我正在尝试在R中创建95％的轮廓。我被建议在我最近的帖子中更具体地讨论我的问题，因此将其作为一个不同的问题发布。我使用了另一个帖子（R - How to find points within specific Contour）中的现有代码，但我不确定为什么我得到'NA'。这导致后来使用的ls和point.in.polygon中的错误
library(MASS)
set.seed(1234)
p1 <- .136
p2 <- .069
nn <- 60
Y <- structure(list(Y1 = c(27L, 8L, 2L, 36L, 5L, 10L, 14L, 12L, 12L, 22L, 11L, 24L, 13L, 6L, 2L, 10L, 12L, 11L, 16L, 2L), Y2 = c(8L, 4L, 2L, 24L, 4L, 1L, 7L, 8L, 6L, 11L, 7L, 7L, 6L, 3L, 1L, 1L, 12L, 8L, 11L, 0L)), .Names = c("Y1", "Y2"), class = "data.frame", row.names = c(NA, -20L))
Y <- as.matrix(Y)
xx <- ifelse(Y==0,Y+.5,Y)
nnn <- ifelse(Y==0,nn+.5,nn)
xx <- as.matrix(xx)
Y1<-xx/nnn # estimates of p
sigma2 <- matrix(c(var(Y1[,1]),cov(Y1[,1],Y1[,2]),cov(Y1[,1],Y1[,2]),var(Y1[,2])),2,2)
rho <- sigma2[1,2]/sqrt(sigma2[1,1]*sigma2[2,2])
rate<-Y1[2,] # change for each site
print(rate)
# Y1 Y2
# 0.13333333 0.06666667
rate1 <- rate/(1-rate)
rate2 <- log(rate1)
Sigma11 <- (1/(rate[1]*(1-rate[1]))^2)*sigma2[1,1]
Sigma22 <- (1/(rate[2]*(1-rate[2]))^2)*sigma2[2,2]
Sigma12 <- (1/((rate[1]*(1-rate[1]))*(rate[2]*(1-rate[2]))))*sigma2[1,2]
Sigma2 <- matrix(c(Sigma11,Sigma12,Sigma12,Sigma22),2,2)
print(Sigma2)
# [,1] [,2]
# [1,] 1.604805 1.503483
# [2,] 1.503483 2.102154
rate3 <- mvrnorm(1000, mu=c(rate2[1],rate2[2]), Sigma2)
x <- exp(rate3[,1])/(1+exp(rate3[,1]))
y <- exp(rate3[,2])/(1+exp(rate3[,2]))
## Points within polygons
library(MASS)
dens <- kde2d(x, y, n=100)
image(dens)
prob <- c(0.975, 0.025)
dx <- diff(dens$x[1:2])
dy <- diff(dens$y[1:2])
sz <- sort(dens$z)
c1 <- cumsum(sz) * dx * dy
levels <- sapply(prob, function(x) {
approx(c1, sz, xout = 1 - x)$y
})
print(levels)
# [1] 0.2480976 NA** # <- Why NA?
#plot(p1,p2)
#contour(dens, levels=levels, labels=prob, add=T)
ls <- contourLines(dens, level=levels)
library(sp)
inner <- point.in.polygon(p1, p2, ls[[2]]$x, ls[[2]]$y) # whether points in inner ellipse
out <- point.in.polygon(p1, p2, ls[[1]]$x, ls[[1]]$y) # whether points in outter ellipse
within<-(inner+out)
print(within)
# [1] 0