From 4f62f39b8979cb3a5c52d65d425e530dc0770665 Mon Sep 17 00:00:00 2001
From: Johannes Ranke
Date: Sun, 16 Feb 2025 17:27:18 +0100
Subject: Fix solution type "deSolve" for a special case
The special case occurs if not observed data for time zero
are available. Fixes #16. Write NEWS and update docs.
A lot of html was regenerated, because I had checked out
the main branch in between, which made pkgdown believe that
I have changed the help files.
---
docs/dev/reference/confint.mkinfit.html | 4 ++--
docs/dev/reference/create_deg_func.html | 8 ++++----
docs/dev/reference/dimethenamid_2018.html | 6 +++---
docs/dev/reference/mkinfit.html | 16 ++++++++--------
docs/dev/reference/mkinmod.html | 4 ++--
docs/dev/reference/mkinpredict.html | 4 ++--
docs/dev/reference/mmkin.html | 4 ++--
docs/dev/reference/saem.html | 8 ++++----
docs/dev/reference/summary.mkinfit.html | 6 +++---
docs/dev/reference/summary.mmkin.html | 2 +-
docs/dev/reference/summary.nlme.mmkin.html | 6 +++---
docs/dev/reference/summary.saem.mmkin.html | 6 +++---
12 files changed, 37 insertions(+), 37 deletions(-)
(limited to 'docs/dev/reference')
diff --git a/docs/dev/reference/confint.mkinfit.html b/docs/dev/reference/confint.mkinfit.html
index a0051a85..aca693cc 100644
--- a/docs/dev/reference/confint.mkinfit.html
+++ b/docs/dev/reference/confint.mkinfit.html
@@ -217,7 +217,7 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37,
f_d_1 <- mkinfit(SFO_SFO, subset(FOCUS_2006_D, value != 0), quiet = TRUE)
system.time(ci_profile <- confint(f_d_1, method = "profile", cores = 1, quiet = TRUE))
#> user system elapsed
-#> 1.182 0.004 1.186
+#> 1.247 0.000 1.246
# Using more cores does not save much time here, as parent_0 takes up most of the time
# If we additionally exclude parent_0 (the confidence of which is often of
# minor interest), we get a nice performance improvement if we use at least 4 cores
@@ -225,7 +225,7 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37,
c("k_parent_sink", "k_parent_m1", "k_m1_sink", "sigma"), cores = n_cores))
#> Profiling the likelihood
#> user system elapsed
-#> 0.429 0.171 0.324
+#> 0.444 0.131 0.303
ci_profile
#> 2.5% 97.5%
#> parent_0 96.456003640 1.027703e+02
diff --git a/docs/dev/reference/create_deg_func.html b/docs/dev/reference/create_deg_func.html
index 4c66c02b..75d21481 100644
--- a/docs/dev/reference/create_deg_func.html
+++ b/docs/dev/reference/create_deg_func.html
@@ -104,8 +104,8 @@
replications = 2)
#> Loading required package: rbenchmark
#> test replications elapsed relative user.self sys.self user.child
-#> 1 analytical 2 0.249 1.000 0.249 0 0
-#> 2 deSolve 2 0.307 1.233 0.306 0 0
+#> 1 analytical 2 0.243 1.000 0.244 0 0
+#> 2 deSolve 2 0.302 1.243 0.301 0 0
#> sys.child
#> 1 0
#> 2 0
@@ -118,8 +118,8 @@
deSolve = mkinfit(DFOP_SFO, FOCUS_D, solution_type = "deSolve", quiet = TRUE),
replications = 2)
#> test replications elapsed relative user.self sys.self user.child
-#> 1 analytical 2 0.391 1.000 0.391 0 0
-#> 2 deSolve 2 0.543 1.389 0.542 0 0
+#> 1 analytical 2 0.393 1.000 0.392 0 0
+#> 2 deSolve 2 0.534 1.359 0.535 0 0
#> sys.child
#> 1 0
#> 2 0
diff --git a/docs/dev/reference/dimethenamid_2018.html b/docs/dev/reference/dimethenamid_2018.html
index 4bd35bc6..209405a9 100644
--- a/docs/dev/reference/dimethenamid_2018.html
+++ b/docs/dev/reference/dimethenamid_2018.html
@@ -185,8 +185,8 @@ specific pieces of information in the comments.
#> saemix version used for fitting: 3.3
#> mkin version used for pre-fitting: 1.2.10
#> R version used for fitting: 4.4.2
-#> Date of fit: Fri Feb 14 07:29:22 2025
-#> Date of summary: Fri Feb 14 07:29:22 2025
+#> Date of fit: Sun Feb 16 16:58:17 2025
+#> Date of summary: Sun Feb 16 16:58:17 2025
#>
#> Equations:
#> d_DMTA/dt = - k_DMTA * DMTA
@@ -199,7 +199,7 @@ specific pieces of information in the comments.
#>
#> Model predictions using solution type deSolve
#>
-#> Fitted in 295.57 s
+#> Fitted in 294.206 s
#> Using 300, 100 iterations and 9 chains
#>
#> Variance model: Two-component variance function
diff --git a/docs/dev/reference/mkinfit.html b/docs/dev/reference/mkinfit.html
index 1c84b9b2..aa9c3d8f 100644
--- a/docs/dev/reference/mkinfit.html
+++ b/docs/dev/reference/mkinfit.html
@@ -368,8 +368,8 @@ Degradation Data. Environments 6(12) 124
summary(fit)
#> mkin version used for fitting: 1.2.10
#> R version used for fitting: 4.4.2
-#> Date of fit: Fri Feb 14 07:30:02 2025
-#> Date of summary: Fri Feb 14 07:30:02 2025
+#> Date of fit: Sun Feb 16 16:58:54 2025
+#> Date of summary: Sun Feb 16 16:58:54 2025
#>
#> Equations:
#> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
@@ -517,9 +517,9 @@ Degradation Data. Environments 6(12) 124
solution_type = "analytical"))
}
#> test relative elapsed
-#> 3 analytical 1.000 0.242
-#> 2 eigen 1.913 0.463
-#> 1 deSolve_compiled 1.917 0.464
+#> 3 analytical 1.000 0.240
+#> 2 eigen 1.908 0.458
+#> 1 deSolve_compiled 1.933 0.464
# }
# Use stepwise fitting, using optimised parameters from parent only fit, FOMC-SFO
@@ -547,8 +547,8 @@ Degradation Data. Environments 6(12) 124
#> Warning: diag(V) had non-positive or NA entries; the non-finite result may be dubious
#> mkin version used for fitting: 1.2.10
#> R version used for fitting: 4.4.2
-#> Date of fit: Fri Feb 14 07:30:07 2025
-#> Date of summary: Fri Feb 14 07:30:07 2025
+#> Date of fit: Sun Feb 16 16:58:58 2025
+#> Date of summary: Sun Feb 16 16:58:58 2025
#>
#> Equations:
#> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
@@ -557,7 +557,7 @@ Degradation Data. Environments 6(12) 124
#>
#> Model predictions using solution type deSolve
#>
-#> Fitted using 4062 model solutions performed in 0.77 s
+#> Fitted using 4062 model solutions performed in 0.776 s
#>
#> Error model: Two-component variance function
#>
diff --git a/docs/dev/reference/mkinmod.html b/docs/dev/reference/mkinmod.html
index d26086eb..9824bf3a 100644
--- a/docs/dev/reference/mkinmod.html
+++ b/docs/dev/reference/mkinmod.html
@@ -290,7 +290,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media
m1 = mkinsub("SFO", full_name = "Metabolite M1"),
name = "SFO_SFO", dll_dir = DLL_dir, unload = TRUE, overwrite = TRUE)
#> Temporary DLL for differentials generated and loaded
-#> Copied DLL from /tmp/RtmpSeNGYy/file226312370605e2.so to /home/jranke/.local/share/mkin/SFO_SFO.so
+#> Copied DLL from /tmp/RtmpHpDSpx/file2445be5e83d15b.so to /home/jranke/.local/share/mkin/SFO_SFO.so
# Now we can save the model and restore it in a new session
saveRDS(SFO_SFO.2, file = "~/SFO_SFO.rds")
# Terminate the R session here if you would like to check, and then do
@@ -343,7 +343,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media
#> })
#> return(predicted)
#> }
-#> <environment: 0x5555577ec6d0>
+#> <environment: 0x55555f1f7f68>
# If we have several parallel metabolites
# (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)
diff --git a/docs/dev/reference/mkinpredict.html b/docs/dev/reference/mkinpredict.html
index e11dacdf..4b6c54e3 100644
--- a/docs/dev/reference/mkinpredict.html
+++ b/docs/dev/reference/mkinpredict.html
@@ -353,10 +353,10 @@ as these always return mapped output.
solution_type = "analytical", use_compiled = FALSE)[201,])
}
#> test relative elapsed
-#> 2 deSolve_compiled 1.0 0.002
#> 4 analytical 1.0 0.002
+#> 2 deSolve_compiled 1.5 0.003
#> 1 eigen 4.0 0.008
-#> 3 deSolve 30.5 0.061
+#> 3 deSolve 31.0 0.062
# \dontrun{
# Predict from a fitted model
diff --git a/docs/dev/reference/mmkin.html b/docs/dev/reference/mmkin.html
index c2bbd3c4..275ac5d9 100644
--- a/docs/dev/reference/mmkin.html
+++ b/docs/dev/reference/mmkin.html
@@ -158,10 +158,10 @@ plotting.
time_default
#> user system elapsed
-#> 1.522 0.957 0.720
+#> 1.617 0.819 0.699
time_1
#> user system elapsed
-#> 1.991 0.024 2.015
+#> 1.908 0.036 1.944
endpoints(fits.0[["SFO_lin", 2]])
#> $ff
diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html
index 25eb03c7..d2ea6e1a 100644
--- a/docs/dev/reference/saem.html
+++ b/docs/dev/reference/saem.html
@@ -397,8 +397,8 @@ using mmkin.
#> saemix version used for fitting: 3.3
#> mkin version used for pre-fitting: 1.2.10
#> R version used for fitting: 4.4.2
-#> Date of fit: Fri Feb 14 07:32:13 2025
-#> Date of summary: Fri Feb 14 07:32:13 2025
+#> Date of fit: Sun Feb 16 17:01:05 2025
+#> Date of summary: Sun Feb 16 17:01:05 2025
#>
#> Equations:
#> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -413,7 +413,7 @@ using mmkin.
#>
#> Model predictions using solution type analytical
#>
-#> Fitted in 3.605 s
+#> Fitted in 3.489 s
#> Using 300, 100 iterations and 10 chains
#>
#> Variance model: Constant variance
@@ -695,7 +695,7 @@ using mmkin.
#>
#> In above message, R1 = 91
#>
-#> Error in deSolve::lsoda(y = odeini, times = outtimes, func = lsoda_func, :
+#> Error in deSolve::lsoda(y = odeini, times = outtimes_deSolve, func = lsoda_func, :
#> illegal input detected before taking any integration steps - see written message
#anova(
diff --git a/docs/dev/reference/summary.mkinfit.html b/docs/dev/reference/summary.mkinfit.html
index 63a08d05..a9d124b9 100644
--- a/docs/dev/reference/summary.mkinfit.html
+++ b/docs/dev/reference/summary.mkinfit.html
@@ -193,15 +193,15 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
summary(mkinfit("SFO", FOCUS_2006_A, quiet = TRUE))
#> mkin version used for fitting: 1.2.10
#> R version used for fitting: 4.4.2
-#> Date of fit: Fri Feb 14 07:34:16 2025
-#> Date of summary: Fri Feb 14 07:34:16 2025
+#> Date of fit: Sun Feb 16 17:03:11 2025
+#> Date of summary: Sun Feb 16 17:03:11 2025
#>
#> Equations:
#> d_parent/dt = - k_parent * parent
#>
#> Model predictions using solution type analytical
#>
-#> Fitted using 131 model solutions performed in 0.009 s
+#> Fitted using 131 model solutions performed in 0.01 s
#>
#> Error model: Constant variance
#>
diff --git a/docs/dev/reference/summary.mmkin.html b/docs/dev/reference/summary.mmkin.html
index dad19e59..27b8c8a5 100644
--- a/docs/dev/reference/summary.mmkin.html
+++ b/docs/dev/reference/summary.mmkin.html
@@ -113,7 +113,7 @@ and gives an overview of ill-defined parameters calculated by #> false convergence (8)
summary(fits)
#> Error model: Constant variance
-#> Fitted in 0.512 s
+#> Fitted in 0.471 s
#>
#> Status:
#> dataset
diff --git a/docs/dev/reference/summary.nlme.mmkin.html b/docs/dev/reference/summary.nlme.mmkin.html
index dd4c4771..a1206833 100644
--- a/docs/dev/reference/summary.nlme.mmkin.html
+++ b/docs/dev/reference/summary.nlme.mmkin.html
@@ -214,8 +214,8 @@ José Pinheiro and Douglas Bates for the components inherited from nlme
#> nlme version used for fitting: 3.1.166
#> mkin version used for pre-fitting: 1.2.10
#> R version used for fitting: 4.4.2
-#> Date of fit: Fri Feb 14 07:34:18 2025
-#> Date of summary: Fri Feb 14 07:34:18 2025
+#> Date of fit: Sun Feb 16 17:03:13 2025
+#> Date of summary: Sun Feb 16 17:03:13 2025
#>
#> Equations:
#> d_parent/dt = - k_parent * parent
@@ -225,7 +225,7 @@ José Pinheiro and Douglas Bates for the components inherited from nlme
#>
#> Model predictions using solution type analytical
#>
-#> Fitted in 0.187 s using 4 iterations
+#> Fitted in 0.189 s using 4 iterations
#>
#> Variance model: Two-component variance function
#>
diff --git a/docs/dev/reference/summary.saem.mmkin.html b/docs/dev/reference/summary.saem.mmkin.html
index e6138f37..271dddfa 100644
--- a/docs/dev/reference/summary.saem.mmkin.html
+++ b/docs/dev/reference/summary.saem.mmkin.html
@@ -290,8 +290,8 @@ saemix authors for the parts inherited from saemix.
#> saemix version used for fitting: 3.3
#> mkin version used for pre-fitting: 1.2.10
#> R version used for fitting: 4.4.2
-#> Date of fit: Fri Feb 14 07:34:33 2025
-#> Date of summary: Fri Feb 14 07:34:33 2025
+#> Date of fit: Sun Feb 16 17:03:28 2025
+#> Date of summary: Sun Feb 16 17:03:28 2025
#>
#> Equations:
#> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -306,7 +306,7 @@ saemix authors for the parts inherited from saemix.
#>
#> Model predictions using solution type analytical
#>
-#> Fitted in 8.903 s
+#> Fitted in 8.612 s
#> Using 300, 100 iterations and 10 chains
#>
#> Variance model: Two-component variance function
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