04_Master.Rmd

---
title: "04_Master.Rmd"
author: "Radost Stanimirova"
date: "February 17, 2016"
output: html_document
---

## Master script for phenology analysis

## Load required functions

```{r}
if(file.exists("01_download.phenocam.R")) source("01_download.phenocam.R")
if(file.exists("02_plot.phenocam.R"))     source("02_plot.phenocam.R")
if(file.exists("03_logistic.R"))          source("03_logistic.R")
```

## Download phenology data
```{r}
URL = "http://phenocam.sr.unh.edu/data/archive/uiefprairie/ROI/uiefprairie_GR_0001_1day_v4.csv"
prairie.pheno <- download.phenocam(URL)
```

## Plot overall phenology data

```{r}
plot.phenocam(prairie.pheno)
```


## Create and visualize subset of data for leaf out

```{r}
spring = as.Date(c("2015-01-01","2015-06-01"))
dat = subset(prairie.pheno,date > spring[1] & date < spring[2], select=c(date,gcc_mean,gcc_std))
plot.phenocam(dat)
```

## Fit logistic model

```{r}
dat$doy = as.POSIXlt(dat$date)$yday
par = c(0.33,0.11,-10,0.1)
fit = fit.logistic(dat,par)
```

## Visualize model and data

```{r}
plot.phenocam(dat)
lines(dat$date,pred.logistic(fit$par,dat$doy),col=2)
```