Include output in README, use mkinsub() in example code

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