vignettes/ComparisonR.Rmd
ComparisonR.Rmdvignettes/SpikeAndSlab.Rmd
SpikeAndSlab.RmdBartoš F (2021). BayesTools: Tools for Bayesian Analyses. -R package version 0.2.16, https://CRAN.R-project.org/package=BayesTools. +R package version 0.2.17, https://CRAN.R-project.org/package=BayesTools.
@Manual{,
title = {BayesTools: Tools for Bayesian Analyses},
author = {František Bartoš},
year = {2021},
- note = {R package version 0.2.16},
+ note = {R package version 0.2.17},
url = {https://CRAN.R-project.org/package=BayesTools},
}
diff --git a/index.html b/index.html
index 10182a58..33fc9d1b 100644
--- a/index.html
+++ b/index.html
@@ -39,7 +39,7 @@
diff --git a/news/index.html b/news/index.html
index 3eca98d4..367f39b0 100644
--- a/news/index.html
+++ b/news/index.html
@@ -17,7 +17,7 @@
@@ -60,6 +60,19 @@ NEWS.md
+ prior_informed() functionbridge_object() (fixes: https://github.com/FBartos/BayesTools/issues/28)Na/NaN tests for check_ functions (fixes: https://github.com/FBartos/BayesTools/issues/26)prepares a 'bridgesampling' object with a given +log marginal likelihood.
+bridgesampling_object(logml = -Inf)log marginal likelihood. Defaults to -Inf.
JAGS_bridgesampling returns an object of class 'bridge'.
check_bool(x, name, check_length = 1, allow_NULL = FALSE, call = "")
+ check_bool(
+ x,
+ name,
+ check_length = 1,
+ allow_NULL = FALSE,
+ allow_NA = TRUE,
+ call = ""
+)
check_char(
x,
@@ -76,6 +83,7 @@ Check input
check_length = 1,
allow_values = NULL,
allow_NULL = FALSE,
+ allow_NA = TRUE,
call = ""
)
@@ -87,6 +95,7 @@ Check input
allow_bound = TRUE,
check_length = 1,
allow_NULL = FALSE,
+ allow_NA = TRUE,
call = ""
)
@@ -98,6 +107,7 @@ Check input
allow_bound = TRUE,
check_length = 1,
allow_NULL = FALSE,
+ allow_NA = TRUE,
call = ""
)
@@ -134,6 +144,11 @@ Arguments
If so, no checks are executed.
+allow_NA
+whether the object can contain NA or NaN
+values.
call
string to be placed as a prefix to the error call.
diff --git a/reference/contr.meandif.html b/reference/contr.meandif.html
index 2beb2a42..d6e50517 100644
--- a/reference/contr.meandif.html
+++ b/reference/contr.meandif.html
@@ -23,7 +23,7 @@
add_column()
Adds column to BayesTools table
Create a 'bridgesampling' object
check_bool() check_char() check_real() check_int() check_list()
Wagenmakers E, Beek TF, Rotteveel M, Gierholz A, Matzke D, Steingroever H, Ly A, Verhagen J, Selker R, Sasiadek A, others (2015). “Turning the hands of time again: a purely confirmatory replication study and a Bayesian analysis.” -Frontiers in Psychology, 6, 494. +Frontiers in Psychology, 6, 1--6. doi:10.3389/fpsyg.2015.00494 .
diff --git a/reference/lines.prior.html b/reference/lines.prior.html index c12178b7..0fe8ab3a 100644 --- a/reference/lines.prior.html +++ b/reference/lines.prior.html @@ -17,7 +17,7 @@ diff --git a/reference/lines_prior_list.html b/reference/lines_prior_list.html index c8364f3c..d6e53dab 100644 --- a/reference/lines_prior_list.html +++ b/reference/lines_prior_list.html @@ -17,7 +17,7 @@ diff --git a/reference/marginal_inference.html b/reference/marginal_inference.html index 34b09449..859d5e4f 100644 --- a/reference/marginal_inference.html +++ b/reference/marginal_inference.html @@ -23,7 +23,7 @@ diff --git a/reference/marginal_posterior.html b/reference/marginal_posterior.html index 36337327..c3401936 100644 --- a/reference/marginal_posterior.html +++ b/reference/marginal_posterior.html @@ -19,7 +19,7 @@ diff --git a/reference/mean.prior.html b/reference/mean.prior.html index c6315ead..3eeb6a1c 100644 --- a/reference/mean.prior.html +++ b/reference/mean.prior.html @@ -20,7 +20,7 @@ diff --git a/reference/mix_posteriors.html b/reference/mix_posteriors.html index 9110ff44..edb81b4e 100644 --- a/reference/mix_posteriors.html +++ b/reference/mix_posteriors.html @@ -20,7 +20,7 @@ diff --git a/reference/mpoint.html b/reference/mpoint.html index e59ad26c..1ccfafba 100644 --- a/reference/mpoint.html +++ b/reference/mpoint.html @@ -18,7 +18,7 @@ diff --git a/reference/parameter_names.html b/reference/parameter_names.html index bc8a55a0..8c01c720 100644 --- a/reference/parameter_names.html +++ b/reference/parameter_names.html @@ -18,7 +18,7 @@ diff --git a/reference/plot.prior.html b/reference/plot.prior.html index 588a6a74..aeff4c11 100644 --- a/reference/plot.prior.html +++ b/reference/plot.prior.html @@ -17,7 +17,7 @@ diff --git a/reference/plot_marginal.html b/reference/plot_marginal.html index e4552a9a..8e0c33c3 100644 --- a/reference/plot_marginal.html +++ b/reference/plot_marginal.html @@ -17,7 +17,7 @@ diff --git a/reference/plot_models.html b/reference/plot_models.html index 49754124..b7a1b479 100644 --- a/reference/plot_models.html +++ b/reference/plot_models.html @@ -17,7 +17,7 @@ diff --git a/reference/plot_posterior.html b/reference/plot_posterior.html index 8845f319..01539d5e 100644 --- a/reference/plot_posterior.html +++ b/reference/plot_posterior.html @@ -17,7 +17,7 @@ diff --git a/reference/plot_prior_list.html b/reference/plot_prior_list.html index ddd7370b..b661450d 100644 --- a/reference/plot_prior_list.html +++ b/reference/plot_prior_list.html @@ -17,7 +17,7 @@ diff --git a/reference/point.html b/reference/point.html index 5118071f..2e58230f 100644 --- a/reference/point.html +++ b/reference/point.html @@ -18,7 +18,7 @@ diff --git a/reference/print.BayesTools_table.html b/reference/print.BayesTools_table.html index e13caf63..213dd469 100644 --- a/reference/print.BayesTools_table.html +++ b/reference/print.BayesTools_table.html @@ -17,7 +17,7 @@ diff --git a/reference/print.prior.html b/reference/print.prior.html index f8c760fe..9e9705fa 100644 --- a/reference/print.prior.html +++ b/reference/print.prior.html @@ -17,7 +17,7 @@ diff --git a/reference/prior.html b/reference/prior.html index 61ec67b4..7a10e474 100644 --- a/reference/prior.html +++ b/reference/prior.html @@ -18,7 +18,7 @@ diff --git a/reference/prior_PP.html b/reference/prior_PP.html index 5eb911b1..14393e11 100644 --- a/reference/prior_PP.html +++ b/reference/prior_PP.html @@ -19,7 +19,7 @@ diff --git a/reference/prior_factor.html b/reference/prior_factor.html index 240f3c51..fbda37ae 100644 --- a/reference/prior_factor.html +++ b/reference/prior_factor.html @@ -19,7 +19,7 @@ diff --git a/reference/prior_functions.html b/reference/prior_functions.html index 500a81bd..145e4ef1 100644 --- a/reference/prior_functions.html +++ b/reference/prior_functions.html @@ -21,7 +21,7 @@ diff --git a/reference/prior_functions_methods.html b/reference/prior_functions_methods.html index d9e79b00..3312531c 100644 --- a/reference/prior_functions_methods.html +++ b/reference/prior_functions_methods.html @@ -21,7 +21,7 @@ diff --git a/reference/prior_informed.html b/reference/prior_informed.html index 521711ef..2ae4f211 100644 --- a/reference/prior_informed.html +++ b/reference/prior_informed.html @@ -18,7 +18,7 @@ @@ -91,8 +91,11 @@For medicine, the possible options are based on Bartoš et al. (2021)
+and Bartoš et al. (2023)
+
who developed empirical prior distributions for the effect size and heterogeneity parameters of the
-continuous standardized outcomes based on the Cochrane database of systematic reviews.
+continuous outcomes (standardized mean differences), dichotomous outcomes (logOR, logRR, and risk differences),
+and time to event outcomes (logHR) based on the Cochrane database of systematic reviews.
Use "Cochrane" for a prior distribution based on the whole database or call
print(prior_informed_medicine_names) to inspect the names of
all 46 subfields and set the appropriate parameter and type.
prior type describing what prior distribution is supposed to be produced in cases
where the name and parameter correspond to multiple prior distributions. Relevant only for
-the empirical medical prior distributions.
"smd"for standardized mean differences
"logOR"for log odds ratios
"logRR"for log risk ratios
"RD"for risk differences
"logHR"for hazard ratios
Bartoš F, Gronau QF, Timmers B, Otte WM, Ly A, Wagenmakers E (2021).
“Bayesian model-averaged meta-analysis in medicine.”
-Statistics in Medicine.
+Statistics in Medicine, 40(30), 6743--6761.
doi:10.1002/sim.9170
-.
Gronau QF, Van Erp S, Heck DW, Cesario J, Jonas KJ, Wagenmakers E (2017).
+.
Bartoš F, Otte WM, Gronau QF, Timmers B, Ly A, Wagenmakers E (2023).
+“Empirical prior distributions for Bayesian meta-analyses of binary and time-to-event outcomes.”
+doi:10.48550/arXiv.2306.11468
+, preprint at https://doi.org/10.48550/arXiv.2306.11468.
Gronau QF, Van Erp S, Heck DW, Cesario J, Jonas KJ, Wagenmakers E (2017).
“A Bayesian model-averaged meta-analysis of the power pose effect with informed and default priors: The case of felt power.”
Comprehensive Results in Social Psychology, 2(1), 123--138.
doi:10.1080/23743603.2017.1326760
@@ -152,7 +174,7 @@
An object of class character of length 47.
An object of class character of length 57.