Description Usage Arguments Details Value Author(s) References Examples

Bayesian estimation of centre (*μ*) and scale (*σ*) of a normal distribution based on a sample. `Bnormal`

uses a gamma prior on the precision, *τ = 1/σ^2*, while `Bnormal2`

applies a gamma prior to *σ*.

1 2 3 4 5 6 |

`y` |
a vector (length > 1) with observed sample values; missing values not allowed. |

`priors` |
an optional list with elements specifying the priors for the centre and scale; see Details. |

`doPriorsOnly` |
if TRUE, |

`chains` |
the number of MCMC chains to run. |

`sample` |
the number of MCMC observations per chain to be returned. |

`thin` |
thinning rate. If set to n > 1, n steps of the MCMC chain are calculated for each one returned. This is useful if autocorrelation is high. |

`burnin` |
number of steps to discard as burn-in at the beginning of each chain. |

`adapt` |
number of steps for adaptation. |

`seed` |
a positive integer (or NULL): the seed for the random number generator, used to obtain reproducible samples if required. |

`parallel` |
if NULL or TRUE and > 3 cores are available, the MCMC chains are run in parallel. (If TRUE and < 4 cores are available, a warning is given.) |

The function generates vectors of random draws from the posterior distributions of the population centre (*μ*) and scale (*σ*). `Bnormal`

uses a Gibbs sampler implemented in R, while `Bnormal2`

uses JAGS (Plummer 2003).

Priors for all parameters can be specified by including elements in the `priors`

list. For both functions, *μ* has a normal prior, with mean `muMean`

and standard deviation `muSD`

. For `Bnormal`

, a gamma prior is used for the precision, *τ = 1\σ^2*, with parameters specified by `tauShape`

and `tauRate`

. For `Bnormal2`

, a gamma prior is placed on *σ*, with parameters specified by mode, `sigmaMode`

, and SD, `sigmaSD`

.

When `priors = NULL`

(the default), `Bnormal`

uses improper flat priors for both *μ* and *τ*, while `Bnormal2`

uses a broad normal prior (muMean = mean(y), muSD = sd(y)*5) for *μ* and a uniform prior on (sd(y) / 1000, sd(y) * 1000) for *σ*.

Returns an object of class `Bwiqid`

, which is a data frame with a column for each parameter in the model.

There are `print`

and `plot`

methods for class `Bwiqid`

, as well as diagnostic plots.

Mike Meredith, `Bnormal`

based on code by Brian Neelon, `Bnormal2`

adapted from code by John Kruschke.

Kruschke, J K. 2013. Bayesian estimation supersedes the *t* test. *Journal of Experimental Psychology: General* 142(2):573-603. doi: 10.1037/a0029146

Plummer, Martyn (2003). JAGS: A Program for Analysis of Bayesian Graphical Models Using Gibbs Sampling, *Proceedings of the 3rd International Workshop on Distributed Statistical Computing (DSC 2003)*, March 20-22, Vienna, Austria. ISSN 1609-395X

1 2 3 4 5 6 7 8 9 10 | ```
# Generate a sample from a normal distribution, maybe the head-body length of a
# carnivore in mm:
HB <- rnorm(10, 900, 15)
Bnormal(HB) # with improper flat priors for mu and tau
Bnormal(HB, priors=list(muMean=1000, muSD=200))
Bnormal(HB, priors=list(muMean=1, muSD=0.2)) # a silly prior produces a warning.
Bnormal2(HB) # with broad normal prior for mu, uniform for sigma
Bnormal2(HB, priors=list(muMean=1000, muSD=200, sigmaMode=20, sigmaSD=10))
``` |

wiqid documentation built on Sept. 10, 2017, 9:02 a.m.

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