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authorJohannes Ranke <jranke@uni-bremen.de>2015-05-19 10:11:44 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2015-05-19 10:11:44 +0200
commit01d0f98ad63ebd1ff9a067cba374d1dbed7383d1 (patch)
tree3ddb2e457c2b16ebd3a26e801ca5b3aee5fdbe41 /README.md
parentf91363d665ce4c3a1a5bd0b502919142459325d4 (diff)
Code highlighting, use of mkinsub() in README.md
Diffstat (limited to 'README.md')
-rw-r--r--README.md54
1 files changed, 30 insertions, 24 deletions
diff --git a/README.md b/README.md
index a9102a8e..ca256f92 100644
--- a/README.md
+++ b/README.md
@@ -10,7 +10,7 @@ if several compartments are involved.
You can install the latest released version from
[CRAN](http://cran.r-project.org/package=mkin) from within R:
-```s
+```{r}
install.packages("mkin")
```
@@ -19,7 +19,7 @@ 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.
-```s
+```{r}
require(devtools)
install_github("jranke/mkin", quick = TRUE)
```
@@ -37,38 +37,44 @@ 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
- library(mkin)
- fit <- mkinfit("SFO", FOCUS_2006_C)
- plot(fit, show_residuals = TRUE)
- summary(fit)
+```{r}
+library(mkin)
+fit <- mkinfit("SFO", FOCUS_2006_C)
+plot(fit, show_residuals = TRUE)
+summary(fit)
+```
A still very simple usage example including the definition of the same data in R
code would be
- 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)
- plot(fit2, show_residuals = TRUE)
+```{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)
+plot(fit2, show_residuals = TRUE)
+```
A fairly complex usage example using another built-in dataset:
- data <- mkin_wide_to_long(schaefer07_complex_case, time = "time")
+```{r}
+data <- mkin_wide_to_long(schaefer07_complex_case, time = "time")
- model <- mkinmod(
- parent = list(type = "SFO", to = c("A1", "B1", "C1"), sink = FALSE),
- A1 = list(type = "SFO", to = "A2"),
- B1 = list(type = "SFO"),
- C1 = list(type = "SFO"),
- A2 = list(type = "SFO"), use_of_ff = "max")
+model <- mkinmod(
+ parent = mkinsub("SFO", c("A1", "B1", "C1"), sink = FALSE),
+ A1 = mkinsub("SFO", "A2"),
+ B1 = mkinsub("SFO"),
+ C1 = mkinsub("SFO"),
+ A2 = mkinsub("SFO"), use_of_ff = "max")
- fit3 <- mkinfit(model, data, method.modFit = "Port")
+fit3 <- mkinfit(model, data, method.modFit = "Port")
- plot(fit3, show_residuals = TRUE)
- summary(fit3)
- mkinparplot(fit3)
+plot(fit3, show_residuals = TRUE)
+summary(fit3)
+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)

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