BEANSP (version 1.0)

BEANSP-package: BEANSP

Description

Package BEANSP computes age specific nest survival rates based on a Bayesian hierarchical model.

Details

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.

References

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.

Examples

## 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