R Markdown

Introduction to R markdown

#Here is a document.
A single # represents a tittle, 2 represents a subtittle)

`Back quotes (``)are use to represent the inside text in a type writter format` 

*The star signs between a text  italicize the text* 

**Double stars make the text  bold**

* **Bulleting items, star space then item. This will not only bullet but also make the bulleted text bold**

        *Four spaces than a star creates sub-bullets

  >Pushes the text inside
  
$For subscript notation$
  
##Let us create a data set
```{r include=TRUE}
library(stats)
x <- c(0,10,20,30,40,50)
y <- c(2748,3162,3307,3571,3576,3544)
dat <- as.data.frame(cbind(x,y))
```
lets plot the data
```{r echo=TRUE,fig.width=3 ,fig.height=3.5}
plot(dat)
```

Some notes on the function we are about to fit
SSasymp is the same function that Charlie is using, just slightly re-parameterized
you need at least 4 xy pairs to fit this relationship
y = a + (b - a) * exp(-exp(c)*x)
a is the asymptote
b is the intercept at 0 input
c is log rate constant ... the corresponding half saturation value is ln(2)/c
also see ?SSasymp
```{r}
fit <- nls(y~SSasymp(x, a, b, c), data=dat)
summary(fit)

plot(y~x, ylab="Yield (kg)", xlab="P input (kg)", dat)
a <-coef(fit)[1]
b <-coef(fit)[2]
c <-coef(fit)[3]
lines(x<-c(0:50),a+(b-a)*exp(-exp(c)*x),col='red')
```