diff options
| -rw-r--r-- | DESCRIPTION | 4 | ||||
| -rw-r--r-- | GNUmakefile | 4 | ||||
| -rw-r--r-- | NEWS.md | 12 | ||||
| -rw-r--r-- | R/endpoints.R | 38 | ||||
| -rw-r--r-- | check.log | 10 | ||||
| -rw-r--r-- | test.log | 1 | ||||
| -rw-r--r-- | vignettes/FOCUS_Z.pdf | bin | 225060 -> 219834 bytes | |||
| -rw-r--r-- | vignettes/compiled_models.Rmd | 101 |
8 files changed, 46 insertions, 124 deletions
diff --git a/DESCRIPTION b/DESCRIPTION index a8cfb15b..85846fa0 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: 0.9-40 -Date: 2015-06-29 +Date: 2015-06-30 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "jranke@uni-bremen.de"), person("Katrin", "Lindenberger", role = "ctb"), @@ -18,7 +18,7 @@ Description: Calculation routines based on the FOCUS Kinetics Report (2006). Please note that no warranty is implied for correctness of results or fitness for a particular purpose. Depends: minpack.lm, rootSolve, inline, parallel -Imports: FME, deSolve +Imports: stats, graphics, FME, deSolve Suggests: knitr, testthat, microbenchmark License: GPL LazyLoad: yes diff --git a/GNUmakefile b/GNUmakefile index 80b88eb4..b6bec285 100644 --- a/GNUmakefile +++ b/GNUmakefile @@ -61,8 +61,12 @@ quickcheck: build-no-vignettes clean: $(RM) -r $(PKGNAME).Rcheck/ + $(RM) -r vignettes/*.bbl + $(RM) -r vignettes/*.blg $(RM) -r vignettes/*.fls $(RM) -r vignettes/*.fdb_latexmk + $(RM) -r vignettes/cache + $(RM) -r vignettes/files $(RM) -r vignettes/*_cache $(RM) -r vignettes/*_files $(RM) -r vignettes/*-concordance.tex @@ -1,6 +1,16 @@ # NEWS for package 'mkin' -## CHANGES in mkin VERSION 0.9-39 +## CHANGES in mkin VERSION 0.9-40 + +### BUG FIXES + +- `endpoints()`: For DFOP and SFORB models, where `optimize()` is used, make use of the fact that the DT50 must be between DT50_k1 and DT50_k2 (DFOP) or DT50_b1 and DT50_b2 (SFORB), as `optimize()` sometimes did not find the minimum. Likewise for finding DT90 values. Also fit on the log scale to make the function more efficient. + +### INTERNAL CHANGES + +- `DESCRIPTION`, `NAMESPACE`, `R/*.R`: Import stats and graphics package, qualify function calls for non-base packages installed with R to avoid NOTES made by R CMD check --as-cran with upcoming R versions. + +## CHANGES in mkin VERSION 0.9-39 (2015-06-26) ### MAJOR CHANGES diff --git a/R/endpoints.R b/R/endpoints.R index 001595bc..a930acb7 100644 --- a/R/endpoints.R +++ b/R/endpoints.R @@ -75,17 +75,20 @@ endpoints <- function(fit) { k1 = parms.all["k1"]
k2 = parms.all["k2"]
g = parms.all["g"]
- f <- function(t, x) {
+ f <- function(log_t, x) {
+ t <- exp(log_t)
fraction <- g * exp( - k1 * t) + (1 - g) * exp( - k2 * t)
(fraction - (1 - x/100))^2
}
- DTmax <- 1000
- DT50.o <- optimize(f, c(0.001, DTmax), x=50)$minimum
- DT50 = ifelse(DTmax - DT50.o < 0.1, NA, DT50.o)
- DT90.o <- optimize(f, c(0.001, DTmax), x=90)$minimum
- DT90 = ifelse(DTmax - DT90.o < 0.1, NA, DT90.o)
DT50_k1 = log(2)/k1
DT50_k2 = log(2)/k2
+ DT90_k1 = log(10)/k1
+ DT90_k2 = log(10)/k2
+ DT50 <- try(exp(optimize(f, c(log(DT50_k1), log(DT50_k2)), x=50)$minimum))
+ DT90 <- try(exp(optimize(f, c(log(DT90_k1), log(DT90_k2)), x=90)$minimum))
+ if (inherits(DT50, "try-error")) DT50 = NA
+ if (inherits(DT90, "try-error")) DT90 = NA
+
ep$distimes[obs_var, c("DT50_k1")] = DT50_k1
ep$distimes[obs_var, c("DT50_k2")] = DT50_k2
}
@@ -119,26 +122,29 @@ endpoints <- function(fit) { b1 = 0.5 * (k_12 + k_21 + k_1output) + sqrt_exp
b2 = 0.5 * (k_12 + k_21 + k_1output) - sqrt_exp
+ DT50_b1 = log(2)/b1
+ DT50_b2 = log(2)/b2
+ DT90_b1 = log(10)/b1
+ DT90_b2 = log(10)/b2
+
+
SFORB_fraction = function(t) {
((k_12 + k_21 - b1)/(b2 - b1)) * exp(-b1 * t) +
((k_12 + k_21 - b2)/(b1 - b2)) * exp(-b2 * t)
}
- f_50 <- function(t) (SFORB_fraction(t) - 0.5)^2
- max_DT <- 1000
- DT50.o <- optimize(f_50, c(0.01, max_DT))$minimum
- if (abs(DT50.o - max_DT) < 0.01) DT50 = NA else DT50 = DT50.o
- f_90 <- function(t) (SFORB_fraction(t) - 0.1)^2
- DT90.o <- optimize(f_90, c(0.01, max_DT))$minimum
- if (abs(DT90.o - max_DT) < 0.01) DT90 = NA else DT90 = DT90.o
+ f_50 <- function(log_t) (SFORB_fraction(exp(log_t)) - 0.5)^2
+ DT50 <- try(exp(optimize(f_50, c(log(DT50_b1), log(DT50_b2)))$minimum))
+ f_90 <- function(log_t) (SFORB_fraction(exp(log_t)) - 0.1)^2
+ DT90 <- try(exp(optimize(f_90, c(log(DT90_b1), log(DT90_b2)))$minimum))
+
+ if (inherits(DT50, "try-error")) DT50 = NA
+ if (inherits(DT90, "try-error")) DT90 = NA
for (k_out_name in k_out_names)
{
ep$ff[[sub("k_", "", k_out_name)]] = parms.all[[k_out_name]] / k_1output
}
- DT50_b1 = log(2)/b1
- DT50_b2 = log(2)/b2
-
# Return the eigenvalues for comparison with DFOP rate constants
ep$SFORB[[paste(obs_var, "b1", sep="_")]] = b1
ep$SFORB[[paste(obs_var, "b2", sep="_")]] = b2
@@ -10,7 +10,7 @@ * checking CRAN incoming feasibility ... NOTE Maintainer: ‘Johannes Ranke <jranke@uni-bremen.de>’ -Days since last update: 3 +Days since last update: 4 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK @@ -56,7 +56,10 @@ Days since last update: 3 * checking data for ASCII and uncompressed saves ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK -* checking files in ‘vignettes’ ... OK +* checking files in ‘vignettes’ ... NOTE +The following files look like leftovers/mistakes: + ‘FOCUS_Z.bbl’, ‘FOCUS_Z.blg’ +Please remove them from your package. * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... SKIPPED @@ -65,7 +68,6 @@ Days since last update: 3 * checking running R code from vignettes ... ‘FOCUS_D.Rmd’ using ‘UTF-8’ ... OK ‘FOCUS_L.Rmd’ using ‘UTF-8’ ... OK - ‘compiled_models.Rmd’ using ‘UTF-8’ ... OK ‘FOCUS_Z.Rnw’ using ‘UTF-8’ ... OK ‘mkin.Rnw’ using ‘UTF-8’ ... OK OK @@ -73,7 +75,7 @@ Days since last update: 3 * checking PDF version of manual ... OK * DONE -Status: 1 NOTE +Status: 2 NOTEs See ‘/home/jranke/git/mkin/mkin.Rcheck/00check.log’ for details. @@ -11,3 +11,4 @@ Fitting of parent only models : ..................... Complex test case from Schaefer et al. (2007) Piacenza paper : .. Results for synthetic data established in expertise for UBA (Ranke 2014) : .... +Way to go! diff --git a/vignettes/FOCUS_Z.pdf b/vignettes/FOCUS_Z.pdf Binary files differindex 8b8f7416..3fb4f69c 100644 --- a/vignettes/FOCUS_Z.pdf +++ b/vignettes/FOCUS_Z.pdf diff --git a/vignettes/compiled_models.Rmd b/vignettes/compiled_models.Rmd deleted file mode 100644 index 8dc74692..00000000 --- a/vignettes/compiled_models.Rmd +++ /dev/null @@ -1,101 +0,0 @@ ----
-title: "Performance benefit by using compiled model definitions in mkin"
-author: "Johannes Ranke"
-date: "`r Sys.Date()`"
-output:
- html_document:
- css: mkin_vignettes.css
- toc: true
- mathjax: null
- theme: united
-vignette: >
- %\VignetteIndexEntry{Performance benefit by using compiled model definitions in mkin}
- %\VignetteEngine{knitr::rmarkdown}
- \usepackage[utf8]{inputenc}
----
-
-```{r, include = FALSE}
-library(knitr)
-opts_chunk$set(tidy = FALSE, cache = TRUE)
-```
-
-## Benchmark for a model that can also be solved with Eigenvalues
-
-This evaluation is taken from the example section of mkinfit. When using an mkin version
-equal to or greater than 0.9-36 and a C compiler (gcc) is available, you will see
-a message that the model is being compiled from autogenerated C code when
-defining a model using mkinmod. The `mkinmod()` function checks for presence of
-the gcc compiler using
-
-```{r check_gcc}
-Sys.which("gcc")
-```
-First, we build a simple degradation model for a parent compound with one metabolite.
-
-```{r create_SFO_SFO}
-library("mkin")
-SFO_SFO <- mkinmod(
- parent = mkinsub("SFO", "m1"),
- m1 = mkinsub("SFO"))
-```
-
-We can compare the performance of the Eigenvalue based solution against the
-compiled version and the R implementation of the differential equations using
-the microbenchmark package.
-
-
-```{r benchmark_SFO_SFO}
-library("microbenchmark")
-mb.1 <- microbenchmark(
- mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve", use_compiled = FALSE,
- quiet = TRUE),
- mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "eigen", quiet = TRUE),
- mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve", quiet = TRUE),
- times = 3, control = list(warmup = 1))
-smb.1 <- summary(mb.1)[-1]
-rownames(smb.1) <- c("deSolve, not compiled", "Eigenvalue based", "deSolve, compiled")
-print(smb.1)
-```
-
-We see that using the compiled model is by a factor of
-`r round(smb.1["deSolve, not compiled", "median"]/smb.1["deSolve, compiled", "median"], 1)`
-faster than using the R version with the default ode solver, and it is even
-faster than the Eigenvalue based solution implemented in R which does not need
-iterative solution of the ODEs:
-
-```{r}
-smb.1["median"]/smb.1["deSolve, compiled", "median"]
-```
-
-## Benchmark for a model that can not be solved with Eigenvalues
-
-This evaluation is also taken from the example section of mkinfit.
-
-```{r benchmark_FOMC_SFO}
-FOMC_SFO <- mkinmod(
- parent = mkinsub("FOMC", "m1"),
- m1 = mkinsub( "SFO"))
-
-mb.2 <- microbenchmark(
- mkinfit(FOMC_SFO, FOCUS_2006_D, use_compiled = FALSE, quiet = TRUE),
- mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE),
- times = 3, control = list(warmup = 1))
-smb.2 <- summary(mb.2)[-1]
-rownames(smb.2) <- c("deSolve, not compiled", "deSolve, compiled")
-print(smb.2)
-smb.2["median"]/smb.2["deSolve, compiled", "median"]
-```
-
-Here we get a performance benefit of a factor of
-`r round(smb.2["deSolve, not compiled", "median"]/smb.2["deSolve, compiled", "median"], 1)`
-using the version of the differential equation model compiled from C code using
-the inline package!
-
-This vignette was built with mkin `r packageVersion("mkin")` on
-
-```{r sessionInfo, echo = FALSE}
-cat(capture.output(sessionInfo())[1:3], sep = "\n")
-if(!inherits(try(cpuinfo <- readLines("/proc/cpuinfo")), "try-error")) {
- cat(gsub("model name\t: ", "CPU model: ", cpuinfo[grep("model name", cpuinfo)[1]]))
-}
-```
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