From 3a62211d9211cd0aedecec055226d66b55a17958 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 20 Apr 2020 18:52:52 +0200 Subject: Prepare release to address failed CRAN check --- DESCRIPTION | 4 ++-- NEWS.md | 2 ++ docs/404.html | 2 +- docs/articles/index.html | 2 +- docs/authors.html | 2 +- docs/index.html | 2 +- docs/news/index.html | 17 +++++++++++++---- docs/reference/index.html | 2 +- docs/reference/mkinds.html | 2 +- docs/reference/mkinfit.html | 44 +++++++++++++++++++------------------------- 10 files changed, 42 insertions(+), 37 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 8273c7df..99a9cc76 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: mkin Type: Package Title: Kinetic Evaluation of Chemical Degradation Data -Version: 0.9.49.10 -Date: 2020-04-18 +Version: 0.9.49.11 +Date: 2020-04-20 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "jranke@uni-bremen.de", comment = c(ORCID = "0000-0003-4371-6538")), diff --git a/NEWS.md b/NEWS.md index 919f413b..790e2e03 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # mkin 0.9.49.11 (unreleased) +- Increase a test tolerance to make it pass on all CRAN check machines + # mkin 0.9.49.10 (2020-04-18) - 'nlme.mmkin': An nlme method for mmkin row objects and an associated S3 class with print, plot, anova and endpoint methods diff --git a/docs/404.html b/docs/404.html index dc3c3c18..b3193a23 100644 --- a/docs/404.html +++ b/docs/404.html @@ -67,7 +67,7 @@ mkin - 0.9.49.10 + 0.9.49.11 diff --git a/docs/articles/index.html b/docs/articles/index.html index 4a5087df..9b0cce06 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -67,7 +67,7 @@ mkin - 0.9.49.10 + 0.9.49.11 diff --git a/docs/authors.html b/docs/authors.html index 20c040f9..55121d7c 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -67,7 +67,7 @@ mkin - 0.9.49.10 + 0.9.49.11 diff --git a/docs/index.html b/docs/index.html index 99d580c5..5baaa718 100644 --- a/docs/index.html +++ b/docs/index.html @@ -37,7 +37,7 @@ mkin - 0.9.49.10 + 0.9.49.11 diff --git a/docs/news/index.html b/docs/news/index.html index 5758c284..853c217f 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -67,7 +67,7 @@ mkin - 0.9.49.10 + 0.9.49.11 @@ -129,9 +129,17 @@ -
+

-mkin 0.9.49.10 (unreleased) Unreleased +mkin 0.9.49.11 (unreleased) Unreleased +

+
    +
  • Increase a test tolerance to make it pass on all CRAN check machines
    • +
+
+
+

+mkin 0.9.49.10 (2020-04-18) 2020-04-18

  • ‘nlme.mmkin’: An nlme method for mmkin row objects and an associated S3 class with print, plot, anova and endpoint methods

    • @@ -769,7 +777,8 @@

    Contents

    diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html index 946d40a6..4f5d9f67 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 - 0.9.49.10 + 0.9.49.11
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index ffc8d52b..09837505 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -75,7 +75,7 @@ likelihood function." /> mkin - 0.9.49.9 + 0.9.49.11
@@ -415,17 +415,17 @@ estimators.


 # Use shorthand notation for parent only degradation
 fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
-summary(fit)
#> mkin version used for fitting:    0.9.49.9 
+summary(fit)
#> mkin version used for fitting:    0.9.49.11 
 #> R version used for fitting:       3.6.3 
-#> Date of fit:     Mon Mar 30 21:41:20 2020 
-#> Date of summary: Mon Mar 30 21:41:20 2020 
+#> Date of fit:     Mon Apr 20 18:52:22 2020 
+#> Date of summary: Mon Apr 20 18:52:22 2020 
 #> 
 #> Equations:
 #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted using 222 model solutions performed in 0.463 s
+#> Fitted using 222 model solutions performed in 0.473 s
 #> 
 #> Error model: Constant variance 
 #> 
@@ -497,13 +497,10 @@ estimators.

   m1 = mkinsub("SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
# Fit the model to the FOCUS example dataset D using defaults
 print(system.time(fit <- mkinfit(SFO_SFO, FOCUS_2006_D,
                            solution_type = "eigen", quiet = TRUE)))
#> Warning: Observations with value of zero were removed from the data
#>        User      System verstrichen 
-#>       1.526       0.000       1.530 
coef(fit)
#> NULL
endpoints(fit)
#> $ff
+#>       1.465       0.003       1.474 
coef(fit)
#> NULL
endpoints(fit)
#> $ff
 #> parent_sink   parent_m1     m1_sink 
 #>    0.485524    0.514476    1.000000 
 #> 
-#> $SFORB
-#> logical(0)
-#> 
 #> $distimes
 #>              DT50      DT90
 #> parent   7.022929  23.32967
@@ -570,13 +567,10 @@ estimators.

 #> Sum of squared residuals at call 126: 371.2134
 #> Sum of squared residuals at call 135: 371.2134
 #> Negative log-likelihood at call 145: 97.22429
#> Optimisation successfully terminated.
#>        User      System verstrichen 
-#>       1.083       0.000       1.084 
coef(fit.deSolve)
#> NULL
endpoints(fit.deSolve)
#> $ff
+#>       1.052       0.000       1.068 
coef(fit.deSolve)
#> NULL
endpoints(fit.deSolve)
#> $ff
 #> parent_sink   parent_m1     m1_sink 
 #>    0.485524    0.514476    1.000000 
 #> 
-#> $SFORB
-#> logical(0)
-#> 
 #> $distimes
 #>              DT50      DT90
 #> parent   7.022929  23.32967
@@ -604,10 +598,10 @@ estimators.

 # \dontrun{
 # Weighted fits, including IRLS
 SFO_SFO.ff <- mkinmod(parent = mkinsub("SFO", "m1"),
-                      m1 = mkinsub("SFO"), use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.
f.noweight <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.noweight)
#> mkin version used for fitting:    0.9.49.9 
+                      m1 = mkinsub("SFO"), use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.
f.noweight <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.noweight)
#> mkin version used for fitting:    0.9.49.11 
 #> R version used for fitting:       3.6.3 
-#> Date of fit:     Mon Mar 30 21:41:36 2020 
-#> Date of summary: Mon Mar 30 21:41:36 2020 
+#> Date of fit:     Mon Apr 20 18:52:37 2020 
+#> Date of summary: Mon Apr 20 18:52:37 2020 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -615,7 +609,7 @@ estimators.

 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted using 422 model solutions performed in 1.144 s
+#> Fitted using 422 model solutions performed in 1.087 s
 #> 
 #> Error model: Constant variance 
 #> 
@@ -721,10 +715,10 @@ estimators.

 #>   100       m1    31.04  31.98163 -9.416e-01
 #>   100       m1    33.13  31.98163  1.148e+00
 #>   120       m1    25.15  28.78984 -3.640e+00
-#>   120       m1    33.31  28.78984  4.520e+00
f.obs <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, error_model = "obs", quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.obs)
#> mkin version used for fitting:    0.9.49.9 
+#>   120       m1    33.31  28.78984  4.520e+00
f.obs <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, error_model = "obs", quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.obs)
#> mkin version used for fitting:    0.9.49.11 
 #> R version used for fitting:       3.6.3 
-#> Date of fit:     Mon Mar 30 21:41:39 2020 
-#> Date of summary: Mon Mar 30 21:41:39 2020 
+#> Date of fit:     Mon Apr 20 18:52:40 2020 
+#> Date of summary: Mon Apr 20 18:52:40 2020 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -732,7 +726,7 @@ estimators.

 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted using 979 model solutions performed in 2.576 s
+#> Fitted using 979 model solutions performed in 2.518 s
 #> 
 #> Error model: Variance unique to each observed variable 
 #> 
@@ -853,10 +847,10 @@ estimators.

 #>   100       m1    31.04  31.98773 -9.477e-01
 #>   100       m1    33.13  31.98773  1.142e+00
 #>   120       m1    25.15  28.80429 -3.654e+00
-#>   120       m1    33.31  28.80429  4.506e+00
f.tc <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, error_model = "tc", quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.tc)
#> mkin version used for fitting:    0.9.49.9 
+#>   120       m1    33.31  28.80429  4.506e+00
f.tc <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, error_model = "tc", quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.tc)
#> mkin version used for fitting:    0.9.49.11 
 #> R version used for fitting:       3.6.3 
-#> Date of fit:     Mon Mar 30 21:41:50 2020 
-#> Date of summary: Mon Mar 30 21:41:50 2020 
+#> Date of fit:     Mon Apr 20 18:52:50 2020 
+#> Date of summary: Mon Apr 20 18:52:50 2020 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -864,7 +858,7 @@ estimators.

 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted using 2552 model solutions performed in 10.593 s
+#> Fitted using 2552 model solutions performed in 10.186 s
 #> 
 #> Error model: Two-component variance function 
 #> 
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