From 8b8703489e202970be6f18c9dbda32107a770f8b Mon Sep 17 00:00:00 2001
From: Dr Nathan Green <n8thangreen@yahoo.co.uk>
Date: Mon, 2 Dec 2024 17:16:32 +0000
Subject: [PATCH] add family the strategy object to be used later with
 different types of models

---
 R/strategy_.R   | 28 +++++++++++++++++++++++++---
 man/gen_data.Rd |  3 ++-
 man/strategy.Rd | 18 +++++++++++-------
 3 files changed, 38 insertions(+), 11 deletions(-)

diff --git a/R/strategy_.R b/R/strategy_.R
index 4707584..9f3fa21 100644
--- a/R/strategy_.R
+++ b/R/strategy_.R
@@ -28,8 +28,11 @@
 #' @export
 #'
 strategy_maic <- function(formula = NULL,
+                          family = gaussian(link = "identity"),
                           R = 1000) {
   check_formula(formula)
+  check_family(family)
+  
   default_args <- formals()
   args <- c(formula = formula, as.list(match.call())[-c(1,2)])
   args <- modifyList(default_args, args)
@@ -57,8 +60,10 @@ strategy_maic <- function(formula = NULL,
 #' @importFrom utils modifyList
 #' @export
 # 
-strategy_stc <- function(formula = NULL) {
+strategy_stc <- function(formula = NULL,
+                         family = gaussian(link = "identity")) {
   check_formula(formula)
+  check_family(family)
   
   default_args <- formals()
   args <- c(formula = formula, as.list(match.call())[-c(1,2)])
@@ -103,8 +108,10 @@ strategy_stc <- function(formula = NULL) {
 #' @export
 #'
 strategy_gcomp_ml <- function(formula = NULL,
+                              family = gaussian(link = "identity"),
                               R = 1000) {
   check_formula(formula)
+  check_family(family)
   
   default_args <- formals()
   args <- c(formula = formula, as.list(match.call())[-c(1,2)])
@@ -144,8 +151,10 @@ strategy_gcomp_ml <- function(formula = NULL,
 #' @importFrom utils modifyList
 #' @export
 #'
-strategy_gcomp_stan <- function(formula = NULL) {
+strategy_gcomp_stan <- function(formula = NULL,
+                                family = gaussian(link = "identity")) {
   check_formula(formula)
+  check_family(family)
   
   default_args <- formals()
   args <- c(formula = formula, as.list(match.call())[-c(1,2)])
@@ -160,8 +169,10 @@ strategy_gcomp_stan <- function(formula = NULL) {
 #' @importFrom utils modifyList
 #' @export
 # 
-strategy_mim <- function(formula = NULL) {
+strategy_mim <- function(formula = NULL,
+                         family = gaussian(link = "identity")) {
   check_formula(formula)
+  check_family(family)
   
   default_args <- formals()
   args <- c(formula = formula, as.list(match.call())[-c(1,2)])
@@ -177,6 +188,7 @@ strategy_mim <- function(formula = NULL) {
 #'
 #' @param strategy Class name from `strategy_maic`, `strategy_stc`, `strategy_gcomp_ml`, `strategy_gcomp_stan`
 #' @param formula Linear regression `formula` object
+#' @param family `family` object from the `stats` library
 #' @param ... Additional arguments
 #'
 #' @export
@@ -184,3 +196,13 @@ strategy_mim <- function(formula = NULL) {
 new_strategy <- function(strategy, ...) {
   structure(list(...), class = c(strategy, "strategy", "list"))
 }
+
+#
+is_family <- function(obj) inherits(obj, "family")
+
+#
+check_family <- function(obj) {
+  if (!is_family(obj)) {
+    stop("family must be a family object")
+  }
+}
diff --git a/man/gen_data.Rd b/man/gen_data.Rd
index 78c7f9a..2e862c8 100644
--- a/man/gen_data.Rd
+++ b/man/gen_data.Rd
@@ -35,6 +35,7 @@ Generate simulated datasets of IPD covariates and outcome for a trial
 }
 \examples{
 
+\dontrun{
 x <- gen_data(
  N = 100,
  b_trt = log(0.17),
@@ -48,6 +49,6 @@ x <- gen_data(
  allocation = 2/3) 
 
 head(x)
-
+}
 }
 \keyword{internal}
diff --git a/man/strategy.Rd b/man/strategy.Rd
index 1e5c0ed..524a9e8 100644
--- a/man/strategy.Rd
+++ b/man/strategy.Rd
@@ -10,28 +10,32 @@
 \alias{new_strategy}
 \title{New strategy objects}
 \usage{
-strategy_maic(formula = NULL, R = 1000)
+strategy_maic(formula = NULL, family = gaussian(link = "identity"), R = 1000)
 
-strategy_stc(formula = NULL)
+strategy_stc(formula = NULL, family = gaussian(link = "identity"))
 
-strategy_gcomp_ml(formula = NULL, R = 1000)
+strategy_gcomp_ml(
+  formula = NULL,
+  family = gaussian(link = "identity"),
+  R = 1000
+)
 
-strategy_gcomp_stan(formula = NULL)
+strategy_gcomp_stan(formula = NULL, family = gaussian(link = "identity"))
 
-strategy_mim(formula = NULL)
+strategy_mim(formula = NULL, family = gaussian(link = "identity"))
 
 new_strategy(strategy, ...)
 }
 \arguments{
 \item{formula}{Linear regression \code{formula} object}
 
+\item{family}{\code{family} object from the \code{stats} library}
+
 \item{R}{The number of resamples used for the non-parametric bootstrap}
 
 \item{strategy}{Class name from \code{strategy_maic}, \code{strategy_stc}, \code{strategy_gcomp_ml}, \code{strategy_gcomp_stan}}
 
 \item{...}{Additional arguments}
-
-\item{ald}{Aggregate-level data}
 }
 \value{
 \code{maic} class object