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Diffstat (limited to 'README.md')
| -rw-r--r-- | README.md | 182 |
1 files changed, 174 insertions, 8 deletions
@@ -10,7 +10,8 @@ if several compartments are involved. You can install the latest released version from [CRAN](http://cran.r-project.org/package=mkin) from within R: -```{r} + +```r install.packages("mkin") ``` @@ -19,7 +20,8 @@ If looking for the latest features, you can install directly from Using `quick = TRUE` skips docs, multiple-architecture builds, demos, and vignettes, to make installation as fast and painless as possible. -```{r} + +```r require(devtools) install_github("jranke/mkin", quick = TRUE) ``` @@ -37,29 +39,54 @@ detailed guidance and helpful tools have been developed as detailed in The simplest usage example that I can think of, using model shorthand notation (available since mkin 0.9-32) and a built-in dataset is -```{r} + +```r library(mkin) -fit <- mkinfit("SFO", FOCUS_2006_C) +``` + +``` +## Loading required package: minpack.lm +## Loading required package: rootSolve +``` + +```r +fit <- mkinfit("SFO", FOCUS_2006_C, quiet = TRUE) plot(fit, show_residuals = TRUE) +``` + + + + +```r +# Output not shown in this README to avoid distraction summary(fit) ``` A still very simple usage example including the definition of the same data in R code would be -```{r} + +```r example_data = data.frame( name = rep("parent", 9), time = c(0, 1, 3, 7, 14, 28, 63, 91, 119), value = c(85.1, 57.9, 29.9, 14.6, 9.7, 6.6, 4, 3.9, 0.6) ) -fit2 <- mkinfit("FOMC", example_data) +fit2 <- mkinfit("FOMC", example_data, quiet = TRUE) plot(fit2, show_residuals = TRUE) ``` + + A fairly complex usage example using another built-in dataset: -```{r} + +``` +## Loading required package: methods +``` + + +```r data <- mkin_wide_to_long(schaefer07_complex_case, time = "time") model <- mkinmod( @@ -68,14 +95,153 @@ model <- mkinmod( B1 = mkinsub("SFO"), C1 = mkinsub("SFO"), A2 = mkinsub("SFO"), use_of_ff = "max") +``` +``` +## Compiling differential equation model from auto-generated C code... +``` + +```r fit3 <- mkinfit(model, data, method.modFit = "Port") +``` +``` +## Model cost at call 1 : 2511.655 +## Model cost at call 2 : 2511.655 +## Model cost at call 11 : 1436.639 +## Model cost at call 12 : 1436.638 +## Model cost at call 13 : 1436.566 +## Model cost at call 21 : 643.6583 +## Model cost at call 22 : 643.6583 +## Model cost at call 23 : 643.6582 +## Model cost at call 29 : 643.6576 +## Model cost at call 31 : 454.0244 +## Model cost at call 32 : 454.0241 +## Model cost at call 34 : 454.0229 +## Model cost at call 43 : 378.1144 +## Model cost at call 45 : 378.1143 +## Model cost at call 53 : 357.245 +## Model cost at call 55 : 357.2449 +## Model cost at call 56 : 357.2447 +## Model cost at call 63 : 354.3415 +## Model cost at call 64 : 354.3415 +## Model cost at call 65 : 354.3413 +## Model cost at call 73 : 332.49 +## Model cost at call 74 : 332.49 +## Model cost at call 81 : 332.4899 +## Model cost at call 83 : 315.2962 +## Model cost at call 84 : 306.3085 +## Model cost at call 86 : 306.3084 +## Model cost at call 87 : 306.3084 +## Model cost at call 92 : 306.3083 +## Model cost at call 94 : 290.6377 +## Model cost at call 96 : 290.6375 +## Model cost at call 98 : 290.6375 +## Model cost at call 101 : 290.6371 +## Model cost at call 105 : 269.09 +## Model cost at call 107 : 269.0899 +## Model cost at call 115 : 259.7551 +## Model cost at call 120 : 259.7549 +## Model cost at call 123 : 259.7547 +## Model cost at call 126 : 253.7973 +## Model cost at call 128 : 253.7972 +## Model cost at call 137 : 251.7358 +## Model cost at call 139 : 251.7358 +## Model cost at call 147 : 250.7394 +## Model cost at call 149 : 250.7393 +## Model cost at call 157 : 249.1148 +## Model cost at call 159 : 249.1148 +## Model cost at call 167 : 246.8768 +## Model cost at call 169 : 246.8768 +## Model cost at call 177 : 244.9758 +## Model cost at call 179 : 244.9758 +## Model cost at call 187 : 243.2914 +## Model cost at call 189 : 243.2914 +## Model cost at call 190 : 243.2914 +## Model cost at call 194 : 243.2914 +## Model cost at call 199 : 242.9202 +## Model cost at call 201 : 242.9202 +## Model cost at call 202 : 242.9202 +## Model cost at call 209 : 242.7695 +## Model cost at call 211 : 242.7695 +## Model cost at call 216 : 242.7695 +## Model cost at call 219 : 242.5771 +## Model cost at call 221 : 242.5771 +## Model cost at call 229 : 242.4402 +## Model cost at call 231 : 242.4402 +## Model cost at call 239 : 242.1878 +## Model cost at call 241 : 242.1878 +## Model cost at call 249 : 242.0553 +## Model cost at call 251 : 242.0553 +## Model cost at call 256 : 242.0553 +## Model cost at call 259 : 241.8761 +## Model cost at call 260 : 241.7412 +## Model cost at call 261 : 241.6954 +## Model cost at call 264 : 241.6954 +## Model cost at call 275 : 241.5982 +## Model cost at call 277 : 241.5982 +## Model cost at call 285 : 241.5459 +## Model cost at call 287 : 241.5459 +## Model cost at call 295 : 241.4837 +## Model cost at call 297 : 241.4837 +## Model cost at call 305 : 241.3882 +## Model cost at call 306 : 241.3161 +## Model cost at call 307 : 241.2315 +## Model cost at call 309 : 241.2315 +## Model cost at call 314 : 241.2315 +## Model cost at call 317 : 240.9738 +## Model cost at call 322 : 240.9738 +## Model cost at call 327 : 240.8244 +## Model cost at call 329 : 240.8244 +## Model cost at call 337 : 240.7005 +## Model cost at call 339 : 240.7005 +## Model cost at call 342 : 240.7005 +## Model cost at call 347 : 240.629 +## Model cost at call 350 : 240.629 +## Model cost at call 357 : 240.6193 +## Model cost at call 358 : 240.6193 +## Model cost at call 364 : 240.6193 +## Model cost at call 367 : 240.6193 +## Model cost at call 369 : 240.5873 +## Model cost at call 374 : 240.5873 +## Model cost at call 380 : 240.578 +## Model cost at call 382 : 240.578 +## Model cost at call 390 : 240.5723 +## Model cost at call 393 : 240.5723 +## Model cost at call 403 : 240.569 +## Model cost at call 404 : 240.569 +## Model cost at call 413 : 240.569 +## Model cost at call 415 : 240.5688 +## Model cost at call 416 : 240.5688 +## Model cost at call 417 : 240.5688 +## Model cost at call 431 : 240.5686 +## Model cost at call 432 : 240.5686 +## Model cost at call 434 : 240.5686 +## Model cost at call 443 : 240.5686 +## Model cost at call 444 : 240.5686 +## Model cost at call 447 : 240.5686 +## Model cost at call 449 : 240.5686 +## Model cost at call 450 : 240.5686 +## Model cost at call 466 : 240.5686 +## Model cost at call 470 : 240.5686 +## Model cost at call 485 : 240.5686 +## Model cost at call 509 : 240.5686 +## Optimisation by method Port successfully terminated. +``` + +```r plot(fit3, show_residuals = TRUE) -summary(fit3) +``` + + + +```r +#summary(fit3) # Commented out to avoid distraction from README content mkinparplot(fit3) ``` + + For more examples and to see results, have a look at the examples provided in the [`mkinfit`](http://kinfit.r-forge.r-project.org/mkin_static/mkinfit.html) documentation or the package vignettes referenced from the |