Nothing
inst/doc/v03-feature-coverage.R
In RoBMA: Robust Bayesian Meta-Analyses
## ----vignette-nowrap-options, include = FALSE, eval = TRUE----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
options(width = 10000)
## ----setup, include = FALSE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
message = FALSE,
warning = FALSE
)
tick <- '<span class="yes">✓</span>'
limited <- '<span class="limited">limited</span>'
no <- '<span class="no">No</span>'
na_cell <- '<span class="na-cell">n/a</span>'
model_columns <- c(
"brma.norm", "brma.glmm", "bselmodel", "bPET/bPEESE",
"BMA.norm", "BMA.glmm", "RoBMA"
)
reference_links <- c(
"add_loo()" = "../reference/add_loo.brma.html",
"add_marglik()" = "../reference/add_marglik.brma.html",
"add_waic()" = "../reference/add_waic.brma.html",
"as_draws()" = "../reference/as_draws.brma.html",
"as_draws_array()" = "../reference/as_draws.brma.html",
"as_draws_df()" = "../reference/as_draws.brma.html",
"as_draws_list()" = "../reference/as_draws.brma.html",
"as_draws_matrix()" = "../reference/as_draws.brma.html",
"as_draws_rvars()" = "../reference/as_draws.brma.html",
"as_zplot()" = "../reference/as_zplot.brma.html",
"bayes_factor()" = "../reference/bf.brma.html",
"bf()" = "../reference/bf.brma.html",
"blup()" = "../reference/blup.brma.html",
"bPET()" = "../reference/bPET.html",
"bPEESE()" = "../reference/bPEESE.html",
"brma()" = "../reference/brma.html",
"brma.glmm()" = "../reference/brma.glmm.html",
"BMA()" = "../reference/BMA.html",
"BMA.glmm()" = "../reference/BMA.glmm.html",
"bridge_sampler()" = "../reference/bridge_sampler.brma.html",
"bselmodel()" = "../reference/bselmodel.html",
"check_loo()" = "../reference/check_loo.brma.html",
"coef()" = "../reference/coef.brma.html",
"contr.meandif()" = "../reference/contr.BayesTools.html",
"contr.orthonormal()" = "../reference/contr.BayesTools.html",
"contr.treatment()" = "https://stat.ethz.ch/R-manual/R-devel/library/stats/html/contrast.html",
"cooks.distance()" = "../reference/cooks.distance.brma.html",
"covratio()" = "../reference/covratio.brma.html",
"dfbetas()" = "../reference/dfbetas.brma.html",
"dffits()" = "../reference/dffits.brma.html",
"estimate_unit_information_sd()" = "../reference/estimate_unit_information_sd.html",
"fitted()" = "../reference/fitted.brma.html",
"funnel()" = "../reference/funnel.html",
"galbraith()" = "../reference/radial.html",
"hatvalues()" = "../reference/hatvalues.brma.html",
"influence()" = "../reference/influence.brma.html",
"interpret()" = "../reference/interpret.html",
"logLik()" = "../reference/logLik.brma.html",
"logml()" = "../reference/logml.brma.html",
"loo()" = "../reference/loo.brma.html",
"loo::pareto_k_ids()" = "https://mc-stan.org/loo/reference/pareto-k-diagnostic.html",
"loo::pareto_k_table()" = "https://mc-stan.org/loo/reference/pareto-k-diagnostic.html",
"loo_compare()" = "../reference/loo_compare.brma.html",
"loo_weights()" = "../reference/loo_weights.brma.html",
"marginal_means()" = "../reference/marginal_means.brma.html",
"nobs()" = "../reference/nobs.brma.html",
"plot()" = "../reference/plot.brma.html",
"plot_diagnostic()" = "../reference/plot_diagnostic.html",
"plot_diagnostic_autocorrelation()" = "../reference/plot_diagnostic.html",
"plot_diagnostic_density()" = "../reference/plot_diagnostic.html",
"plot_diagnostic_trace()" = "../reference/plot_diagnostic.html",
"plot_pet_peese()" = "../reference/plot_pet_peese.html",
"plot_prior()" = "../reference/plot_prior.html",
"plot_weightfunction()" = "../reference/plot_weightfunction.html",
"pooled_effect()" = "../reference/pooled_effect.brma.html",
"pooled_heterogeneity()" = "../reference/pooled_heterogeneity.brma.html",
"post_prob()" = "../reference/post_prob.brma.html",
"predict()" = "../reference/predict.brma.html",
"print_prior()" = "../reference/print_prior.html",
"prior()" = "../reference/prior.html",
"prior_factor()" = "../reference/prior_factor.html",
"prior_informed()" = "../reference/prior_informed.html",
"prior_none()" = "../reference/prior_none.html",
"prior_PEESE()" = "../reference/prior_PEESE.html",
"prior_PET()" = "../reference/prior_PET.html",
"prior_weightfunction()" = "../reference/prior_weightfunction.html",
"qqnorm()" = "../reference/qqnorm.brma.html",
"radial()" = "../reference/radial.html",
"ranef()" = "../reference/ranef.brma.html",
"regplot()" = "../reference/regplot.html",
"residuals()" = "../reference/residuals.brma.html",
"RoBMA()" = "../reference/RoBMA.html",
"rstandard()" = "../reference/rstandard.brma.html",
"rstudent()" = "../reference/rstudent.brma.html",
"simulate()" = "https://stat.ethz.ch/R-manual/R-devel/library/stats/html/simulate.html",
"summary()" = "../reference/summary.brma.html",
"summary_heterogeneity()" = "../reference/summary_heterogeneity.brma.html",
"summary_models()" = "../reference/summary_models.html",
"true_effects()" = "../reference/true_effects.brma.html",
"update()" = "../reference/update.brma.html",
"vcov()" = "https://stat.ethz.ch/R-manual/R-devel/library/stats/html/vcov.html",
"vif()" = "../reference/vif.brma.html",
"waic()" = "../reference/waic.brma.html",
"weights()" = "https://stat.ethz.ch/R-manual/R-devel/library/stats/html/weights.html",
"wf_cumulative()" = "../reference/prior_weightfunction.html",
"wf_fixed()" = "../reference/prior_weightfunction.html",
"wf_independent()" = "../reference/prior_weightfunction.html",
"forest()" = "https://wviechtb.github.io/metafor/reference/forest.rma.html",
"baujat()" = "https://wviechtb.github.io/metafor/reference/baujat.html",
"gosh()" = "https://wviechtb.github.io/metafor/reference/gosh.html",
"labbe()" = "https://wviechtb.github.io/metafor/reference/labbe.html"
)
model_column_links <- list(
"brma.norm" = "../reference/brma.html",
"brma.glmm" = "../reference/brma.glmm.html",
"bselmodel" = "../reference/bselmodel.html",
"bPET/bPEESE" = c("../reference/bPET.html", "../reference/bPEESE.html"),
"BMA.norm" = "../reference/BMA.html",
"BMA.glmm" = "../reference/BMA.glmm.html",
"RoBMA" = "../reference/RoBMA.html"
)
status_map <- c(
Y = tick,
L = limited,
N = no,
A = na_cell
)
feature_row <- function(topic, feature, pattern) {
values <- strsplit(pattern, "", fixed = TRUE)[[1]]
if (length(values) != length(model_columns)) {
stop("Status pattern has wrong length: ", pattern, call. = FALSE)
}
out <- c(
list(Topic = topic, Feature = feature),
stats::setNames(as.list(status_map[values]), model_columns)
)
return(out)
}
feature_table <- function(rows) {
rows <- as.data.frame(do.call(rbind, rows), stringsAsFactors = FALSE, check.names = FALSE)
rows[] <- lapply(rows, function(x) {
if (is.list(x)) {
return(vapply(x, function(y) paste0(as.character(y), collapse = ""), character(1)))
}
return(as.character(x))
})
cat('
<style>
.feature-matrix {
border-collapse: collapse;
width: 100%;
font-size: 0.84em;
}
.feature-matrix th,
.feature-matrix td {
border: 1px solid #d0d7de;
padding: 4px 6px;
vertical-align: top;
}
.feature-matrix th {
background: #f6f8fa;
}
.feature-matrix .topic-head {
min-width: 60px;
width: 60px;
}
.feature-matrix .feature-head {
min-width: 25em;
}
.feature-matrix .model-head {
height: 118px;
min-width: 34px;
max-width: 34px;
width: 34px;
padding: 0;
position: relative;
vertical-align: bottom;
}
.feature-matrix .rotated-header {
bottom: 6px;
display: block;
left: 50%;
line-height: 1;
position: absolute;
transform: rotate(-90deg);
transform-origin: left center;
white-space: nowrap;
}
.feature-matrix .topic-cell {
background: #f6f8fa;
min-width: 60px;
width: 60px;
padding: 0;
text-align: center;
vertical-align: middle;
}
.feature-matrix .topic-cell span {
display: inline-block;
transform: rotate(-90deg);
white-space: normal;
width: 8em;
text-align: center;
font-weight: 700;
line-height: 1.1;
}
.feature-matrix .feature-cell {
min-width: 25em;
}
.feature-matrix .feature-cell a {
color: #0969da;
text-decoration: none;
}
.feature-matrix .feature-cell a:hover {
text-decoration: underline;
}
.feature-matrix .feature-cell a code {
color: inherit;
}
.feature-matrix .status-cell {
text-align: center;
vertical-align: middle;
white-space: nowrap;
width: 34px;
}
.feature-matrix .yes {
color: #1a7f37;
font-weight: 700;
}
.feature-matrix .limited {
color: #9a6700;
}
.feature-matrix .no,
.feature-matrix .na-cell {
color: #6e7781;
}
</style>
')
escape_html_text <- function(x) {
x <- as.character(x)
x <- gsub("&", "&", x, fixed = TRUE)
x <- gsub("<", "<", x, fixed = TRUE)
x <- gsub(">", ">", x, fixed = TRUE)
x <- gsub('"', """, x, fixed = TRUE)
return(x)
}
format_code_span <- function(code) {
code_html <- paste0("<code>", escape_html_text(code), "</code>")
link <- if (code %in% names(reference_links)) reference_links[[code]] else NA_character_
if (!is.na(link)) {
return(paste0('<a href="', escape_html_text(link), '">', code_html, "</a>"))
}
return(code_html)
}
escape_html <- function(x) {
x <- as.character(x)
matches <- gregexpr("`[^`]+`", x, perl = TRUE)[[1]]
if (matches[1] == -1L) {
return(escape_html_text(x))
}
match_lengths <- attr(matches, "match.length")
pieces <- character(0)
position <- 1L
for (j in seq_along(matches)) {
match_start <- matches[j]
match_end <- match_start + match_lengths[j] - 1L
if (match_start > position) {
pieces <- c(pieces, escape_html_text(substr(x, position, match_start - 1L)))
}
code <- substr(x, match_start + 1L, match_end - 1L)
pieces <- c(pieces, format_code_span(code))
position <- match_end + 1L
}
if (position <= nchar(x)) {
pieces <- c(pieces, escape_html_text(substr(x, position, nchar(x))))
}
return(paste0(pieces, collapse = ""))
}
format_model_column <- function(model_column) {
link <- model_column_links[[model_column]]
if (length(link) == 2L) {
return(paste0(
'<a href="', escape_html_text(link[[1]]), '">bPET</a>/',
'<a href="', escape_html_text(link[[2]]), '">bPEESE</a>'
))
}
return(paste0(
'<a href="', escape_html_text(link), '">',
escape_html_text(model_column),
"</a>"
))
}
topic_runs <- rle(rows$Topic)
topic_start <- cumsum(c(1L, head(topic_runs$lengths, -1L)))
topic_span <- rep(0L, nrow(rows))
topic_span[topic_start] <- topic_runs$lengths
cat('<div style="overflow-x: auto;">\n')
cat('<table class="feature-matrix">\n')
cat("<thead><tr>")
cat('<th class="topic-head">Topic</th>')
cat('<th class="feature-head">Feature</th>')
for (model_column in model_columns) {
cat('<th class="model-head"><span class="rotated-header">', format_model_column(model_column), "</span></th>", sep = "")
}
cat("</tr></thead>\n")
cat("<tbody>\n")
for (i in seq_len(nrow(rows))) {
cat("<tr>")
if (topic_span[i] > 0L) {
cat(
'<td class="topic-cell" rowspan="', topic_span[i], '"><span>',
escape_html(rows$Topic[i]),
"</span></td>",
sep = ""
)
}
cat('<td class="feature-cell">', escape_html(rows$Feature[i]), "</td>", sep = "")
for (model_column in model_columns) {
cat('<td class="status-cell">', rows[[model_column]][i], "</td>", sep = "")
}
cat("</tr>\n")
}
cat("</tbody>\n")
cat("</table>\n")
cat("</div>\n")
}
## ----feature-matrix, echo = FALSE, results = "asis"-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
rows <- list(
feature_row("Model / Structure", "Fixed- and random-effects models", "YYYYYYY"),
feature_row("Model / Structure", "Moderation (`mods`)", "YYYYYYY"),
feature_row("Model / Structure", "Location-scale models (`scale`)", "YYYYYYY"),
feature_row("Model / Structure", "Multilevel models (`cluster`)", "YYYYYYY"),
feature_row("Model / Structure", "Model averaging", "NNNNYYY"),
feature_row("Model / Structure", "Inclusion Bayes factors", "NNNNYYY"),
feature_row("Model / Structure", "General multivariate / covariance structures", "NNNNNNN"),
feature_row("Model / Structure", "Robust / sandwich inference", "NNNNNNN"),
feature_row("Model / Structure", "Refit / update (`update()`)", "YYYYYYY"),
feature_row("Priors", "Default prior distributions", "YYYYYYY"),
feature_row("Priors", "Empirical/informed prior distributions (`prior_informed()`)", "YYYYYYY"),
feature_row("Priors", "Custom prior distributions (`prior()`, `prior_factor()`, `prior_weightfunction()`, `prior_none()`)", "YYYYYYY"),
feature_row("Priors", "PET / PEESE prior distributions (`prior_PET()`, `prior_PEESE()`)", "NNNYNNY"),
feature_row("Priors", "Prior-only inspection (`only_priors = TRUE`)", "YYYYYYY"),
feature_row("Priors", "Weight-function shape (`wf_cumulative()`, `wf_fixed()`, `wf_independent()`)", "NNYNNNY"),
feature_row("Priors", "Factor contrasts (`contr.treatment()`, `contr.meandif()`, `contr.orthonormal()`)", "YYYYYYY"),
feature_row("Priors", "UISD estimation (`estimate_unit_information_sd()`)", "YYYYYYY"),
feature_row("Publication Bias", "Selection models", "NNYNNNY"),
feature_row("Publication Bias", "PET / PEESE models", "NNNYNNY"),
feature_row("Publication Bias", "Model averaging over bias models", "NNNNNNY"),
feature_row("Publication Bias", "Bias-adjusted summaries / predictions", "NNYYNNY"),
feature_row("Publication Bias", "Trim-fill / fail-safe N", "NNNNNNN"),
feature_row("Prediction", "Pooled effect / heterogeneity summaries (`pooled_effect()`, `pooled_heterogeneity()`)", "YYYYYYY"),
feature_row("Prediction", "Heterogeneity decomposition (`summary_heterogeneity()`, tau², I², H²)", "YYYYYYY"),
feature_row("Prediction", "Fitted-value extraction (`fitted()`)", "YYYYYYY"),
feature_row("Prediction", "Prediction for new covariate values (`predict()`)", "YYYYYYY"),
feature_row("Prediction", "Posterior predictive response summaries (`predict()`)", "YYYYYYY"),
feature_row("Prediction", "True effects / BLUPs / random effects (`true_effects()`, `blup()`, `ranef()`)", "YYYYYYY"),
feature_row("Prediction", "Estimated marginal means (`marginal_means()`)", "YYYYYYY"),
feature_row("Plots", "Posterior plots (`plot()`)", "YYYYYYY"),
feature_row("Plots", "Prior plots (`plot_prior()`)", "YYYYYYY"),
feature_row("Plots", "Marginal means plots (`marginal_means()` + `plot()`)", "YYYYYYY"),
feature_row("Plots", "Regression plots (`regplot()`)", "YYYYYYY"),
feature_row("Plots", "Funnel plots (`funnel()`)", "YYYYYYY"),
feature_row("Plots", "zplot diagnostics (`as_zplot()`/`zplot()`)", "YYYYYYY"),
feature_row("Plots", "Weight-function plots (`plot_weightfunction()`)", "NNYNNNY"),
feature_row("Plots", "PET-PEESE plots (`plot_pet_peese()`)", "NNNYNNY"),
feature_row("Plots", "Radial / Galbraith plots (`radial()`, `galbraith()`)", "YLYYYLY"),
feature_row("Plots", "Forest plots (`forest()`)", "NNNNNNN"),
feature_row("Plots", "Baujat plots (`baujat()`)", "NNNNNNN"),
feature_row("Plots", "GOSH plots (`gosh()`)", "NNNNNNN"),
feature_row("Plots", "L'Abbe plots (`labbe()`)", "NNNNNNN"),
feature_row("Residuals / Diagnostics", "Raw residuals (`residuals()`)", "YYYYYYY"),
feature_row("Residuals / Diagnostics", "Pearson / standardized residuals (`rstandard()`)", "YNNYYNL"),
feature_row("Residuals / Diagnostics", "Studentized residuals (LOO-PIT) (`rstudent()`)", "YYYYYYY"),
feature_row("Residuals / Diagnostics", "Q-Q plots (`qqnorm()`)", "YYYYYYY"),
feature_row("Residuals / Diagnostics", "Cook's distances (`cooks.distance()`)", "YNNYYNN"),
feature_row("Residuals / Diagnostics", "DFBETAS (`dfbetas()`)", "YYYYYYY"),
feature_row("Residuals / Diagnostics", "DFFITS (`dffits()`)", "YNNYYNN"),
feature_row("Residuals / Diagnostics", "Covariance ratios (`covratio()`)", "YYYYYYY"),
feature_row("Residuals / Diagnostics", "Hat values (`hatvalues()`)", "YNNYYNN"),
feature_row("Residuals / Diagnostics", "Combined influence summary (`influence()`)", "YLLYYLL"),
feature_row("Residuals / Diagnostics", "LOO / WAIC diagnostics (`check_loo()`, `loo::pareto_k_ids()`, `loo::pareto_k_table()`)", "YYYYYYY"),
feature_row("Residuals / Diagnostics", "Moderator collinearity diagnostics (`vif()`)", "YYYYYYY"),
feature_row("Residuals / Diagnostics", "Refit leave-one-out / permutation tests", "NNNNNNN"),
feature_row("MCMC Diagnostics", "Posterior summaries (Rhat, ESS, MCMC error) (`summary()`)", "YYYYYYY"),
feature_row("MCMC Diagnostics", "Trace plots (`plot_diagnostic_trace()`)", "YYYYYYY"),
feature_row("MCMC Diagnostics", "Density plots (`plot_diagnostic_density()`)", "YYYYYYY"),
feature_row("MCMC Diagnostics", "Autocorrelation plots (`plot_diagnostic_autocorrelation()`)", "YYYYYYY"),
feature_row("MCMC Diagnostics", "Diagnostic-plot wrapper (`plot_diagnostic()`)", "YYYYYYY"),
feature_row("Model Comparison", "Marginal likelihood (`add_marglik()`, `logml()`)", "YYYYNNN"),
feature_row("Model Comparison", "WAIC/LOO (`add_waic()`, `add_loo()`, `waic()`, `loo()`)", "YYYYYYY"),
feature_row("Model Comparison", "Bayes factors (`bf()`, `bayes_factor()`, `post_prob()`)", "YYYYYYY"),
feature_row("Model Comparison", "WAIC comparison (`loo_compare()`, `loo_weights()`)", "YYYYYYY"),
feature_row("Model Comparison", "LOO comparison (`loo_compare()`, `loo_weights()`)", "YYYYYYY"),
feature_row("Model Comparison", "AIC / BIC", "NNNNNNN"),
feature_row("Reporting", "Plain-text interpretation (`interpret()`)", "YYYYYYY"),
feature_row("Reporting", "Sub-model summary (`summary_models()`)", "NNNNYYY"),
feature_row("Reporting", "Prior inspection (`print_prior()`)", "YYYYYYY"),
feature_row("Extraction", "Posterior draw extraction (`as_draws()`, `as_draws_array()`, `as_draws_df()`, `as_draws_list()`, `as_draws_matrix()`, `as_draws_rvars()`)", "YYYYYYY"),
feature_row("Extraction", "Coefficients (`coef()`)", "YYYYYYY"),
feature_row("Extraction", "Point-wise log-likelihood (`logLik()`)", "YYYYYYY"),
feature_row("Extraction", "Sample size (`nobs()`)", "YYYYYYY"),
feature_row("Extraction", "Variance-covariance matrix (`vcov()`)", "NNNNNNN"),
feature_row("Extraction", "Credible intervals (`summary()`, `summary_heterogeneity()`, `pooled_effect()`, `pooled_heterogeneity()`)", "YYYYYYY"),
feature_row("Extraction", "Model weights (`weights()`)", "NNNNNNN"),
feature_row("Extraction", "Simulated responses (`simulate()`)", "NNNNNNN")
)
# Intentionally skipped exported functions in this feature table:
# bridge_sampler(), contr.independent(), RoBMA.options(), RoBMA.get_option(),
# set_autofit_control(), set_convergence_checks().
feature_table(rows)
Try the RoBMA package in your browser
Any scripts or data that you put into this service are public.
RoBMA documentation built on May 7, 2026, 5:08 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
## ----vignette-nowrap-options, include = FALSE, eval = TRUE----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
options(width = 10000)
## ----setup, include = FALSE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
message = FALSE,
warning = FALSE
)
tick <- '<span class="yes">✓</span>'
limited <- '<span class="limited">limited</span>'
no <- '<span class="no">No</span>'
na_cell <- '<span class="na-cell">n/a</span>'
model_columns <- c(
"brma.norm", "brma.glmm", "bselmodel", "bPET/bPEESE",
"BMA.norm", "BMA.glmm", "RoBMA"
)
reference_links <- c(
"add_loo()" = "../reference/add_loo.brma.html",
"add_marglik()" = "../reference/add_marglik.brma.html",
"add_waic()" = "../reference/add_waic.brma.html",
"as_draws()" = "../reference/as_draws.brma.html",
"as_draws_array()" = "../reference/as_draws.brma.html",
"as_draws_df()" = "../reference/as_draws.brma.html",
"as_draws_list()" = "../reference/as_draws.brma.html",
"as_draws_matrix()" = "../reference/as_draws.brma.html",
"as_draws_rvars()" = "../reference/as_draws.brma.html",
"as_zplot()" = "../reference/as_zplot.brma.html",
"bayes_factor()" = "../reference/bf.brma.html",
"bf()" = "../reference/bf.brma.html",
"blup()" = "../reference/blup.brma.html",
"bPET()" = "../reference/bPET.html",
"bPEESE()" = "../reference/bPEESE.html",
"brma()" = "../reference/brma.html",
"brma.glmm()" = "../reference/brma.glmm.html",
"BMA()" = "../reference/BMA.html",
"BMA.glmm()" = "../reference/BMA.glmm.html",
"bridge_sampler()" = "../reference/bridge_sampler.brma.html",
"bselmodel()" = "../reference/bselmodel.html",
"check_loo()" = "../reference/check_loo.brma.html",
"coef()" = "../reference/coef.brma.html",
"contr.meandif()" = "../reference/contr.BayesTools.html",
"contr.orthonormal()" = "../reference/contr.BayesTools.html",
"contr.treatment()" = "https://stat.ethz.ch/R-manual/R-devel/library/stats/html/contrast.html",
"cooks.distance()" = "../reference/cooks.distance.brma.html",
"covratio()" = "../reference/covratio.brma.html",
"dfbetas()" = "../reference/dfbetas.brma.html",
"dffits()" = "../reference/dffits.brma.html",
"estimate_unit_information_sd()" = "../reference/estimate_unit_information_sd.html",
"fitted()" = "../reference/fitted.brma.html",
"funnel()" = "../reference/funnel.html",
"galbraith()" = "../reference/radial.html",
"hatvalues()" = "../reference/hatvalues.brma.html",
"influence()" = "../reference/influence.brma.html",
"interpret()" = "../reference/interpret.html",
"logLik()" = "../reference/logLik.brma.html",
"logml()" = "../reference/logml.brma.html",
"loo()" = "../reference/loo.brma.html",
"loo::pareto_k_ids()" = "https://mc-stan.org/loo/reference/pareto-k-diagnostic.html",
"loo::pareto_k_table()" = "https://mc-stan.org/loo/reference/pareto-k-diagnostic.html",
"loo_compare()" = "../reference/loo_compare.brma.html",
"loo_weights()" = "../reference/loo_weights.brma.html",
"marginal_means()" = "../reference/marginal_means.brma.html",
"nobs()" = "../reference/nobs.brma.html",
"plot()" = "../reference/plot.brma.html",
"plot_diagnostic()" = "../reference/plot_diagnostic.html",
"plot_diagnostic_autocorrelation()" = "../reference/plot_diagnostic.html",
"plot_diagnostic_density()" = "../reference/plot_diagnostic.html",
"plot_diagnostic_trace()" = "../reference/plot_diagnostic.html",
"plot_pet_peese()" = "../reference/plot_pet_peese.html",
"plot_prior()" = "../reference/plot_prior.html",
"plot_weightfunction()" = "../reference/plot_weightfunction.html",
"pooled_effect()" = "../reference/pooled_effect.brma.html",
"pooled_heterogeneity()" = "../reference/pooled_heterogeneity.brma.html",
"post_prob()" = "../reference/post_prob.brma.html",
"predict()" = "../reference/predict.brma.html",
"print_prior()" = "../reference/print_prior.html",
"prior()" = "../reference/prior.html",
"prior_factor()" = "../reference/prior_factor.html",
"prior_informed()" = "../reference/prior_informed.html",
"prior_none()" = "../reference/prior_none.html",
"prior_PEESE()" = "../reference/prior_PEESE.html",
"prior_PET()" = "../reference/prior_PET.html",
"prior_weightfunction()" = "../reference/prior_weightfunction.html",
"qqnorm()" = "../reference/qqnorm.brma.html",
"radial()" = "../reference/radial.html",
"ranef()" = "../reference/ranef.brma.html",
"regplot()" = "../reference/regplot.html",
"residuals()" = "../reference/residuals.brma.html",
"RoBMA()" = "../reference/RoBMA.html",
"rstandard()" = "../reference/rstandard.brma.html",
"rstudent()" = "../reference/rstudent.brma.html",
"simulate()" = "https://stat.ethz.ch/R-manual/R-devel/library/stats/html/simulate.html",
"summary()" = "../reference/summary.brma.html",
"summary_heterogeneity()" = "../reference/summary_heterogeneity.brma.html",
"summary_models()" = "../reference/summary_models.html",
"true_effects()" = "../reference/true_effects.brma.html",
"update()" = "../reference/update.brma.html",
"vcov()" = "https://stat.ethz.ch/R-manual/R-devel/library/stats/html/vcov.html",
"vif()" = "../reference/vif.brma.html",
"waic()" = "../reference/waic.brma.html",
"weights()" = "https://stat.ethz.ch/R-manual/R-devel/library/stats/html/weights.html",
"wf_cumulative()" = "../reference/prior_weightfunction.html",
"wf_fixed()" = "../reference/prior_weightfunction.html",
"wf_independent()" = "../reference/prior_weightfunction.html",
"forest()" = "https://wviechtb.github.io/metafor/reference/forest.rma.html",
"baujat()" = "https://wviechtb.github.io/metafor/reference/baujat.html",
"gosh()" = "https://wviechtb.github.io/metafor/reference/gosh.html",
"labbe()" = "https://wviechtb.github.io/metafor/reference/labbe.html"
)
model_column_links <- list(
"brma.norm" = "../reference/brma.html",
"brma.glmm" = "../reference/brma.glmm.html",
"bselmodel" = "../reference/bselmodel.html",
"bPET/bPEESE" = c("../reference/bPET.html", "../reference/bPEESE.html"),
"BMA.norm" = "../reference/BMA.html",
"BMA.glmm" = "../reference/BMA.glmm.html",
"RoBMA" = "../reference/RoBMA.html"
)
status_map <- c(
Y = tick,
L = limited,
N = no,
A = na_cell
)
feature_row <- function(topic, feature, pattern) {
values <- strsplit(pattern, "", fixed = TRUE)[[1]]
if (length(values) != length(model_columns)) {
stop("Status pattern has wrong length: ", pattern, call. = FALSE)
}
out <- c(
list(Topic = topic, Feature = feature),
stats::setNames(as.list(status_map[values]), model_columns)
)
return(out)
}
feature_table <- function(rows) {
rows <- as.data.frame(do.call(rbind, rows), stringsAsFactors = FALSE, check.names = FALSE)
rows[] <- lapply(rows, function(x) {
if (is.list(x)) {
return(vapply(x, function(y) paste0(as.character(y), collapse = ""), character(1)))
}
return(as.character(x))
})
cat('
<style>
.feature-matrix {
border-collapse: collapse;
width: 100%;
font-size: 0.84em;
}
.feature-matrix th,
.feature-matrix td {
border: 1px solid #d0d7de;
padding: 4px 6px;
vertical-align: top;
}
.feature-matrix th {
background: #f6f8fa;
}
.feature-matrix .topic-head {
min-width: 60px;
width: 60px;
}
.feature-matrix .feature-head {
min-width: 25em;
}
.feature-matrix .model-head {
height: 118px;
min-width: 34px;
max-width: 34px;
width: 34px;
padding: 0;
position: relative;
vertical-align: bottom;
}
.feature-matrix .rotated-header {
bottom: 6px;
display: block;
left: 50%;
line-height: 1;
position: absolute;
transform: rotate(-90deg);
transform-origin: left center;
white-space: nowrap;
}
.feature-matrix .topic-cell {
background: #f6f8fa;
min-width: 60px;
width: 60px;
padding: 0;
text-align: center;
vertical-align: middle;
}
.feature-matrix .topic-cell span {
display: inline-block;
transform: rotate(-90deg);
white-space: normal;
width: 8em;
text-align: center;
font-weight: 700;
line-height: 1.1;
}
.feature-matrix .feature-cell {
min-width: 25em;
}
.feature-matrix .feature-cell a {
color: #0969da;
text-decoration: none;
}
.feature-matrix .feature-cell a:hover {
text-decoration: underline;
}
.feature-matrix .feature-cell a code {
color: inherit;
}
.feature-matrix .status-cell {
text-align: center;
vertical-align: middle;
white-space: nowrap;
width: 34px;
}
.feature-matrix .yes {
color: #1a7f37;
font-weight: 700;
}
.feature-matrix .limited {
color: #9a6700;
}
.feature-matrix .no,
.feature-matrix .na-cell {
color: #6e7781;
}
</style>
')
escape_html_text <- function(x) {
x <- as.character(x)
x <- gsub("&", "&", x, fixed = TRUE)
x <- gsub("<", "<", x, fixed = TRUE)
x <- gsub(">", ">", x, fixed = TRUE)
x <- gsub('"', """, x, fixed = TRUE)
return(x)
}
format_code_span <- function(code) {
code_html <- paste0("<code>", escape_html_text(code), "</code>")
link <- if (code %in% names(reference_links)) reference_links[[code]] else NA_character_
if (!is.na(link)) {
return(paste0('<a href="', escape_html_text(link), '">', code_html, "</a>"))
}
return(code_html)
}
escape_html <- function(x) {
x <- as.character(x)
matches <- gregexpr("`[^`]+`", x, perl = TRUE)[[1]]
if (matches[1] == -1L) {
return(escape_html_text(x))
}
match_lengths <- attr(matches, "match.length")
pieces <- character(0)
position <- 1L
for (j in seq_along(matches)) {
match_start <- matches[j]
match_end <- match_start + match_lengths[j] - 1L
if (match_start > position) {
pieces <- c(pieces, escape_html_text(substr(x, position, match_start - 1L)))
}
code <- substr(x, match_start + 1L, match_end - 1L)
pieces <- c(pieces, format_code_span(code))
position <- match_end + 1L
}
if (position <= nchar(x)) {
pieces <- c(pieces, escape_html_text(substr(x, position, nchar(x))))
}
return(paste0(pieces, collapse = ""))
}
format_model_column <- function(model_column) {
link <- model_column_links[[model_column]]
if (length(link) == 2L) {
return(paste0(
'<a href="', escape_html_text(link[[1]]), '">bPET</a>/',
'<a href="', escape_html_text(link[[2]]), '">bPEESE</a>'
))
}
return(paste0(
'<a href="', escape_html_text(link), '">',
escape_html_text(model_column),
"</a>"
))
}
topic_runs <- rle(rows$Topic)
topic_start <- cumsum(c(1L, head(topic_runs$lengths, -1L)))
topic_span <- rep(0L, nrow(rows))
topic_span[topic_start] <- topic_runs$lengths
cat('<div style="overflow-x: auto;">\n')
cat('<table class="feature-matrix">\n')
cat("<thead><tr>")
cat('<th class="topic-head">Topic</th>')
cat('<th class="feature-head">Feature</th>')
for (model_column in model_columns) {
cat('<th class="model-head"><span class="rotated-header">', format_model_column(model_column), "</span></th>", sep = "")
}
cat("</tr></thead>\n")
cat("<tbody>\n")
for (i in seq_len(nrow(rows))) {
cat("<tr>")
if (topic_span[i] > 0L) {
cat(
'<td class="topic-cell" rowspan="', topic_span[i], '"><span>',
escape_html(rows$Topic[i]),
"</span></td>",
sep = ""
)
}
cat('<td class="feature-cell">', escape_html(rows$Feature[i]), "</td>", sep = "")
for (model_column in model_columns) {
cat('<td class="status-cell">', rows[[model_column]][i], "</td>", sep = "")
}
cat("</tr>\n")
}
cat("</tbody>\n")
cat("</table>\n")
cat("</div>\n")
}
## ----feature-matrix, echo = FALSE, results = "asis"-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
rows <- list(
feature_row("Model / Structure", "Fixed- and random-effects models", "YYYYYYY"),
feature_row("Model / Structure", "Moderation (`mods`)", "YYYYYYY"),
feature_row("Model / Structure", "Location-scale models (`scale`)", "YYYYYYY"),
feature_row("Model / Structure", "Multilevel models (`cluster`)", "YYYYYYY"),
feature_row("Model / Structure", "Model averaging", "NNNNYYY"),
feature_row("Model / Structure", "Inclusion Bayes factors", "NNNNYYY"),
feature_row("Model / Structure", "General multivariate / covariance structures", "NNNNNNN"),
feature_row("Model / Structure", "Robust / sandwich inference", "NNNNNNN"),
feature_row("Model / Structure", "Refit / update (`update()`)", "YYYYYYY"),
feature_row("Priors", "Default prior distributions", "YYYYYYY"),
feature_row("Priors", "Empirical/informed prior distributions (`prior_informed()`)", "YYYYYYY"),
feature_row("Priors", "Custom prior distributions (`prior()`, `prior_factor()`, `prior_weightfunction()`, `prior_none()`)", "YYYYYYY"),
feature_row("Priors", "PET / PEESE prior distributions (`prior_PET()`, `prior_PEESE()`)", "NNNYNNY"),
feature_row("Priors", "Prior-only inspection (`only_priors = TRUE`)", "YYYYYYY"),
feature_row("Priors", "Weight-function shape (`wf_cumulative()`, `wf_fixed()`, `wf_independent()`)", "NNYNNNY"),
feature_row("Priors", "Factor contrasts (`contr.treatment()`, `contr.meandif()`, `contr.orthonormal()`)", "YYYYYYY"),
feature_row("Priors", "UISD estimation (`estimate_unit_information_sd()`)", "YYYYYYY"),
feature_row("Publication Bias", "Selection models", "NNYNNNY"),
feature_row("Publication Bias", "PET / PEESE models", "NNNYNNY"),
feature_row("Publication Bias", "Model averaging over bias models", "NNNNNNY"),
feature_row("Publication Bias", "Bias-adjusted summaries / predictions", "NNYYNNY"),
feature_row("Publication Bias", "Trim-fill / fail-safe N", "NNNNNNN"),
feature_row("Prediction", "Pooled effect / heterogeneity summaries (`pooled_effect()`, `pooled_heterogeneity()`)", "YYYYYYY"),
feature_row("Prediction", "Heterogeneity decomposition (`summary_heterogeneity()`, tau², I², H²)", "YYYYYYY"),
feature_row("Prediction", "Fitted-value extraction (`fitted()`)", "YYYYYYY"),
feature_row("Prediction", "Prediction for new covariate values (`predict()`)", "YYYYYYY"),
feature_row("Prediction", "Posterior predictive response summaries (`predict()`)", "YYYYYYY"),
feature_row("Prediction", "True effects / BLUPs / random effects (`true_effects()`, `blup()`, `ranef()`)", "YYYYYYY"),
feature_row("Prediction", "Estimated marginal means (`marginal_means()`)", "YYYYYYY"),
feature_row("Plots", "Posterior plots (`plot()`)", "YYYYYYY"),
feature_row("Plots", "Prior plots (`plot_prior()`)", "YYYYYYY"),
feature_row("Plots", "Marginal means plots (`marginal_means()` + `plot()`)", "YYYYYYY"),
feature_row("Plots", "Regression plots (`regplot()`)", "YYYYYYY"),
feature_row("Plots", "Funnel plots (`funnel()`)", "YYYYYYY"),
feature_row("Plots", "zplot diagnostics (`as_zplot()`/`zplot()`)", "YYYYYYY"),
feature_row("Plots", "Weight-function plots (`plot_weightfunction()`)", "NNYNNNY"),
feature_row("Plots", "PET-PEESE plots (`plot_pet_peese()`)", "NNNYNNY"),
feature_row("Plots", "Radial / Galbraith plots (`radial()`, `galbraith()`)", "YLYYYLY"),
feature_row("Plots", "Forest plots (`forest()`)", "NNNNNNN"),
feature_row("Plots", "Baujat plots (`baujat()`)", "NNNNNNN"),
feature_row("Plots", "GOSH plots (`gosh()`)", "NNNNNNN"),
feature_row("Plots", "L'Abbe plots (`labbe()`)", "NNNNNNN"),
feature_row("Residuals / Diagnostics", "Raw residuals (`residuals()`)", "YYYYYYY"),
feature_row("Residuals / Diagnostics", "Pearson / standardized residuals (`rstandard()`)", "YNNYYNL"),
feature_row("Residuals / Diagnostics", "Studentized residuals (LOO-PIT) (`rstudent()`)", "YYYYYYY"),
feature_row("Residuals / Diagnostics", "Q-Q plots (`qqnorm()`)", "YYYYYYY"),
feature_row("Residuals / Diagnostics", "Cook's distances (`cooks.distance()`)", "YNNYYNN"),
feature_row("Residuals / Diagnostics", "DFBETAS (`dfbetas()`)", "YYYYYYY"),
feature_row("Residuals / Diagnostics", "DFFITS (`dffits()`)", "YNNYYNN"),
feature_row("Residuals / Diagnostics", "Covariance ratios (`covratio()`)", "YYYYYYY"),
feature_row("Residuals / Diagnostics", "Hat values (`hatvalues()`)", "YNNYYNN"),
feature_row("Residuals / Diagnostics", "Combined influence summary (`influence()`)", "YLLYYLL"),
feature_row("Residuals / Diagnostics", "LOO / WAIC diagnostics (`check_loo()`, `loo::pareto_k_ids()`, `loo::pareto_k_table()`)", "YYYYYYY"),
feature_row("Residuals / Diagnostics", "Moderator collinearity diagnostics (`vif()`)", "YYYYYYY"),
feature_row("Residuals / Diagnostics", "Refit leave-one-out / permutation tests", "NNNNNNN"),
feature_row("MCMC Diagnostics", "Posterior summaries (Rhat, ESS, MCMC error) (`summary()`)", "YYYYYYY"),
feature_row("MCMC Diagnostics", "Trace plots (`plot_diagnostic_trace()`)", "YYYYYYY"),
feature_row("MCMC Diagnostics", "Density plots (`plot_diagnostic_density()`)", "YYYYYYY"),
feature_row("MCMC Diagnostics", "Autocorrelation plots (`plot_diagnostic_autocorrelation()`)", "YYYYYYY"),
feature_row("MCMC Diagnostics", "Diagnostic-plot wrapper (`plot_diagnostic()`)", "YYYYYYY"),
feature_row("Model Comparison", "Marginal likelihood (`add_marglik()`, `logml()`)", "YYYYNNN"),
feature_row("Model Comparison", "WAIC/LOO (`add_waic()`, `add_loo()`, `waic()`, `loo()`)", "YYYYYYY"),
feature_row("Model Comparison", "Bayes factors (`bf()`, `bayes_factor()`, `post_prob()`)", "YYYYYYY"),
feature_row("Model Comparison", "WAIC comparison (`loo_compare()`, `loo_weights()`)", "YYYYYYY"),
feature_row("Model Comparison", "LOO comparison (`loo_compare()`, `loo_weights()`)", "YYYYYYY"),
feature_row("Model Comparison", "AIC / BIC", "NNNNNNN"),
feature_row("Reporting", "Plain-text interpretation (`interpret()`)", "YYYYYYY"),
feature_row("Reporting", "Sub-model summary (`summary_models()`)", "NNNNYYY"),
feature_row("Reporting", "Prior inspection (`print_prior()`)", "YYYYYYY"),
feature_row("Extraction", "Posterior draw extraction (`as_draws()`, `as_draws_array()`, `as_draws_df()`, `as_draws_list()`, `as_draws_matrix()`, `as_draws_rvars()`)", "YYYYYYY"),
feature_row("Extraction", "Coefficients (`coef()`)", "YYYYYYY"),
feature_row("Extraction", "Point-wise log-likelihood (`logLik()`)", "YYYYYYY"),
feature_row("Extraction", "Sample size (`nobs()`)", "YYYYYYY"),
feature_row("Extraction", "Variance-covariance matrix (`vcov()`)", "NNNNNNN"),
feature_row("Extraction", "Credible intervals (`summary()`, `summary_heterogeneity()`, `pooled_effect()`, `pooled_heterogeneity()`)", "YYYYYYY"),
feature_row("Extraction", "Model weights (`weights()`)", "NNNNNNN"),
feature_row("Extraction", "Simulated responses (`simulate()`)", "NNNNNNN")
)
# Intentionally skipped exported functions in this feature table:
# bridge_sampler(), contr.independent(), RoBMA.options(), RoBMA.get_option(),
# set_autofit_control(), set_convergence_checks().
feature_table(rows)
Try the RoBMA package in your browser
Any scripts or data that you put into this service are public.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.