diff options
author | Johannes Ranke <jranke@uni-bremen.de> | 2015-05-18 16:58:44 +0200 |
---|---|---|
committer | Johannes Ranke <jranke@uni-bremen.de> | 2015-05-18 16:58:44 +0200 |
commit | d337a9665d9261d18734d81edc8fe4b569635e71 (patch) | |
tree | 794ca4b3df97b083e7c05678abac785a575ed808 | |
parent | 4cc0da3b67ec78534271eaef23ff2b13abfb86d9 (diff) |
Make checking faster, testing is done by tests
-rw-r--r-- | DESCRIPTION | 2 | ||||
-rw-r--r-- | GNUmakefile | 2 | ||||
-rw-r--r-- | man/mkinfit.Rd | 19 | ||||
-rw-r--r-- | man/synthetic_data_for_UBA.Rd | 2 | ||||
-rw-r--r-- | man/transform_odeparms.Rd | 2 |
5 files changed, 12 insertions, 15 deletions
diff --git a/DESCRIPTION b/DESCRIPTION index 295eaac6..59b653f4 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -3,7 +3,7 @@ Type: Package Title: Routines for Fitting Kinetic Models with One or More State Variables to Chemical Degradation Data Version: 0.9-36 -Date: 2015-05-15 +Date: 2015-05-18 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "jranke@uni-bremen.de"), person("Katrin", "Lindenberger", role = "ctb"), diff --git a/GNUmakefile b/GNUmakefile index 30576682..613c124c 100644 --- a/GNUmakefile +++ b/GNUmakefile @@ -60,7 +60,7 @@ check: build check-no-vignettes: build-no-vignettes mv $(TGZVNR) $(TGZ) - "$(RBIN)/R" CMD check --as-cran --no-tests $(TGZ) + "$(RBIN)/R" CMD check --as-cran --no-tests --no-build-vignettes --no-vignettes $(TGZ) mv $(TGZ) $(TGZVNR) clean: diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd index 34e5bbae..2d8d3726 100644 --- a/man/mkinfit.Rd +++ b/man/mkinfit.Rd @@ -243,20 +243,14 @@ SFO_SFO <- mkinmod( # Fit the model to the FOCUS example dataset D using defaults system.time(fit <- mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "eigen")) -system.time(fit.deSolve <- mkinfit(SFO_SFO, FOCUS_2006_D, - solution_type = "deSolve", use_compiled = FALSE)) -system.time(fit.deSolve.compiled <- mkinfit(SFO_SFO, FOCUS_2006_D, - solution_type = "deSolve", use_compiled = TRUE)) -# The performance benefit of using the compiled version is immense compared -# with deSolve without compilation, and about a factor of two compared with the -# eigenvalue based solution coef(fit) -coef(fit.deSolve) -coef(fit.deSolve.compiled) endpoints(fit) +\dontrun{ +system.time(fit.deSolve <- mkinfit(SFO_SFO, FOCUS_2006_D, + solution_type = "deSolve")) +coef(fit.deSolve) endpoints(fit.deSolve) -# Check compiled model versions against other solutions - +} # Use stepwise fitting, using optimised parameters from parent only fit, FOMC \dontrun{ @@ -282,6 +276,7 @@ fit.SFORB_SFO.deSolve <- mkinfit(SFORB_SFO, FOCUS_2006_D, solution_type = "deSol # Use starting parameters from parent only SFORB fit (not really needed in this case) fit.SFORB = mkinfit(SFORB, FOCUS_2006_D) fit.SFORB_SFO <- mkinfit(SFORB_SFO, FOCUS_2006_D, parms.ini = fit.SFORB$bparms.ode) +} \dontrun{ # Weighted fits, including IRLS @@ -309,7 +304,5 @@ f.w.man.irls <- mkinfit(SFO_SFO.ff, dw, err = "err.man", reweight.method = "obs") summary(f.w.man.irls) } - } -\keyword{ models } \keyword{ optimize } diff --git a/man/synthetic_data_for_UBA.Rd b/man/synthetic_data_for_UBA.Rd index 5d924afd..468e3731 100644 --- a/man/synthetic_data_for_UBA.Rd +++ b/man/synthetic_data_for_UBA.Rd @@ -41,6 +41,7 @@ measurement error in analytical chemistry. Technometrics 37(2), 176-184.
}
\examples{
+\dontrun{
m_synth_SFO_lin <- mkinmod(parent = list(type = "SFO", to = "M1"),
M1 = list(type = "SFO", to = "M2"),
M2 = list(type = "SFO"), use_of_ff = "max")
@@ -62,4 +63,5 @@ m_synth_DFOP_par <- mkinmod(parent = list(type = "DFOP", to = c("M1", "M2"), mkinfit(m_synth_SFO_lin, synthetic_data_for_UBA_2014[[1]]$data)
}
+}
\keyword{datasets}
diff --git a/man/transform_odeparms.Rd b/man/transform_odeparms.Rd index ba93af7d..1385a896 100644 --- a/man/transform_odeparms.Rd +++ b/man/transform_odeparms.Rd @@ -76,6 +76,7 @@ names(transformed) <- rownames(fit$start_transformed) transform_odeparms(initials, SFO_SFO) backtransform_odeparms(transformed, SFO_SFO) +\dontrun{ # The case of formation fractions SFO_SFO.ff <- mkinmod( parent = list(type = "SFO", to = "m1", sink = TRUE), @@ -98,4 +99,5 @@ SFO_SFO.ff.2 <- mkinmod( fit.ff.2 <- mkinfit(SFO_SFO.ff.2, FOCUS_2006_D) summary(fit.ff.2, data = FALSE) } +} \keyword{ manip } |