R version 2.13.0 alpha (2011-03-18 r54865)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: i686-pc-linux-gnu (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(bbmle)
Loading required package: stats4
Loading required package: numDeriv
Loading required package: lattice
Loading required package: MASS
> 
> ## goby data in dump format
> 
> x <- structure(list(indiv = structure(as.integer(c(20, 77, 79, 21, 
+ 33, 40, 11, 28, 43, 85, 56, 49, 29, 37, 57, 36, 66, 65, 19, 69, 
+ 47, 60, 23, 25, 39, 84, 12, 5, 76, 55, 32, 10, 75, 4, 78, 80, 
+ 86, 48, 54, 22, 18, 61, 41, 74, 68, 14, 53, 45, 30, 17, 62, 3, 
+ 7, 50, 34, 82, 8, 70, 38, 52, 2, 63, 81, 15, 44, 58, 13, 26, 
+ 73, 83, 59, 42, 72, 67, 35, 16, 1, 46, 27, 64, 51, 24, 71, 6, 
+ 9, 31)), .Label = c("f10al1", "f10al2", "f10al3", "f10r1", "f10r2", 
+ "f11al1", "f11al2", "f11al3", "f11al4", "f11r1", "f11r2", "f11r3", 
+ "f12al1", "f12al2", "f12al3", "f12al4", "f12al5", "f12r1", "f12r2", 
+ "f12r3", "f12r4", "f12r5", "f12r6", "f13al1", "f13r1", "f14al1", 
+ "f14al2", "f14r1", "f14r2", "f15al1", "f15al2", "f15r1", "f15r2", 
+ "f18al1", "f18al2", "f18r1", "f18r2", "f19al1", "f19r1", "f19r2", 
+ "f1al1", "f1al2", "f1r1", "f20al1", "f20al2", "f20al3", "f20r1", 
+ "f20r2", "f20r3", "f2al1", "f2al2", "f2al3", "f2al4", "f2r1", 
+ "f2r2", "f2r3", "f2r4", "f3al1", "f3al2", "f3r1", "f3r2", "f4al1", 
+ "f5al1", "f5al2", "f5r1", "f5r2", "f6al1", "f6al2", "f6r1", "f7al1", 
+ "f7al2", "f7al3", "f7al4", "f7al5", "f7r1", "f7r2", "f7r3", "f7r4", 
+ "f7r5", "f7r6", "f9al1", "f9al2", "f9al4", "f9r1", "f9r2", "f9r3"
+ ), class = "factor"), group = structure(as.integer(c(5, 5, 5, 
+ 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 
+ 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 
+ 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1)), .Label = c("AL", 
+ "AL-Rat5th", "AL-RatOv", "R", "R-ALat5th"), class = "factor"), 
+     lifespan = as.integer(c(391, 370, 346, 341, 334, 320, 319, 
+     317, 314, 307, 295, 260, 30, 10, 397, 380, 364, 355, 352, 
+     341, 340, 339, 336, 320, 314, 312, 308, 302, 296, 290, 284, 
+     267, 263, 263, 255, 253, 242, 222, 220, 181, 64, 36, 192, 
+     192, 189, 186, 183, 181, 180, 176, 173, 171, 170, 169, 166, 
+     11, 247, 235, 234, 233, 232, 224, 221, 220, 215, 210, 210, 
+     204, 202, 17, 13, 301, 300, 296, 281, 271, 253, 250, 241, 
+     239, 232, 221, 220, 214, 33, 30))), .Names = c("indiv", "group", 
+ "lifespan"), class = "data.frame", row.names = c("1", "2", "3", 
+ "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", 
+ "16", "17", "18", "19", "20", "21", "22", "23", "24", "25", "26", 
+ "27", "28", "29", "30", "31", "32", "33", "34", "35", "36", "37", 
+ "38", "39", "40", "41", "42", "43", "44", "45", "46", "47", "48", 
+ "49", "50", "51", "52", "53", "54", "55", "56", "57", "58", "59", 
+ "60", "61", "62", "63", "64", "65", "66", "67", "68", "69", "70", 
+ "71", "72", "73", "74", "75", "76", "77", "78", "79", "80", "81", 
+ "82", "83", "84", "85", "86"))
> 
> mlife <- log(mean(x$lifespan))
> Bm0w <- mle2(lifespan~dweibull(scale=exp(llambda),shape=alpha),
+              start=list(llambda=mlife,alpha=1),
+              data=x)
> Bm1w <- mle2(lifespan~dweibull(scale=exp(llambda),shape=alpha),
+            start=list(llambda=mlife,alpha=1),
+            parameters=list(llambda~group),
+            data=x)
Warning message:
In dweibull(x, shape, scale, log) : NaNs produced
> Bm2w <- mle2(lifespan~dweibull(scale=exp(llambda),shape=alpha),
+              start=list(llambda=mlife,alpha=1),
+              parameters=list(llambda~group,alpha~group),
+              data=x)           
Warning messages:
1: In dweibull(x, shape, scale, log) : NaNs produced
2: In dweibull(x, shape, scale, log) : NaNs produced
> Bm3w <- mle2(lifespan~dweibull(scale=exp(llambda),shape=alpha),
+            start=list(llambda=mlife,alpha=3),
+            parameters=list(alpha~group),
+            data=x)
Warning messages:
1: In dweibull(x, shape, scale, log) : NaNs produced
2: In dweibull(x, shape, scale, log) : NaNs produced
3: In dweibull(x, shape, scale, log) : NaNs produced
4: In dweibull(x, shape, scale, log) : NaNs produced
> anova(Bm0w,Bm1w)
Likelihood Ratio Tests
Model 1: Bm0w, lifespan~dweibull(scale=exp(llambda),shape=alpha)
Model 2: Bm1w, lifespan~dweibull(scale=exp(llambda),shape=alpha): llambda~group
  Tot Df Deviance  Chisq Df Pr(>Chisq)    
1      2   1043.5                         
2      6   1015.5 27.945  4   1.28e-05 ***
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 
> anova(Bm0w,Bm1w,Bm2w)
Likelihood Ratio Tests
Model 1: Bm0w, lifespan~dweibull(scale=exp(llambda),shape=alpha)
Model 2: Bm1w, lifespan~dweibull(scale=exp(llambda),shape=alpha): llambda~group
Model 3: Bm2w, lifespan~dweibull(scale=exp(llambda),shape=alpha):
          llambda~group, alpha~group
  Tot Df Deviance  Chisq Df Pr(>Chisq)    
1      2   1043.5                         
2      6   1015.5 27.945  4   1.28e-05 ***
3     10   1008.8  6.736  4     0.1505    
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 
> anova(Bm0w,Bm3w,Bm2w)
Likelihood Ratio Tests
Model 1: Bm0w, lifespan~dweibull(scale=exp(llambda),shape=alpha)
Model 2: Bm3w, lifespan~dweibull(scale=exp(llambda),shape=alpha): alpha~group
Model 3: Bm2w, lifespan~dweibull(scale=exp(llambda),shape=alpha):
          llambda~group, alpha~group
  Tot Df Deviance   Chisq Df Pr(>Chisq)    
1      2   1043.5                          
2      6   1038.5  4.9434  4     0.2932    
3     10   1008.8 29.7377  4  5.535e-06 ***
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 
> AICctab(Bm0w,Bm1w,Bm2w,Bm3w,sort=TRUE,nobs=nrow(x),delta=TRUE)
     dAICc df
Bm1w  0.0  6 
Bm2w  3.1  10
Bm0w 19.0  2 
Bm3w 23.0  6 
> 
> 
> proc.time()
   user  system elapsed 
  1.556   0.144   1.688