14-tidyr.Rmd

---
title: Dataframe Manipulation with tidyr
teaching: 30
exercises: 15
questions:
- "How can I change the format of dataframes?"
objectives:
- "To be understand the concepts of 'long' and 'wide' data formats and be able to convert between them with `tidyr`."
keypoints:
- "Use the `tidyr` package to change the layout of dataframes."
- "Use `gather()` to go from wide to long format."
- "Use `spread()` to go from long to wide format."
source: Rmd
---

```{r, include=FALSE}
source("../bin/chunk-options.R")
knitr_fig_path("14-")
# Silently load in the data so the rest of the lesson works
gapminder <- read.csv("data/gapminder-FiveYearData.csv", header=TRUE, stringsAsFactors = FALSE)

# To create gapminder_wide.csv:
# library("dplyr")
# library("tidyr")
#
# #transform the data to the wide format
# gap_wide <- gapminder %>% gather(obs_type,obs_values,-continent,-country,-year) %>%
#     unite(ID_var,continent,country,sep="_") %>%
#     unite(var_names,obs_type,year,sep="_") %>%
#     spread(var_names,obs_values) %>%
#     separate(ID_var,into=c('continent','country'),sep='_')
#
# #write our the .csv so students can use it
# write.csv(gap_wide_betterID,"data/gapminder_wide.csv",row.names = FALSE)

#load the "student" data
gap_wide <- read.csv("data/gapminder_wide.csv", header=TRUE, stringsAsFactors = FALSE)
```

Researchers often want to manipulate their data from the 'wide' to the 'long'
format, or vice-versa. The 'long' format is where:

 - each column is a variable
 - each row is an observation

In the 'long' format, you usually have 1 column for the observed variable and
the other columns are ID variables.


For the 'wide' format each row is often a site/subject/patient and you have
multiple observation variables containing the same type of data. These can be
either repeated observations over time, or observation of multiple variables (or
a mix of both). You may find data input may be simpler or some other
applications may prefer the 'wide' format. However, many of `R`'s functions have
been designed assuming you have 'long' format data. This tutorial will help you
efficiently transform your data regardless of original format.

![](../fig/14-tidyr-fig1.png)

These data formats mainly affect readability. For humans, the wide format is
often more intuitive since we can often see more of the data on the screen due
to its shape. However, the long format is more machine readable and is closer
to the formatting of databases. The ID variables in our dataframes are similar to
the fields in a database and observed variables are like the database values.

## Getting started

First install the packages if you haven't already done so (you probably
installed dplyr in the previous lesson):

```{r,eval=FALSE}
#install.packages("tidyr")
#install.packages("dplyr")
```

Load the packages

```{r,message=FALSE}
library("tidyr")
library("dplyr")
```

First, lets look at the structure of our original gapminder dataframe:

```{r}
str(gapminder)
```

> ## Challenge 1
>
> Is gapminder a purely long, purely wide, or some intermediate format?
>
>
> > ## Solution to Challenge 1
> >
> > The original gapminder data.frame is in an intermediate format. It is not
> > purely long since it had multiple observation variables
> > (`pop`,`lifeExp`,`gdpPercap`).
> {: .solution}
{: .challenge}


Sometimes, as with the gapminder dataset, we have multiple types of observed
data. It is somewhere in between the purely 'long' and 'wide' data formats. We
have 3 "ID variables" (`continent`, `country`, `year`) and 3 "Observation
variables" (`pop`,`lifeExp`,`gdpPercap`). I usually prefer my data in this
intermediate format in most cases despite not having ALL observations in 1
column given that all 3 observation variables have different units. There are
few operations that would need us to stretch out this dataframe any longer
(i.e. 4 ID variables and 1 Observation variable).

While using many of the functions in R, which are often vector based, you
usually do not want to do mathematical operations on values with different
units. For example, using the purely long format, a single mean for all of the
values of population, life expectancy, and GDP would not be meaningful since it
would return the mean of values with 3 incompatible units. The solution is that
we first manipulate the data either by grouping (see the lesson on `dplyr`), or
we change the structure of the dataframe.  **Note:** Some plotting functions in
R actually work better in the wide format data.

## From wide to long format with gather()

Until now, we've been using the nicely formatted original gapminder dataset, but
'real' data (i.e. our own research data) will never be so well organized. Here
let's start with the wide format version of the gapminder dataset.

> Download the wide version of the gapminder data from [here](https://raw.githubusercontent.com/swcarpentry/r-novice-gapminder/gh-pages/_episodes_rmd/data/gapminder_wide.csv)
and save it in your data folder.

We'll load the data file and look at it.  Note: we don't want our continent and
country columns to be factors, so we use the stringsAsFactors argument for
`read.csv()` to disable that.

```{r}
gap_wide <- read.csv("data/gapminder_wide.csv", stringsAsFactors = FALSE)
str(gap_wide)
```

![](../fig/14-tidyr-fig2.png)

The first step towards getting our nice intermediate data format is to first
convert from the wide to the long format. The `tidyr` function `gather()` will
'gather' your observation variables into a single variable.

![](../fig/14-tidyr-fig3.png)

```{r}
gap_long <- gap_wide %>%
    gather(obstype_year, obs_values, starts_with('pop'),
           starts_with('lifeExp'), starts_with('gdpPercap'))
str(gap_long)
```

Here we have used piping syntax which is similar to what we were doing in the
previous lesson with dplyr. In fact, these are compatible and you can use a mix
of tidyr and dplyr functions by piping them together

Inside `gather()` we first name the new column for the new ID variable
(`obstype_year`), the name for the new amalgamated observation variable
(`obs_value`), then the names of the old observation variable. We could have
typed out all the observation variables, but as in the `select()` function (see
`dplyr` lesson), we can use the `starts_with()` argument to select all variables
that starts with the desired character string. Gather also allows the alternative
syntax of using the `-` symbol to identify which variables are not to be
gathered (i.e. ID variables)

![](../fig/14-tidyr-fig4.png)

```{r}
gap_long <- gap_wide %>% gather(obstype_year,obs_values,-continent,-country)
str(gap_long)
```

That may seem trivial with this particular dataframe, but sometimes you have 1
ID variable and 40 Observation variables with irregular variables names. The
flexibility is a huge time saver!


Now `obstype_year` actually contains 2 pieces of information, the observation
type (`pop`,`lifeExp`, or `gdpPercap`) and the `year`. We can use the
`separate()` function to split the character strings into multiple variables

```{r}
gap_long <- gap_long %>% separate(obstype_year,into=c('obs_type','year'),sep="_")
gap_long$year <- as.integer(gap_long$year)
```


> ## Challenge 2
>
> Using `gap_long`, calculate the mean life expectancy, population, and gdpPercap for each continent.
>**Hint:** use the `group_by()` and `summarize()` functions we learned in the `dplyr` lesson
>
> > ## Solution to Challenge 2
> >```{r}
> >gap_long %>% group_by(continent,obs_type) %>%
> >    summarize(means=mean(obs_values))
> >```
> {: .solution}
{: .challenge}

## From long to intermediate format with spread()

It is always good to check work. So, let's use the opposite of `gather()` to
spread our observation variables back out with the aptly named `spread()`. We
can then spread our `gap_long()` to the original intermediate format or the
widest format. Let's start with the intermediate format.

```{r}
gap_normal <- gap_long %>% spread(obs_type,obs_values)
dim(gap_normal)
dim(gapminder)
names(gap_normal)
names(gapminder)
```

Now we've got an intermediate dataframe `gap_normal` with the same dimensions as
the original `gapminder`, but the order of the variables is different. Let's fix
that before checking if they are `all.equal()`.

```{r}
gap_normal <- gap_normal[,names(gapminder)]
all.equal(gap_normal,gapminder)
head(gap_normal)
head(gapminder)
```

We're almost there, the original was sorted by `country`, `continent`, then
`year`.

```{r}
gap_normal <- gap_normal %>% arrange(country,continent,year)
all.equal(gap_normal,gapminder)
```

That's great! We've gone from the longest format back to the intermediate and we
didn't introduce any errors in our code.

Now lets convert the long all the way back to the wide. In the wide format, we
will keep country and continent as ID variables and spread the observations
across the 3 metrics (`pop`,`lifeExp`,`gdpPercap`) and time (`year`). First we
need to create appropriate labels for all our new variables (time*metric
combinations) and we also need to unify our ID variables to simplify the process
of defining `gap_wide`

```{r}
gap_temp <- gap_long %>% unite(var_ID,continent,country,sep="_")
str(gap_temp)

gap_temp <- gap_long %>%
    unite(ID_var,continent,country,sep="_") %>%
    unite(var_names,obs_type,year,sep="_")
str(gap_temp)
```

Using `unite()` we now have a single ID variable which is a combination of
`continent`,`country`,and we have defined variable names. We're now ready to
pipe in `spread()`

```{r}
gap_wide_new <- gap_long %>%
    unite(ID_var,continent,country,sep="_") %>%
    unite(var_names,obs_type,year,sep="_") %>%
    spread(var_names,obs_values)
str(gap_wide_new)
```

> ## Challenge 3
>
> Take this 1 step further and create a `gap_ludicrously_wide` format data by spreading over countries, year and the 3 metrics?
>**Hint** this new dataframe should only have 5 rows.
>
> > ## Solution to Challenge 3
> >```{r}
> >gap_ludicrously_wide <- gap_long %>%
> >    unite(var_names,obs_type,year,country,sep="_") %>%
> >    spread(var_names,obs_values)
> >```
> {: .solution}
{: .challenge}

Now we have a great 'wide' format dataframe, but the `ID_var` could be more
usable, let's separate it into 2 variables with `separate()`


```{r}
gap_wide_betterID <- separate(gap_wide_new,ID_var,c("continent","country"),sep="_")
gap_wide_betterID <- gap_long %>%
    unite(ID_var, continent,country,sep="_") %>%
    unite(var_names, obs_type,year,sep="_") %>%
    spread(var_names, obs_values) %>%
    separate(ID_var, c("continent","country"),sep="_")
str(gap_wide_betterID)

all.equal(gap_wide, gap_wide_betterID)
```

There and back again!


## Other great resources

* [R for Data Science](r4ds.had.co.nz)
* [Data Wrangling Cheat sheet](https://www.rstudio.com/wp-content/uploads/2015/02/data-wrangling-cheatsheet.pdf)
* [Introduction to tidyr](https://cran.r-project.org/web/packages/tidyr/vignettes/tidy-data.html)
* [Data wrangling with R and RStudio](https://www.rstudio.com/resources/webinars/data-wrangling-with-r-and-rstudio/)