BFpack-package {BFpack}

BFpack: Flexible Bayes factor testing of scientific expectations

Description

The R package BFpack provides tools for exploratory and confirmatory Bayesian hypothesis testing using Bayes factors and posterior probabilities under common statistical models. The main function 'BF' needs a fitted model 'x' as input argument. Depending on the class of the fitted model, a standard hypothesis test is executed by default. For example, if 'x' is a fitted regression model of class 'lm' then posterior probabilities are computed of whether each separate coefficient is zero, negative, or positive (assuming equal prior probabilities). If one has specific hypotheses with equality and/or order constraints on the parameters under the fitted model 'x' then these can be formulated using the 'hypothesis' argument (a character string), possibly together prior probabilities for the hypotheses via the 'prior' argument (default all hypotheses are equally likely a priori), and the 'complement' argument which is a logical stating whether the complement hypotheses should be included in the case ('TRUE' by default).

Use compilation for Fortran functions

Author(s)

Maintainer: Joris Mulder [e-mail]

Authors:

• Caspar van Lissa [e-mail] [contributor]

• Donald R. Williams [e-mail] [contributor]

• Xin Gu [e-mail] [contributor]

• Anton Olsson-Collentine [e-mail] [contributor]

• Florian Boeing-Messing [e-mail] [contributor]

• Jean-Paul Fox [e-mail] [contributor]

Other contributors:

• Janosch Menke [e-mail] [contributor]

• Robbie van Aert [e-mail] [contributor]

• Barry Brown [contributor]

• James Lovato [contributor]

• Kathy Russell [contributor]

• Lapack 3.8 [contributor]

• Jack Dongarra [contributor]

• Jim Bunch [contributor]

• Cleve Moler [contributor]

• Gilbert Stewart [contributor]

• John Burkandt [contributor]

• Ashwith Rego [contributor]

• Alexander Godunov [contributor]

• Alan Miller [contributor]

• Jean-Pierre Moreau [contributor]

• The R Core Team [copyright holder]

References

Mulder, J., D.R. Williams, Gu, X., A. Tomarken, F. Böing-Messing, J.A.O.C. Olsson-Collentine, Marlyne Meyerink, J. Menke, J.-P. Fox, Y. Rosseel, E.J. Wagenmakers, H. Hoijtink., and van Lissa, C. (submitted). BFpack: Flexible Bayes Factor Testing of Scientific Theories in R. https://arxiv.org/abs/1911.07728

Mulder, J., van Lissa, C., Gu, X., Olsson-Collentine, A., Boeing-Messing, F., Williams, D. R., Fox, J.-P., Menke, J., et al. (2019). BFpack: Flexible Bayes Factor Testing of Scientific Expectations. (Version 0.2.1) https://CRAN.R-project.org/package=BFpack

See Also

Useful links:

• https://github.com/jomulder/BFpack

• Report bugs at https://github.com/jomulder/BFpack/issues

Examples

## Not run: 
# EXAMPLE 1. One-sample t test
ttest1 <- t_test(therapeutic, mu = 5)
print(ttest1)
# confirmatory Bayesian one sample t test
BF1 <- BF(ttest1, hypothesis = "mu = 5")
summary(BF1)
# exploratory Bayesian one sample t test
BF(ttest1)

# EXAMPLE 2. ANOVA
aov1 <- aov(price ~ anchor * motivation,data = tvprices)
BF1 <- BF(aov1, hypothesis = "anchorrounded = motivationlow;
                              anchorrounded < motivationlow")
summary(BF1)

# EXAMPLE 3. Logistic regression
fit <- glm(sent ~ ztrust + zfWHR + zAfro + glasses + attract + maturity +
   tattoos, family = binomial(), data = wilson)
BF1 <- BF(fit, hypothesis = "ztrust > zfWHR > 0;
                             ztrust > 0 & zfWHR = 0")
summary(BF1)

# EXAMPLE 4. Correlation analysis
set.seed(123)
cor1 <- cor_test(memory[1:20,1:3])
BF1 <- BF(cor1)
summary(BF1)
BF2 <- BF(cor1, hypothesis = "Wmn_with_Im > Wmn_with_Del > 0;
                              Wmn_with_Im = Wmn_with_Del = 0")
summary(BF2)

## End(Not run)