04_Master.Rmd

---
title: "04_Master.Rmd"
author: "Qianning Qin"
date: "February 11, 2019"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

## R Markdown

This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.

When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:

```{r cars}
## Master script for phenology analysis
## Load required functions
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
URL = "http://phenocam.sr.unh.edu/data/archive/uiefprairie/ROI/uiefprairie_GR_1000_1day.csv"
prairie.pheno <- download.phenocam(URL)
## Plot overall phenology data
plot.phenocam(prairie.pheno)
## Create and visualize subset of data for leaf out
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
dat$doy = as.POSIXlt(dat$date)$yday
par = c(0.33,0.11,-10,0.1)
fit = fit.logistic(dat,par)
## Visualize model and data
plot.phenocam(dat)
lines(dat$date,pred.logistic(fit$par,dat$doy),col=2)
```