From 7777ff3b019e54364947ff393e2dab782d7cfe3c Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 10 Apr 2020 08:26:44 +0200 Subject: Improve nlme function docs --- docs/reference/endpoints.html | 2 +- docs/reference/index.html | 4 +- docs/reference/mkinds.html | 2 +- docs/reference/mmkin.html | 14 +++-- docs/reference/nlme.html | 114 ++++++++++++++++++++++++++++++++++----- docs/reference/plot.mmkin.html | 2 +- docs/reference/print.mkinds.html | 2 +- 7 files changed, 114 insertions(+), 26 deletions(-) (limited to 'docs/reference') diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index f201294d..68af5fcf 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -75,7 +75,7 @@ advantage that the SFORB model can also be used for metabolites." /> mkin - 0.9.49.9 + 0.9.49.10 diff --git a/docs/reference/index.html b/docs/reference/index.html index a3547e29..31f7678c 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -67,7 +67,7 @@ mkin - 0.9.49.9 + 0.9.49.10 @@ -273,7 +273,7 @@ of an mmkin object

-

mean_degparms() nlme_data() nlme_function()

+

nlme_function() mean_degparms() nlme_data()

Estimation of parameter distributions from mmkin row objects

diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html index ef6fb35c..946d40a6 100644 --- a/docs/reference/mkinds.html +++ b/docs/reference/mkinds.html @@ -72,7 +72,7 @@ provided by this package come as mkinds objects nevertheless." /> mkin - 0.9.49.9 + 0.9.49.10 diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index 8e1ea54f..c1f62be7 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -72,7 +72,7 @@ datasets specified in its first two arguments." /> mkin - 0.9.49.9 + 0.9.49.10 @@ -183,8 +183,9 @@ for parallel execution.

Value

-

A matrix of mkinfit objects that can be indexed using - the model and dataset names as row and column indices.

+

A two-dimensional array of mkinfit + objects that can be indexed using the model names for the first index (row index) + and the dataset names for the second index (column index).

See also

[.mmkin for subsetting, plot.mmkin for @@ -207,15 +208,12 @@ for parallel execution.

time_1 <- system.time(fits.4 <- mmkin(models, datasets, cores = 1, quiet = TRUE)) time_default
#> User System verstrichen -#> 18.739 0.379 6.198
time_1
#> User System verstrichen -#> 19.910 0.000 19.925
+#> 16.471 0.352 5.654
time_1
#> User System verstrichen +#> 19.578 0.000 19.590
endpoints(fits.0[["SFO_lin", 2]])
#> $ff #> parent_M1 parent_sink M1_M2 M1_sink #> 0.7340480 0.2659520 0.7505686 0.2494314 #> -#> $SFORB -#> logical(0) -#> #> $distimes #> DT50 DT90 #> parent 0.8777689 2.915885 diff --git a/docs/reference/nlme.html b/docs/reference/nlme.html index b939d1c3..696916a0 100644 --- a/docs/reference/nlme.html +++ b/docs/reference/nlme.html @@ -6,7 +6,7 @@ -Estimation of parameter distributions from mmkin row objects — mean_degparms • mkin +Estimation of parameter distributions from mmkin row objects — nlme_function • mkin @@ -35,8 +35,8 @@ - - + @@ -72,7 +72,7 @@ datasets." /> mkin - 0.9.49.9 + 0.9.49.10
@@ -136,17 +136,17 @@ datasets." />
-

This function sets up and attempts to fit a mixed effects model to +

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.

- 
mean_degparms(object)
+    
nlme_function(object)
 
-nlme_data(object)
+mean_degparms(object)
 
-nlme_function(object)

+nlme_data(object)

Arguments

@@ -159,12 +159,102 @@ datasets.

Value

-

A named vector containing mean values of the fitted degradation model parameters

-

A groupedData data object

-

A function that can be used with nlme

+

A function that can be used with link{nlme}

+

A named vector containing mean values of the fitted degradation model parameters

+

A groupedData object

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, cores = 1, quiet = TRUE)
+mean_dp <- mean_degparms(f)
+grouped_data <- nlme_data(f)
+nlme_f <- nlme_function(f)
+
+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)
#> Error in nlme_f(name, time, parent_0, log_k_parent_sink): konnte Funktion "nlme_f" nicht finden
summary(m_nlme)
#> Error in summary(m_nlme): Objekt 'm_nlme' nicht gefunden

+# \dontrun{
+  # Test on some real data
+  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")
#> Successfully compiled differential equation model from auto-generated C code.
  m_sfo_sfo_ff <- mkinmod(parent = mkinsub("SFO", "A1"),
+    A1 = mkinsub("SFO"), use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.
  m_fomc_sfo <- mkinmod(parent = mkinsub("FOMC", "A1"),
+    A1 = mkinsub("SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
  m_dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "A1"),
+    A1 = mkinsub("SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
  m_sforb_sfo <- mkinmod(parent = mkinsub("SFORB", "A1"),
+    A1 = mkinsub("SFO"))
#> Successfully compiled differential equation model from auto-generated C code.

+  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)
+
+  grouped_data_2 <- nlme_data(f_2["SFO-SFO", ])
+
+  mean_dp_sfo_sfo <- mean_degparms(f_2["SFO-SFO", ])
+  mean_dp_sfo_sfo_ff <- mean_degparms(f_2["SFO-SFO-ff", ])
+  mean_dp_fomc_sfo <- mean_degparms(f_2["FOMC-SFO", ])
+  mean_dp_dfop_sfo <- mean_degparms(f_2["DFOP-SFO", ])
+  mean_dp_sforb_sfo <- mean_degparms(f_2["SFORB-SFO", ])
+
+  nlme_f_sfo_sfo <- nlme_function(f_2["SFO-SFO", ])
+  nlme_f_sfo_sfo_ff <- nlme_function(f_2["SFO-SFO-ff", ])
+  nlme_f_fomc_sfo <- nlme_function(f_2["FOMC-SFO", ])
+
+  # Allowing for correlations between random effects leads to non-convergence
+  f_nlme_sfo_sfo <- nlme(value ~ nlme_f_sfo_sfo(name, time,
+       parent_0, log_k_parent_sink, log_k_parent_A1, log_k_A1_sink),
+     data = grouped_data_2,
+     fixed = parent_0 + log_k_parent_sink + log_k_parent_A1 + log_k_A1_sink ~ 1,
+     random = pdDiag(parent_0 + log_k_parent_sink + log_k_parent_A1 + log_k_A1_sink ~ 1),
+     start = mean_dp_sfo_sfo)
#> Error in nlme_f_sfo_sfo(name, time, parent_0, log_k_parent_sink, log_k_parent_A1,     log_k_A1_sink): konnte Funktion "nlme_f_sfo_sfo" nicht finden

+  # The same model fitted with transformed formation fractions does not converge
+  f_nlme_sfo_sfo_ff <- nlme(value ~ nlme_f_sfo_sfo_ff(name, time,
+       parent_0, log_k_parent, log_k_A1, f_parent_ilr_1),
+     data = grouped_data_2,
+     fixed = parent_0 + log_k_parent + log_k_A1 + f_parent_ilr_1 ~ 1,
+     random = pdDiag(parent_0 + log_k_parent + log_k_A1 + f_parent_ilr_1 ~ 1),
+     start = mean_dp_sfo_sfo_ff)
#> Error in nlme_f_sfo_sfo_ff(name, time, parent_0, log_k_parent, log_k_A1,     f_parent_ilr_1): konnte Funktion "nlme_f_sfo_sfo_ff" nicht finden

+  # It does converge with this version of reduced random effects
+  f_nlme_sfo_sfo_ff <- nlme(value ~ nlme_f_sfo_sfo_ff(name, time,
+       parent_0, log_k_parent, log_k_A1, f_parent_ilr_1),
+     data = grouped_data_2,
+     fixed = parent_0 + log_k_parent + log_k_A1 + f_parent_ilr_1 ~ 1,
+     random = pdDiag(parent_0 + log_k_parent ~ 1),
+     start = mean_dp_sfo_sfo_ff)
#> Error in nlme_f_sfo_sfo_ff(name, time, parent_0, log_k_parent, log_k_A1,     f_parent_ilr_1): konnte Funktion "nlme_f_sfo_sfo_ff" nicht finden

+  f_nlme_fomc_sfo <- nlme(value ~ nlme_f_fomc_sfo(name, time,
+       parent_0, log_alpha, log_beta, log_k_A1, f_parent_ilr_1),
+     data = grouped_data_2,
+     fixed = parent_0 + log_alpha + log_beta + log_k_A1 + f_parent_ilr_1 ~ 1,
+     random = pdDiag(parent_0 + log_alpha + log_beta + log_k_A1 + f_parent_ilr_1 ~ 1),
+     start = mean_dp_fomc_sfo)
#> Error in nlme_f_fomc_sfo(name, time, parent_0, log_alpha, log_beta, log_k_A1,     f_parent_ilr_1): konnte Funktion "nlme_f_fomc_sfo" nicht finden

+  # DFOP-SFO and SFORB-SFO did not converge with full random effects
+
+  anova(f_nlme_fomc_sfo, f_nlme_sfo_sfo)
#> Error in anova(f_nlme_fomc_sfo, f_nlme_sfo_sfo): Objekt 'f_nlme_fomc_sfo' nicht gefunden
# }
+

 
diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html
index de1a2410..824d961b 100644
--- a/docs/reference/print.mkinds.html
+++ b/docs/reference/print.mkinds.html
@@ -69,7 +69,7 @@
       
         mkin
-        0.9.49.9
+        0.9.49.10
       
 
-- 
cgit v1.2.1