---
title: "Lab 20: Summarizing Bird Data"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE)
knitr::opts_chunk$set(warning = FALSE)
knitr::opts_chunk$set(message = FALSE)
knitr::opts_chunk$set(fig.height = 5)
knitr::opts_chunk$set(fig.width = 8.5)
knitr::opts_chunk$set(out.width = "100%")
knitr::opts_chunk$set(dpi = 300)

library(readr)
library(ggplot2)
library(dplyr)
library(viridis)
library(smodels)
theme_set(theme_minimal())
```

## Instructions

Below you will find several empty R code scripts.
Your task is to fill in the required code snippets.

## Birds Data

Today you will be working with a datasets of birds:

```{r}
birds <- read_csv("https://statsmaths.github.io/stat_data/birds.csv")
```

Here is a full data dictionary describing all of the variables

- **genus** (chr): taxonomic rank of the bird
- **species** (chr): scientific species name of the bird
- **name** (chr): common name of the bird
- **type** (chr): common name of the type of bird
- **egg_mass** (dbl): average mass of an egg when laid (grams)
- **male_mass** (dbl): average observed mass of an adult male (grams)
- **mating_system** (int): scores of mating system. Intensity of male-male competition increases from 1 to 5.
    - (1) polyandry
    - (2) monogamy (<5% polygyny)
    - (3) mostly monogamy, but occasional polygyny (5–15% polygyny)
    - (4) mostly polygyny (> 15% polygyny)
    - (5) lek or promiscuous
- **display** (int): mating display agility
    - (1) ground displays only, including displays on trees and bushes
    - (2) ground displays, but with occasional jumps/leaps into the air
    - (3) both ground and non-acrobatic flight displays
    - (4) mainly aerial displays, non-acrobatic
    - (5) mainly aerial displays, acrobatic
- **resource** (int): scores of territoriality and between-mate resource sharing
    - (0) males and females don't share resources and they feed away from their breeding territory
    - (1) males and females share resources on their territory only during the breeding season
    - (2) males and females share resources on their territory all year round.
- **clutch_size** (dbl): average number of eggs produced per clutch

Notice that the last two variables are integer codes. They are stored as numbers but
correspond to a category.

## Starting plot

Create a scatter plot showing the mass of a male bird (x-axis) and the mass of an egg:

```{r}

```

You should notice that the plot's scale makes it hard to see the relationship between the two variables.

## Changing the scale

Now add the layers `scale_x_log10` and `scale_y_log10`

```{r}

```

## Parrots

Create a new dataset called `parrots` consisting of just those birds that are
parrots:

```{r}

```

Now add a layer to the previous plot (keeping the log scales) where the
parrots are highlighted in the color "red". To make them stand out, make the
base layer have an alpha value of 0.15. Finally, add a text annotation
describing to the reader that the red points are parrots.

```{r}

```

## Outliers

If you look at the plot, you'll see one bird in particular who has a very
large egg size given the mass of the bird itself. This is the the Red-tailed
tropicbird (also, you can add pictures to Rmarkdown!):

![](https://upload.wikimedia.org/wikipedia/commons/thumb/4/47/Red-tailed_Tropicbird_RWD2.jpg/640px-Red-tailed_Tropicbird_RWD2.jpg)

The tropicbird as a male mass of 218.7g and an egg mass of 87.00g. Annotate
this point on the graph and give a label for it, but instead of using the
annotate function, make use of the `filter` command:

```{r}

```

## Summarizing the Data

Create a new dataset which summarizes everything to the level of a bird
type using the `group_summarize` function:

```{r}

```

Create a log-log plot of the median egg mass and median male mass for each
bird type.

```{r}

```

Now create a new dataset filtered to only those bird types with 5 or more
birds in the original dataset:

```{r}

```

Finally, add two layers to the first plot that (1) colors the smaller set
of birds in red and (2) provides a textual label for the red colored points.
Try to make the labels readable (hint: perhaps add the `alpha` aesthetic
to the first set of points and/or jitter the y-axis of the labels):

```{r}

```