From ac183c732317cf6ede26a2ee127604a407f0a6b3 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 4 Feb 2021 11:24:22 +0100 Subject: Documentation improvements, mainly fixing example code The errors in the example code were in the \dontrun sections, so they were not caught by CRAN checks. In addition, the static help files generated with pkgdown were cached, so I noticed the errors only after completely regenerating the documentation for version 1.0.0. --- docs/reference/transform_odeparms.html | 78 ++++++++++++++++++++-------------- 1 file changed, 46 insertions(+), 32 deletions(-) (limited to 'docs/reference/transform_odeparms.html') diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index efaf7b46..e2cb876b 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -77,7 +77,7 @@ the ilr transformation is used." /> mkin - 1.0.0 + 1.0.1 @@ -231,50 +231,64 @@ This is no problem for the internal use in mkinfit.
SFO_SFO <- mkinmod( parent = list(type = "SFO", to = "m1", sink = TRUE), - m1 = list(type = "SFO")) -
#> Temporary DLL for differentials generated and loaded
# 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) + m1 = list(type = "SFO"), use_of_ff = "min") +
#> Temporary DLL for differentials generated and loaded
+# Fit the model to the FOCUS example dataset D using defaults +FOCUS_D <- subset(FOCUS_2006_D, value != 0) # remove zero values to avoid warning +fit <- mkinfit(SFO_SFO, FOCUS_D, quiet = TRUE) +fit.s <- summary(fit) # Transformed and backtransformed parameters print(fit.s$par, 3) -
#> Estimate Std. Error Lower Upper -#> parent_0 99.5985 1.5702 96.404 102.79 -#> log_k_parent -2.3157 0.0409 -2.399 -2.23 -#> log_k_m1 -5.2475 0.1332 -5.518 -4.98 -#> f_parent_qlogis 0.0579 0.0893 -0.124 0.24 -#> sigma 3.1255 0.3585 2.396 3.85
print(fit.s$bpar, 3) -
#> Estimate se_notrans t value Pr(>t) Lower Upper -#> parent_0 99.59848 1.57022 63.43 2.30e-36 96.40383 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
+
#> 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$bpar, 3) +
#> Estimate se_notrans t value Pr(>t) Lower Upper +#> parent_0 99.59848 1.57022 63.43 2.30e-36 96.40384 102.7931 +#> k_parent_sink 0.04792 0.00365 13.11 6.13e-15 0.04103 0.0560 +#> k_parent_m1 0.05078 0.00205 24.80 3.27e-23 0.04678 0.0551 +#> k_m1_sink 0.00526 0.00070 7.51 6.16e-09 0.00401 0.0069 +#> sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.8549
# \dontrun{ -# Compare to the version without transforming rate parameters -fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE, quiet = TRUE) -
#> Warning: Observations with value of zero were removed from the data
#> Error in if (cost < cost.current) { assign("cost.current", cost, inherits = TRUE) if (!quiet) cat(ifelse(OLS, "Sum of squared residuals", "Negative log-likelihood"), " at call ", calls, ": ", signif(cost.current, 6), "\n", sep = "")}: missing value where TRUE/FALSE needed
#> Timing stopped at: 0.003 0 0.003
fit.2.s <- summary(fit.2) -
#> Error in summary(fit.2): object 'fit.2' not found
print(fit.2.s$par, 3) -
#> Error in print(fit.2.s$par, 3): object 'fit.2.s' not found
print(fit.2.s$bpar, 3) -
#> Error in print(fit.2.s$bpar, 3): object 'fit.2.s' not found
# } +# Compare to the version without transforming rate parameters (does not work +# with analytical solution, we get NA values for m1 in predictions) +fit.2 <- mkinfit(SFO_SFO, FOCUS_D, transform_rates = FALSE, + solution_type = "deSolve", quiet = TRUE) +fit.2.s <- summary(fit.2) +print(fit.2.s$par, 3) +
#> Estimate Std. Error Lower Upper +#> parent_0 99.59849 1.57022 96.40385 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$bpar, 3) +
#> Estimate se_notrans t value Pr(>t) Lower Upper +#> parent_0 99.59849 1.57022 63.43 2.30e-36 96.40385 1.03e+02 +#> k_parent_sink 0.04792 0.00365 13.11 6.13e-15 0.04049 5.54e-02 +#> k_parent_m1 0.05078 0.00205 24.80 3.27e-23 0.04661 5.49e-02 +#> k_m1_sink 0.00526 0.00070 7.51 6.16e-09 0.00384 6.69e-03 +#> sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.85e+00
# } initials <- fit$start$value names(initials) <- rownames(fit$start) transformed <- fit$start_transformed$value names(transformed) <- rownames(fit$start_transformed) transform_odeparms(initials, SFO_SFO) -
#> parent_0 log_k_parent log_k_m1 f_parent_qlogis -#> 100.750000 -2.302585 -2.301586 0.000000
backtransform_odeparms(transformed, SFO_SFO) -
#> parent_0 k_parent k_m1 f_parent_to_m1 -#> 100.7500 0.1000 0.1001 0.5000
+
#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 100.750000 -2.302585 -2.301586 -2.300587
backtransform_odeparms(transformed, SFO_SFO) +
#> parent_0 k_parent_sink k_parent_m1 k_m1_sink +#> 100.7500 0.1000 0.1001 0.1002
# \dontrun{ -# The case of formation fractions +# The case of formation fractions (this is now the default) SFO_SFO.ff <- mkinmod( parent = list(type = "SFO", to = "m1", sink = TRUE), m1 = list(type = "SFO"), use_of_ff = "max")
#> Temporary DLL for differentials generated and loaded
-fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE) -
#> Warning: Observations with value of zero were removed from the data
fit.ff.s <- summary(fit.ff) +fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_D, quiet = TRUE) +fit.ff.s <- summary(fit.ff) print(fit.ff.s$par, 3)
#> Estimate Std. Error Lower Upper #> parent_0 99.5985 1.5702 96.404 102.79 @@ -299,8 +313,8 @@ This is no problem for the internal use in mkinfit.= "max")
#> Temporary DLL for differentials generated and loaded
-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) +fit.ff.2 <- mkinfit(SFO_SFO.ff.2, FOCUS_D, quiet = TRUE) +fit.ff.2.s <- summary(fit.ff.2) print(fit.ff.2.s$par, 3)
#> Estimate Std. Error Lower Upper #> parent_0 84.79 3.012 78.67 90.91 -- cgit v1.2.1