.frame(a_pbmle, b_pbmle)
    pbmle_df <- setNames(pbmle_df, c("a", "b"))
    pbmle_df$method <- "PB_MLE"

    return(list(MLE = mle_df,
                PBMLE = pbmle_df))
}

然后，使用lapply，您可以将函数应用于y1, y2, y3, y4，而无需四次写下相同的内容：

tmplist <- list(y1, y2, y3, y4)
tmplist2 <- lapply(tmplist, tmp)

这部分很草率，但这是我能想到的：

mL <- melt(tmplist2)
mL$par[is.na(mL$par)] <- mL$variable[is.na(mL$par)]
mL <- mL[,-6]
for(i in 2:4){
    mL[,i] <- as.numeric(as.character(mL[,i]))
}

mL_a <- subset(mL, par == "a")
mL_b <- subset(mL, par == "b")

然后，你用它绘制图形：

g1 <- ggplot(mL_a) + geom_boxplot(aes(method, value)) +
    geom_point(aes(method, y = mean)) +
    geom_errorbar(aes(method, ymin = lower, ymax = upper)) +
    facet_grid(L1~.) +
    ylab("a") +
    coord_flip()

g2 <- g1 %+% mL_b +
    ylab("b")

g1.a <- g1 + theme(strip.text.y = element_blank())
g2.a <- g2 + theme(axis.text.y = element_blank(),
                   axis.ticks.y = element_blank(),
                   axis.title.y = element_blank())

grid.arrange(g1.a, g2.a, nrow = 1,
             widths = c(1.2, 1))

你得到了

OLD ANSWER

哦..我在发布数据之前就开始研究这个了，所以我使用了一个假的例子。这是我的代码：

sL <- list()

for(i in c("FW&SW", "FW", "FW|S")){
    sL[[i]] <- rbind(data.frame(name = "MLE",
                          a = runif(10, -2, 0),
                          b = runif(10, 3, 5),
                          c = runif(10, -1, 2)),
    data.frame(name = "P-B MLE",
                          a = runif(10, -2, 0),
                          b = runif(10, 3, 5),
                          c = runif(10, -1, 2)),
    data.frame(name = "NP-B MLE",
                          a = runif(10, -2, 0),
                          b = runif(10, 3, 5),
                          c = runif(10, -1, 2)))
}
library(reshape2)
library(ggplot2); theme_set(theme_bw())
library(gridExtra)
library(grid)

mL <- melt(sL)
mL$L1 <- factor(mL$L1, levels = c("FW|S", "FW", "FW&SW"))

g1 <- ggplot(subset(mL, variable == "a"), aes(name, value)) + geom_boxplot() +
    coord_flip() +
    facet_grid(L1~.) + 
    theme(panel.margin=grid::unit(0,"lines"),
          axis.title.y = element_blank(),
          plot.margin = unit(c(1,0.1,1,0), "cm"))

g2 <- g1 %+% subset(mL, variable == "b")
g3 <- g1 %+% subset(mL, variable == "c")

text1 <- textGrob("FW|S", gp=gpar(fontsize=12, fontface = "bold"))
text2 <- textGrob("FW", gp=gpar(fontsize=12))
text3 <- textGrob("FW&SW", gp=gpar(fontsize=12))



g1.a <- g1 + 
    ylab("a") +
    scale_y_continuous(breaks = c(-1.5, -1, -.5)) +
    theme(strip.text.y = element_blank())

g2.a <- g2 + ylab("b") +
    scale_y_continuous(breaks = c(3.5, 4, 4.5)) +
    theme(axis.title.y = element_blank(),
        axis.text.y = element_blank(),
        axis.ticks.y = element_blank(),
        strip.text.y = element_blank())
g3.a <- g3 + ylab("c") +
    scale_y_continuous(breaks = c(-0.5, 0.5, 1.5)) +
    theme(axis.title.y = element_blank(),
        axis.text.y = element_blank(),
        axis.ticks.y = element_blank())

grid.arrange(g1.a, g2.a, g3.a, nrow = 1,
             widths = c(1.5, 1, 1.1))

让我尝试使用您提供的数据......

编辑（旧编辑旧数据）

根据您提供的数据，我会这样做：

m <- confint(fit.mle)
MLE <- as.data.frame(cbind(c(a,b),m))
PBMLE <- as.data.frame(summary(b1)$CI)
sL <- list(MLE, PBMLE)
methods <- c("MLE", "P-B MLE")

myList <- lapply(1:2, function(i){
    x <- sL[[i]]
    colnames(x) <- c("Median", "low","high")
    x <- cbind(pars = c("a", "b"), method = methods[i], x)
})

df <- do.call("rbind", myList)

ggplot(df, aes(x = method, y = Median)) +
    geom_point(size = 4) +
    geom_errorbar(aes(ymax = high, ymin = low)) +
    facet_wrap(~pars, scale = "free") +
    xlab("") +
    ylab("")

这比我上面的要简单得多。您应该查看facet_wrap和grid_arrange。

R：如何使用不同类型的数据创建箱线图？

1 个答案:

更新

OLD ANSWER

编辑（旧编辑旧数据）