From 45c511f61d3e617c97e847bcb995f8976bd91c97 Mon Sep 17 00:00:00 2001
From: Dr Nathan Green <n8thangreen@yahoo.co.uk>
Date: Thu, 29 Aug 2024 16:09:55 +0100
Subject: [PATCH] new build

---
 NAMESPACE        |  2 ++
 R/mim.R          |  6 +++---
 man/IPD_stats.Rd |  7 +++++++
 man/mim.Rd       | 16 ++++++++++++++++
 man/outstandR.Rd |  2 +-
 man/strategy.Rd  |  9 +++++++++
 6 files changed, 38 insertions(+), 4 deletions(-)
 create mode 100644 man/mim.Rd

diff --git a/NAMESPACE b/NAMESPACE
index d3a1ac4..d87c877 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -4,6 +4,7 @@ S3method(IPD_stats,default)
 S3method(IPD_stats,gcomp_ml)
 S3method(IPD_stats,gcomp_stan)
 S3method(IPD_stats,maic)
+S3method(IPD_stats,mim)
 S3method(IPD_stats,stc)
 export(ALD_stats)
 export(IPD_stats)
@@ -14,6 +15,7 @@ export(outstandR)
 export(strategy_gcomp_ml)
 export(strategy_gcomp_stan)
 export(strategy_maic)
+export(strategy_mim)
 export(strategy_stc)
 export(trial_treatment_effect)
 export(trial_variance)
diff --git a/R/mim.R b/R/mim.R
index f4d3fe4..0a48d3e 100644
--- a/R/mim.R
+++ b/R/mim.R
@@ -6,10 +6,10 @@
 #'
 mim <- function(ipd.index,
                 ipd.target,
-                M = 1,
+                M = 1000,
                 n.chains = 2,
-                warmup = 10,
-                iters = 1000) {
+                warmup = 1000,
+                iters = 4000) {
   
   ## SYNTHESIS STAGE ##
   
diff --git a/man/IPD_stats.Rd b/man/IPD_stats.Rd
index 0cb8601..bd1bff7 100644
--- a/man/IPD_stats.Rd
+++ b/man/IPD_stats.Rd
@@ -7,6 +7,7 @@
 \alias{IPD_stats.stc}
 \alias{IPD_stats.gcomp_ml}
 \alias{IPD_stats.gcomp_stan}
+\alias{IPD_stats.mim}
 \title{Calculate individual-level patient data statistics}
 \usage{
 IPD_stats(strategy, ipd, ald, ...)
@@ -20,6 +21,8 @@ IPD_stats(strategy, ipd, ald, ...)
 \method{IPD_stats}{gcomp_ml}(strategy, ipd, ald)
 
 \method{IPD_stats}{gcomp_stan}(strategy, ipd, ald)
+
+\method{IPD_stats}{mim}(strategy, ipd, ald)
 }
 \arguments{
 \item{strategy}{A list corresponding to different approaches}
@@ -61,3 +64,7 @@ Using Stan, compute marginal log-odds ratio for \emph{A} vs \emph{C} for each MC
 by transforming from probability to linear predictor scale.
 }
 
+\section{Multiple imputation marginalisation}{
+
+}
+
diff --git a/man/mim.Rd b/man/mim.Rd
new file mode 100644
index 0000000..4e843b2
--- /dev/null
+++ b/man/mim.Rd
@@ -0,0 +1,16 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/mim.R
+\name{mim}
+\alias{mim}
+\title{Multiple imputation marginalization (MIM)}
+\usage{
+mim(ipd.index, ipd.target, M = 1000, n.chains = 2, warmup = 1000, iters = 4000)
+}
+\arguments{
+\item{ipd.index, ipd.target}{Index RCT and target covariate datasets}
+
+\item{M}{Number of syntheses used in analysis stage (high for low Monte Carlo error)}
+}
+\description{
+Multiple imputation marginalization (MIM)
+}
diff --git a/man/outstandR.Rd b/man/outstandR.Rd
index 89b3ef5..7ea99f7 100644
--- a/man/outstandR.Rd
+++ b/man/outstandR.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/ModStanR.R
+% Please edit documentation in R/outstandR.R
 \name{outstandR}
 \alias{outstandR}
 \title{Calculate the difference between treatments using all evidence}
diff --git a/man/strategy.Rd b/man/strategy.Rd
index 8bc2e89..1e5c0ed 100644
--- a/man/strategy.Rd
+++ b/man/strategy.Rd
@@ -5,6 +5,7 @@
 \alias{strategy_stc}
 \alias{strategy_gcomp_ml}
 \alias{strategy_gcomp_stan}
+\alias{strategy_mim}
 \alias{strategy}
 \alias{new_strategy}
 \title{New strategy objects}
@@ -17,6 +18,8 @@ strategy_gcomp_ml(formula = NULL, R = 1000)
 
 strategy_gcomp_stan(formula = NULL)
 
+strategy_mim(formula = NULL)
+
 new_strategy(strategy, ...)
 }
 \arguments{
@@ -38,6 +41,8 @@ new_strategy(strategy, ...)
 \code{gcomp_ml} class object
 
 \code{gcomp_stan} class object
+
+\code{mim} class object
 }
 \description{
 Create a type of strategy class for each modelling approach.
@@ -140,3 +145,7 @@ In practice, the integrals above can be approximated numerically, using full Bay
 estimation via Markov chain Monte Carlo (MCMC) sampling.
 }
 
+\section{Multiple imputation marginalization (MIM)}{
+
+}
+