===================================================================
RCS file: /cvs/ext/extinction_risk_1.R,v
retrieving revision 1.11
retrieving revision 1.12
diff -u -p -r1.11 -r1.12
--- ext/extinction_risk_1.R	2015/08/06 11:08:24	1.11
+++ ext/extinction_risk_1.R	2015/08/06 13:09:31	1.12
@@ -1,5 +1,5 @@
 # extinction_risk_1.R
-# $Id: extinction_risk_1.R,v 1.11 2015/08/06 11:08:24 hako Exp $
+# $Id: extinction_risk_1.R,v 1.12 2015/08/06 13:09:31 hako Exp $
 #
 # Author: Hiroshi Hakoyama <hako@affrc.go.jp>
 # Copyright (c) 2013-2015 Hiroshi Hakoyama <hako@affrc.go.jp>, All rights reserved.
@@ -130,14 +130,14 @@ ext1 <- function(dat, t = 100, ne = 1, alpha = 0.05, v
     c(lower.CL.P, upper.CL.P)
   }
 
-  CI.rand <- function(mu.obs, s.obs, xd, t, q, tq, alpha) {
+  CI.rand <- function(mu.obs, xd, s.obs, t, tq, q, alpha) {
     mu <- rnorm(1, mean = mu.obs, sd = sqrt(s.obs / q))
     s <-  rchisq(1, df = q - 1) * s.obs / q
     confidence.interval(mu, xd, s, t, tq, q, alpha)
   }
 
-  CI.sim <- function(n.sim, gam, alpha, q, tq, t, xd, mu.obs, s.obs) {
-    CI.dist <- replicate(n.sim, CI.rand(mu.obs, s.obs, xd, t, q, tq, alpha))
+  CI.sim <- function(n.sim, gam, alpha, mu.obs, xd, s.obs, t, tq, q) {
+    CI.dist <- replicate(n.sim, CI.rand(mu.obs, xd, s.obs, t, tq, q, alpha))
     w.obs <- w(mu.obs, xd, s.obs, t)
     z.obs <- z(mu.obs, xd, s.obs, t)
     P.obs <- pr(w.obs, z.obs)
@@ -155,8 +155,8 @@ ext1 <- function(dat, t = 100, ne = 1, alpha = 0.05, v
     c(binom$estimate[[1]], binom$p.value, ci)
   }
 
-  asymptotically.exact.confidence.interval <- function(n.sim, alpha.sim, alpha, q, t, xd, mu.obs, s.obs) {
-    res <- CI.sim(n.sim, alpha, alpha, q, tq, t, xd, mu.obs, s.obs)
+  asymptotically.exact.confidence.interval <- function(n.sim, alpha.sim, mu.obs, xd, s.obs, t, tq, q, alpha) {
+    res <- CI.sim(n.sim, alpha, alpha, mu.obs, xd, s.obs, t, tq, q)
     gg <- res[[1]]
     pp <- res[[2]]
     a <- alpha
@@ -164,7 +164,7 @@ ext1 <- function(dat, t = 100, ne = 1, alpha = 0.05, v
       return(confidence.interval(mu, xd, s, t, tq, q, alpha))
     } else {
     while (pp < alpha.sim) {
-      res <- CI.sim(n.sim, alpha, a, q, tq, t, xd, mu.obs, s.obs)
+      res <- CI.sim(n.sim, alpha, a, mu.obs, xd, s.obs, t, tq, q)
       gg <- res[[1]]
       pp <- res[[2]]
       a <- a * alpha / gg
@@ -174,7 +174,7 @@ ext1 <- function(dat, t = 100, ne = 1, alpha = 0.05, v
   }
 
   if (exact.CL == TRUE) {
-  	CL.P <- asymptotically.exact.confidence.interval(n.sim, alpha.sim, alpha, q, t, xd, mu, s)
+  	CL.P <- asymptotically.exact.confidence.interval(n.sim, alpha.sim, mu, xd, s, t, tq, q, alpha)
   	} else {
   	CL.P <- confidence.interval(mu, xd, s, t, tq, q, alpha)
   	}