diff --git a/R/IPD_stats.R b/R/IPD_stats.R index 67fc7c2..ef7c9ef 100644 --- a/R/IPD_stats.R +++ b/R/IPD_stats.R @@ -147,8 +147,8 @@ IPD_stats.default <- function() { #' using bootstrapping #' #' @param strategy -#' @param ipd -#' @param ald +#' @template args-ipd +#' @template args-ald #' #' @export #' @@ -174,8 +174,8 @@ IPD_stats.maic <- function(strategy, #' IPD_stats.stc #' #' @param strategy -#' @param ipd -#' @param ald +#' @template args-ipd +#' @template args-ald #' @export #' IPD_stats.stc <- function(strategy, @@ -196,8 +196,8 @@ IPD_stats.stc <- function(strategy, #' IPD_stats.gcomp_ml #' #' @param strategy -#' @param ipd -#' @param ald +#' @template args-ipd +#' @template args-ald #' #' @return #' @export @@ -220,8 +220,8 @@ IPD_stats.gcomp_ml <- function(strategy, #' IPD_stats.gcomp_stan #' #' @param strategy -#' @param ipd -#' @param ald +#' @template args-ipd +#' @template args-ald #' #' @return #' @export @@ -230,7 +230,7 @@ IPD_stats.gcomp_stan <- function(strategy, ipd, ald) { ppv <- gcomp_stan(formula = strategy$formula, - dat = ipd) + ipd = ipd, ald = ald) # compute marginal log-odds ratio for A vs C for each MCMC sample # by transforming from probability to linear predictor scale diff --git a/R/gcomp_stan.R b/R/gcomp_stan.R index 2fa4123..51673b4 100644 --- a/R/gcomp_stan.R +++ b/R/gcomp_stan.R @@ -2,8 +2,8 @@ #' G-computation using Stan #' #' @param formula -#' @param ipd -#' @param ald +#' @template args-ipd +#' @template args-ald #' #' @return #' @export @@ -15,9 +15,7 @@ gcomp_stan <- function(formula = as.formula("y ~ X3 + X4 + trt*X1 + trt*X2"), # remove treatment cov_names <- cov_names[cov_names != treat_names] - - n_covariates <- length(covariate_names) - + n_covariates <- length(cov_names) rho <- cor(ipd[, cov_names]) # covariate simulation for BC trial using copula package @@ -40,7 +38,6 @@ gcomp_stan <- function(formula = as.formula("y ~ X3 + X4 + trt*X1 + trt*X2"), # simulated BC pseudo-population of size 1000 x_star <- as.data.frame(rMvdc(1000, mvd)) - browser() colnames(x_star) <- cov_names # outcome logistic regression fitted to IPD using MCMC (Stan) diff --git a/man-roxygen/args-ald.R b/man-roxygen/args-ald.R new file mode 100644 index 0000000..7e99408 --- /dev/null +++ b/man-roxygen/args-ald.R @@ -0,0 +1 @@ +#' @param ald Aggregate-level data \ No newline at end of file diff --git a/man-roxygen/args-ipd.R b/man-roxygen/args-ipd.R new file mode 100644 index 0000000..57a7bd5 --- /dev/null +++ b/man-roxygen/args-ipd.R @@ -0,0 +1 @@ +#' @param ipd Individual-level data \ No newline at end of file diff --git a/man/gcomp_stan.Rd b/man/gcomp_stan.Rd index 9408fb9..0fd669f 100644 --- a/man/gcomp_stan.Rd +++ b/man/gcomp_stan.Rd @@ -2,15 +2,17 @@ % Please edit documentation in R/gcomp_stan.R \name{gcomp_stan} \alias{gcomp_stan} -\title{gcomp_stan} +\title{G-computation using Stan} \usage{ -gcomp_stan(formula = as.formula("y ~ X3 + X4 + trt*X1 + trt*X2"), dat = AC.IPD) +gcomp_stan(formula = as.formula("y ~ X3 + X4 + trt*X1 + trt*X2"), ipd, ald) } \arguments{ \item{formula}{} -\item{dat}{} +\item{ipd}{Individual-level data} + +\item{ald}{Aggregate-level data} } \description{ -gcomp_stan +G-computation using Stan }