R/bdplogit.R
In balcomes/mdictools: Tools for the Bayesian Discount Prior Function
#' @title Bayesian Discount Prior: Two-Arm Logistic Regression
#' @description \code{bdplogit} is used to estimate the treatment effect
#' in the presence of covariates using the logistic regression analysis
#' implementation of the Bayesian discount prior. \code{summary} and
#' \code{print} methods are supported. Currently, the function only supports
#' a two-arm clinical trial where all of current treatment, current control,
#' historical treatment, and historical control data are present
#' @param formula an object of class "formula." See "Details" for
#' more information, including specification of treatment
#' data indicators.
#' @param data a data frame containing the current data variables in the model.
#' A column named \code{treatment} must be present; \code{treatment} must
#' be binary and indicate treatment group vs. control group.
#' @param data0 a data frame containing the historical data variables in the model.
#' The column labels of data and data0 must match.
#' @param prior_treatment_effect scalar. The historical adjusted treatment effect.
#' If left \code{NULL}, value is estimated from the historical data.
#' @param prior_control_effect scalar. The historical adjusted control effect.
#' If left \code{NULL}, value is estimated from the historical data.
#' @param prior_treatment_sd scalar. The standard deviation of the historical
#' adjusted treatment effect. If left \code{NULL}, value is estimated from
#' the historical data.
#' @param prior_control_sd scalar. The standard deviation of the historical
#' adjusted control effect. If left \code{NULL}, value is estimated from
#' the historical data.
#' @param prior_covariate_effect vector. The prior mean(s) of the covariate
#' effect(s). Default value is zero. If a single value is input, the
#' the scalar is repeated to the length of the input covariates. Otherwise,
#' care must be taken to ensure the length of the input matches the number of
#' covariates.
#' @param prior_covariate_sd vector. The prior standard deviation(s) of the
#' covariate effect(s). Default value is 1e4. If a single value is input, the
#' the scalar is repeated to the length of the input covariates. Otherwise,
#' care must be taken to ensure the length of the input matches the number of
#' covariates.
#' @param discount_function character. Specify the discount function to use.
#' Currently supports \code{weibull}, \code{scaledweibull}, and
#' \code{identity}. The discount function \code{scaledweibull} scales
#' the output of the Weibull CDF to have a max value of 1. The \code{identity}
#' discount function uses the posterior probability directly as the discount
#' weight. Default value is "\code{identity}".
#' @param alpha_max scalar. Maximum weight the discount function can apply.
#' Default is 1. Users may specify a vector of two values where the first
#' value is used to weight the historical treatment group and
#' the second value is used to weight the historical control group.
#' @param fix_alpha logical. Fix alpha at alpha_max? Default value is FALSE.
#' @param number_mcmc_alpha scalar. Number of Monte Carlo
#' simulations for estimating the historical data weight. Default is 5000.
#' @param number_mcmc_beta scalar. Number of Monte Carlo simulations for
#' estimating beta, the vector of regression coefficients. Default is 10000.
#' @param weibull_shape scalar. Shape parameter of the Weibull discount function
#' used to compute alpha, the weight parameter of the historical data. Default
#' value is 3. Users may specify a vector of two values
#' where the first value is used to estimate the weight of the historical
#' treatment group and the second value is used to estimate the weight of the
#' historical control group. Not used when \code{discount_function} = "identity".
#' @param weibull_scale scalar. Scale parameter of the Weibull discount function
#' used to compute alpha, the weight parameter of the historical data. Default
#' value is 0.135. Users may specify a vector of two
#' values where the first value is used to estimate the weight of the
#' historical treatment group and the second value is used to estimate the
#' weight of the historical control group.
#' Not used when \code{discount_function} = "identity".
#' @param method character. Analysis method with respect to estimation of the weight
#' paramter alpha. Default method "\code{mc}" estimates alpha for each
#' Monte Carlo iteration. Alternate value "\code{fixed}" estimates alpha once and
#' holds it fixed throughout the analysis. See the the \code{bdplm} vignette \cr
#' \code{vignette("bdplm-vignette", package="bayesDP")} for more details.
#' @details \code{bdplogit} uses a two-stage approach for determining the
#' strength of historical data in estimation of an adjusted mean or covariate
#' effect. In the first stage, a \emph{discount function} is used that
#' that defines the maximum strength of the
#' historical data and discounts based on disagreement with the current data.
#' Disagreement between current and historical data is determined by stochastically
#' comparing the respective posterior distributions under noninformative priors.
#' Here with a two-arm regression analysis, the comparison is the
#' proability (\code{p}) that the covariate effect of an historical data indicator is
#' significantly different from zero. The comparison metric \code{p} is then
#' input into the discount function and the final strength of the
#' historical data is returned (\code{alpha}).
#'
#' In the second stage, posterior estimation is performed where the discount
#' function parameter, \code{alpha}, is used to weight the historical data
#' effects.
#'
#' The formula must include an intercept (i.e., do not use \code{-1} in
#' the formula) and both data and data0 must be present.
#' The column names of data and data0 must match. See \code{examples} below for
#' example usage.
#'
#' The underlying model uses the \code{MCMClogit} function of the MCMCpack
#' package to carryout posterior estimation. Add more.
#'
#' @return \code{bdplogit} returns an object of class "bdplogit".
#'
#' An object of class "\code{bdplogit}" is a list containing at least
#' the following components:
#' \describe{
#' \item{\code{posterior}}{
#' data frame. The posterior draws of the covariates, the intercept, and
#' the treatment effect. The grid of sigma values are included.}
#' \item{\code{alpha_discount}}{
#' vector. The posterior probability of the stochastic comparison
#' between the current and historical data for each of the treatment
#' and control arms. If \code{method="mc"}, the result is a matrix of
#' estimates, otherwise for \code{method="fixed"}, the result is a vector
#' of estimates.}
#' \item{\code{estimates}}{
#' list. The posterior means and standard errors of the intercept,
#' treatment effect, covariate effect(s) and error variance.}
#' }
#'
#' @examples
#' # Set sample sizes
#' n_t <- 30 # Current treatment sample size
#' n_c <- 30 # Current control sample size
#' n_t0 <- 80 # Historical treatment sample size
#' n_c0 <- 80 # Historical control sample size
#'
#' # Treatment group vectors for current and historical data
#' treatment <- c(rep(1,n_t), rep(0,n_c))
#' treatment0 <- c(rep(1,n_t0), rep(0,n_c0))
#'
#' # Simulate a covariate effect for current and historical data
#' x <- rnorm(n_t+n_c, 1, 5)
#' x0 <- rnorm(n_t0+n_c0, 1, 5)
#'
#' # Simulate outcome:
#' # - Intercept of 10 for current and historical data
#' # - Treatment effect of 31 for current data
#' # - Treatment effect of 30 for historical data
#' # - Covariate effect of 3 for current and historical data
#' Y <- 10 + 31*treatment + x*3 + rnorm(n_t+n_c,0,5)
#' Y0 <- 10 + 30*treatment0 + x0*3 + rnorm(n_t0+n_c0,0,5)
#'
#' # Place data into separate treatment and control data frames and
#' # assign historical = 0 (current) or historical = 1 (historical)
#' df_ <- data.frame(Y=Y, treatment=treatment, x=x)
#' df0 <- data.frame(Y=Y0, treatment=treatment0, x=x0)
#'
#' # Fit model using default settings
#' fit <- bdplm(formula=Y ~ treatment+x, data=df_, data0=df0,
#' method="fixed")
#'
#' # Look at estimates and discount weight
#' summary(fit)
#' print(fit)
#'
#' @rdname bdplogit
#' @import methods
#' @importFrom stats density is.empty.model median model.offset model.response pweibull pnorm quantile rbeta rgamma rnorm var vcov contrasts<- dt gaussian lm.fit model.frame model.matrix.default offset terms terms.formula coefficients lm qgamma runif
#' @importFrom MCMCpack MCMClogit
#' @aliases bdplogit,ANY-method
#' @useDynLib bayesDP
#' @export bdplogit
bdplogit <- setClass("bdplogit", slots = c(posterior_treatment = "list",
posterior_control = "list",
args1 = "list"))
setGeneric("bdplogit",
function(formula = formula,
data = data,
data0 = NULL,
prior_treatment_effect = NULL, #0,
prior_control_effect = NULL, #0,
prior_treatment_sd = NULL, #1e4,
prior_control_sd = NULL, #1e4,
prior_covariate_effect = 0,
prior_covariate_sd = 1e4,
number_mcmc_alpha = 5000,
number_mcmc_beta = 10000,
discount_function = "identity",
alpha_max = 1,
fix_alpha = FALSE,
weibull_scale = 0.135,
weibull_shape = 3,
method = "mc"){
standardGeneric("bdplogit")
})
setMethod("bdplogit",
signature(),
function(formula = formula,
data = data,
data0 = NULL,
prior_treatment_effect = NULL, #0,
prior_control_effect = NULL, #0,
prior_treatment_sd = NULL, #1e4,
prior_control_sd = NULL, #1e4,
prior_covariate_effect = 0,
prior_covariate_sd = 1e4,
number_mcmc_alpha = 5000,
number_mcmc_beta = 10000,
discount_function = "identity",
alpha_max = 1,
fix_alpha = FALSE,
weibull_scale = 0.135,
weibull_shape = 3,
method = "mc"){
### Check validity of data input
call <- match.call()
if (missing(data)) {
stop("Current data not input correctly.")
}
if (is.null(data0)) {
stop("Historical data not input correctly.")
}
if(method == "mc"){
stop("Method 'mc' not currently supported.")
}
### Parse current data
mf <- mf0 <- match.call(expand.dots = FALSE)
m <- match(c("formula", "data"), names(mf), 0L)
mf <- mf[c(1L, m)]
mf$na.action <- NULL
mf[[1L]] <- quote(stats::model.frame)
mf <- eval(mf, parent.frame())
mt <- attr(mf, "terms")
Y <- model.response(mf, "any")
if (length(dim(Y)) == 1L) {
nm <- rownames(Y)
dim(Y) <- NULL
if (!is.null(nm)) {
names(Y) <- nm
}
}
X <- if (!is.empty.model(mt)) {
model.matrixBayes(object = mt, data = data, contrasts.arg = NULL,
keep.order = TRUE, drop.baseline = TRUE)
} else {
matrix(, NROW(Y), 0L)
}
### Alter intercept column name, if present
imatch <- match("(Intercept)", colnames(X))
if(!is.na(imatch)) colnames(X)[imatch] <- "intercept"
# Create indicator of whether each column is present
cmatch <- match(c("intercept","treatment") , colnames(X))
cmatch <- !is.na(cmatch) ### == TRUE == present
if(!all(cmatch)){
stop("Current data is input incorrectly. Intercept and treatment must be present.")
}
### Count levels of treatment data and sure 0 and 1 are present
trt_levels <- levels(as.factor(X[,"treatment"]))
if(!(all(trt_levels %in% c(0,1)))){
stop("Treatment input has wrong levels. Values should be 0 and 1.")
}
### Parse historical data
if(missing(data0)){
stop("Historical data is required.")
} else{
m00 <- match("data0", names(mf0), 0L)
m01 <- match("data", names(mf0), 0L)
mf0[m01] <- mf0[m00]
m0 <- match(c("formula", "data"), names(mf0), 0L)
mf0 <- mf0[c(1L, m0)]
mf0$na.action <- NULL
mf0[[1L]] <- quote(stats::model.frame)
mf0 <- eval(mf0, parent.frame())
mt0 <- attr(mf0, "terms")
Y0 <- model.response(mf0, "any")
if (length(dim(Y0)) == 1L) {
nm0 <- rownames(Y0)
dim(Y0) <- NULL
if (!is.null(nm0)) {
names(Y0) <- nm0
}
}
X0 <- if (!is.empty.model(mt0)) {
model.matrixBayes(object = mt0, data = data0, contrasts.arg = NULL,
keep.order = TRUE, drop.baseline = TRUE)
} else {
matrix(, NROW(Y0), 0L)
}
### Alter intercept column name, if present
imatch <- match("(Intercept)", colnames(X0))
if(!is.na(imatch)) colnames(X0)[imatch] <- "intercept"
# Create indicator of whether each column is present
cmatch <- match(c("intercept","treatment") , colnames(X0))
cmatch <- !is.na(cmatch) ### == TRUE == present
if(!all(cmatch)){
stop("Historical data is input incorrectly. Intercept and treatment must be present.")
}
cnames <- colnames(X)
cnames0 <- colnames(X0)
if(!all(cnames==cnames0)){
stop("Column names in the historical data must match the current data.")
}
### Count levels of treatment data and ensure 0 and 1 are present
trt_levels0 <- levels(as.factor(X0[,"treatment"]))
# Check that the levels are 0 and/or 1
if(!(all(trt_levels0 %in% c(0,1)))){
stop("Treatment input has wrong levels. Values should be 0 and 1.")
}
}
### If method == "mc", fix_alpha must be FALSE
if(method=="mc" & fix_alpha){
stop("mc method not possible with fix_alpha == TRUE. Set fix_alpha == FALSE." )
}
# Check that discount_function is input correctly
all_functions <- c("weibull", "scaledweibull", "identity")
function_match <- match(discount_function, all_functions)
if(is.na(function_match)) {
stop("discount_function input incorrectly.")
}
historical <- NULL
treatment <- NULL
intercept <- NULL
##############################################################################
# Quick check, if alpha_max, weibull_scale, or weibull_shape have length 1,
# repeat input twice
##############################################################################
if(length(alpha_max)==1){
alpha_max <- rep(alpha_max, 2)
}
if(length(weibull_scale)==1){
weibull_scale <- rep(weibull_scale, 2)
}
if(length(weibull_shape)==1){
weibull_shape <- rep(weibull_shape, 2)
}
##############################################################################
# Format input data
##############################################################################
### Create a master dataframe
df <- data.frame(Y=Y, data.frame(X), historical=0)
df0 <- data.frame(Y=Y0, data.frame(X0), historical=1)
df <- rbind(df, df0)
### Split data into separate treatment & control dataframes
df_t <- subset(df, treatment == 1)
df_c <- subset(df, treatment == 0)
### Also create current data dataframe
df_current <- subset(df, historical == 0, select=-intercept)
### Count number of covariates
names_df <- names(df)
covs_df <- names_df[!(names_df %in% c("Y", "intercept", "treatment", "historical"))]
n_covs <- length(covs_df)
##############################################################################
# Estimate discount weights for each of the treatment and control arms
##############################################################################
discount_treatment <- discount_logit(df = df_t,
discount_function = discount_function,
alpha_max = alpha_max[1],
fix_alpha = fix_alpha,
number_mcmc_alpha = number_mcmc_alpha,
weibull_shape = weibull_shape[1],
weibull_scale = weibull_scale[1],
method = method)
discount_control <- discount_logit(df = df_c,
discount_function = discount_function,
alpha_max = alpha_max[2],
fix_alpha = fix_alpha,
number_mcmc_alpha = number_mcmc_alpha,
weibull_shape = weibull_shape[2],
weibull_scale = weibull_scale[2],
method = method)
##############################################################################
# Estimate historical adjusted treatment and control effects to use as the
# priors for the current data
##############################################################################
if(is.null(prior_treatment_effect) | is.null(prior_control_effect) |
is.null(prior_treatment_sd) | is.null(prior_control_sd)){
df0$control <- 1-df0$treatment
cnames0 <- names(df0)
cnames0 <- cnames0[!(cnames0 %in% c("Y", "intercept", "historical","treatment","control"))]
cnames0 <- c("treatment","control", cnames0)
f0 <- paste0("Y~ -1+",paste0(cnames0,collapse="+"))
fit_0 <- glm(f0, data=df0, family=binomial)
summ_0 <- summary(fit_0)
if(is.null(prior_treatment_effect)) prior_treatment_effect <- summ_0$coef[1,1]
if(is.null(prior_control_effect)) prior_control_effect <- summ_0$coef[2,1]
if(is.null(prior_treatment_sd)) prior_treatment_sd <- summ_0$coef[1,2]
if(is.null(prior_control_sd)) prior_control_sd <- summ_0$coef[2,2]
}
### Prior covariate effects
if(length(prior_covariate_effect) == 1){
prior_covariate_effect <- rep(prior_covariate_effect,n_covs)
}
if(length(prior_covariate_sd) == 1){
prior_covariate_sd <- rep(prior_covariate_sd,n_covs)
}
##############################################################################
# Estimate augmented treatment effect
##############################################################################
### Compute prior terms
### - Covarance/variance needs to be parameterized as precision
tau2 <- c(1/prior_treatment_sd, 1/prior_control_sd, 1/prior_covariate_sd)^2
mu0 <- c(prior_treatment_effect, prior_control_effect, prior_covariate_effect)
### Calculate constants from current data
df_current$control <- 1-df_current$treatment
# Create analysis formula
df_analysis <- df_current[,c("treatment", "control",covs_df)]
cnames <- names(df_analysis)
f <- paste0("Y~ -1 +",paste0(cnames,collapse="+"))
### Estimation scheme differs conditional on discounting method
if(method == "fixed"){
### Extract alpha0, append "zero" weight for the covariate effect(s)
alpha0 <- c(discount_treatment$alpha_discount + 1e-12,
discount_control$alpha_discount + 1e-12,
rep(1e-12, n_covs))
### Create precision matrix
B0 <- diag(alpha0/tau2)
### Get Bayesian fit
fit <- MCMCpack::MCMClogit(f, data=df_analysis,
mcmc = number_mcmc_beta,
b0 = mu0,
B0 = diag(tau2))
beta_samples <- data.frame(fit)
} else if(method == "mc"){
stop("Method 'mc' not currently supported.")
}
### Estimate posterior of intercept and treatment effect
beta_samples$intercept <- beta_samples$control
beta_samples$treatment <- beta_samples$treatment-beta_samples$control
### Format posterior table
m <- ncol(beta_samples)
beta_samples <- beta_samples[,c(m,1,3:(m-1))]
### Format alpha_discount values
alpha_discount <- data.frame(treatment = discount_treatment$alpha_discount,
control = discount_control$alpha_discount)
### Format estimates
estimates <- list()
estimates$coefficients <- data.frame(t(colMeans(beta_samples)))
estimates$coefficients <- estimates$coefficients[c("intercept", "treatment", covs_df)]
estimates$se <- data.frame(t(apply(beta_samples,2,sd)))
estimates$se <- estimates$se[c("intercept", "treatment", covs_df)]
### Format input arguments
args1 <- list(call = call,
data = df)
### Format output
me <- list(posterior = beta_samples,
alpha_discount = alpha_discount,
estimates = estimates,
args1 = args1)
class(me) <- "bdplm"
return(me)
})
################################################################################
# Logistic Regression discount weight estimation
# 1) Estimate the discount function
# - Test that the historical effect is different from zero
# - Estimate alpha based on the above comparison
################################################################################
discount_logit <- function(df, discount_function, alpha_max, fix_alpha,
number_mcmc_alpha,
weibull_shape, weibull_scale,
method){
# Create formula
cnames <- names(df)
cnames <- cnames[!(cnames %in% c("Y", "intercept", "historical","treatment"))]
cnames <- c("historical", cnames)
f <- paste0("Y~",paste0(cnames,collapse="+"))
### Get Bayesian fit
fit <- MCMCpack::MCMClogit(f, data=df, mcmc = number_mcmc_alpha)
posterior <- data.frame(fit)
### Monte Carlo simulations of historical effect
beta <- posterior$historical
### Compute posterior comparison
if(method == "fixed"){
p_hat <- mean(beta>0)
p_hat <- 2*ifelse(p_hat > 0.5, 1 - p_hat, p_hat)
} else if(method == "mc"){
Z <- abs(beta)/sigma2_beta
p_hat <- 2*(1-pnorm(Z))
}
### Compute alpha, the discount weight
if(fix_alpha){
alpha_discount <- alpha_max
} else{
# Compute alpha discount based on distribution
if(discount_function == "weibull"){
alpha_discount <- pweibull(p_hat, shape=weibull_shape,
scale=weibull_scale)*alpha_max
} else if(discount_function == "scaledweibull"){
max_p <- pweibull(1, shape=weibull_shape, scale=weibull_scale)
alpha_discount <- pweibull(p_hat, shape=weibull_shape,
scale=weibull_scale)*alpha_max/max_p
} else if(discount_function == "identity"){
alpha_discount <- p_hat*alpha_max
}
}
res <- list(p_hat = p_hat,
alpha_discount = alpha_discount)
res
}
model.matrixBayes <- function(object, data=environment(object), contrasts.arg=NULL,
xlev=NULL, keep.order=FALSE, drop.baseline=FALSE,...){
t <- if( missing( data ) ) {
terms( object )
} else{
terms.formula(object, data = data, keep.order=keep.order)
}
attr(t, "intercept") <- attr(object, "intercept")
if (is.null(attr(data, "terms"))){
data <- model.frame(object, data, xlev=xlev)
} else {
reorder <- match(sapply(attr(t,"variables"), deparse, width.cutoff=500)[-1], names(data))
if (anyNA(reorder)) {
stop( "model frame and formula mismatch in model.matrix()" )
}
if(!identical(reorder, seq_len(ncol(data)))) {
data <- data[,reorder, drop = FALSE]
}
}
int <- attr(t, "response")
if(length(data)) { # otherwise no rhs terms, so skip all this
if (drop.baseline){
contr.funs <- as.character(getOption("contrasts"))
}else{
contr.funs <- as.character(list("contr.bayes.unordered", "contr.bayes.ordered"))
}
namD <- names(data)
## turn character columns into factors
for(i in namD)
if(is.character( data[[i]] ) ) {
data[[i]] <- factor(data[[i]])
warning( gettextf( "variable '%s' converted to a factor", i ), domain = NA)
}
isF <- vapply(data, function(x) is.factor(x) || is.logical(x), NA)
isF[int] <- FALSE
isOF <- vapply(data, is.ordered, NA)
for( nn in namD[isF] ) # drop response
if( is.null( attr( data[[nn]], "contrasts" ) ) ) {
contrasts( data[[nn]] ) <- contr.funs[1 + isOF[nn]]
}
## it might be safer to have numerical contrasts:
## get(contr.funs[1 + isOF[nn]])(nlevels(data[[nn]]))
if ( !is.null( contrasts.arg ) && is.list( contrasts.arg ) ) {
if ( is.null( namC <- names( contrasts.arg ) ) ) {
stop( "invalid 'contrasts.arg' argument" )
}
for (nn in namC) {
if ( is.na( ni <- match( nn, namD ) ) ) {
warning( gettextf( "variable '%s' is absent, its contrast will be ignored", nn ), domain = NA )
}
else {
ca <- contrasts.arg[[nn]]
if( is.matrix( ca ) ) {
contrasts( data[[ni]], ncol( ca ) ) <- ca
}
else {
contrasts( data[[ni]] ) <- contrasts.arg[[nn]]
}
}
}
}
} else {
isF <- FALSE
data <- data.frame(x=rep(0, nrow(data)))
}
ans <- model.matrix.default(object=t, data=data)
cons <- if(any(isF)){
lapply( data[isF], function(x) attr( x, "contrasts") )
}else { NULL }
attr(ans, "contrasts" ) <- cons
ans
}
# library(MCMCpack)
# df0 <- data.frame(y = c(1,1,1,rep(0,138)),
# x = rnorm(141,5,0.5),
# historical = 1)
#
# df <- data.frame(y = rbinom(100,1,0.03),
# x = rnorm(100,3,1),
# historical = 0)
#
# df_ <- rbind(df0,df)
#
# fit <- MCMClogit(y~x+historical, data=df_,
# mcmc = 1e4)
#
# posterior <- data.frame(fit)
# p_hat <- mean(posterior$historical > 0)
# p_hat <- 2*ifelse(p_hat > 0.5, 1 - p_hat, p_hat)
#
#
#
# # b0=c(0,0,1),
# # B0=B0)
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#' @title Bayesian Discount Prior: Two-Arm Logistic Regression
#' @description \code{bdplogit} is used to estimate the treatment effect
#' in the presence of covariates using the logistic regression analysis
#' implementation of the Bayesian discount prior. \code{summary} and
#' \code{print} methods are supported. Currently, the function only supports
#' a two-arm clinical trial where all of current treatment, current control,
#' historical treatment, and historical control data are present
#' @param formula an object of class "formula." See "Details" for
#' more information, including specification of treatment
#' data indicators.
#' @param data a data frame containing the current data variables in the model.
#' A column named \code{treatment} must be present; \code{treatment} must
#' be binary and indicate treatment group vs. control group.
#' @param data0 a data frame containing the historical data variables in the model.
#' The column labels of data and data0 must match.
#' @param prior_treatment_effect scalar. The historical adjusted treatment effect.
#' If left \code{NULL}, value is estimated from the historical data.
#' @param prior_control_effect scalar. The historical adjusted control effect.
#' If left \code{NULL}, value is estimated from the historical data.
#' @param prior_treatment_sd scalar. The standard deviation of the historical
#' adjusted treatment effect. If left \code{NULL}, value is estimated from
#' the historical data.
#' @param prior_control_sd scalar. The standard deviation of the historical
#' adjusted control effect. If left \code{NULL}, value is estimated from
#' the historical data.
#' @param prior_covariate_effect vector. The prior mean(s) of the covariate
#' effect(s). Default value is zero. If a single value is input, the
#' the scalar is repeated to the length of the input covariates. Otherwise,
#' care must be taken to ensure the length of the input matches the number of
#' covariates.
#' @param prior_covariate_sd vector. The prior standard deviation(s) of the
#' covariate effect(s). Default value is 1e4. If a single value is input, the
#' the scalar is repeated to the length of the input covariates. Otherwise,
#' care must be taken to ensure the length of the input matches the number of
#' covariates.
#' @param discount_function character. Specify the discount function to use.
#' Currently supports \code{weibull}, \code{scaledweibull}, and
#' \code{identity}. The discount function \code{scaledweibull} scales
#' the output of the Weibull CDF to have a max value of 1. The \code{identity}
#' discount function uses the posterior probability directly as the discount
#' weight. Default value is "\code{identity}".
#' @param alpha_max scalar. Maximum weight the discount function can apply.
#' Default is 1. Users may specify a vector of two values where the first
#' value is used to weight the historical treatment group and
#' the second value is used to weight the historical control group.
#' @param fix_alpha logical. Fix alpha at alpha_max? Default value is FALSE.
#' @param number_mcmc_alpha scalar. Number of Monte Carlo
#' simulations for estimating the historical data weight. Default is 5000.
#' @param number_mcmc_beta scalar. Number of Monte Carlo simulations for
#' estimating beta, the vector of regression coefficients. Default is 10000.
#' @param weibull_shape scalar. Shape parameter of the Weibull discount function
#' used to compute alpha, the weight parameter of the historical data. Default
#' value is 3. Users may specify a vector of two values
#' where the first value is used to estimate the weight of the historical
#' treatment group and the second value is used to estimate the weight of the
#' historical control group. Not used when \code{discount_function} = "identity".
#' @param weibull_scale scalar. Scale parameter of the Weibull discount function
#' used to compute alpha, the weight parameter of the historical data. Default
#' value is 0.135. Users may specify a vector of two
#' values where the first value is used to estimate the weight of the
#' historical treatment group and the second value is used to estimate the
#' weight of the historical control group.
#' Not used when \code{discount_function} = "identity".
#' @param method character. Analysis method with respect to estimation of the weight
#' paramter alpha. Default method "\code{mc}" estimates alpha for each
#' Monte Carlo iteration. Alternate value "\code{fixed}" estimates alpha once and
#' holds it fixed throughout the analysis. See the the \code{bdplm} vignette \cr
#' \code{vignette("bdplm-vignette", package="bayesDP")} for more details.
#' @details \code{bdplogit} uses a two-stage approach for determining the
#' strength of historical data in estimation of an adjusted mean or covariate
#' effect. In the first stage, a \emph{discount function} is used that
#' that defines the maximum strength of the
#' historical data and discounts based on disagreement with the current data.
#' Disagreement between current and historical data is determined by stochastically
#' comparing the respective posterior distributions under noninformative priors.
#' Here with a two-arm regression analysis, the comparison is the
#' proability (\code{p}) that the covariate effect of an historical data indicator is
#' significantly different from zero. The comparison metric \code{p} is then
#' input into the discount function and the final strength of the
#' historical data is returned (\code{alpha}).
#'
#' In the second stage, posterior estimation is performed where the discount
#' function parameter, \code{alpha}, is used to weight the historical data
#' effects.
#'
#' The formula must include an intercept (i.e., do not use \code{-1} in
#' the formula) and both data and data0 must be present.
#' The column names of data and data0 must match. See \code{examples} below for
#' example usage.
#'
#' The underlying model uses the \code{MCMClogit} function of the MCMCpack
#' package to carryout posterior estimation. Add more.
#'
#' @return \code{bdplogit} returns an object of class "bdplogit".
#'
#' An object of class "\code{bdplogit}" is a list containing at least
#' the following components:
#' \describe{
#' \item{\code{posterior}}{
#' data frame. The posterior draws of the covariates, the intercept, and
#' the treatment effect. The grid of sigma values are included.}
#' \item{\code{alpha_discount}}{
#' vector. The posterior probability of the stochastic comparison
#' between the current and historical data for each of the treatment
#' and control arms. If \code{method="mc"}, the result is a matrix of
#' estimates, otherwise for \code{method="fixed"}, the result is a vector
#' of estimates.}
#' \item{\code{estimates}}{
#' list. The posterior means and standard errors of the intercept,
#' treatment effect, covariate effect(s) and error variance.}
#' }
#'
#' @examples
#' # Set sample sizes
#' n_t <- 30 # Current treatment sample size
#' n_c <- 30 # Current control sample size
#' n_t0 <- 80 # Historical treatment sample size
#' n_c0 <- 80 # Historical control sample size
#'
#' # Treatment group vectors for current and historical data
#' treatment <- c(rep(1,n_t), rep(0,n_c))
#' treatment0 <- c(rep(1,n_t0), rep(0,n_c0))
#'
#' # Simulate a covariate effect for current and historical data
#' x <- rnorm(n_t+n_c, 1, 5)
#' x0 <- rnorm(n_t0+n_c0, 1, 5)
#'
#' # Simulate outcome:
#' # - Intercept of 10 for current and historical data
#' # - Treatment effect of 31 for current data
#' # - Treatment effect of 30 for historical data
#' # - Covariate effect of 3 for current and historical data
#' Y <- 10 + 31*treatment + x*3 + rnorm(n_t+n_c,0,5)
#' Y0 <- 10 + 30*treatment0 + x0*3 + rnorm(n_t0+n_c0,0,5)
#'
#' # Place data into separate treatment and control data frames and
#' # assign historical = 0 (current) or historical = 1 (historical)
#' df_ <- data.frame(Y=Y, treatment=treatment, x=x)
#' df0 <- data.frame(Y=Y0, treatment=treatment0, x=x0)
#'
#' # Fit model using default settings
#' fit <- bdplm(formula=Y ~ treatment+x, data=df_, data0=df0,
#' method="fixed")
#'
#' # Look at estimates and discount weight
#' summary(fit)
#' print(fit)
#'
#' @rdname bdplogit
#' @import methods
#' @importFrom stats density is.empty.model median model.offset model.response pweibull pnorm quantile rbeta rgamma rnorm var vcov contrasts<- dt gaussian lm.fit model.frame model.matrix.default offset terms terms.formula coefficients lm qgamma runif
#' @importFrom MCMCpack MCMClogit
#' @aliases bdplogit,ANY-method
#' @useDynLib bayesDP
#' @export bdplogit
bdplogit <- setClass("bdplogit", slots = c(posterior_treatment = "list",
posterior_control = "list",
args1 = "list"))
setGeneric("bdplogit",
function(formula = formula,
data = data,
data0 = NULL,
prior_treatment_effect = NULL, #0,
prior_control_effect = NULL, #0,
prior_treatment_sd = NULL, #1e4,
prior_control_sd = NULL, #1e4,
prior_covariate_effect = 0,
prior_covariate_sd = 1e4,
number_mcmc_alpha = 5000,
number_mcmc_beta = 10000,
discount_function = "identity",
alpha_max = 1,
fix_alpha = FALSE,
weibull_scale = 0.135,
weibull_shape = 3,
method = "mc"){
standardGeneric("bdplogit")
})
setMethod("bdplogit",
signature(),
function(formula = formula,
data = data,
data0 = NULL,
prior_treatment_effect = NULL, #0,
prior_control_effect = NULL, #0,
prior_treatment_sd = NULL, #1e4,
prior_control_sd = NULL, #1e4,
prior_covariate_effect = 0,
prior_covariate_sd = 1e4,
number_mcmc_alpha = 5000,
number_mcmc_beta = 10000,
discount_function = "identity",
alpha_max = 1,
fix_alpha = FALSE,
weibull_scale = 0.135,
weibull_shape = 3,
method = "mc"){
### Check validity of data input
call <- match.call()
if (missing(data)) {
stop("Current data not input correctly.")
}
if (is.null(data0)) {
stop("Historical data not input correctly.")
}
if(method == "mc"){
stop("Method 'mc' not currently supported.")
}
### Parse current data
mf <- mf0 <- match.call(expand.dots = FALSE)
m <- match(c("formula", "data"), names(mf), 0L)
mf <- mf[c(1L, m)]
mf$na.action <- NULL
mf[[1L]] <- quote(stats::model.frame)
mf <- eval(mf, parent.frame())
mt <- attr(mf, "terms")
Y <- model.response(mf, "any")
if (length(dim(Y)) == 1L) {
nm <- rownames(Y)
dim(Y) <- NULL
if (!is.null(nm)) {
names(Y) <- nm
}
}
X <- if (!is.empty.model(mt)) {
model.matrixBayes(object = mt, data = data, contrasts.arg = NULL,
keep.order = TRUE, drop.baseline = TRUE)
} else {
matrix(, NROW(Y), 0L)
}
### Alter intercept column name, if present
imatch <- match("(Intercept)", colnames(X))
if(!is.na(imatch)) colnames(X)[imatch] <- "intercept"
# Create indicator of whether each column is present
cmatch <- match(c("intercept","treatment") , colnames(X))
cmatch <- !is.na(cmatch) ### == TRUE == present
if(!all(cmatch)){
stop("Current data is input incorrectly. Intercept and treatment must be present.")
}
### Count levels of treatment data and sure 0 and 1 are present
trt_levels <- levels(as.factor(X[,"treatment"]))
if(!(all(trt_levels %in% c(0,1)))){
stop("Treatment input has wrong levels. Values should be 0 and 1.")
}
### Parse historical data
if(missing(data0)){
stop("Historical data is required.")
} else{
m00 <- match("data0", names(mf0), 0L)
m01 <- match("data", names(mf0), 0L)
mf0[m01] <- mf0[m00]
m0 <- match(c("formula", "data"), names(mf0), 0L)
mf0 <- mf0[c(1L, m0)]
mf0$na.action <- NULL
mf0[[1L]] <- quote(stats::model.frame)
mf0 <- eval(mf0, parent.frame())
mt0 <- attr(mf0, "terms")
Y0 <- model.response(mf0, "any")
if (length(dim(Y0)) == 1L) {
nm0 <- rownames(Y0)
dim(Y0) <- NULL
if (!is.null(nm0)) {
names(Y0) <- nm0
}
}
X0 <- if (!is.empty.model(mt0)) {
model.matrixBayes(object = mt0, data = data0, contrasts.arg = NULL,
keep.order = TRUE, drop.baseline = TRUE)
} else {
matrix(, NROW(Y0), 0L)
}
### Alter intercept column name, if present
imatch <- match("(Intercept)", colnames(X0))
if(!is.na(imatch)) colnames(X0)[imatch] <- "intercept"
# Create indicator of whether each column is present
cmatch <- match(c("intercept","treatment") , colnames(X0))
cmatch <- !is.na(cmatch) ### == TRUE == present
if(!all(cmatch)){
stop("Historical data is input incorrectly. Intercept and treatment must be present.")
}
cnames <- colnames(X)
cnames0 <- colnames(X0)
if(!all(cnames==cnames0)){
stop("Column names in the historical data must match the current data.")
}
### Count levels of treatment data and ensure 0 and 1 are present
trt_levels0 <- levels(as.factor(X0[,"treatment"]))
# Check that the levels are 0 and/or 1
if(!(all(trt_levels0 %in% c(0,1)))){
stop("Treatment input has wrong levels. Values should be 0 and 1.")
}
}
### If method == "mc", fix_alpha must be FALSE
if(method=="mc" & fix_alpha){
stop("mc method not possible with fix_alpha == TRUE. Set fix_alpha == FALSE." )
}
# Check that discount_function is input correctly
all_functions <- c("weibull", "scaledweibull", "identity")
function_match <- match(discount_function, all_functions)
if(is.na(function_match)) {
stop("discount_function input incorrectly.")
}
historical <- NULL
treatment <- NULL
intercept <- NULL
##############################################################################
# Quick check, if alpha_max, weibull_scale, or weibull_shape have length 1,
# repeat input twice
##############################################################################
if(length(alpha_max)==1){
alpha_max <- rep(alpha_max, 2)
}
if(length(weibull_scale)==1){
weibull_scale <- rep(weibull_scale, 2)
}
if(length(weibull_shape)==1){
weibull_shape <- rep(weibull_shape, 2)
}
##############################################################################
# Format input data
##############################################################################
### Create a master dataframe
df <- data.frame(Y=Y, data.frame(X), historical=0)
df0 <- data.frame(Y=Y0, data.frame(X0), historical=1)
df <- rbind(df, df0)
### Split data into separate treatment & control dataframes
df_t <- subset(df, treatment == 1)
df_c <- subset(df, treatment == 0)
### Also create current data dataframe
df_current <- subset(df, historical == 0, select=-intercept)
### Count number of covariates
names_df <- names(df)
covs_df <- names_df[!(names_df %in% c("Y", "intercept", "treatment", "historical"))]
n_covs <- length(covs_df)
##############################################################################
# Estimate discount weights for each of the treatment and control arms
##############################################################################
discount_treatment <- discount_logit(df = df_t,
discount_function = discount_function,
alpha_max = alpha_max[1],
fix_alpha = fix_alpha,
number_mcmc_alpha = number_mcmc_alpha,
weibull_shape = weibull_shape[1],
weibull_scale = weibull_scale[1],
method = method)
discount_control <- discount_logit(df = df_c,
discount_function = discount_function,
alpha_max = alpha_max[2],
fix_alpha = fix_alpha,
number_mcmc_alpha = number_mcmc_alpha,
weibull_shape = weibull_shape[2],
weibull_scale = weibull_scale[2],
method = method)
##############################################################################
# Estimate historical adjusted treatment and control effects to use as the
# priors for the current data
##############################################################################
if(is.null(prior_treatment_effect) | is.null(prior_control_effect) |
is.null(prior_treatment_sd) | is.null(prior_control_sd)){
df0$control <- 1-df0$treatment
cnames0 <- names(df0)
cnames0 <- cnames0[!(cnames0 %in% c("Y", "intercept", "historical","treatment","control"))]
cnames0 <- c("treatment","control", cnames0)
f0 <- paste0("Y~ -1+",paste0(cnames0,collapse="+"))
fit_0 <- glm(f0, data=df0, family=binomial)
summ_0 <- summary(fit_0)
if(is.null(prior_treatment_effect)) prior_treatment_effect <- summ_0$coef[1,1]
if(is.null(prior_control_effect)) prior_control_effect <- summ_0$coef[2,1]
if(is.null(prior_treatment_sd)) prior_treatment_sd <- summ_0$coef[1,2]
if(is.null(prior_control_sd)) prior_control_sd <- summ_0$coef[2,2]
}
### Prior covariate effects
if(length(prior_covariate_effect) == 1){
prior_covariate_effect <- rep(prior_covariate_effect,n_covs)
}
if(length(prior_covariate_sd) == 1){
prior_covariate_sd <- rep(prior_covariate_sd,n_covs)
}
##############################################################################
# Estimate augmented treatment effect
##############################################################################
### Compute prior terms
### - Covarance/variance needs to be parameterized as precision
tau2 <- c(1/prior_treatment_sd, 1/prior_control_sd, 1/prior_covariate_sd)^2
mu0 <- c(prior_treatment_effect, prior_control_effect, prior_covariate_effect)
### Calculate constants from current data
df_current$control <- 1-df_current$treatment
# Create analysis formula
df_analysis <- df_current[,c("treatment", "control",covs_df)]
cnames <- names(df_analysis)
f <- paste0("Y~ -1 +",paste0(cnames,collapse="+"))
### Estimation scheme differs conditional on discounting method
if(method == "fixed"){
### Extract alpha0, append "zero" weight for the covariate effect(s)
alpha0 <- c(discount_treatment$alpha_discount + 1e-12,
discount_control$alpha_discount + 1e-12,
rep(1e-12, n_covs))
### Create precision matrix
B0 <- diag(alpha0/tau2)
### Get Bayesian fit
fit <- MCMCpack::MCMClogit(f, data=df_analysis,
mcmc = number_mcmc_beta,
b0 = mu0,
B0 = diag(tau2))
beta_samples <- data.frame(fit)
} else if(method == "mc"){
stop("Method 'mc' not currently supported.")
}
### Estimate posterior of intercept and treatment effect
beta_samples$intercept <- beta_samples$control
beta_samples$treatment <- beta_samples$treatment-beta_samples$control
### Format posterior table
m <- ncol(beta_samples)
beta_samples <- beta_samples[,c(m,1,3:(m-1))]
### Format alpha_discount values
alpha_discount <- data.frame(treatment = discount_treatment$alpha_discount,
control = discount_control$alpha_discount)
### Format estimates
estimates <- list()
estimates$coefficients <- data.frame(t(colMeans(beta_samples)))
estimates$coefficients <- estimates$coefficients[c("intercept", "treatment", covs_df)]
estimates$se <- data.frame(t(apply(beta_samples,2,sd)))
estimates$se <- estimates$se[c("intercept", "treatment", covs_df)]
### Format input arguments
args1 <- list(call = call,
data = df)
### Format output
me <- list(posterior = beta_samples,
alpha_discount = alpha_discount,
estimates = estimates,
args1 = args1)
class(me) <- "bdplm"
return(me)
})
################################################################################
# Logistic Regression discount weight estimation
# 1) Estimate the discount function
# - Test that the historical effect is different from zero
# - Estimate alpha based on the above comparison
################################################################################
discount_logit <- function(df, discount_function, alpha_max, fix_alpha,
number_mcmc_alpha,
weibull_shape, weibull_scale,
method){
# Create formula
cnames <- names(df)
cnames <- cnames[!(cnames %in% c("Y", "intercept", "historical","treatment"))]
cnames <- c("historical", cnames)
f <- paste0("Y~",paste0(cnames,collapse="+"))
### Get Bayesian fit
fit <- MCMCpack::MCMClogit(f, data=df, mcmc = number_mcmc_alpha)
posterior <- data.frame(fit)
### Monte Carlo simulations of historical effect
beta <- posterior$historical
### Compute posterior comparison
if(method == "fixed"){
p_hat <- mean(beta>0)
p_hat <- 2*ifelse(p_hat > 0.5, 1 - p_hat, p_hat)
} else if(method == "mc"){
Z <- abs(beta)/sigma2_beta
p_hat <- 2*(1-pnorm(Z))
}
### Compute alpha, the discount weight
if(fix_alpha){
alpha_discount <- alpha_max
} else{
# Compute alpha discount based on distribution
if(discount_function == "weibull"){
alpha_discount <- pweibull(p_hat, shape=weibull_shape,
scale=weibull_scale)*alpha_max
} else if(discount_function == "scaledweibull"){
max_p <- pweibull(1, shape=weibull_shape, scale=weibull_scale)
alpha_discount <- pweibull(p_hat, shape=weibull_shape,
scale=weibull_scale)*alpha_max/max_p
} else if(discount_function == "identity"){
alpha_discount <- p_hat*alpha_max
}
}
res <- list(p_hat = p_hat,
alpha_discount = alpha_discount)
res
}
model.matrixBayes <- function(object, data=environment(object), contrasts.arg=NULL,
xlev=NULL, keep.order=FALSE, drop.baseline=FALSE,...){
t <- if( missing( data ) ) {
terms( object )
} else{
terms.formula(object, data = data, keep.order=keep.order)
}
attr(t, "intercept") <- attr(object, "intercept")
if (is.null(attr(data, "terms"))){
data <- model.frame(object, data, xlev=xlev)
} else {
reorder <- match(sapply(attr(t,"variables"), deparse, width.cutoff=500)[-1], names(data))
if (anyNA(reorder)) {
stop( "model frame and formula mismatch in model.matrix()" )
}
if(!identical(reorder, seq_len(ncol(data)))) {
data <- data[,reorder, drop = FALSE]
}
}
int <- attr(t, "response")
if(length(data)) { # otherwise no rhs terms, so skip all this
if (drop.baseline){
contr.funs <- as.character(getOption("contrasts"))
}else{
contr.funs <- as.character(list("contr.bayes.unordered", "contr.bayes.ordered"))
}
namD <- names(data)
## turn character columns into factors
for(i in namD)
if(is.character( data[[i]] ) ) {
data[[i]] <- factor(data[[i]])
warning( gettextf( "variable '%s' converted to a factor", i ), domain = NA)
}
isF <- vapply(data, function(x) is.factor(x) || is.logical(x), NA)
isF[int] <- FALSE
isOF <- vapply(data, is.ordered, NA)
for( nn in namD[isF] ) # drop response
if( is.null( attr( data[[nn]], "contrasts" ) ) ) {
contrasts( data[[nn]] ) <- contr.funs[1 + isOF[nn]]
}
## it might be safer to have numerical contrasts:
## get(contr.funs[1 + isOF[nn]])(nlevels(data[[nn]]))
if ( !is.null( contrasts.arg ) && is.list( contrasts.arg ) ) {
if ( is.null( namC <- names( contrasts.arg ) ) ) {
stop( "invalid 'contrasts.arg' argument" )
}
for (nn in namC) {
if ( is.na( ni <- match( nn, namD ) ) ) {
warning( gettextf( "variable '%s' is absent, its contrast will be ignored", nn ), domain = NA )
}
else {
ca <- contrasts.arg[[nn]]
if( is.matrix( ca ) ) {
contrasts( data[[ni]], ncol( ca ) ) <- ca
}
else {
contrasts( data[[ni]] ) <- contrasts.arg[[nn]]
}
}
}
}
} else {
isF <- FALSE
data <- data.frame(x=rep(0, nrow(data)))
}
ans <- model.matrix.default(object=t, data=data)
cons <- if(any(isF)){
lapply( data[isF], function(x) attr( x, "contrasts") )
}else { NULL }
attr(ans, "contrasts" ) <- cons
ans
}
# library(MCMCpack)
# df0 <- data.frame(y = c(1,1,1,rep(0,138)),
# x = rnorm(141,5,0.5),
# historical = 1)
#
# df <- data.frame(y = rbinom(100,1,0.03),
# x = rnorm(100,3,1),
# historical = 0)
#
# df_ <- rbind(df0,df)
#
# fit <- MCMClogit(y~x+historical, data=df_,
# mcmc = 1e4)
#
# posterior <- data.frame(fit)
# p_hat <- mean(posterior$historical > 0)
# p_hat <- 2*ifelse(p_hat > 0.5, 1 - p_hat, p_hat)
#
#
#
# # b0=c(0,0,1),
# # B0=B0)
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