Exported internal helper functions

NAMESPACE

@@ -46,7 +46,9 @@ export(Stack)
 export(add_class)
 export(analyse)
 export(ancova)
+export(as_analysis)
 export(as_class)
+export(as_simple_formula)
 export(as_vcov)
 export(control_bayes)
 export(delta_template)
@@ -57,11 +59,13 @@ export(extract_imputed_dfs)
 export(fill_locf)
 export(getStrategies)
 export(get_example_data)
+export(get_pool_components)
 export(has_class)
 export(impute)
 export(jackknife_se)
 export(locf)
 export(longDataConstructor)
+export(lsmeans)
 export(make_rbmi_cluster)
 export(mcse)
 export(mcse_combine_all_pars)
@@ -70,8 +74,10 @@ export(method_approxbayes)
 export(method_bayes)
 export(method_bmlmi)
 export(method_condmean)
+export(parametric_ci)
 export(pool)
 export(pool_internal)
+export(rubin_rules)
 export(set_simul_pars)
 export(set_vars)
 export(simulate_data)
@@ -80,6 +86,7 @@ export(strategy_CR)
 export(strategy_JR)
 export(strategy_LMCF)
 export(strategy_MAR)
+export(transpose_results)
 export(validate)
 export(validate_analyse_pars)
 import(R6)

NEWS.md

@@ -1,5 +1,10 @@
 # rbmi (development version)
 
+## Added
+
+* Exported internal helper functions: `extract_covariates`, `as_simple_formula`, `lsmeans`, `as_analysis`, `transpose_results`, `get_pool_components`, `rubin_rules`, and `parametric_ci`.
+
+
 ## Bug Fixes
 * Added en-GB spell-check and a corresponding test to the package
 * Fixed numerous spelling errors and standardised nomenclature for missing not

R/analyse.R

@@ -419,6 +419,7 @@ extract_imputed_df <- function(imputation, ld, delta = NULL, idmap = FALSE) {
 #' @param fun The analysis function that was used.
 #' @param fun_name The character name of the analysis function (used for printing)
 #' purposes.
+#' @export
 as_analysis <- function(
     results,
     method,

R/lsmeans.R

@@ -80,6 +80,7 @@
 #' lsmeans(mod, Species = "versicolor", Petal.Length = 1)
 #' }
 #' @importFrom stats model.matrix terms reformulate
+#' @export
 lsmeans <- function(
     model,
     ...,

R/pool.R

@@ -118,6 +118,7 @@ pool <- function(
 #'
 #' @param x Character name of the analysis method, must one of
 #' either `"rubin"`, `"jackknife"`, "`bootstrap"` or `"bmlmi"`.
+#' @export
 get_pool_components <- function(x) {
     switch(
         x,
@@ -383,6 +384,7 @@ rubin_df <- function(v_com, var_b, var_t, M) {
 #' Roderick J. A. Little and Donald B. Rubin. Statistical Analysis with Missing
 #' Data, Second Edition. John Wiley & Sons, Hoboken, New Jersey, 2002. \[Section 5.4\]
 #' @importFrom stats var
+ #' @export
 rubin_rules <- function(ests, ses, v_com) {
     M <- length(ests)
     est_point <- mean(ests)
@@ -568,6 +570,7 @@ pool_bootstrap_normal <- function(est, conf.level, alternative) {
 #'
 #' @param ... additional arguments passed on `qfun` and `pfun` i.e. `df = 102`.
 #'
+#' @export
 parametric_ci <- function(point, se, alpha, alternative, qfun, pfun, ...) {
     ci <- switch(
         alternative,
@@ -652,6 +655,7 @@ parametric_ci <- function(point, se, alpha, alternative, qfun, pfun, ...) {
 #'     )
 #' )
 #' ```
+ #' @export
 transpose_results <- function(results, components) {
     elements <- names(results[[1]])
     results_transpose <- list()

R/utilities.R

@@ -51,6 +51,7 @@ has_class <- function(x, cls) {
 #' @param covars character (vector). Name of covariates
 #' @return
 #' A formula
+#' @export
 as_simple_formula <- function(outcome, covars) {
     frm <- stats::as.formula(
         paste0(

tests/testthat/test-helpers.R

@@ -0,0 +1,32 @@
+library(testthat)
+
+test_that("utilities exports behave sensibly", {
+  expect_true(is.character(extract_covariates(c("v1", "v2:v3"))))
+  expect_setequal(extract_covariates(c("v1", "v2:v3")), c("v1", "v2", "v3"))
+  f <- as_simple_formula("y", c("a", "b"))
+  expect_s3_class(f, "formula")
+})
+
+test_that("pool helpers and CI functions", {
+  expect_equal(get_pool_components("rubin"), c("est", "df", "se"))
+  rr <- rubin_rules(ests = c(1, 2, 3), ses = c(1, 1, 1), v_com = 10)
+  expect_named(rr, c("est_point", "var_t", "df"))
+  pc <- parametric_ci(1, 1, 0.05, "two.sided", qnorm, pnorm)
+  expect_named(pc, c("est", "ci", "se", "pvalue"))
+  tr_in <- list(list(a = list(est = 1, se = 2)), list(a = list(est = 3, se = 4)))
+  tr_out <- transpose_results(tr_in, c("est", "se"))
+  expect_true(is.list(tr_out))
+  expect_named(tr_out, "a")
+})
+
+test_that("as_analysis constructs analysis object", {
+  method <- list(n_samples = 3, D = 1)
+  class(method) <- c("method", "bayes")
+  results <- list(
+  list(par1 = list(est = 1, df = 1, se = 2)),
+  list(par1 = list(est = 2, df = 1, se = 2)),
+  list(par1 = list(est = 3, df = 1, se = 2))
+  )
+  ana <- as_analysis(results, method = method, delta = NULL, fun = NULL, fun_name = "fn")
+  expect_s3_class(ana, "analysis")
+})