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Add option for analysis mode for perc divergent #124

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Add option for analysis mode for perc divergent #124

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2 changes: 2 additions & 0 deletions R/get-analysis-mode.R
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,7 @@
#' \item{mb.nreanalyses}{A count specifying the maximum number of reanalyses.}
#' \item{mb.rhat}{A number specifying the rhat threshold.}
#' \item{mb.esr}{A number specifying the minimum effective sampling rate.}
#' \item{mb.perc_divergent}{A number specifying the maximum percent divergent transitions.}
#' \item{mb.duration}{The maximum total time to spend on analysis and reanalysis.}
#' \item{mb.conf_level}{A number specifying the confidence level.}
#' }
Expand All @@ -37,6 +38,7 @@ get_analysis_mode <- function() {
mb.nreanalyses = getOption("mb.nreanalyses"),
mb.rhat = getOption("mb.rhat"),
mb.esr = getOption("mb.esr"),
mb.perc_divergent = getOption("mb.perc_divergent"),
mb.duration = getOption("mb.duration"),
mb.conf_level = getOption("mb.conf_level")
)
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7 changes: 7 additions & 0 deletions R/set-analysis-mode.R
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Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,7 @@
#' \item{mb.nreanalyses}{A count specifying the maximum number of reanalyses.}
#' \item{mb.rhat}{A number specifying the rhat threshold.}
#' \item{mb.esr}{A number specifying the minimum effective sampling rate.}
#' \item{mb.perc_divergent}{A number specifying the maximum percent divergent transitions.}
#' \item{mb.duration}{The maximum total time to spend on analysis and reanalysis.}
#' \item{mb.conf_level}{A number specifying the confidence level.}
#' }
Expand All @@ -50,6 +51,7 @@ set_analysis_mode <- function(mode = "report") {
mb.nreanalyses = NULL,
mb.rhat = NULL,
mb.esr = NULL,
mb.perc_divergent = NULL,
mb.duration = NULL,
mb.conf_level = NULL
)
Expand All @@ -65,6 +67,7 @@ set_analysis_mode <- function(mode = "report") {
mb.nreanalyses = 0L,
mb.rhat = 1.05,
mb.esr = 0.1,
mb.perc_divergent = 0.2,
mb.duration = dminutes(1),
mb.conf_level = 0.95
)
Expand All @@ -80,6 +83,7 @@ set_analysis_mode <- function(mode = "report") {
mb.nreanalyses = 0L,
mb.rhat = 1.05,
mb.esr = 0.1,
mb.perc_divergent = 0.2,
mb.duration = dminutes(1),
mb.conf_level = 0.95
)
Expand All @@ -95,6 +99,7 @@ set_analysis_mode <- function(mode = "report") {
mb.nreanalyses = 1L,
mb.rhat = 1.0,
mb.esr = 1.0,
mb.perc_divergent = 0,
mb.duration = dminutes(2),
mb.conf_level = 0.95
)
Expand All @@ -110,6 +115,7 @@ set_analysis_mode <- function(mode = "report") {
mb.nreanalyses = 1L,
mb.rhat = 1.05,
mb.esr = 0.1,
mb.perc_divergent = 0.2,

@joethorley joethorley Aug 24, 2026

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I think this is too high for report (its what we use most of the time).

Would 0.01 be more appropriate. Be good to get Nicole's thoughts.

mb.duration = dhours(1),
mb.conf_level = 0.95
)
Expand All @@ -125,6 +131,7 @@ set_analysis_mode <- function(mode = "report") {
mb.nreanalyses = 2L,
mb.rhat = 1.01,
mb.esr = 0.25,
mb.perc_divergent = 0,
mb.duration = dhours(6),
mb.conf_level = 0.95
)
Expand Down
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