Review of doing Bayesian data analysis: a tutorial with R, JAGS, and Stan (second edition)

Gaudet, Charles E.

doi:10.1080/13854046.2017.1306111

Cited by 12 publications

(11 citation statements)

References 7 publications

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“…Bayesian methods were used to assess predictors of HBsAg clearance in a multivariable analysis by estimating HBsAg loss posterior probability (mixed logistic model) with non-informative priors (centered at the value of no effect, with very tight precision of 0.001) [22] and using a time-varying approach. Modeling results were expressed as Odd-ratios (OR) with credibility intervals at 95% (CrI) of HBsAg clearance.…”

Section: Methodsmentioning

confidence: 99%

Higher rates of HBsAg clearance with tenofovir-containing therapy in HBV/HIV co-infection

Gantner¹,

Cotte²,

Allavena³

et al. 2019

PLoS ONE

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Introduction Achieving functional cure of chronic HBV infection (Hepatitis B surface antigen [HBsAg] clearance, eventually followed by acquisition of anti-hepatitis B surface antigen [Anti-HBs]) in individuals with HIV and HBV infections is a rare event. In this setting, factors related to HBV cure have not yet been fully characterized. Methods HIV-infected individuals with chronic HBV infection enrolled in the French Dat’AIDS cohort (NCT02898987), who started combined antiretroviral (cART)-anti-HBV treatment were retrospectively analyzed for HBsAg loss and Anti-HBs seroconversion. Results Overall, 1419 naïve-subjects received three different cART-anti-HBV treatment schedule: (1) 3TC or FTC only (n = 150), (2) TDF with or without 3TC or FTC (n = 489) and (3) 3TC or FTC as first line followed by adding/switching to TDF as second line (n = 780). Individuals were followed-up for a median of 89 months (IQR, 56–118). HBV-DNA was < 15 IU/mL in 91% of individuals at the end of the follow-up. Overall, 97 individuals cleared HBsAg (0.7/100 patient-years), of whom, 67 seroconverted for Anti-HBs (0.5/100 patient-years). A high CD4 nadir, a short delay between HBV diagnosis and treatment, a longer time on HBV therapy, an African origin and TDF-based therapy were independent predictors of HBsAg clearance (Probability of odds ratio [OR]>1, >95%) suggested by Bayesian analysis. Also, TDF-based regimen as first line (OR, 3.03) or second line (OR, 2.95) increased rates of HBsAg clearance compared to 3TC or FTC alone, with a 99% probability. Conclusions HBsAg clearance rate was low in HIV-HBV co-infected cART-anti-HBV treated individuals, but was slightly improved on TDF-based regimen.

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Section: Methodsmentioning

confidence: 99%

Higher rates of HBsAg clearance with tenofovir-containing therapy in HBV/HIV co-infection

Gantner¹,

Cotte²,

Allavena³

et al. 2019

PLoS ONE

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“…We aim to provide probabilistic interpretations of the CLASSIC results to aid researchers and clinicians with decision‐making. The Bayesian analysis provides direct probabilities and allows a more straightforward way to quantify uncertainties using credible intervals (CrI) representing a range within which the true parameter value falls with a certain probability 6–12 . This is often clearer and more intuitive to interpretate compared to the frequentist confidence intervals.…”

Section: Introductionmentioning

confidence: 99%

“…This is often clearer and more intuitive to interpretate compared to the frequentist confidence intervals. Additionally, we sought to nuance the interpretation as the Bayesian framework enables integration of pre‐existing knowledge such as findings from recent meta‐analyses 6,12 . This enhances sequential updating as new evidence emerges, making it suitable for addressing evolving research questions.…”

Section: Introductionmentioning

confidence: 99%

Restrictive versus standard IV fluid therapy in adult ICU patients with septic shock—Bayesian analyses of the CLASSIC trial

Sivapalan,

Meyhoff,

Hjortrup

et al. 2023

Acta Anaesthesiol Scand

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BackgroundThe CLASSIC trial assessed the effects of restrictive versus standard intravenous (IV) fluid therapy in adult intensive care unit (ICU) patients with septic shock. This pre‐planned study provides a probabilistic interpretation and evaluates heterogeneity in treatment effects (HTE).MethodsWe analysed mortality, serious adverse events (SAEs), serious adverse reactions (SARs) and days alive without life‐support within 90 days using Bayesian models with weakly informative priors. HTE on mortality was assessed according to five baseline variables: disease severity, vasopressor dose, lactate levels, creatinine values and IV fluid volumes given before randomisation.ResultsThe absolute difference in mortality was 0.2%‐points (95% credible interval: −5.0 to 5.4; 47% posterior probability of benefit [risk difference <0.0%‐points]) with restrictive IV fluid. The posterior probabilities of benefits with restrictive IV fluid were 72% for SAEs, 52% for SARs and 61% for days alive without life‐support. The posterior probabilities of no clinically important differences (absolute risk difference ≤2%‐points) between the groups were 56% for mortality, 49% for SAEs, 90% for SARs and 38% for days alive without life‐support. There was 97% probability of HTE for previous IV fluid volumes analysed continuously, that is, potentially relatively lower mortality of restrictive IV fluids with higher previous IV fluids. No substantial evidence of HTE was found in the other analyses.ConclusionWe could not rule out clinically important effects of restrictive IV fluid therapy on mortality, SAEs or days alive without life‐support, but substantial effects on SARs were unlikely. IV fluids given before randomisation might interact with IV fluid strategy.

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“…Due to the low prevalence of T. solium cysticercosis (12 of 1281 pigs were positive) regression coefficients for the mixed-effects logistic regression model were estimated using a Bayesian approach implemented in JAGS [ 18 , 19 ]. Flat (uninformed) prior distributions were assumed for the intercept β 0 and each of the regression coefficients for the fixed effects β 1 ⋯ β m .…”

Section: Methodsmentioning

confidence: 99%

The epidemiology of porcine Taenia solium cysticercosis in communities of the Central Highlands in Vietnam

et al. 2018

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BackgroundTaenia solium cysticercosis, recognized as a neglected tropical disease by the WHO, is distributed mostly in developing countries of Latin America, sub-Saharan Africa and Asia. Pigs and humans act as intermediate hosts, acquiring T. solium cysticerci (larval stage) in their tissue, through the ingestion of T. solium eggs shed in the faeces of humans infected with adult tapeworms. The disease has a negative impact on rural economies due to losses in productivity arising from human disease, pork carcass condemnations and loss of market access. The aim of this study was to estimate the prevalence of T. solium cysticercosis in pigs in Dak Lak Province in the Central Highlands of Vietnam and to identify household level characteristics associated with T. solium porcine cysticercosis.MethodsThis was a cross-sectional study of household pigs in three districts of Dak Lak Province. A total of 408 households in six villages in three districts were visited between June and October 2015. A questionnaire was administered to the head of each household, and within each household, serum samples were collected from three pigs. Serum samples were analyzed using the recombinant T24H antigen in enzyme-linked immunoelectrotransfer blot assay and lentil lectin purified glycoprotein in EITB assay. A Bayesian, mixed-effects logistic regression model was developed to identify management factors associated with the probability of a household having at least one cysticercosis-positive pig.ResultsThe prevalence of porcine T. solium cysticercosis in this study was low at 0.94 [95% confidence interval (CI) 0.51–1.68] cases per 100 pigs at risk, in agreement with other studies conducted throughout Vietnam. Scavenging of food and coprophagy were associated with T. solium cysticercosis [odds ratios 1.98 (95% CrI: 0.55–4.74) and 2.57 (95% CrI: 1.22–4.66), respectively].ConclusionsThis study proves that the seroprevalence of porcine cysticercosis in Dak Lak Province was as low as that of other studies conducted throughout Vietnam. Scavenging of food and coprophagy are modifiable factors, providing the opportunity to decrease the prevalence of porcine cysticercosis further in the province.

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Review of doing Bayesian data analysis: a tutorial with R, JAGS, and Stan (second edition)

Cited by 12 publications

References 7 publications

Higher rates of HBsAg clearance with tenofovir-containing therapy in HBV/HIV co-infection

Higher rates of HBsAg clearance with tenofovir-containing therapy in HBV/HIV co-infection

Restrictive versus standard IV fluid therapy in adult ICU patients with septic shock—Bayesian analyses of the CLASSIC trial

The epidemiology of porcine Taenia solium cysticercosis in communities of the Central Highlands in Vietnam

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