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1 files changed, 174 insertions, 8 deletions
diff --git a/README.md b/README.md
index ca256f92..454b0cd6 100644
--- a/README.md
+++ b/README.md
@@ -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)
+```
+
+![plot of chunk unnamed-chunk-3](figure/unnamed-chunk-3-1.png)
+
+
+```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)
```
+![plot of chunk unnamed-chunk-5](figure/unnamed-chunk-5-1.png)
+
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)
+```
+
+![plot of chunk unnamed-chunk-7](figure/unnamed-chunk-7-1.png)
+
+```r
+#summary(fit3) # Commented out to avoid distraction from README content
mkinparplot(fit3)
```
+![plot of chunk unnamed-chunk-7](figure/unnamed-chunk-7-2.png)
+
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

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