nlme_function {mkin} | R Documentation |
These functions facilitate setting up a nonlinear mixed effects model for
an mmkin row object. An mmkin row object is essentially a list of mkinfit
objects that have been obtained by fitting the same model to a list of
datasets. They are used internally by the nlme.mmkin()
method.
nlme_function(object) nlme_data(object)
object |
An mmkin row object containing several fits of the same model to different datasets |
A function that can be used with nlme
A groupedData
object
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 = 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 = 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 = 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, cores = 1, quiet = TRUE) mean_dp <- mean_degparms(f) grouped_data <- nlme_data(f) nlme_f <- nlme_function(f) # These assignments are necessary for these objects to be # visible to nlme and augPred when evaluation is done by # pkgdown to generate the html docs. assign("nlme_f", nlme_f, globalenv()) assign("grouped_data", grouped_data, globalenv()) library(nlme) m_nlme <- nlme(value ~ nlme_f(name, time, parent_0, log_k_parent_sink), data = grouped_data, fixed = parent_0 + log_k_parent_sink ~ 1, random = pdDiag(parent_0 + log_k_parent_sink ~ 1), start = mean_dp) summary(m_nlme) plot(augPred(m_nlme, level = 0:1), layout = c(3, 1)) # augPred does not work on fits with more than one state # variable # # The procedure is greatly simplified by the nlme.mmkin function f_nlme <- nlme(f) plot(f_nlme)