R: Reproductive data from seven dairy cows

reprocows {mhsmm} | R Documentation

## Reproductive data from seven dairy cows

### Description

This data set contains hourly observations on progesterone and an activity index at hourly intervals since calving on seven dairy cows.

### Usage

    reprocows

### Format

`reprocows` is a data frame containing 13040 rows. `id` is the cow ID, `progesterone` is a measurement of the hormone in ng/L taken from a milk sample, activity is a relative measure of activity calculated from a pedometer.

There are a large number of missing values as progesterone is measured only at milking time (and at a farm manager's discretion). Missing values in activity occur due to hardware problems can occur with pedometers.

### Source

Danish Cattle Research Centre

### References

Peters, A. and Ball, P. (1995), "Reproduction in Cattle," 2nd ed.

### Examples

    data(reprocows)
    data(reproai)
    data(reproppa)
    tm = 1600

    J <- 3
    init <- c(1,0,0)
    trans <- matrix(c(0,0,0,1,0,1,0,1,0),nrow=J)
    emis <- list(mu=c(0,2.5,0),sigma=c(1,1,1))

    N <- as.numeric(table(reprocows$id))
    train <- list(x=reprocows$activity,N=N)
    class(train) <- "hsmm.data"
    tmp <- gammafit(reproppa * 24)
    M <- max(N)

    d <- cbind(dgamma(1:M,shape=tmp$shape,scale=tmp$scale),
     # ppa sojourn directly estimated from ppa data set
    dunif(1:M,4,30),
     # oestrus between 4 and 30 hours
    dunif(1:M,15*24,40*24))
     #not-oestrus between 15 and 40 days

    startval <- hsmmspec(init,trans,parms.emission=emis,list(d=d,type='gamma'),
      dens.emission=dnorm.hsmm)
    #not run (takes some time)
    #h.activity <- hsmmfit(train,startval,mstep=mstep.norm,maxit=10,M=M,lock.transition=TRUE)

[Package mhsmm version 0.4.16 Index]