Add three functions to facilitate the use of nlme

1 files changed, 0 insertions, 84 deletions

diff --git a/man/memkin.Rd b/man/memkin.Rd
deleted file mode 100644
index 8ae6100a..00000000
--- a/man/memkin.Rd
+++ /dev/null
@@ -1,84 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/memkin.R
-\name{memkin}
-\alias{memkin}
-\title{Estimation of parameter distributions from mmkin row objects}
-\usage{
-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{
-An nlme object
-}
-\description{
-This function sets up and attempts to fit a mixed effects model to
-an mmkin row object which is essentially a list of mkinfit objects
-that have been obtained by fitting the same model to a list of
-datasets.
-}
-\examples{
-sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
-m_SFO <- mkinmod(parent = mkinsub("SFO"))
-d_SFO_1 <- mkinpredict(m_SFO,
-  c(k_parent_sink = 0.1),
-  c(parent = 98), sampling_times)
-d_SFO_1_long <- mkin_wide_to_long(d_SFO_1, time = "time")
-d_SFO_2 <- mkinpredict(m_SFO,
-  c(k_parent_sink = 0.05),
-  c(parent = 102), sampling_times)
-d_SFO_2_long <- mkin_wide_to_long(d_SFO_2, time = "time")
-d_SFO_3 <- mkinpredict(m_SFO,
-  c(k_parent_sink = 0.02),
-  c(parent = 103), sampling_times)
-d_SFO_3_long <- mkin_wide_to_long(d_SFO_3, time = "time")
-
-d1 <- add_err(d_SFO_1, function(value) 3, n = 1)
-d2 <- add_err(d_SFO_2, function(value) 2, n = 1)
-d3 <- add_err(d_SFO_3, function(value) 4, n = 1)
-ds <- c(d1 = d1, d2 = d2, d3 = d3)
-
-f <- mmkin("SFO", ds)
-x <- memkin(f)
-summary(x)
-
-ds_2 <- lapply(experimental_data_for_UBA_2019[6:10],
- function(x) x$data[c("name", "time", "value")])
-m_sfo_sfo <- mkinmod(parent = mkinsub("SFO", "A1"),
-  A1 = mkinsub("SFO"), use_of_ff = "min")
-m_sfo_sfo_ff <- mkinmod(parent = mkinsub("SFO", "A1"),
-  A1 = mkinsub("SFO"), use_of_ff = "max")
-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,
- "SFORB-SFO" = m_sforb_sfo),
-  ds_2)
-
-f_nlme_sfo_sfo <- memkin(f_2[1, ])
-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
-  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)
-}