---
title: "R Markdown Example"
author: "Karl Broman"
date: "1/9/2018"
output: html_document
---

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

## Set up

This document illustrates R markdown, which is super cool.

First I'll load some packages.

```{r load_libraries}
# this comment will be shown
library(dplyr)
library(ggplot2)
```

```{r comments_on_that, echo=FALSE}
# this is a comment that will not be shown
```



Then I'll load the data.

```{r load_data}
surveys <- read.csv("../clean_data/portal_clean.csv")
```

This dataset has `r nrow(surveys)` observations.

## Create some datasets

```{r create_datasets}
# create some datasets
# 1. only the obs with species_id=="DM"
just_dm <- surveys %>% filter(species_id == "DM")
# 2. average weight and hindfoot length and count of each species
stat_summary <- surveys %>% group_by(species_id) %>% 
    summarize(mean_wt=mean(weight),
              mean_hfl=mean(hindfoot_length),
              n=n())
# 3. average wt, hfl, count by year, species, sex
year_summary <- surveys %>% group_by(species_id, year, sex) %>% 
    summarize(mean_wt=mean(weight),
              mean_hfl=mean(hindfoot_length),
              n=n())
```

Here's a scatterplot of hindfoot length vs weight for species DM.

```{r plot_hfl_vs_weight_for_DM, fig.height=8}
ggplot(just_dm, aes(x=weight, y=hindfoot_length)) +
    geom_point()
```

## R markdown 

This is _italics_ this is **bold**.

- This is a bulleted list.
- This is the second item.