From c322a8102a399cbb1fe38c4c4ca4485cea8bc4e8 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 7 May 2019 08:43:12 +0200 Subject: Fix hessian calculations Static documentation rebuilt by pkgdown --- docs/reference/NAFTA_SOP_2015.html | 32 ++--- docs/reference/NAFTA_SOP_Attachment.html | 32 ++--- docs/reference/logistic.solution.html | 18 ++- docs/reference/mccall81_245T.html | 45 ++++--- docs/reference/mkinfit.html | 176 ++++++++++++++++------------ docs/reference/mkinmod.html | 2 +- docs/reference/mkinparplot-1.png | Bin 17306 -> 16549 bytes docs/reference/mkinparplot.html | 2 +- docs/reference/mkinpredict.html | 4 +- docs/reference/mmkin.html | 4 +- docs/reference/nafta.html | 32 ++--- docs/reference/summary.mkinfit.html | 30 +++-- docs/reference/test_data_from_UBA_2014.html | 54 ++++++--- docs/reference/transform_odeparms.html | 90 +++++++------- 14 files changed, 300 insertions(+), 221 deletions(-) (limited to 'docs/reference') diff --git a/docs/reference/NAFTA_SOP_2015.html b/docs/reference/NAFTA_SOP_2015.html index 9fbc71c6..84341a17 100644 --- a/docs/reference/NAFTA_SOP_2015.html +++ b/docs/reference/NAFTA_SOP_2015.html @@ -155,7 +155,7 @@

Examples

- 
  nafta_evaluation <- nafta(NAFTA_SOP_Appendix_D, cores = 1)
#> Warning: Could not calculate correlation; no covariance matrix
#> Warning: Could not calculate correlation; no covariance matrix
#> Warning: Could not calculate correlation; no covariance matrix
#> The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
#> The representative half-life of the IORE model is longer than the one corresponding
#> to the terminal degradation rate found with the DFOP model.
#> The representative half-life obtained from the DFOP model may be used
  print(nafta_evaluation)
#> Sums of squares:
+    
  nafta_evaluation <- nafta(NAFTA_SOP_Appendix_D, cores = 1)
#> The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
#> The representative half-life of the IORE model is longer than the one corresponding
#> to the terminal degradation rate found with the DFOP model.
#> The representative half-life obtained from the DFOP model may be used
  print(nafta_evaluation)
#> Sums of squares:
 #>       SFO      IORE      DFOP 
 #> 1378.6832  615.7730  517.8836 
 #> 
@@ -164,25 +164,25 @@
 #> 
 #> Parameters:
 #> $SFO
-#>               Estimate Pr(>t) Lower Upper
-#> parent_0       83.7558     NA    NA    NA
-#> k_parent_sink   0.0017     NA    NA    NA
-#> sigma           8.7518     NA    NA    NA
+#>               Estimate   Pr(>t)    Lower   Upper
+#> parent_0       83.7558 1.80e-14 77.18268 90.3288
+#> k_parent_sink   0.0017 7.43e-05  0.00112  0.0026
+#> sigma           8.7518 1.22e-05  5.64278 11.8608
 #> 
 #> $IORE
-#>                     Estimate Pr(>t) Lower Upper
-#> parent_0            9.69e+01     NA    NA    NA
-#> k__iore_parent_sink 8.40e-14     NA    NA    NA
-#> N_parent            6.68e+00     NA    NA    NA
-#> sigma               5.85e+00     NA    NA    NA
+#>                     Estimate Pr(>t)    Lower    Upper
+#> parent_0            9.69e+01     NA 8.88e+01 1.05e+02
+#> k__iore_parent_sink 8.40e-14     NA 1.79e-18 3.94e-09
+#> N_parent            6.68e+00     NA 4.19e+00 9.17e+00
+#> sigma               5.85e+00     NA 3.76e+00 7.94e+00
 #> 
 #> $DFOP
-#>          Estimate Pr(>t) Lower Upper
-#> parent_0 9.76e+01     NA    NA    NA
-#> k1       4.24e-02     NA    NA    NA
-#> k2       8.24e-04     NA    NA    NA
-#> g        2.88e-01     NA    NA    NA
-#> sigma    5.36e+00     NA    NA    NA
+#>          Estimate   Pr(>t)    Lower    Upper
+#> parent_0 9.76e+01 1.94e-13 9.02e+01 1.05e+02
+#> k1       4.24e-02 5.92e-03 2.03e-02 8.88e-02
+#> k2       8.24e-04 6.48e-03 3.89e-04 1.75e-03
+#> g        2.88e-01 2.47e-05 1.95e-01 4.03e-01
+#> sigma    5.36e+00 2.22e-05 3.43e+00 7.30e+00
 #> 
 #> 
 #> DTx values:
diff --git a/docs/reference/NAFTA_SOP_Attachment.html b/docs/reference/NAFTA_SOP_Attachment.html
index 149b4d82..76d91c40 100644
--- a/docs/reference/NAFTA_SOP_Attachment.html
+++ b/docs/reference/NAFTA_SOP_Attachment.html
@@ -152,7 +152,7 @@
     
 
     
Examples

-    
  nafta_att_p5a <- nafta(NAFTA_SOP_Attachment[["p5a"]], cores = 1)
#> Warning: Could not calculate correlation; no covariance matrix
#> Warning: Could not calculate correlation; no covariance matrix
#> Warning: Could not calculate correlation; no covariance matrix
#> The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
#> The half-life obtained from the IORE model may be used
  print(nafta_att_p5a)
#> Sums of squares:
+    
  nafta_att_p5a <- nafta(NAFTA_SOP_Attachment[["p5a"]], cores = 1)
#> The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
#> The half-life obtained from the IORE model may be used
  print(nafta_att_p5a)
#> Sums of squares:
 #>       SFO      IORE      DFOP 
 #> 465.21753  56.27506  32.06401 
 #> 
@@ -161,25 +161,25 @@
 #> 
 #> Parameters:
 #> $SFO
-#>               Estimate Pr(>t) Lower Upper
-#> parent_0       95.8401     NA    NA    NA
-#> k_parent_sink   0.0102     NA    NA    NA
-#> sigma           4.8230     NA    NA    NA
+#>               Estimate   Pr(>t)  Lower   Upper
+#> parent_0       95.8401 4.67e-21 92.245 99.4357
+#> k_parent_sink   0.0102 3.92e-12  0.009  0.0117
+#> sigma           4.8230 3.81e-06  3.214  6.4318
 #> 
 #> $IORE
-#>                     Estimate Pr(>t) Lower Upper
-#> parent_0            1.01e+02     NA    NA    NA
-#> k__iore_parent_sink 1.54e-05     NA    NA    NA
-#> N_parent            2.57e+00     NA    NA    NA
-#> sigma               1.68e+00     NA    NA    NA
+#>                     Estimate Pr(>t)    Lower    Upper
+#> parent_0            1.01e+02     NA 9.91e+01 1.02e+02
+#> k__iore_parent_sink 1.54e-05     NA 4.08e-06 5.84e-05
+#> N_parent            2.57e+00     NA 2.25e+00 2.89e+00
+#> sigma               1.68e+00     NA 1.12e+00 2.24e+00
 #> 
 #> $DFOP
-#>          Estimate Pr(>t) Lower Upper
-#> parent_0 9.99e+01     NA    NA    NA
-#> k1       2.67e-02     NA    NA    NA
-#> k2       2.86e-12     NA    NA    NA
-#> g        6.47e-01     NA    NA    NA
-#> sigma    1.27e+00     NA    NA    NA
+#>          Estimate   Pr(>t)   Lower    Upper
+#> parent_0 9.99e+01 1.41e-26 98.8116 101.0810
+#> k1       2.67e-02 5.05e-06  0.0243   0.0295
+#> k2       2.86e-12 5.00e-01  0.0000      Inf
+#> g        6.47e-01 3.67e-06  0.6248   0.6677
+#> sigma    1.27e+00 8.91e-06  0.8395   1.6929
 #> 
 #> 
 #> DTx values:
diff --git a/docs/reference/logistic.solution.html b/docs/reference/logistic.solution.html
index 082cd4fb..3b45b14f 100644
--- a/docs/reference/logistic.solution.html
+++ b/docs/reference/logistic.solution.html
@@ -205,12 +205,18 @@
     n = 1, reps = 2, digits = 5, LOD = 0.1, seed = 123456)[[1]]
 
   m <- mkinfit("logistic", d_2_1, quiet = TRUE)
-  plot_sep(m)
  summary(m)$bpar
#> Warning: Could not calculate correlation; no covariance matrix
#>              Estimate se_notrans t value Pr(>t) Lower Upper
-#> parent_0 1.057896e+02         NA      NA     NA    NA    NA
-#> kmax     6.398190e-02         NA      NA     NA    NA    NA
-#> k0       1.612775e-04         NA      NA     NA    NA    NA
-#> r        2.263946e-01         NA      NA     NA    NA    NA
-#> sigma    5.332935e+00         NA      NA     NA    NA    NA
  endpoints(m)$distimes
#>            DT50     DT90  DT50_k0 DT50_kmax
+  plot_sep(m)
  summary(m)$bpar
#>              Estimate   se_notrans   t value       Pr(>t)        Lower
+#> parent_0 1.057896e+02 1.9023449649 55.610120 3.768361e-16 1.016451e+02
+#> kmax     6.398190e-02 0.0143201029  4.467978 3.841828e-04 3.929235e-02
+#> k0       1.612775e-04 0.0005866813  0.274898 3.940351e-01 5.846685e-08
+#> r        2.263946e-01 0.1718110773  1.317695 1.061044e-01 4.335843e-02
+#> sigma    5.332935e+00 0.9145907310  5.830952 4.036926e-05 3.340213e+00
+#>                Upper
+#> parent_0 109.9341588
+#> kmax       0.1041853
+#> k0         0.4448750
+#> r          1.1821121
+#> sigma      7.3256566
  endpoints(m)$distimes
#>            DT50     DT90  DT50_k0 DT50_kmax
 #> parent 36.86533 62.41511 4297.854  10.83349