From bc3825ae2d12c18ea3d3caf17eb23c93fef180b8 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 8 Oct 2020 09:31:35 +0200 Subject: Fix issues for release --- docs/dev/reference/transform_odeparms.html | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) (limited to 'docs/dev/reference/transform_odeparms.html') diff --git a/docs/dev/reference/transform_odeparms.html b/docs/dev/reference/transform_odeparms.html index b0994d33..58a1e9a1 100644 --- a/docs/dev/reference/transform_odeparms.html +++ b/docs/dev/reference/transform_odeparms.html @@ -226,7 +226,7 @@ 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"))
#> 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) +fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
#> Warning: Shapiro-Wilk test for standardized residuals: p = 0.0165
fit.s <- summary(fit) # Transformed and backtransformed parameters print(fit.s$par, 3)
#> Estimate Std. Error Lower Upper #> parent_0 99.598 1.5702 96.4038 102.793 @@ -241,7 +241,7 @@ This is no problem for the internal use in mkinfit< #> sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.8549
# \dontrun{ # Compare to the version without transforming rate parameters -fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
#> Error in if (cost < cost.current) { assign("cost.current", cost, inherits = TRUE) if (!quiet) cat(ifelse(OLS, "Sum of squared residuals", "Negative log-likelihood"), " at call ", calls, ": ", cost.current, "\n", sep = "")}: missing value where TRUE/FALSE needed
#> Timing stopped at: 0 0.002 0.002
fit.2.s <- summary(fit.2)
#> Error in summary(fit.2): object 'fit.2' not found
print(fit.2.s$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$bpar, 3): object 'fit.2.s' not found
# } +fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
#> Error in if (cost < cost.current) { assign("cost.current", cost, inherits = TRUE) if (!quiet) cat(ifelse(OLS, "Sum of squared residuals", "Negative log-likelihood"), " at call ", calls, ": ", signif(cost.current, 6), "\n", sep = "")}: missing value where TRUE/FALSE needed
#> Timing stopped at: 0.002 0 0.003
fit.2.s <- summary(fit.2)
#> Error in summary(fit.2): object 'fit.2' not found
print(fit.2.s$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$bpar, 3): object 'fit.2.s' not found
# } initials <- fit$start$value names(initials) <- rownames(fit$start) @@ -256,7 +256,7 @@ This is no problem for the internal use in mkinfit< 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)
#> Warning: Observations with value of zero were removed from the data
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
#> Warning: Shapiro-Wilk test for standardized residuals: p = 0.0165
fit.ff.s <- summary(fit.ff) print(fit.ff.s$par, 3)
#> Estimate Std. Error Lower Upper #> parent_0 99.598 1.5702 96.4038 102.793 #> log_k_parent -2.316 0.0409 -2.3988 -2.233 @@ -277,7 +277,7 @@ This is no problem for the internal use in mkinfit< m1 = list(type = "SFO"), use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.
-fit.ff.2 <- mkinfit(SFO_SFO.ff.2, FOCUS_2006_D, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
fit.ff.2.s <- summary(fit.ff.2) +fit.ff.2 <- mkinfit(SFO_SFO.ff.2, FOCUS_2006_D, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
#> Warning: Shapiro-Wilk test for standardized residuals: p = 0.0242
fit.ff.2.s <- summary(fit.ff.2) print(fit.ff.2.s$par, 3)
#> Estimate Std. Error Lower Upper #> parent_0 84.79 3.012 78.67 90.91 #> log_k_parent -2.76 0.082 -2.92 -2.59 -- cgit v1.2.1