Help for package bayespmtools

Title:

Bayesian Sample Size and Precision Considerations for Risk Prediction Models

Version:

0.0.1

Maintainer:

Mohsen Sadatsafavi <mohsen.sadatsafavi@ubc.ca>

Description:

Performs Bayesian sample size, precision, and value-of-information analysis for external validation of existing multi-variable prediction models using the approach proposed by Sadatsafavi and colleagues (2025) <doi:10.1002/sim.70389>.

License:

GPL-3

Encoding:

UTF-8

RoxygenNote:

7.3.3

Depends:

R (≥ 3.5.0)

Imports:

fastLogisticRegressionWrap, logitnorm, mc2d, mcmapper, pROC, cobs, OOR, quantreg

LazyData:

true

Suggests:

knitr, rmarkdown, ggplot2

VignetteBuilder:

knitr

NeedsCompilation:

Packaged:

2026-03-08 21:09:05 UTC; annaluo

Author:

Mohsen Sadatsafavi

[aut, cre], Anna Luo [ctb]

Repository:

CRAN

Date/Publication:

2026-03-29 15:40:09 UTC

bayespmtools: Bayesian Sample Size and Precision Considerations for Risk Prediction Models

Description

Author(s)

Maintainer: Mohsen Sadatsafavi mohsen.sadatsafavi@ubc.ca (ORCID)

Other contributors:

Anna Luo aannaluo@gmail.com [contributor]

Bayesian Precision / VoI Calculator

Description

Bayesian precision and value-of-information calculator for external validation studies of risk prediction models at fixed sample sizes.

Usage

bpm_valprec(
  N,
  evidence,
  targets,
  n_sim = NULL,
  method = "sample",
  threshold = NULL,
  dist_type = "logitnorm",
  impute_cor = TRUE,
  ex_args = NULL
)

Arguments

N

Numeric vector of sample sizes to evaluate.

evidence

A named list containing prior evidence components for model performance parameters (e.g., prevalence, discrimination, calibration). Alternatively, evidence may be a data frame of pre-posterior draws (element $sample) returned by a previous call to this function or to bpm_valprec(), in which case those draws are used directly.

targets

A named list of targets to compute.

eciw.metric: Logical; compute expected CI width.
qciw.metric: Numeric scalar in (0,1); CI width quantile.
oa.nb: Logical; compute optimality assurance for net benefit.
voi.nb: Logical; compute EVSI and EVSI/EVPI.

n_sim

#' Number of Monte Carlo simulations used to generate the pre-posterior distribution. If evidence is a data frame from previous calls to relevant functions, n_sim will automatically be set to the number of rows of the data frame.

method

Method to compute CI widths. One of "sample" or "2s".

threshold

Decision threshold for net benefit calculations. Required if oa.nb or voi.nb are requested.

dist_type

Distribution for calibrated risks. Default is "logitnorm".

impute_cor

Logical; whether to induce correlation between parameters.

ex_args

Optional list of extra arguments. May include f_progress, a custom progress function.

Value

A list with elements:

results: Matrix of requested metrics by sample size.
sample: Monte Carlo sample used for computations.
evidence: Processed evidence object.
targets: Targets as supplied by the user.
ciws: Simulated CI widths for requested metrics.

Examples

evidence <- list(
  prev ~ beta(116, 155),           # Outcome prevalence
  cstat ~ beta(3628, 1139),        # C-statistic
  cal_mean ~ norm(-0.009, 0.125),  # Mean calibration error
  cal_slp ~ norm(0.995, 0.024)     # Calibration slope
)

res <- bpm_valprec(
  N = c(1000, 1500),
  evidence = evidence,
  targets = list(eciw.cstat = TRUE, qciw.cal_slp=0.9, voi.nb=0.8),
  threshold=0.2,
  n_sim = 100            # faster and safer on CRAN. Please increase this value for real-world use.
)

print(res$results)

Bayesian Sample Size Calculator for External Validation

Description

Bayesian sample size calculation for external validation studies of clinical risk prediction models. The function evaluates sample sizes required to meet precision-, assurance-, or decision-based targets using pre-posterior simulation.

Usage

bpm_valsamp(
  evidence,
  targets,
  n_sim = NULL,
  method = "sample",
  threshold = NULL,
  dist_type = "logitnorm",
  impute_cor = TRUE,
  ex_args = NULL
)

Arguments

evidence

targets

A named list specifying sample size targets.

Supported targets include:

Precision-based targets using expected 95\ (prefix eciw).
Assurance-based targets specifying the probability that the 95\ (prefix qciw).
Net benefit targets, including optimality assurance (oa.nb) and value-of-information ratios (voi.nb = EVSI / EVPI).

For example, eciw.cstat = 0.1 targets an expected interval width of 0.1 for the c-statistic, while qciw.cal_slp = c(0.90, 0.22) targets a 90 percent assurance that the calibration slope interval width does not exceed 0.22. Finally, oa.nb = 0.80 targets a sample size that would correspond to 80 percent assurance that the strategy with the highest NB in the sample will be the strategy with the highest NB in the population.

n_sim

Number of Monte Carlo simulations used to generate the pre-posterior distribution. If evidence is a data frame from previous calls to relevant functions, n_sim will automatically be set to the number of rows of the data frame.

method

Method used to compute the pre-posterior distribution of 95\ One of "sample" (simulation-based) or "2s" (two-stage approximation). Default is "sample".

threshold

Risk threshold used for decision-analytic quantities and net benefit calculations. Required if oa.nb or voi.nb targets are specified.

dist_type

Distribution assumed for calibrated risks. Default is "logitnorm".

impute_cor

Logical indicating whether correlation between performance measures should be induced when simulating from marginal evidence distributions. Default is TRUE.

ex_args

Optional list of additional arguments passed to internal simulation or root-finding routines (experimental feature).

Value

A list with the following components:

results: Estimated sample sizes required to meet each target.
sample: Data frame of pre-posterior simulation draws.
evidence: Processed evidence object used in the analysis.
trace: Trace output from the stochastic root-finding algorithm.
targets: The targets argument supplied to the function.

Examples


evidence <- list(
  prev ~ beta(116, 155),           # Outcome prevalence
  cstat ~ beta(3628, 1139),        # C-statistic
  cal_mean ~ norm(-0.009, 0.125),  # Mean calibration error
  cal_slp ~ norm(0.995, 0.024)     # Calibration slope
)

targets <- list(
  eciw.cstat = 0.1,
  qciw.cstat = c(0.9, 0.1),
  oa.nb      = 0.8
)

samp <- bpm_valsamp(
  evidence  = evidence,
  targets   = targets,
  n_sim     = 1000,
  threshold = 0.2
)

samp$results

Calculates Pre-Posterior Distribution of 95% CI Widths Using Two-step Method

Description

Calculates pre-posterior distribution of 95% CI widths using two-step method.

Usage

calc_ciw_2s(N, parms)

Arguments

N

A vector of sample sizes

parms

Parameters for the distribution containing: cal_int: calibration intercept cal_slp: calibration slope prev: prevalence dist_type: distribution type cstat: c-statistic dist_type: one of ("logitnorm", "beta, "probitnorm") dist_parm1: first parameter of the distribution dist_parm2: second parameter of the distribution

Value

List of length N, of vectors containing 95% confidence interval width for each of: cstat: c-statistic cal_oe: observed to expected ratio cal_mean: mean calibration cal_int: calibration intercept cal_slp: calibration slope

#'Calculates Pre-Posterior Distribution of 95% CI Widths Based on Given Method

Description

Calculates pre-posterior distribution of 95% CI widths based on given method

Usage

calc_ciw_mc(N, parms_sample, method)

Arguments

N

A vector of sample sizes

parms_sample

Matrix of parameters for the distribution each row with appropriate parameters: cstat: c-statistic prev: prevalence dist_type: distribution type dist_parm1: first parameter of distribution dist_parm2: second parameter of distribution cal_int: calibration intercept cal_slp: calibration slope

method

Method to calculate 95% confident interval width, one of sample, 2s

Value

List of matrices each with dimension (number of rows in parms_sample x length N) containing 95% confidence interval width for each of: cstat: c-statistic cal_oe: observed to expected ratio cal_mean: mean calibration cal_int: calibration intercept cal_slp: calibration slope

Calculates Pre-Posterior Distribution of 95% CI Widths Using Sampling-based Simulation

Description

Calculates pre-posterior distribution of 95% CI widths using sampling-based simulation

Usage

calc_ciw_sample(N, parms)

Arguments

N

A vector of sample sizes

parms

Parameters for the distribution containing: prev: prevalence dist_type: distribution type dist_parm1: first parameter of distribution dist_parm2: second parameter of distribution cal_int: calibration intercept cal_slp: calibration slope

Value

Calculates the C-statistic of Model

Description

Calculates the c-statistic given the model type and parameters.

Usage

calc_cstat(type, parms, m = NULL)

Arguments

type

A character string; one of c("beta", "logitnorm", "probitnorm") indicating the model type.

parms

A numeric vector containing parameters relevant to the model.

m

Mean, default is NULL

Value

The C-statistic

Calculates Approximate Variances and Covariance for Performance Metrics

Description

Calculates approximate variances performance metrics and covariance of calibration intercept and slope using the Riley framework

Usage

calc_riley_vars(N, parms)

Arguments

N

sample size of the validation dataset

parms

list containing model and distribution parameters: prev: expected prevalence cstat: c-statistic of the model dist_type: one of ("logitnorm", "beta, "probitnorm") dist_parm1: first parameter of the distribution dist_parm2: second parameter of the distribution cal_int: calibration intercept cal_slp: calibration slope

Value

list of approximate variances and covariance of the performance metrics.

Calculates the Sensitivity and Specificity

Description

Calculate the sensitivity and specificity of the model at given threshold

Usage

calc_se_sp(dist_type, dist_parms, cal_int, cal_slp, threshold, prev)

Arguments

dist_type

The distribution type, one of c("logitnorm", "beta", "probitnorm").

dist_parms

Vector of the two parameters of interest given the distribution.

cal_int

The calibration intercept.

cal_slp

The calibration slope.

threshold

The risk threshold

prev

The outcome prevalence, the expectation of the model

Value

A vector containing sensitivity and specificity

Examples

calc_se_sp("beta", c(1,1), 0.9, 0.75, 0.5, 0.5)

Calculates Sample Size Given Target Mean CI

Description

Calculates sample size N, so that the mean confidence interval is equal to given target, assumes function is decreasing and convex

Usage

find_n_mean(target, N, ciws, decreasing = TRUE, convex = TRUE)

Arguments

target

The target mean confidence interval width

N

Sample sizes corresponding to each row of ciws,=

ciws

Matrix of confidence intervals widths, each row corresponding to N

decreasing

Logical. Constraining function to decreasing

convex

Logical. Constraining function to convex

Value

Integer. Estimated sample size needed to achieve the target

Calculates Sample Size Given Target Quantile

Description

Find sample size N, so that the specified quantile is equal to given target

Usage

find_n_quantile(target, N, q, ciws)

Arguments

target

The desired quantile target value

N

Sample sizes corresponding to each row of ciws

q

Desired quantile level, between 0 and 1.

ciws

A matrix of confidence intervals widths, each row corresponding to N

Value

Estimated sample size needed to achieve the target

Infer Calibration Intercept from Mean Calibration

Description

Infer calibration intercept from mean calibration given a fixed calibration slope and a given distribution for calibrated risks

Usage

infer_cal_int_from_mean(dist_type, dist_parms, cal_mean, cal_slp, prev = NULL)

Arguments

dist_type

The distribution type, one of c("logitnorm", "probitnorm", "beta").

dist_parms

The two parameters that index the type.

cal_mean

The mean calibration.

cal_slp

The calibration slope.

prev

Outcome prevalence. Optional; if not provided, estimate is as the expected value of the distribution of calibrated risks.

Value

The estimated calibration intercept

Infer Calibration Intercept from O/E ratio

Description

Infer calibration intercept from observed-to-expected outcome ratio given a fixed calibration slope and a given distribution for calibrated risks

Usage

infer_cal_int_from_oe(dist_type, dist_parms, cal_oe, cal_slp, prev = NULL)

Arguments

dist_type

The distribution type, one of c("logitnorm", "probitnorm", "beta").

dist_parms

The two parameters that index the type.

cal_oe

The observed-to-expected outcome ratio.

cal_slp

The calibration slope.

prev

Outcome prevalence. Optional; if not provided, estimate is as the expected value of the distribution of calibrated risks.

Value

The estimated calibration intercept

Calculates Correlation

Description

Calculates correlation based on simulated data

Usage

infer_correlation(dist_type, dist_parms, cal_int, cal_slp, n, n_sim)

Arguments

dist_type

The distribution type

dist_parms

The two parameters of interest for the given distribution type

cal_int

The calibration intercept.

cal_slp

The calibration slope.

n

number of observations for each simulation.

n_sim

number of simulations

Value

correlation among the simulated data

Calculates the Model Parameters Given Quantile

Description

Calculate the model parameters given the distribution type, mean, quantile, and percentile.

Usage

inv_mean_quantile(type, m, q, p)

Arguments

type

The distribution type, one of c("norm", "beta", "logitnorm", "probitnorm").

m

Mean of the of distribution.

q

The quantile value.

p

The percentile at which the quantile occurs.

Value

The model parameters of the given type.

Calculates the Model Parameters Given Moments

Description

Calculates the model parameters of interest given the first two moments.

Usage

inv_moments(type, moments)

Arguments

type

The distribution type, one of c("norm", "beta", "logitnorm").

moments

A numeric vector containing the first two moments of the model

Value

Returns the two parameters for each model. mean and sd for norm mu and sigma for logitnorm shape1 (alpha) and shape2 (beta) for beta

Isaric Dataset

Description

Data from the International Severe Acute Respiratory and Emerging Infection Consortium regarding Regions in the UK.

Usage

isaric

Format

A data frame with 8 rows and 10 columns

Region: Region where the sample was drawn
Sample_Size: Raw number of total subjects available in the region's dataset
n: Number of subjects used in analysis after exclusions
n_events: Number of positive subjects
cstat: C-statistic
cstat_l: Lower bound for the confidence interval of the C-statistic
cal_mean: Calibration Mean
cal_mean_l: Lower bound for the confidence interval of the calibration mean
cal_slope: Calibration slope
cal_slope_l: Lower bound of the confidence interval of the calibration slope

Source

Simulated Data

Mean and Variance Calculator

Description

Calculates the first two moments (mean and variance) of the given model type and parameters.

Usage

moments(type, parms)

Arguments

type

The distribution type, one of c("norm", "beta", "logitnorm", "probitnorm").

parms

A numeric vector containing parameters relevant to the model.

Value

A numeric vector representing the mean and variance.

Plots Calibration Distance from Simulation Curves

Description

simulates calibration curves based on given method, and uses plot to visualize calibration distance (difference between predicted and observed)

Usage

plot_cal_distance(N, sample, method = "loess", X = (1:99)/100)

Arguments

N

Number of observations to simulate in each sample

sample

Data frame with columns: dist_type: distribution type dist_parm1: first distribution parameter (e.g. mean, alpha, shape1) dist_parm2: second distribution parameter (e.g. sd, beta, shape2) cal_int: calibration intercept cal_slp: calibration slope

method

One of loess or line, on default is loess

X

Vector of predicted probabilities, on default is 0.01 to 0.99

Value

Plot of simulated calibration curves

Examples

sample <- data.frame(
dist_type = rep("beta", 3),
dist_parm1 = c(1,2,3),
dist_parm2 = c(3,4,5),
cal_int = c(0, 0.05, 0.1),
cal_slp = c(1, 0.9, 0.8))
plot_cal_distance(N=200, sample=sample)

Plots Calibration Instability from Simulated Calibration Curves

Description

Simulates calibration curves based on given method, and uses plot to visualize calibration instability.

Usage

plot_cal_instability(N, sample, method = "loess", X = (1:99)/100)

Arguments

N

Number of observations to simulate in each sample

sample

method

One of loess or line, on default is loess

X

Vector of predicted probabilities, on default is 0.01 to 0.99

Value

Plot of simulated calibration curves

Examples

sample <- data.frame(
dist_type = rep("beta", 3),
dist_parm1 = c(1,2,3),
dist_parm2 = c(3,4,5),
cal_int = c(0, 0.05, 0.1),
cal_slp = c(1, 0.9, 0.8))
plot_cal_instability(N=200, sample=sample)

Transforms Evidence Into Standardized Format

Description

Verifies evidence object has correct members, and standardizes it

Usage

process_evidence(evidence)

Arguments

evidence

named list of evidence elements including: prev: prevalence cstat: c-statistic cal_slp: calibration slope and, one of cal_mean (mean calibration), cal_oe (observed to expected ratio), or cal_int (calibration intercept)

Value

Modified evidence object that has been standardized and restructured

Examples

evidence <- list(
prev=list(type="beta", mean=0.38, sd=0.2),
cstat=list(mean=0.7, sd=0.05),
cal_int=list(mean=0.2, sd=0.2),
cal_slp=list(mean=0.8, sd=0.3))
process_evidence(evidence=evidence)

Generates Samples From Normal Distribution

Description

generates samples from a normal distribution using marginal means, variances, and covariance

Usage

rbnorm(n, mu1, mu2, var1, var2, cov)

Arguments

n

Number of samples to be generated

mu1

Mean of first variable

mu2

Mean of second variable

var1

Variance of first variable

var2

Variance of second variable

cov

Covariance between the two variables

Value

Matrix of nx2 where column 1 contains samples for the first variable, and column 2 contains samples for the second variable conditioned on the first

Calculates Sample Size that Achieves Target CI Widths

Description

Calculates sample size that achieves target confidence interval widths using Riley's framework

Usage

riley_samp(target_ciws, parms)

Arguments

target_ciws

Named list containing target confidence interval width for at least one of: prev: prevalence cstat: c-statistic cal_mean: mean calibration cal_oe: observed to expected outcome ratio cal_int: calibration intercept cal_slp: calibration slope

parms

List containing model parameters and distribution: prev: expected prevalence cstat: c-statistic of the model dist_type: one of ("logitnorm", "beta, "probitnorm") dist_parm1: first parameter of the distribution dist_parm2: second parameter of the distribution cal_int: calibration intercept cal_slp: calibration slope

Value

A named list of estimated sample sizes that achieve target confidence interval widths: fciw.prev, fciw.cstat, fciw.cal_mean, fciw.cal_oe, fciw.cal_int, fciw.cal_slp