Description Details Author(s) References Examples
Package BEANSP computes age specific nest survival rates based on a Bayesian hierarchical model.
Package: | BEANSP |
Type: | Package |
Version: | 1.0 |
Date: | 2014-08-09 |
License: | GPL-2 |
The package BEANSP can be applied on either one of the two simple data formats, interval format and date format. For more details of data format, see example 1 and example 2 instruction. For either data format, first use the function "nestconv" to convert a data to the standard format including (ul,ur,zl,zr,y); then apply the function "nestsr" to generate the nest survival summary.
Chong He, Yiqun Yang, Jing Cao
Maintainer:Yiqun Yang <yyry2@mail.missouri.edu>
Cao, J., He, C., Suedkamp Wells, K.M., Millspaugh, J.J., and Ryan, M.R. (2009). Modeling age and nest-specific survival using a hierarchical Bayesian approach. Biometrics, 65, 1052-1062.
He, C.,Yang, Y.. User Instruction for Program BEANSP.
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 | ## Data Input with Date Format
## For the details of all variables in the date format, refer to the "example 2" part.
library(BEANSP)
data(example2)
data<-example2
jj<-as.integer(20)
nx<-as.integer(2)
nn<-as.integer(233)
x1<-example2[1:nn,6]
x2<-example2[1:nn,7]
x<-cbind(as.double(x1),as.double(x2))
temp<-nestconv(1,nn,jj,data)
## Data Input with Interval Format
## For the details of all variables in the interval format, refer to the "example 1" part.
library(BEANSP)
data(example1)
data<-example1
jj<-as.integer(19)
nx<-as.integer(2)
nn<-as.integer(217)
x1<-example1[1:nn,7]
x2<-example1[1:nn,8]
x<-cbind(as.double(x1),as.double(x2))
temp<-nestconv(0,nn,jj,data)
## After converting data to the standard format (ul,ur,zl,zr,y)
## set initial values (a,b,sigma,day,enc,covar) and burnin number (n0,ntotal)
ul<-as.integer(temp[,2])
ur<-as.integer(temp[,3])
zl<-as.integer(temp[,4])
zr<-as.integer(temp[,5])
y<-as.integer(temp[,6])
a<-as.double(rep(2.0,2))
b<-as.double(rep(1.0,2))
sigma<-as.double(rep(1.0,2))
day<-as.double(rep(0.0,jj))
enc<-as.double(rep(0.0,jj-1))
covar<-as.double(rep(0.0,nx))
n0<-as.integer(10)
ntotal<-as.integer(110)
out<-nestsr(jj,nx,nn,ul,ur,zl,zr,x,y,a,b,sigma,day,enc,covar,n0,ntotal)
## After applying the function "nestsr"
## some trace plots or survival plots can be created using the folloing functions.
plot.asr(out$asr,out$jj)
plot.casr(out$casr,out$jj)
plot.del(out$del,out$jj)
plot.q(out$q,1,out$jj) # 1 is the first nest age-specific outcome rates
plot.sr(out$sr,1,out$jj)# 1 is the first nest age-specific survival rates
i1=1
i2=ntotal
plot.trace1(out$trace1,i1,i2,1) # trace plot for E_1
plot.trace2(out$trace2,i1,i2,1) # trace plot for A_1
plot.trace3(out$trace3,i1,i2,1) # trace plot for covar_1
plot.trace4(out$trace4,i1,i2,1) # trace plot for sigma_1
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.