From 194659fcaccdd1ee37851725b8c72e99daa3a8cf Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 10 Apr 2019 10:17:35 +0200 Subject: Adapt tests, vignettes and examples - Write the NEWS - Static documentation rebuilt by pkgdown - Adapt mkinerrmin - Fix (hopefully all) remaining problems in mkinfit --- docs/reference/transform_odeparms.html | 82 ++++++++++++++++++---------------- 1 file changed, 43 insertions(+), 39 deletions(-) (limited to 'docs/reference/transform_odeparms.html') diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index fbc792f1..7e05480e 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -71,7 +71,7 @@ The transformation of sets of formation fractions is fragile, as it supposes mkin - 0.9.48.1 + 0.9.49.4 @@ -202,30 +202,32 @@ The transformation of sets of formation fractions is fragile, as it supposes 
SFO_SFO <- mkinmod(
   parent = list(type = "SFO", to = "m1", sink = TRUE),
   m1 = list(type = "SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
# Fit the model to the FOCUS example dataset D using defaults
-fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
-fit.s <- summary(fit)
+fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
fit.s <- summary(fit)
 # Transformed and backtransformed parameters
 print(fit.s$par, 3)
#>                   Estimate Std. Error Lower  Upper
-#> parent_0             99.60     1.6137 96.33 102.87
-#> log_k_parent_sink    -3.04     0.0783 -3.20  -2.88
-#> log_k_parent_m1      -2.98     0.0412 -3.06  -2.90
-#> log_k_m1_sink        -5.25     0.1361 -5.52  -4.97
print(fit.s$bpar, 3)
#>               Estimate se_notrans t value   Pr(>t)    Lower    Upper
-#> parent_0      99.59848   1.613712   61.72 2.02e-38 96.32572 1.03e+02
-#> k_parent_sink  0.04792   0.003750   12.78 3.05e-15  0.04089 5.62e-02
-#> k_parent_m1    0.05078   0.002094   24.25 3.41e-24  0.04670 5.52e-02
-#> k_m1_sink      0.00526   0.000716    7.35 5.76e-09  0.00399 6.93e-03

+#> parent_0             99.60     1.5702 96.40 102.79
+#> log_k_parent_sink    -3.04     0.0763 -3.19  -2.88
+#> log_k_parent_m1      -2.98     0.0403 -3.06  -2.90
+#> log_k_m1_sink        -5.25     0.1332 -5.52  -4.98
+#> sigma                 3.13     0.3585  2.40   3.85
print(fit.s$bpar, 3)
#>               Estimate se_notrans t value   Pr(>t)    Lower    Upper
+#> parent_0      99.59848    1.57022   63.43 2.30e-36 96.40384 102.7931
+#> k_parent_sink  0.04792    0.00365   13.11 6.13e-15  0.04103   0.0560
+#> k_parent_m1    0.05078    0.00205   24.80 3.27e-23  0.04678   0.0551
+#> k_m1_sink      0.00526    0.00070    7.51 6.16e-09  0.00401   0.0069
+#> sigma          3.12550    0.35852    8.72 2.24e-10  2.39609   3.8549

 
# Compare to the version without transforming rate parameters
-fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE, quiet = TRUE)
-fit.2.s <- summary(fit.2)
+fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
fit.2.s <- summary(fit.2)
 print(fit.2.s$par, 3)
#>               Estimate Std. Error    Lower    Upper
-#> parent_0      99.59848   1.613710 96.32573 1.03e+02
-#> k_parent_sink  0.04792   0.003750  0.04031 5.55e-02
-#> k_parent_m1    0.05078   0.002094  0.04653 5.50e-02
-#> k_m1_sink      0.00526   0.000716  0.00381 6.71e-03
print(fit.2.s$bpar, 3)
#>               Estimate se_notrans t value   Pr(>t)    Lower    Upper
-#> parent_0      99.59848   1.613710   61.72 2.02e-38 96.32573 1.03e+02
-#> k_parent_sink  0.04792   0.003750   12.78 3.05e-15  0.04031 5.55e-02
-#> k_parent_m1    0.05078   0.002094   24.25 3.41e-24  0.04653 5.50e-02
-#> k_m1_sink      0.00526   0.000716    7.35 5.76e-09  0.00381 6.71e-03

+#> parent_0      99.59848    1.57022 96.40384 1.03e+02
+#> k_parent_sink  0.04792    0.00365  0.04049 5.54e-02
+#> k_parent_m1    0.05078    0.00205  0.04661 5.49e-02
+#> k_m1_sink      0.00526    0.00070  0.00384 6.69e-03
+#> sigma          3.12550    0.35852  2.39609 3.85e+00
print(fit.2.s$bpar, 3)
#>               Estimate se_notrans t value   Pr(>t)    Lower    Upper
+#> parent_0      99.59848    1.57022   63.43 2.30e-36 96.40384 1.03e+02
+#> k_parent_sink  0.04792    0.00365   13.11 6.13e-15  0.04049 5.54e-02
+#> k_parent_m1    0.05078    0.00205   24.80 3.27e-23  0.04661 5.49e-02
+#> k_m1_sink      0.00526    0.00070    7.51 6.16e-09  0.00384 6.69e-03
+#> sigma          3.12550    0.35852    8.72 2.24e-10  2.39609 3.85e+00

 initials <- fit$start$value
 names(initials) <- rownames(fit$start)
 transformed <- fit$start_transformed$value
@@ -238,17 +240,18 @@ The transformation of sets of formation fractions is fragile, as it supposes
   parent = list(type = "SFO", to = "m1", sink = TRUE),
   m1 = list(type = "SFO"),
   use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.

-fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
-fit.ff.s <- summary(fit.ff)
+fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
fit.ff.s <- summary(fit.ff)
 print(fit.ff.s$par, 3)
#>                Estimate Std. Error   Lower   Upper
-#> parent_0         99.598     1.6137 96.3257 102.871
-#> log_k_parent     -2.316     0.0419 -2.4006  -2.231
-#> log_k_m1         -5.248     0.1361 -5.5235  -4.972
-#> f_parent_ilr_1    0.041     0.0648 -0.0904   0.172
print(fit.ff.s$bpar, 3)
#>                Estimate se_notrans t value   Pr(>t)    Lower    Upper
-#> parent_0       99.59848   1.613712   61.72 2.02e-38 96.32574 1.03e+02
-#> k_parent        0.09870   0.004132   23.88 5.70e-24  0.09066 1.07e-01
-#> k_m1            0.00526   0.000716    7.35 5.76e-09  0.00399 6.93e-03
-#> f_parent_to_m1  0.51448   0.022880   22.49 4.37e-23  0.46808 5.61e-01
initials <- c("f_parent_to_m1" = 0.5)
+#> parent_0         99.598     1.5702 96.4038 102.793
+#> log_k_parent     -2.316     0.0409 -2.3988  -2.233
+#> log_k_m1         -5.248     0.1332 -5.5184  -4.977
+#> f_parent_ilr_1    0.041     0.0631 -0.0875   0.169
+#> sigma             3.126     0.3585  2.3961   3.855
print(fit.ff.s$bpar, 3)
#>                Estimate se_notrans t value   Pr(>t)    Lower    Upper
+#> parent_0       99.59848    1.57022   63.43 2.30e-36 96.40384 102.7931
+#> k_parent        0.09870    0.00403   24.47 4.96e-23  0.09082   0.1073
+#> k_m1            0.00526    0.00070    7.51 6.16e-09  0.00401   0.0069
+#> f_parent_to_m1  0.51448    0.02230   23.07 3.10e-22  0.46912   0.5596
+#> sigma           3.12550    0.35852    8.72 2.24e-10  2.39609   3.8549
initials <- c("f_parent_to_m1" = 0.5)
 transformed <- transform_odeparms(initials, SFO_SFO.ff)
 backtransform_odeparms(transformed, SFO_SFO.ff)
#> f_parent_to_m1 
 #>            0.5 

@@ -258,15 +261,16 @@ The transformation of sets of formation fractions is fragile, as it supposes
   m1 = list(type = "SFO"),
   use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.

 
-fit.ff.2 <- mkinfit(SFO_SFO.ff.2, FOCUS_2006_D, quiet = TRUE)
-fit.ff.2.s <- summary(fit.ff.2)
+fit.ff.2 <- mkinfit(SFO_SFO.ff.2, FOCUS_2006_D, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
fit.ff.2.s <- summary(fit.ff.2)
 print(fit.ff.2.s$par, 3)
#>              Estimate Std. Error Lower Upper
-#> parent_0        84.79     2.9651 78.78 90.80
-#> log_k_parent    -2.76     0.0809 -2.92 -2.59
-#> log_k_m1        -4.21     0.1115 -4.44 -3.99
print(fit.ff.2.s$bpar, 3)
#>          Estimate se_notrans t value   Pr(>t)   Lower   Upper
-#> parent_0  84.7916    2.96505   28.60 3.94e-27 78.7838 90.7994
-#> k_parent   0.0635    0.00514   12.36 5.24e-15  0.0539  0.0748
-#> k_m1       0.0148    0.00165    8.97 4.11e-11  0.0118  0.0185
+#> parent_0 84.79 3.012 78.67 90.91 +#> log_k_parent -2.76 0.082 -2.92 -2.59 +#> log_k_m1 -4.21 0.123 -4.46 -3.96 +#> sigma 8.22 0.943 6.31 10.14
print(fit.ff.2.s$bpar, 3)
#> Estimate se_notrans t value Pr(>t) Lower Upper +#> parent_0 84.7916 3.01203 28.15 1.92e-25 78.6704 90.913 +#> k_parent 0.0635 0.00521 12.19 2.91e-14 0.0538 0.075 +#> k_m1 0.0148 0.00182 8.13 8.81e-10 0.0115 0.019 +#> sigma 8.2229 0.94323 8.72 1.73e-10 6.3060 10.140