The Bayesian counterpart of the paired t test, the analysis of
bayes_one_sample_t applied to the within-pair differences.
It reports the posterior of the standardized difference
\(\delta = \mu_D / \sigma_D\) under the default
Jeffreys-Zellner-Siow (JZS) prior, a Cauchy prior on \(\delta\) with
Jeffreys priors on the nuisance parameters (the variance), summarized by
its median, mean, a credible interval, and the probability statement
\(P(\delta > 0 \mid \mathrm{data})\). The JZS default Bayes factor
(Rouder, Speckman, Sun, Morey, & Iverson, 2009) is also reported. See
bayes_one_sample_t for the model, the package's
interpretive stance, and the computational details (exact quadrature,
no Monte Carlo error).
bayes_paired_t(
x = NULL,
y = NULL,
mean_diff = NULL,
sd_diff = NULL,
n = NULL,
prior_location = 0,
prior_scale = sqrt(2)/2,
prior_mean = NULL,
prior_sd = NULL,
conf_level = 0.95
)A data.frame (class dmar_tbl) with the same
rows as bayes_one_sample_t, where \(\delta\) is the
standardized within-pair difference and the raw rows are on the
difference scale; n is the number of pairs.
Specifying the prior. The default prior on the standardized
effect \(\delta\) is the JZS Cauchy centered at zero. Its
prior_scale
\(r\) is not a standard deviation: a Cauchy has no mean and no variance (those integrals diverge), so beliefs stated as prior moments cannot be expressed through it. What the scale does fix is the quartiles: half the prior mass lies within \(\pm r\) of the location, so the default \(r = \sqrt{2}/2\)
says a 50 percent prior bet that \(|\delta| < 0.71\). A directional
prior keeps the Cauchy and moves prior_location (Gronau, Ly, &
Wagenmakers, 2020). A researcher who thinks in prior moments instead
sets prior_mean and prior_sd, which use a normal prior
with exactly those moments; the two families are exclusive.
The families are also linked by an exact identity: a Cauchy with
location \(\mu\) and scale \(r\) is a normal prior
\(N(\mu, r^2/z^2)\) whose \(z\) is standard normal, that is, a
normal prior whose variance you are not sure of. Choosing the Cauchy
is therefore choosing a normal prior with built-in doubt about its
own width, which is why its tails are heavier and its Bayes factors
more conservative. A normal matched to the Cauchy's interquartile
range has prior_sd = 1.4826 * prior_scale. The full posterior
of \(\delta\) is returned in the "posterior" attribute as a
data frame of delta and density, so any posterior
probability, not only the reported ones, can be computed from it.
Numeric vectors of paired observations, the same length, in
matching order. The analysis is of x - y. Omit both to supply
summary statistics of the differences instead.
Summary statistics of the paired differences: their mean, their standard deviation, and the number of pairs. These are the quantities a paper's paired t test reports. Supply either raw data or all three summary values, never both.
Location of the Cauchy prior on \(\delta\). Defaults to 0, the JZS prior; a nonzero value centers the prior on an expected effect (Gronau, Ly, & Wagenmakers, 2020).
The way to adjust the prior. It is the scale (width)
of the Cauchy prior on the standardized effect \(\delta\) (the JZS
prior), so a user who wants a more or less informative prior sets
prior_scale: larger values say larger effects are plausible a
priori, smaller values concentrate the prior near zero. The default
\(\sqrt{2}/2 \approx 0.707\) is the JZS “medium” prior. Fully
custom or subjective priors beyond the Cauchy family are not supported
by the BayesFactor engine.
Mean and standard deviation of a normal prior on \(\delta\), for prior beliefs stated as moments. Supplying them selects the normal prior; they cannot be combined with the Cauchy arguments. See the prior section of Details.
Probability mass of the credible interval.
Ken Kelley [email protected]
Gronau, Q. F., Ly, A., & Wagenmakers, E.-J. (2020). Informed Bayesian t-tests. The American Statistician, 74(2), 137--143. tools:::Rd_expr_doi("10.1080/00031305.2018.1562983")
Rouder, J. N., Speckman, P. L., Sun, D., Morey, R. D., & Iverson, G. (2009). Bayesian t tests for accepting and rejecting the null hypothesis. Psychonomic Bulletin & Review, 16(2), 225--237. tools:::Rd_expr_doi("10.3758/PBR.16.2.225")
Jeffreys, H. (1961). Theory of probability (3rd ed.). Oxford University Press.
Zellner, A., & Siow, A. (1980). Posterior odds ratios for selected regression hypotheses. In J. M. Bernardo, M. H. DeGroot, D. V. Lindley, & A. F. M. Smith (Eds.), Bayesian statistics: Proceedings of the First International Meeting (pp. 585--603). University of Valencia Press.
bayes_one_sample_t for the model and stance;
bayes_independent_t for unpaired groups;
probability_of_superiority_paired and
randomization_test_paired for other paired analyses.
Other Bayesian t analyses:
bayes_independent_t(),
bayes_one_sample_t()
set.seed(113)
before <- rnorm(30, 100, 12)
after <- before + rnorm(30, 3, 6)
bayes_paired_t(after, before)
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