From 07346be10c96c25e3da77aa501eb1c9f08111afa Mon Sep 17 00:00:00 2001
From: Matthew Fidler <matthew.fidler@gmail.com>
Date: Fri, 18 Oct 2024 12:37:29 -0500
Subject: [PATCH] Add babelBpopIdx

---
 NAMESPACE           |  1 +
 man/babelBpopIdx.Rd | 71 +++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 72 insertions(+)
 create mode 100644 man/babelBpopIdx.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 562719b8..a751a813 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -144,6 +144,7 @@ export(as.nlmixr)
 export(as.nlmixr2)
 export(as.nonmem2rx)
 export(babel.poped.database)
+export(babelBpopIdx)
 export(bblDatToMonolix)
 export(bblDatToMrgsolve)
 export(bblDatToNonmem)
diff --git a/man/babelBpopIdx.Rd b/man/babelBpopIdx.Rd
new file mode 100644
index 00000000..1210a249
--- /dev/null
+++ b/man/babelBpopIdx.Rd
@@ -0,0 +1,71 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/poped.R
+\name{babelBpopIdx}
+\alias{babelBpopIdx}
+\title{Get the bpop_idx by variable name for a poped database created by \code{babelmixr2}}
+\usage{
+babelBpopIdx(popedInput, var)
+}
+\arguments{
+\item{popedInput}{The babaelmixr2 created database}
+
+\item{var}{variable to query}
+}
+\value{
+index of the variable
+}
+\description{
+This may work for other poped databases if the population parameters are named.
+}
+\examples{
+
+if (requireNamespace("PopED", quietly=TRUE)) {
+
+f <- function() {
+  ini({
+    tV <- 72.8
+    tKa <- 0.25
+    tCl <- 3.75
+    tF <- fix(0.9)
+    pedCL <- 0.8
+
+    eta.v ~ 0.09
+    eta.ka ~ 0.09
+    eta.cl ~0.25^2
+
+    prop.sd <- fix(sqrt(0.04))
+    add.sd <- fix(sqrt(5e-6))
+
+  })
+  model({
+    V<-tV*exp(eta.v)
+    KA<-tKa*exp(eta.ka) * (pedCL**isPediatric) # add covariate for pediatrics
+    CL<-tCl*exp(eta.cl)
+    Favail <- tF
+
+    N <-  floor(t/TAU)+1
+    y <- (DOSE*Favail/V)*(KA/(KA - CL/V)) *
+      (exp(-CL/V * (t - (N - 1) * TAU)) *
+         (1 - exp(-N * CL/V * TAU))/(1 - exp(-CL/V * TAU)) -
+         exp(-KA * (t - (N - 1) * TAU)) * (1 - exp(-N * KA * TAU))/(1 - exp(-KA * TAU)))
+
+    y ~ prop(prop.sd) + add(add.sd)
+  })
+}
+
+e <- et(c( 1,8,10,240,245))
+
+babel.db <- nlmixr2(f, e, "poped",
+                    popedControl(m = 2,
+                                 groupsize=20,
+                                 bUseGrouped_xt=TRUE,
+                                 a=list(c(DOSE=20,TAU=24,isPediatric = 0),
+                                        c(DOSE=40, TAU=24,isPediatric = 0))))
+
+babelBpopIdx(babel.db, "pedCL")
+
+}
+}
+\author{
+Matthew L. Fidler
+}