# BFpack v0.2.1

Monthly downloads

## Flexible Bayes Factor Testing of Scientific Expectations

Implementation of various default Bayes factors
for testing statistical hypotheses. The package is
intended for applied quantitative researchers in the
social and behavioral sciences, medical research,
and related fields. The Bayes factor tests can be
executed for statistical models such as
univariate and multivariate normal linear models,
generalized linear models, special cases of
linear mixed models, survival models, relational
event models. Parameters that can be tested are
location parameters (e.g., regression coefficients),
variances (e.g., group variances), and measures of
association (e.g,. bivariate correlations).
The statistical underpinnings are
described in
Mulder, Hoijtink, and Xin (2019) <arXiv:1904.00679>,
Mulder and Gelissen (2019) <arXiv:1807.05819>,
Mulder (2016) <DOI:10.1016/j.jmp.2014.09.004>,
Mulder and Fox (2019) <DOI:10.1214/18-BA1115>,
Mulder and Fox (2013) <DOI:10.1007/s11222-011-9295-3>,
Boeing-Messing, van Assen, Hofman, Hoijtink, and Mulder <DOI:10.1037/met0000116>,
Hoijtink, Mulder, van Lissa, and Gu, (2018) <DOI:10.31234/osf.io/v3shc>,
Gu, Mulder, and Hoijtink, (2018) <DOI:10.1111/bmsp.12110>,
Hoijtink, Gu, and Mulder, (2018) <DOI:10.1111/bmsp.12145>, and
Hoijtink, Gu, Mulder, and Rosseel, (2018) <DOI:10.1037/met0000187>.

## Readme

# BFpack

R-functions for Bayesian exploratory (equal vs negative vs postive) and confirmatory (equality and/or order constraints) hypothesis testing for commonly used statistical models, including (but not limited to) univariate/multivariate t testing, (M)AN(C)OVA, multivariate/univariate regression, random intercept models. The functions need fitted models (e.g., lm) as input as well as a string that specifies a set of order constraints on the regression coefficients.

Developers and collaborators: Joris Mulder, Caspar van Lissa, Donald R. Williams, Xin Gu, Anton Olsson-Collentine, Florian Böing-Messing, Andrew Tomarken, Marlyne Bosman-Meijerink, Eric-Jan Wagenmakers, Yves Rosseel, Jean-Paul Fox, Janosch Menke, and Herbert Hoijtink.

Licensed under the GNU General Public License version 2 (June, 1991)

## Installation

You can install BFpack from GitHub with:

``` r

# install.packages("devtools")

devtools::install_github("jomulder/BFpack")

## Example analyses

# Aapplication 1

# load R package BFpack and bain

library(BFpack) library(bain)

# Frequentist one sample t test at the null point mu=5 on the therapeutic data

ttest1 <- t_test(therapeutic,mu=5) print(ttest1)

# confirmatory Bayesian one sample t test

BF1 <- BF(ttest1,"mu=5") summary(BF1)

# Application 2

# Fit an anova model on the tvprices data

aov1 <- aov(price ~ anchor*motivation,data=tvprices)

# Perform exploratory Bayes factor tests for ANOVA design

BF(aov1)

# Application 3

# Perform classical Bartlett test for homogeneity of group varianceson the accuracy data

bartlett <- bartlett_test(x = attention$accuracy, g = attention$group)

# Specify informative hypotheses on the group variances based on substantive expectations

hypothesis <- c("Controls=TS<ADHD; Controls<TS=ADHD; Controls=TS=ADHD") set.seed(358)

# Perform the Bayesian hypothesis tests

BF_var <- BF(bartlett, hypothesis) summary(BF_var)

# Application 4

# Fit the multivariate regression model on the fmri data

fmri.lm <- lm(cbind(Superficial,Middle,Deep) ~ Face + Vehicle, data=fmri)

# Specify informative hypotheses on the coefficients across predictor and dependent variables

# based on substantive expectations

constraints.fmri <- "Face_on_Deep = Face_on_Superficial = Face_on_Middle < 0 < Vehicle_on_Deep = Vehicle_on_Superficial = Vehicle_on_Middle; Face_on_Deep < Face_on_Superficial = Face_on_Middle < 0 < Vehicle_on_Deep = Vehicle_on_Superficial = Vehicle_on_Middle"

# Perform the Bayesian hypothesis tests

set.seed(123) BF_fmri <- BF(fmri.lm, hypothesis = constraints.fmri) summary(BF_fmri)

# Application 4b

constraints.fmri2 <- "Face_on_Deep = Face_on_Superficial = Face_on_Middle < 0; Face_on_Deep < Face_on_Superficial = Face_on_Middle < 0" fmri.lm2 <- lm(cbind(Superficial,Middle,Deep) ~ Face + Vehicle, data=fmri) BF.fmri2 <- BF(fmri.lm2, hypothesis=constraints.fmri2)

#Application 5

# Fit logistic regression model

fit <- glm(sent ~ ztrust + zfWHR + zAfro + glasses + attract + maturity + tattoos, family = binomial(), data = wilson)

# Perform the Bayesian hypothesis tests

set.seed(123) BF_glm <- BF(fit, hypothesis="ztrust > (zfWHR, zAfro) > 0; ztrust > (zfWHR, zAfro) = 0") summary(BF_glm)

# Application 6: Correlation analysis

#Fit multivariate normal model lm6 <- lm(cbind(Im,Del,Wmn,Cat,Fas,Rat) ~ -1 + Group, data=memory) set.seed(123)

#Perform Bayes factor test of the order hypothesis against its compleplement BF6_cor <- BF(lm6,parameter="correlation", hypothesis= "Del_with_Im_in_GroupHC > Del_with_Im_in_GroupSZ & Del_with_Wmn_in_GroupHC > Del_with_Wmn_in_GroupSZ & Del_with_Cat_in_GroupHC > Del_with_Cat_in_GroupSZ & Del_with_Fas_in_GroupHC > Del_with_Fas_in_GroupSZ & Del_with_Rat_in_GroupHC > Del_with_Rat_in_GroupSZ & Im_with_Wmn_in_GroupHC > Im_with_Wmn_in_GroupSZ & Im_with_Cat_in_GroupHC > Im_with_Cat_in_GroupSZ & Im_with_Fas_in_GroupHC > Im_with_Fas_in_GroupSZ & Im_with_Rat_in_GroupHC > Im_with_Rat_in_GroupSZ & Wmn_with_Cat_in_GroupHC > Wmn_with_Cat_in_GroupSZ & Wmn_with_Fas_in_GroupHC > Wmn_with_Fas_in_GroupSZ & Wmn_with_Rat_in_GroupHC > Wmn_with_Rat_in_GroupSZ & Cat_with_Fas_in_GroupHC > Cat_with_Fas_in_GroupSZ & Cat_with_Rat_in_GroupHC > Cat_with_Rat_in_GroupSZ & Fas_with_Rat_in_GroupHC > Fas_with_Rat_in_GroupSZ") summary(BF6_cor)

# Application 7. Testing intraclas correlations

library(lme4)

#Only consider the timssICC data for the measurements of the four counteries in 2011 timssICC_subset <- timssICC[(timssICC$groupNL11==1)+(timssICC$groupHR11==1)+ (timssICC$groupDE11==1)+(timssICC$groupDK11==1)>0,]

#Fit a random intercept model with country specific random effect variances across schools outlme1 <- lmer(math ~ -1 + gender + weight + lln + groupNL11 + (0+groupNL11 | schoolID) + groupHR11 + (0+groupHR11 | schoolID) + groupDE11 + (0+groupDE11 | schoolID) + groupDK11 + (0+groupDK11 | schoolID), data=timssICC_subset)

#Perform Bayes factor test on intraclass correlations across countries in 2011 set.seed(123) BFout <- BF(outlme1,hypothesis= "groupNL11<groupHR11<groupDE11<groupDK11; groupNL11=groupHR11=groupDE11=groupDK11") summary(BFout)

## Functions in BFpack

Name | Description | |

BF | Bayes factors for Bayesian exploratory and confirmatory hypothesis testing | |

actors | Actors from a consultancy firm | |

therapeutic | Data come from an experimental study (Rosa, Rosa, Sarner, and Barrett, 1998) that were also used in Howell (2012, p.196). An experiment was conducted to investigate if Therapeutic Touch practitioners who were blindfolded can effectively identify which of their hands is below the experimenter<U+00A1><U+00AF>s. Twenty-eight practitioners were involved and tested 10 times in the experiment. Researchers expected an average of 5 correct answers from each practitioner as it is the number by chance if they do not outperform others. | |

timssICC | Trends in International Mathematics and Science Study (TIMSS) 2011-2015 | |

attention | Multiple Sources of Attentional Dysfunction in Adults With Tourette's Syndrome | |

bartlett_test | Bartlett Test of Homogeneity of Variances | |

cor_test | Bayesian correlation analysis | |

relevents | A sequence of innovation-related e-mail messages | |

fmri | fMRI data | |

memory | Memory data on health and schizophrenic patients | |

tvprices | Precision of the Anchor Influences the Amount of Adjustment | |

wilson | Facial trustworthiness and criminal sentencing | |

sivan | Wason task performance and morality | |

same_division | Same division event statistic | |

same_hierarchy | Same hierarchical position event statistic | |

same_building | Same building event statistic | |

No Results! |

## Last month downloads

## Details

Type | Package |

Date | 2020-05-11 |

License | GPL (>= 3) |

URL | https://github.com/jomulder/BFpack |

BugReports | https://github.com/jomulder/BFpack/issues |

Encoding | UTF-8 |

LazyData | true |

NeedsCompilation | yes |

RoxygenNote | 6.1.1 |

Packaged | 2020-05-11 16:04:12 UTC; jorismulder |

Repository | CRAN |

Date/Publication | 2020-05-11 17:50:02 UTC |

depends | bain , R (>= 3.0.0) |

imports | lme4 , MASS , Matrix , mvtnorm , pracma , stats |

suggests | polycor , pscl , survival , testthat |

Contributors | the R Core Team, James Lovato, Alan Miller, Barry Brown, Cleve Moler, Caspar van Lissa, Xin Gu, Anton Olsson-Collentine, Florian Boeing-Messing, Jean-Paul Fox, Janosch Menke, Kathy Russell, Lapack 3.8 , Jack Dongarra, Jim Bunch, Gilbert Stewart, John Burkandt, Ashwith Rego, Alexander Godunov, Jean-Pierre Moreau, Donald Williams |

#### Include our badge in your README

```
[![Rdoc](http://www.rdocumentation.org/badges/version/BFpack)](http://www.rdocumentation.org/packages/BFpack)
```