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authorJohannes Ranke <jranke@uni-bremen.de>2020-03-30 14:16:29 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2020-03-30 14:16:29 +0200
commitc3c39413a040a7d6eb36d7ebade551fa830499f8 (patch)
treeb7b4edbe984cc5ccda0163d75c1ebcf0ebfdfbf3 /man/memkin.Rd
parent405cde11f9f26fcab0742e84c110cf3dcb2a4c1f (diff)
Fixed example code
Diffstat (limited to 'man/memkin.Rd')
-rw-r--r--man/memkin.Rd28
1 files changed, 20 insertions, 8 deletions
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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