From b9be19af5e3085216d0cd5af439332f631fa8b92 Mon Sep 17 00:00:00 2001
From: Johannes Ranke
nlme.m
nlme_function(object)
-mean_degparms(object, random = FALSE)
+mean_degparms(object, random = FALSE, test_log_parms = FALSE, conf.level = 0.6)
nlme_data(object)
@@ -170,6 +170,17 @@ datasets. They are used internally by the nlme.m
random
Should a list with fixed and random effects be returned?
+
+ test_log_parms
+ If TRUE, log parameters are only considered in
+the mean calculations if their untransformed counterparts (most likely
+rate constants) pass the t-test for significant difference from zero.
+
+
+ conf.level
+ Possibility to adjust the required confidence level
+for parameter that are tested if requested by 'test_log_parms'.
+
Value
@@ -211,7 +222,7 @@ nlme for the case of a single grouping variable ds.
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 generated the html docs.
+# pkgdown to generate the html docs.
assign("nlme_f", nlme_f, globalenv())
assign("grouped_data", grouped_data, globalenv())
@@ -226,28 +237,28 @@ nlme for the case of a single grouping variable ds.
#> Model: value ~ nlme_f(name, time, parent_0, log_k_parent_sink)
#> Data: grouped_data
#> AIC BIC logLik
-#> 300.6824 310.2426 -145.3412
+#> 298.2781 307.7372 -144.1391
#>
#> Random effects:
#> Formula: list(parent_0 ~ 1, log_k_parent_sink ~ 1)
#> Level: ds
#> Structure: Diagonal
#> parent_0 log_k_parent_sink Residual
-#> StdDev: 1.697361 0.6801209 3.666073
+#> StdDev: 0.937473 0.7098105 3.83543
#>
#> Fixed effects: parent_0 + log_k_parent_sink ~ 1
#> Value Std.Error DF t-value p-value
-#> parent_0 100.99378 1.3890416 46 72.70753 0
-#> log_k_parent_sink -3.07521 0.4018589 46 -7.65246 0
+#> parent_0 101.76838 1.1445443 45 88.91607 0
+#> log_k_parent_sink -3.05444 0.4195622 45 -7.28008 0
#> Correlation:
#> prnt_0
-#> log_k_parent_sink 0.027
+#> log_k_parent_sink 0.034
#>
#> Standardized Within-Group Residuals:
-#> Min Q1 Med Q3 Max
-#> -1.9942823 -0.5622565 0.1791579 0.7165038 2.0704781
+#> Min Q1 Med Q3 Max
+#> -2.61693595 -0.21853231 0.05740682 0.57209372 3.04598764
#>
-#> Number of Observations: 50
+#> Number of Observations: 49
#> Number of Groups: 3
# augPred does not work on fits with more than one state
# variable
--
cgit v1.2.1
From 0c9b2f0e3c8ce65cb790c9e048476784cbbea070 Mon Sep 17 00:00:00 2001
From: Johannes Ranke
Date: Fri, 11 Jun 2021 11:14:45 +0200
Subject: Finished 'summary.nlmixr.mmkin', checks, docs
---
docs/dev/reference/nlme.html | 41 ++++++++++-------------------------------
1 file changed, 10 insertions(+), 31 deletions(-)
(limited to 'docs/dev/reference/nlme.html')
diff --git a/docs/dev/reference/nlme.html b/docs/dev/reference/nlme.html
index 78d132e9..55a94443 100644
--- a/docs/dev/reference/nlme.html
+++ b/docs/dev/reference/nlme.html
@@ -75,7 +75,7 @@ datasets. They are used internally by the nlme.mmkin() method." />
@@ -155,8 +155,6 @@ datasets. They are used internally by the nlme.m
nlme_function(object)
-mean_degparms(object, random = FALSE, test_log_parms = FALSE, conf.level = 0.6)
-
nlme_data(object)
Arguments
@@ -166,30 +164,11 @@ datasets. They are used internally by the nlme.m
object
An mmkin row object containing several fits of the same model to different datasets
-
- random
- Should a list with fixed and random effects be returned?
-
-
- test_log_parms
- If TRUE, log parameters are only considered in
-the mean calculations if their untransformed counterparts (most likely
-rate constants) pass the t-test for significant difference from zero.
-
-
- conf.level
- Possibility to adjust the required confidence level
-for parameter that are tested if requested by 'test_log_parms'.
-
Value
A function that can be used with nlme
-If random is FALSE (default), a named vector containing mean values
-of the fitted degradation model parameters. If random is TRUE, a list with
-fixed and random effects, in the format required by the start argument of
-nlme for the case of a single grouping variable ds.
A groupedData
object
See also
@@ -217,7 +196,7 @@ nlme for the case of a single grouping variable ds.
ds <- c(d1 = d1, d2 = d2, d3 = d3)
f <- mmkin("SFO", ds, cores = 1, quiet = TRUE)
-mean_dp <- mean_degparms(f)
+mean_dp <- mean_degparms(f)
grouped_data <- nlme_data(f)
nlme_f <- nlme_function(f)
# These assignments are necessary for these objects to be
@@ -237,28 +216,28 @@ nlme for the case of a single grouping variable ds.
#> Model: value ~ nlme_f(name, time, parent_0, log_k_parent_sink)
#> Data: grouped_data
#> AIC BIC logLik
-#> 298.2781 307.7372 -144.1391
+#> 300.6824 310.2426 -145.3412
#>
#> Random effects:
#> Formula: list(parent_0 ~ 1, log_k_parent_sink ~ 1)
#> Level: ds
#> Structure: Diagonal
#> parent_0 log_k_parent_sink Residual
-#> StdDev: 0.937473 0.7098105 3.83543
+#> StdDev: 1.697361 0.6801209 3.666073
#>
#> Fixed effects: parent_0 + log_k_parent_sink ~ 1
#> Value Std.Error DF t-value p-value
-#> parent_0 101.76838 1.1445443 45 88.91607 0
-#> log_k_parent_sink -3.05444 0.4195622 45 -7.28008 0
+#> parent_0 100.99378 1.3890416 46 72.70753 0
+#> log_k_parent_sink -3.07521 0.4018589 46 -7.65246 0
#> Correlation:
#> prnt_0
-#> log_k_parent_sink 0.034
+#> log_k_parent_sink 0.027
#>
#> Standardized Within-Group Residuals:
-#> Min Q1 Med Q3 Max
-#> -2.61693595 -0.21853231 0.05740682 0.57209372 3.04598764
+#> Min Q1 Med Q3 Max
+#> -1.9942823 -0.5622565 0.1791579 0.7165038 2.0704781
#>
-#> Number of Observations: 49
+#> Number of Observations: 50
#> Number of Groups: 3
# augPred does not work on fits with more than one state
# variable
--
cgit v1.2.1
From 0b754ffa91b9496bdd2f892cf3ca2bd887028dea Mon Sep 17 00:00:00 2001
From: Johannes Ranke
Date: Tue, 27 Jul 2021 18:22:01 +0200
Subject: Fix dimethenamid vignette problems and update docs
---
docs/dev/reference/nlme.html | 18 +++++++++---------
1 file changed, 9 insertions(+), 9 deletions(-)
(limited to 'docs/dev/reference/nlme.html')
diff --git a/docs/dev/reference/nlme.html b/docs/dev/reference/nlme.html
index 55a94443..184585df 100644
--- a/docs/dev/reference/nlme.html
+++ b/docs/dev/reference/nlme.html
@@ -75,7 +75,7 @@ datasets. They are used internally by the nlme.mmkin() method." />
@@ -216,28 +216,28 @@ datasets. They are used internally by the nlme.m
#> Model: value ~ nlme_f(name, time, parent_0, log_k_parent_sink)
#> Data: grouped_data
#> AIC BIC logLik
-#> 300.6824 310.2426 -145.3412
+#> 278.1355 287.7946 -134.0677
#>
#> Random effects:
#> Formula: list(parent_0 ~ 1, log_k_parent_sink ~ 1)
#> Level: ds
#> Structure: Diagonal
#> parent_0 log_k_parent_sink Residual
-#> StdDev: 1.697361 0.6801209 3.666073
+#> StdDev: 3.406042 0.6437579 2.620833
#>
#> Fixed effects: parent_0 + log_k_parent_sink ~ 1
#> Value Std.Error DF t-value p-value
-#> parent_0 100.99378 1.3890416 46 72.70753 0
-#> log_k_parent_sink -3.07521 0.4018589 46 -7.65246 0
+#> parent_0 101.50173 2.123709 47 47.79457 0
+#> log_k_parent_sink -3.07597 0.379775 47 -8.09945 0
#> Correlation:
#> prnt_0
-#> log_k_parent_sink 0.027
+#> log_k_parent_sink 0.01
#>
#> Standardized Within-Group Residuals:
-#> Min Q1 Med Q3 Max
-#> -1.9942823 -0.5622565 0.1791579 0.7165038 2.0704781
+#> Min Q1 Med Q3 Max
+#> -2.06889303 -0.50100169 -0.06268253 0.62557544 2.19922001
#>
-#> Number of Observations: 50
+#> Number of Observations: 51
#> Number of Groups: 3
# augPred does not work on fits with more than one state
# variable
--
cgit v1.2.1
From 137612045c23198f10d6e8612c32e266c2a6c00e Mon Sep 17 00:00:00 2001
From: Johannes Ranke
Date: Thu, 29 Jul 2021 12:17:56 +0200
Subject: Go back to 1.0.x version, update docs
---
docs/dev/reference/nlme.html | 18 +++++++++---------
1 file changed, 9 insertions(+), 9 deletions(-)
(limited to 'docs/dev/reference/nlme.html')
diff --git a/docs/dev/reference/nlme.html b/docs/dev/reference/nlme.html
index 184585df..55a94443 100644
--- a/docs/dev/reference/nlme.html
+++ b/docs/dev/reference/nlme.html
@@ -75,7 +75,7 @@ datasets. They are used internally by the nlme.mmkin() method." />
@@ -216,28 +216,28 @@ datasets. They are used internally by the nlme.m
#> Model: value ~ nlme_f(name, time, parent_0, log_k_parent_sink)
#> Data: grouped_data
#> AIC BIC logLik
-#> 278.1355 287.7946 -134.0677
+#> 300.6824 310.2426 -145.3412
#>
#> Random effects:
#> Formula: list(parent_0 ~ 1, log_k_parent_sink ~ 1)
#> Level: ds
#> Structure: Diagonal
#> parent_0 log_k_parent_sink Residual
-#> StdDev: 3.406042 0.6437579 2.620833
+#> StdDev: 1.697361 0.6801209 3.666073
#>
#> Fixed effects: parent_0 + log_k_parent_sink ~ 1
#> Value Std.Error DF t-value p-value
-#> parent_0 101.50173 2.123709 47 47.79457 0
-#> log_k_parent_sink -3.07597 0.379775 47 -8.09945 0
+#> parent_0 100.99378 1.3890416 46 72.70753 0
+#> log_k_parent_sink -3.07521 0.4018589 46 -7.65246 0
#> Correlation:
#> prnt_0
-#> log_k_parent_sink 0.01
+#> log_k_parent_sink 0.027
#>
#> Standardized Within-Group Residuals:
-#> Min Q1 Med Q3 Max
-#> -2.06889303 -0.50100169 -0.06268253 0.62557544 2.19922001
+#> Min Q1 Med Q3 Max
+#> -1.9942823 -0.5622565 0.1791579 0.7165038 2.0704781
#>
-#> Number of Observations: 51
+#> Number of Observations: 50
#> Number of Groups: 3
# augPred does not work on fits with more than one state
# variable
--
cgit v1.2.1
From c41381a961263c28d60976e68923157916c78b15 Mon Sep 17 00:00:00 2001
From: Johannes Ranke
Date: Thu, 16 Sep 2021 15:31:13 +0200
Subject: Adapt and improve the dimethenamid vignette
Adapt to the corrected data and unify control parameters for saemix and
nlmixr with saem. Update docs
---
docs/dev/reference/nlme.html | 18 +++++++++---------
1 file changed, 9 insertions(+), 9 deletions(-)
(limited to 'docs/dev/reference/nlme.html')
diff --git a/docs/dev/reference/nlme.html b/docs/dev/reference/nlme.html
index 55a94443..500ac391 100644
--- a/docs/dev/reference/nlme.html
+++ b/docs/dev/reference/nlme.html
@@ -75,7 +75,7 @@ datasets. They are used internally by the nlme.mmkin() method." />
@@ -216,28 +216,28 @@ datasets. They are used internally by the nlme.m
#> Model: value ~ nlme_f(name, time, parent_0, log_k_parent_sink)
#> Data: grouped_data
#> AIC BIC logLik
-#> 300.6824 310.2426 -145.3412
+#> 289.8295 299.4886 -139.9148
#>
#> Random effects:
#> Formula: list(parent_0 ~ 1, log_k_parent_sink ~ 1)
#> Level: ds
#> Structure: Diagonal
#> parent_0 log_k_parent_sink Residual
-#> StdDev: 1.697361 0.6801209 3.666073
+#> StdDev: 1.839278 0.6988919 3.059894
#>
#> Fixed effects: parent_0 + log_k_parent_sink ~ 1
#> Value Std.Error DF t-value p-value
-#> parent_0 100.99378 1.3890416 46 72.70753 0
-#> log_k_parent_sink -3.07521 0.4018589 46 -7.65246 0
+#> parent_0 100.52780 1.3507449 47 74.42397 0
+#> log_k_parent_sink -3.08477 0.4124053 47 -7.47995 0
#> Correlation:
#> prnt_0
-#> log_k_parent_sink 0.027
+#> log_k_parent_sink 0.019
#>
#> Standardized Within-Group Residuals:
-#> Min Q1 Med Q3 Max
-#> -1.9942823 -0.5622565 0.1791579 0.7165038 2.0704781
+#> Min Q1 Med Q3 Max
+#> -2.22350411 -0.51546184 0.04803417 0.55987705 3.49178405
#>
-#> Number of Observations: 50
+#> Number of Observations: 51
#> Number of Groups: 3
# augPred does not work on fits with more than one state
# variable
--
cgit v1.2.1
From ff83d8b2ba623513d92ac90fac4a1b0ec98c2cb5 Mon Sep 17 00:00:00 2001
From: Johannes Ranke
Date: Tue, 5 Oct 2021 17:33:52 +0200
Subject: Update docs
---
docs/dev/reference/nlme.html | 16 ++++++++--------
1 file changed, 8 insertions(+), 8 deletions(-)
(limited to 'docs/dev/reference/nlme.html')
diff --git a/docs/dev/reference/nlme.html b/docs/dev/reference/nlme.html
index 500ac391..5c88b69d 100644
--- a/docs/dev/reference/nlme.html
+++ b/docs/dev/reference/nlme.html
@@ -216,28 +216,28 @@ datasets. They are used internally by the nlme.m
#> Model: value ~ nlme_f(name, time, parent_0, log_k_parent_sink)
#> Data: grouped_data
#> AIC BIC logLik
-#> 289.8295 299.4886 -139.9148
+#> 300.6824 310.2426 -145.3412
#>
#> Random effects:
#> Formula: list(parent_0 ~ 1, log_k_parent_sink ~ 1)
#> Level: ds
#> Structure: Diagonal
#> parent_0 log_k_parent_sink Residual
-#> StdDev: 1.839278 0.6988919 3.059894
+#> StdDev: 1.697361 0.6801209 3.666073
#>
#> Fixed effects: parent_0 + log_k_parent_sink ~ 1
#> Value Std.Error DF t-value p-value
-#> parent_0 100.52780 1.3507449 47 74.42397 0
-#> log_k_parent_sink -3.08477 0.4124053 47 -7.47995 0
+#> parent_0 100.99378 1.3890416 46 72.70753 0
+#> log_k_parent_sink -3.07521 0.4018589 46 -7.65246 0
#> Correlation:
#> prnt_0
-#> log_k_parent_sink 0.019
+#> log_k_parent_sink 0.027
#>
#> Standardized Within-Group Residuals:
-#> Min Q1 Med Q3 Max
-#> -2.22350411 -0.51546184 0.04803417 0.55987705 3.49178405
+#> Min Q1 Med Q3 Max
+#> -1.9942823 -0.5622565 0.1791579 0.7165038 2.0704781
#>
-#> Number of Observations: 51
+#> Number of Observations: 50
#> Number of Groups: 3
# augPred does not work on fits with more than one state
# variable
--
cgit v1.2.1