===================================================================
RCS file: /cvs/ext/extinction_risk_1.R,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -p -r1.3 -r1.4
--- ext/extinction_risk_1.R	2015/05/25 12:51:56	1.3
+++ ext/extinction_risk_1.R	2015/06/25 15:16:22	1.4
@@ -1,5 +1,4 @@
-# extinction_risk_1.R, ver. 1.5 2015/4/30
-# $Id: extinction_risk_1.R,v 1.3 2015/05/25 12:51:56 hako Exp $
+# extinction_risk_1.R, ver. 1.6 2015/6/24
 #
 # Author: Hiroshi Hakoyama <hako@affrc.go.jp>
 # Copyright (c) 2013-2015 Hiroshi Hakoyama <hako@affrc.go.jp>, All rights reserved.
@@ -51,6 +50,7 @@
 # the ML estimate of the probability of extinction within a specific time period t (G*psi), and
 # a lower 95 % confidence limit of parameter * (Low.CL.*), and
 # a higher 95 % confidence limit of parameter * (High.CL.*)
+# formatted	If set to TRUE, give the result by formatted output. If set to FALSE, give a list of estimates.
 #
 # References:
 #  R. Lande and S. H. Orzack. Extinction dynamics of age-structured populations
@@ -61,7 +61,7 @@
 # 61:115-143, 1991.
 #
 
-ext1 <- function(dat, t = 100, ne = 1, alpha = 0.05, verbose = FALSE) {
+ext1 <- function(dat, t = 100, ne = 1, alpha = 0.05, verbose = FALSE, formatted = TRUE) {
   yr <- ts(dat[, 1], start = c(dat[, 1][1])) # Year
   ps <- ts(dat[, 2], start = c(dat[, 1][1])) # Population size
   complete <- complete.cases(yr, ps)
@@ -159,12 +159,16 @@ ext1 <- function(dat, t = 100, ne = 1, alpha = 0.05, v
       Extinction.probability = G(t, xd, mu, s) * psi(xd, mu, s),
       Low.CL.Gpsi = Low.CL.Gpsi,
       High.CL.Gpsi = High.CL.Gpsi)
-    class(results) <- "ext1"
+    if (formatted == TRUE) {
+      class(results) <- "ext1"
+    }
     return(results)
   } else {
     results <- list(ne = ne, t = t, verbose = verbose, 
       Extinction.probability = G(t, xd, mu, s) * psi(xd, mu, s))
-    class(results) <- "ext1"
+    if (formatted == TRUE) {
+      class(results) <- "ext1"
+    }
     return(results)
   }
 }
@@ -213,7 +217,7 @@ print.ext1 <- function(obj, digits = 5) {
 #
 # Examples
 # Yellowstone grizzly bears (from Dennis et al., 1991)
-# dat <- data.frame(Year = c(1959, 1960, 1961, 1962, 1963, 1964, 1965, 1966, 1967, 1968, 1969, 1970, 1971, 1972, 1973, 1974, 1975, 1976, 1977, 1978, 1979, 1980, 1981, 1982, 1983, 1984, 1985, 1986, 1987), 
+ # dat <- data.frame(Year = c(1959, 1960, 1961, 1962, 1963, 1964, 1965, 1966, 1967, 1968, 1969, 1970, 1971, 1972, 1973, 1974, 1975, 1976, 1977, 1978, 1979, 1980, 1981, 1982, 1983, 1984, 1985, 1986, 1987), 
 # Population = c(44, 47, 46, 44, 46, 45, 46, 40, 39, 39, 42, 44, 41, 40, 33, 36, 34, 39, 35, 34, 38, 36, 37, 41, 39, 51, 47, 57, 47))
 # The probability of extinction (of decline to population size 1) within 100 years
 # ext1(dat, 100)