From 9ac853c7ceece333099021974025d07e75be2b33 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 12 May 2020 08:07:07 +0200 Subject: Documentation improvements, rebuild static docs --- docs/reference/transform_odeparms.html | 95 +++++++++++++++------------------- 1 file changed, 42 insertions(+), 53 deletions(-) (limited to 'docs/reference/transform_odeparms.html') diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index 2a08228d..fc0ffef2 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,6 @@ constants and other paramters that can only take on positive values, a simple log transformation is used. For compositional parameters, such as the formations fractions that should always sum up to 1 and can not be negative, the ilr transformation is used." /> - @@ -60,7 +63,7 @@ the ilr transformation is used." /> - +
@@ -118,7 +121,12 @@ the ilr transformation is used." />
@@ -133,7 +141,7 @@ the ilr transformation is used." />

Functions to transform and backtransform kinetic parameters for fitting

- + Source: R/transform_odeparms.R
@@ -204,7 +212,7 @@ fitting procedure.

Value

A vector of transformed or backtransformed parameters with the same - names as the original parameters.

+names as the original parameters.

Details

The transformation of sets of formation fractions is fragile, as it supposes @@ -224,39 +232,28 @@ This is no problem for the internal use in mkinfit< 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)
#> Warning: Observations with value of zero were removed from the data
fit.s <- summary(fit) # Transformed and backtransformed parameters -print(fit.s$par, 3)
#> Estimate Std. Error Lower Upper -#> parent_0 99.60 1.5702 96.40 102.79 -#> log_k_parent_sink -3.04 0.0763 -3.19 -2.88 -#> log_k_parent_m1 -2.98 0.0403 -3.06 -2.90 -#> log_k_m1_sink -5.25 0.1332 -5.52 -4.98 -#> sigma 3.13 0.3585 2.40 3.85
print(fit.s$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
+print(fit.s$par, 3)
#> Estimate Std. Error Lower Upper +#> parent_0 99.598 1.5702 96.4038 102.793 +#> log_k_parent -2.316 0.0409 -2.3988 -2.233 +#> log_k_m1 -5.248 0.1332 -5.5184 -4.977 +#> f_parent_ilr_1 0.041 0.0631 -0.0875 0.169 +#> sigma 3.126 0.3585 2.3961 3.855
print(fit.s$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
# \dontrun{ # Compare to the version without transforming rate parameters -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$par, 3)
#> Estimate Std. Error Lower Upper -#> parent_0 99.59848 1.57022 96.40384 1.03e+02 -#> k_parent_sink 0.04792 0.00365 0.04049 5.54e-02 -#> k_parent_m1 0.05078 0.00205 0.04661 5.49e-02 -#> k_m1_sink 0.00526 0.00070 0.00384 6.69e-03 -#> sigma 3.12550 0.35852 2.39609 3.85e+00
print(fit.2.s$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
# } +fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
#> Error in if (cost < cost.current) { assign("cost.current", cost, inherits = TRUE) if (!quiet) cat(ifelse(OLS, "Sum of squared residuals", "Negative log-likelihood"), " at call ", calls, ": ", cost.current, "\n", sep = "")}: Fehlender Wert, wo TRUE/FALSE nötig ist
#> Timing stopped at: 0.002 0 0.003
fit.2.s <- summary(fit.2)
#> Error in summary(fit.2): Objekt 'fit.2' nicht gefunden
print(fit.2.s$par, 3)
#> Error in print(fit.2.s$par, 3): Objekt 'fit.2.s' nicht gefunden
print(fit.2.s$bpar, 3)
#> Error in print(fit.2.s$bpar, 3): Objekt 'fit.2.s' nicht gefunden
# } initials <- fit$start$value names(initials) <- rownames(fit$start) transformed <- fit$start_transformed$value names(transformed) <- rownames(fit$start_transformed) -transform_odeparms(initials, SFO_SFO)
#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink -#> 100.750000 -2.302585 -2.301586 -2.300587
backtransform_odeparms(transformed, SFO_SFO)
#> parent_0 k_parent_sink k_parent_m1 k_m1_sink -#> 100.7500 0.1000 0.1001 0.1002
+transform_odeparms(initials, SFO_SFO)
#> parent_0 log_k_parent log_k_m1 f_parent_ilr_1 +#> 100.750000 -2.302585 -2.301586 0.000000
backtransform_odeparms(transformed, SFO_SFO)
#> parent_0 k_parent k_m1 f_parent_to_m1 +#> 100.7500 0.1000 0.1001 0.5000
# \dontrun{ # The case of formation fractions SFO_SFO.ff <- mkinmod( @@ -297,18 +294,10 @@ This is no problem for the internal use in mkinfit<
- @@ -319,7 +308,7 @@ This is no problem for the internal use in mkinfit<
-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.5.1.

-- cgit v1.2.1