From c3c39413a040a7d6eb36d7ebade551fa830499f8 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Mon, 30 Mar 2020 14:16:29 +0200
Subject: Fixed example code

---
 R/memkin.R    |  5 ++---
 man/memkin.Rd | 28 ++++++++++++++++++++--------
 2 files changed, 22 insertions(+), 11 deletions(-)

diff --git a/R/memkin.R b/R/memkin.R
index 5cc00345..8a71484e 100644
--- a/R/memkin.R
+++ b/R/memkin.R
@@ -66,11 +66,10 @@
 #' }
 #' f_nlme_fomc_sfo <- memkin(f_2[3, ])
 #' \dontrun{
-#'   f_nlme_dfop_sfo <- memkin(f_2[4, ])  # apparently underdetermined}
+#'   f_nlme_dfop_sfo <- memkin(f_2[4, ])  # apparently underdetermined
 #'   f_nlme_sforb_sfo <- memkin(f_2[5, ]) # also does not converge
 #' }
-#' anova(f_nlme_sfo_sfo, f_nlme_fomc_sfo)
-#' # The FOMC variant has a lower AIC and has significantly higher likelihood
+#' anova(f_nlme_fomc_sfo, f_nlme_sfo_sfo, f_nlme_sfo_sfo_4)
 #' @export
 memkin <- function(object, random_spec = "auto", ...) {
   if (nrow(object) > 1) stop("Only row objects allowed")
diff --git a/man/memkin.Rd b/man/memkin.Rd
index cda9b468..8ae6100a 100644
--- a/man/memkin.Rd
+++ b/man/memkin.Rd
@@ -4,15 +4,18 @@
 \alias{memkin}
 \title{Estimation of parameter distributions from mmkin row objects}
 \usage{
-memkin(object, ...)
+memkin(object, random_spec = "auto", ...)
 }
 \arguments{
 \item{object}{An mmkin row object containing several fits of the same model to different datasets}
 
+\item{random_spec}{Either "auto" or a specification of random effects for \code{\link{nlme}}
+given as a character vector}
+
 \item{...}{Additional arguments passed to \code{\link{nlme}}}
 }
 \value{
-A fitted object of class 'memkin'
+An nlme object
 }
 \description{
 This function sets up and attempts to fit a mixed effects model to
@@ -55,18 +58,27 @@ m_fomc_sfo <- mkinmod(parent = mkinsub("FOMC", "A1"),
   A1 = mkinsub("SFO"))
 m_dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "A1"),
   A1 = mkinsub("SFO"))
+m_sforb_sfo <- mkinmod(parent = mkinsub("SFORB", "A1"),
+  A1 = mkinsub("SFO"))
 
 f_2 <- mmkin(list("SFO-SFO" = m_sfo_sfo,
  "SFO-SFO-ff" = m_sfo_sfo_ff,
  "FOMC-SFO" = m_fomc_sfo,
- "DFOP-SFO" = m_dfop_sfo),
+ "DFOP-SFO" = m_dfop_sfo,
+ "SFORB-SFO" = m_sforb_sfo),
   ds_2)
 
 f_nlme_sfo_sfo <- memkin(f_2[1, ])
-\dontrun{f_nlme_sfo_sfo_ff <- memkin(f_2[2, ])} # does not converge with maxIter = 50
+f_nlme_sfo_sfo_2 <- memkin(f_2[1, ], "pdDiag(parent_0 + log_k_parent_sink + log_k_parent_A1 + log_k_A1_sink ~ 1)") # explicit
+f_nlme_sfo_sfo_3 <- memkin(f_2[1, ], "pdDiag(parent_0 + log_k_parent_sink + log_k_parent_A1 ~ 1)") # reduced
+f_nlme_sfo_sfo_4 <- memkin(f_2[1, ], "pdDiag(parent_0 + log_k_parent_sink ~ 1)") # further reduced
+\dontrun{
+  f_nlme_sfo_sfo_ff <- memkin(f_2[2, ]) # does not converge with maxIter = 50
+}
 f_nlme_fomc_sfo <- memkin(f_2[3, ])
-\dontrun{f_nlme_dfop_sfo <- memkin(f_2[4, ]) # apparently underdetermined}
-anova(f_nlme_sfo_sfo, f_nlme_fomc_sfo)
-# The FOMC variant has a lower AIC and has significantly higher likelihood
-update(f_nlme_fomc_sfo)
+\dontrun{
+  f_nlme_dfop_sfo <- memkin(f_2[4, ])  # apparently underdetermined
+  f_nlme_sforb_sfo <- memkin(f_2[5, ]) # also does not converge
+}
+anova(f_nlme_fomc_sfo, f_nlme_sfo_sfo, f_nlme_sfo_sfo_4)
 }
-- 
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