moved some functions to internal and rebuild GH pages

StatisticsHealthEconomics · Dec 8, 2023 · 5bb3c3b · 5bb3c3b
1 parent 989b857
commit 5bb3c3b
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Showing 75 changed files with 172 additions and 227 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -9,11 +9,6 @@ export(IPD_stats)
 export(gcomp_ml.boot)
 export(gcomp_ml_log_odds_ratio)
 export(gcomp_stan)
-export(get_covariate_names)
-export(get_effect_modifiers)
-export(get_mean_names)
-export(get_sd_names)
-export(get_treatment_name)
 export(hat_Delta_stats)
 export(marginal_treatment_effect)
 export(marginal_variance)

diff --git a/R/IPD_stats.R b/R/IPD_stats.R
@@ -14,7 +14,7 @@
 #' }
 #' 
 #' @param formula Linear regression formula object 
-#' @param R 
+#' @param R The number of resamples used for the non-parametric bootstrap
 #' @param ald Aggregate-level data 
 #'
 #' @return `maic` class object
@@ -45,9 +45,7 @@ strategy_maic <- function(formula = as.formula("y ~ X3 + X4 + trt*X1 + trt*X2"),
 #' @export
 # 
 strategy_stc <- function(formula =
-                           as.formula("y ~ X3 + X4 +
-                                   trt*I(X1 - mean(X1)) +
-                                   trt*I(X2 - mean(X2))")) {
+                           as.formula("y ~ X3 + X4 + trt*I(X1 - mean(X1)) + trt*I(X2 - mean(X2))")) {
   default_args <- formals()
   args <- as.list(match.call())[-1]
   args <- modifyList(default_args, args)
@@ -64,7 +62,7 @@ strategy_stc <- function(formula =
 #' }
 #'
 #' @param formula Linear regression formula object
-#' @param R 
+#' @param R The number of resamples used for the non-parametric bootstrap
 #' 
 #' @return `gcomp_ml` class object
 #' @export

diff --git a/R/cor2cov.R b/R/cor2cov.R
@@ -4,6 +4,7 @@
 #' @param R correlation matrix
 #' @param S vector of standard deviations covariance matrix
 #' @return Required input for \code{mvrnorm}.
+#' @keywords internal
 #'
 cor2cov <- function(R, S) {
   sweep(sweep(R, 1, S, "*"), 2, S, "*")

diff --git a/R/gen_data.R b/R/gen_data.R
@@ -13,6 +13,8 @@
 #' @param allocation Allocation
 #' @return Data frame of `X`, `trt` and `y`
 #' 
+#' @keywords internal
+#' 
 gen_data <- function(N, b_trt, b_X, b_EM, b_0,
                      meanX, sdX, event_rate, 
                      corX, allocation) {

diff --git a/R/parse_formula.R b/R/parse_formula.R
@@ -4,7 +4,7 @@
 #' @param formula Linear regression formula
 #'
 #' @return Effect modifiers names
-#' @export
+#' @keywords internal
 #'
 get_effect_modifiers <- function(formula) {
 
@@ -22,7 +22,7 @@ get_effect_modifiers <- function(formula) {
 #' @param formula Linear regression formula
 #'
 #' @return Treatment name
-#' @export
+#' @keywords internal
 #'
 get_treatment_name <- function(formula) {
   formula <- as.formula(formula)
@@ -39,7 +39,7 @@ get_treatment_name <- function(formula) {
 #' @param var_names Variable names
 #'
 #' @return Mean names
-#' @export
+#' @keywords internal
 #'
 get_mean_names <- function(dat, var_names) {
   dat_names <- names(dat)
@@ -56,7 +56,7 @@ get_mean_names <- function(dat, var_names) {
 #' @param var_names 
 #'
 #' @return SD names
-#' @export
+#' @keywords internal
 #'
 get_sd_names <- function(dat, var_names) {
   dat_names <- names(dat)
@@ -72,7 +72,7 @@ get_sd_names <- function(dat, var_names) {
 #' @param formula Linear regression formula
 #'
 #' @return covariate names
-#' @export
+#' @keywords internal
 #'
 get_covariate_names <- function(formula) {
   all.vars(formula)[-1]

diff --git a/R/performance_measures.R b/R/performance_measures.R
@@ -5,6 +5,8 @@
 #'
 #' @param beta Beta
 #' @param X X
+#' @keywords internal
+#' 
 Q <- function(beta, X) {
   sum(exp(X %*% beta))
 }
@@ -13,6 +15,8 @@ Q <- function(beta, X) {
 #' 
 #' @param theta.hat Theta hat
 #' @param theta Theta
+#' @keywords internal
+#' 
 bias <- function(theta.hat, theta) {
   nsim <- length(theta.hat)
   sum(theta.hat)/nsim - theta
@@ -21,6 +25,8 @@ bias <- function(theta.hat, theta) {
 #' Monte Carlo SE of bias estimate
 #' @param theta.hat theta hat
 #' @return \eqn{sqrt(1/(nsim*(nsim-1))*tmp)}
+#' @keywords internal
+#' 
 bias.mcse <- function(theta.hat) {
   nsim <- length(theta.hat)
   tmp <- sum((theta.hat - mean(theta.hat))^2)
@@ -33,6 +39,8 @@ bias.mcse <- function(theta.hat) {
 #' @param upp Upper
 #' @param theta Theta
 #' @return \eqn{sum(in_range)/nsim}
+#' @keywords internal
+#' 
 coverage <- function(low, upp, theta) {
   nsim <- length(low)
   theta_inside_range <- theta >= low & theta <= upp
@@ -45,6 +53,8 @@ coverage <- function(low, upp, theta) {
 #' @param coverage Coverage
 #' @param nsim Number of simulations
 #' @return \eqn{sqrt((coverage*(1 - coverage))/nsim)}
+#' @keywords internal
+#' 
 coverage.mcse <- function(coverage, nsim) {
   sqrt((coverage*(1 - coverage))/nsim)
 }
@@ -54,6 +64,8 @@ coverage.mcse <- function(coverage, nsim) {
 #' @param theta.hat Theta hat
 #' @param theta Theta
 #' @return \eqn{sum((theta.hat - theta)^2)/nsim}
+#' @keywords internal
+#' 
 mse <- function(theta.hat, theta) {
   nsim <- length(theta.hat)
   sum((theta.hat - theta)^2)/nsim
@@ -64,6 +76,8 @@ mse <- function(theta.hat, theta) {
 #' @param theta.hat Theta hat
 #' @param theta Theta
 #' @return \eqn{sqrt(sum((tmp - mse.est)^2)/(nsim*(nsim-1)))}
+#' @keywords internal
+#' 
 mse.mcse <- function(theta.hat, theta) {
   nsim <- length(theta.hat)
   tmp <- (theta.hat - theta)^2
@@ -76,6 +90,8 @@ mse.mcse <- function(theta.hat, theta) {
 #' @param theta.hat Theta hat
 #' @param theta Theta
 #' @return \eqn{sum(abs(theta.hat - theta))/nsim}
+#' @keywords internal
+#' 
 mae <- function(theta.hat, theta) {
   nsim <- length(theta.hat)
   sum(abs(theta.hat - theta))/nsim
@@ -85,6 +101,8 @@ mae <- function(theta.hat, theta) {
 #' 
 #' @param pm pm
 #' @return \eqn{sqrt(sum((pm - pm_mean)^2)/(nsim*(nsim-1)))}
+#' @keywords internal
+#' 
 mcse.estimate <- function(pm) {
   nsim <- length(pm)
   pm_mean <- sum(pm)/nsim
@@ -95,6 +113,8 @@ mcse.estimate <- function(pm) {
 #' 
 #' @param theta.hat Theta
 #' @return \eqn{sqrt(tmp/(nsim-1))}
+#' @keywords internal
+#' 
 empse <- function(theta.hat) {
   nsim <- length(theta.hat)
   tmp <- sum((theta.hat - mean(theta.hat))^2)
@@ -106,6 +126,8 @@ empse <- function(theta.hat) {
 #' @param empse EMPSE
 #' @param nsim Number of simulations
 #' @return \eqn{empse/(sqrt(2*(nsim-1)))}
+#' @keywords internal
+#' 
 empse.mcse <- function(empse, nsim) {
   empse/(sqrt(2*(nsim-1)))
 } 
@@ -115,6 +137,8 @@ empse.mcse <- function(empse, nsim) {
 #' @param theta.hat Theta hat
 #' @param std.err Standard error
 #' @return Ratio
+#' @keywords internal
+#' 
 var.ratio <- function(theta.hat, std.err) {
   nsim <- length(theta.hat)
   num <- sum(std.err)/nsim
@@ -135,6 +159,8 @@ var.ratio <- function(theta.hat, std.err) {
 #' @references
 #' \insertRef{wolter2007}{mimR}
 #' 
+#' @keywords internal
+#' 
 var.ratio.mcse <- function(avg.se, emp.se, var.avg.se, var.emp.se) {
 
   sqrt((1/emp.se^2)*var.avg.se + (((avg.se^2)/(emp.se^4))*var.emp.se))

diff --git a/R/process_metrics.R b/R/process_metrics.R
@@ -5,6 +5,8 @@
 #' @param variances Variances
 #' @param truth Truth
 #' 
+#' @keywords internal
+#' 
 process_metrics <- function(means, variances, truth) {
   # remove NAs (an issue for MAIC in Scenario 7, separation issues)
   NAs <- is.na(means)

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -24,36 +24,15 @@ reference:
   desc: "Helper functions"
   contents:
   - ALD_stats
-  - bias.mcse
-  - bias
-  - cor2cov
-  - coverage.mcse
-  - coverage
-  - empse.mcse
-  - empse
   - gcomp_ml.boot
   - gcomp_ml_log_odds_ratio
   - gcomp_stan
-  - gen_data
-  - get_covariate_names
-  - get_effect_modifiers
-  - get_mean_names
-  - get_sd_names
-  - get_treatment_name
   - IPD_stats
-  - mae
   - maic.boot
   - maic_weights
   - marginal_treatment_effect
   - marginal_variance
-  - mcse.estimate
-  - mse.mcse
-  - mse
-  - process_metrics
-  - Q
   - strategy_maic
   - trial_treatment_effect
   - trial_variance
-  - var.ratio.mcse
-  - var.ratio
 
diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/LICENSE.html b/docs/LICENSE.html
diff --git a/docs/articles/Basic_example.html b/docs/articles/Basic_example.html
diff --git a/docs/articles/index.html b/docs/articles/index.html