---
title: "overviewR: Easily Extracting Information About Your Data"
author: "Cosima Meyer and Dennis Hammerschmidt"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{overviewR: Easily Extracting Information About Your Data}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r setup, include = FALSE}
knitr::opts_chunk$set(collapse = TRUE,
                      comment = "#>")
```


```{R,echo=FALSE,results='hide',message=FALSE,include=FALSE, eval=TRUE}
if (!require(knitr))
  install.packages("knitr")
if (!require(devtools))
  install.packages("devtools")
if (!require(dplyr))
  install.packages("dplyr")
if (!require(magrittr))
  install.packages("magrittr")
if (!require(ggplot2))
  install.packages("ggplot2")
if (!require(countrycode))
  install.packages("countrycode")
if (!require(xtable))
  install.packages("xtable")
```


The goal of overviewR is to make it easy to get an overview of a data set by displaying relevant sample information. At the moment, there are the following functions:

- `overview_tab` generates a tabular overview of the sample.  The general sample plots a two-column table that provides information on an id in the left column and a the time frame on the right column. 
- `overview_crosstab` generates a cross table. The conditional column allows to disaggregate the overview table by specifying two conditions, hence resulting a 2x2 table. This way, it is easy to visualize the time and scope conditions as well as theoretical assumptions with examples from the data set.
- `overview_latex` converts the output of both `overview_tab` and `overview_crosstab` into LaTeX code and/or directly into a .tex file. 
- `overview_plot` is an alternative to visualize the sample (a way to present results from `overview_tab`)
- `overview_crossplot` is an alternative to visualize a cross table (a way to present results from `overview_crosstab`)
- `overview_heat` plots a heat map of your time line
- `overview_na` plots an overview of missing values by variable

The plots can be saved using the `ggsave()` command. The output of `overview_tab` and `overview_crosstab` are also compatible with other packages such as [```xtable```](https://CRAN.R-project.org/package=xtable), [```flextable```](https://CRAN.R-project.org/package=flextable), or [`knitr`](https://bookdown.org/yihui/rmarkdown-cookbook/kable.html).

We present a short step-by-step guide as well as the functions in more detail below.

## Installation

A stable version of `overviewR` can be directly accessed on CRAN:
```{r, eval=FALSE}
install.packages("overviewR", force = TRUE)
```

To install the latest development version of `overviewR` directly from [GitHub](https://github.com/cosimameyer/overviewR) use: 

```{r, message=FALSE, warning=FALSE, results = "hide", eval=FALSE}
library(devtools)
devtools::install_github("cosimameyer/overviewR")
```


# Tabular overview
## `overview_tab`

First, load the package.
```{r, include = FALSE, eval = FALSE}
install.packages("overviewR")
```

```{r, message=FALSE, warning=FALSE}
library(overviewR)
```

The following examples use a toy data set (`toydata`) that comes with the package. This data contains artificially generated information in a cross-sectional format on 5 countries, covering the period 1990-1999.

```{r}
data(toydata)
head(toydata)
```
<!-- ``` -->
<!--     ccode   year   month  gdp       population -->
<!--     RWA     1990   Jan    24180.77  14969.988 -->
<!--     RWA     1990   Feb    23650.53  11791.464 -->
<!--     RWA     1990   Mar    21860.14  30047.979 -->
<!--     RWA     1990   Apr    20801.06  19853.556 -->
<!--     RWA     1990   May    18702.84   5148.118 -->
<!--     RWA     1990   Jun    30272.37  48625.140 -->
<!-- ``` -->

There are 264 observations for 5 countries (Angola, Benin, France, Rwanda, and UK) stored in the ```ccode``` variable, over a time period between 1990 to 1999 (```year```) with additional information for the month (```month```). Additionally, two artificially generated fake variables for GDP (```gdp```) and  population size (```population```) are included to illustrate of conditions.

The following functions work best on data sets that have an id-time-structure, in the case of `toydata` this corresponds to country-year with `ccode` and `year`. 
If the data set does not have this format yet, consider using [```pivot_wider()``` or ```pivot_longer()```](https://tidyr.tidyverse.org/reference/pivot_longer.html) to get to the format.

Generate some general overview of the data set using the time and scope conditions with ```overview_tab```.

```{r, message=FALSE, warning=FALSE, eval=FALSE}
output_table <- overview_tab(dat = toydata, id = ccode, time = year)
```

The resulting data frame collapses the time condition for each id by taking into account potential gaps in the time frame. Note that the column name for the time frame is set by default to `time_frame` and internally generated when using `overview_tab`. 

```{r, message=FALSE, eval=FALSE}
output_table
```

```
# ccode   time_frame
# RWA	    1990 - 1995
# AGO	    1990 - 1992
# BEN	    1995 - 1999
# GBR	    1991, 1993, 1995, 1997, 1999
# FRA	    1993, 1996, 1999
```

### Multiple time arguments

As of overviewR version 0.0.7 you can also use multiple time objects in `overview_tab`. You can now pass a list containing multiple time variables with the following format: `time = list(year = NULL, month = NULL, day = NULL)`.

```{r, message=FALSE, eval=FALSE}
output_table_complex <- overview_tab(dat = toydata, id = ccode, 
                                     time = list(year = toydata$year,
                                                 month = toydata$month, 
                                                 day = toydata$day), 
                                     complex_date = TRUE)
```

The resulting data frame collapses again the time condition for each id by taking into account potential gaps in the time frame. Note that the column name for the time frame is set by default to `time_frame` and internally generated when using `overview_tab`. The output resembles something like this:

```{r, message=FALSE, eval=FALSE}
output_table_complex
```

```
 ccode time_frame                                                                                                      # AGO   1990-01-01, 1990-02-02, 1990-03-03, 1990-04-04, 1990-05-05, 1990-06-06, ...
# BEN   1995-01-01, 1995-02-02, 1995-03-03, 1995-04-04, 1995-05-05, 1995-06-06, ...
# FRA   1993-01-01, 1993-02-02, 1993-03-03, 1993-04-04, 1993-05-05, 1993-06-06, ...
# GBR   1991-01-01, 1991-02-02, 1991-03-03, 1991-04-04, 1991-05-05, 1991-06-06, ...
# RWA   1990-01-01 - 1990-01-12, 1991-01-01 - 1991-01-12, 1992-01-01 - 1992-01-12, 1993-01-01 - 1993-01-12, 1994-01-01 
```

## `overview_crosstab`
To generate a cross table that divides the data based on two conditions, for instance GDP and population size, ```overview_crosstab``` can be used. `threshold1` and `threshold2` thereby indicate the cut point for the two conditions (`cond1` and `cond2`), respectively. 

```{r, message=FALSE, warning=FALSE, eval=FALSE}
output_crosstab <- overview_crosstab(
  dat = toydata,
  cond1 = gdp,
  cond2 = population,
  threshold1 = 25000,
  threshold2 = 27000,
  id = ccode,
  time = year
)
```

The data frame output looks as follows:

```{r, message=FALSE, echo=FALSE, eval=FALSE}
output_crosstab
```
```
#   part1                                      part2
# 1 AGO (1990, 1992), FRA (1993), GBR (1997)   BEN (1996, 1999), FRA (1999), GBR (1993), RWA (1992, 1994)
# 2 BEN (1997), RWA (1990)                     AGO (1991), BEN (1995, 1998), FRA (1996), GBR (1991, 1995, 1999), RWA (1991, 1993, 1995)
```

Note, if a data set is used that has multiple observations on the id-time unit, the function automatically aggregates the data set using the mean of condition 1 (`cond1`) and condition 2 (`cond2`). 

## `overview_latex`

> With overviewR v 0.0.11.999 we introduced `overview_latex` instead of `overview_print`

To generate an easily usable LaTeX output for the generated `overview_tab` and `overview_crosstab` objects, `overviewR` offers the function `overview_latex`. 
The following illustrate this using the `output_table` object from `overview_tab`.

```{r, eval=FALSE}
overview_latex(obj = output_table)
```
<details>
  <summary>LaTeX output</summary>
```{r, eval=FALSE, include=FALSE}
overview_latex(obj = output_table)
```
```
% Overview table generated in R version 4.0.0 (2020-04-24) using overviewR 
% Table created on 2020-06-21
\begin{table}[ht] 
 \centering 
 \caption{Time and scope of the sample} 
 \begin{tabular}{ll} 
 \hline 
Sample & Time frame \\ 
\hline 
 RWA & 1990 - 1995 \\ 
 AGO & 1990 - 1992 \\ 
 BEN & 1995 - 1999 \\ 
 GBR & 1991, 1993, 1995, 1997, 1999 \\ 
 FRA & 1993, 1996, 1999 \\ 
 \hline 
 \end{tabular} 
 \end{table}
```
</details>

<p align="center">
<img src='ex1.png' height="150"/>
</p>

The default already provides a title ("Time and scope of the sample") that can be modified in the argument `title`. The same holds for the column names ("Sample" and "Time frame" are set by default but can be modified as shown below). 

```{r, eval = FALSE, eval=FALSE}
overview_latex(
  obj = output_table,
  id = "Countries",
  time = "Years",
  title = "Cool new title for our awesome table"
)
```
<details>
  <summary>LaTeX output</summary>
```{r, eval=FALSE, include=FALSE}
overview_latex(
  obj = output_table,
  id = "Countries",
  time = "Years",
  title = "Cool new title for our awesome table"
)
```

```
% Overview table generated in R version 4.0.0 (2020-04-24) using overviewR 
% Table created on 2020-06-21
\begin{table}[ht] 
 \centering 
 \caption{Cool new title for our awesome table} 
 \begin{tabular}{ll} 
 \hline 
Countries & Years \\ 
\hline 
 RWA & 1990 - 1995 \\ 
 AGO & 1990 - 1992 \\ 
 BEN & 1995 - 1999 \\ 
 GBR & 1991, 1993, 1995, 1997, 1999 \\ 
 FRA & 1993, 1996, 1999 \\ 
 \hline 
 \end{tabular} 
 \end{table} 
```
</details>

<p align="center">
<img src='ex2.png' height="150"/>
</p>



The same function can also be used for outputs from the `overview_crosstab` function by using the argument `crosstab = TRUE`. There are also options to label the respective conditions (```cond1``` and ```cond2```). Note that this should correspond to the conditions (```cond1``` and ```cond2```) specified in the `overview_crosstab` function.

```{r, eval = FALSE}
overview_latex(
  obj = output_crosstab,
  title = "Cross table of the sample",
  crosstab = TRUE,
  cond1 = "GDP",
  cond2 = "Population"
)
```
<details>
  <summary>LaTeX output</summary>
```{r, eval=FALSE, include=FALSE}
overview_latex(
  obj = output_crosstab,
  title = "Cross table of the sample",
  crosstab = TRUE,
  cond1 = "GDP",
  cond2 = "Population"
)
```
```
% Overview table generated in R version 4.0.0 (2020-04-24) using overviewR 
% Table created on 2020-06-21
% Please add the following packages to your document preamble: 
% \usepackage{multirow} 
% \usepackage{tabularx} 
% \newcolumntype{b}{X} 
% \newcolumntype{s}{>{\hsize=.5\hsize}X} 
\begin{table}[ht] 
\caption{Cross table of the sample} 
 \begin{tabularx}{\textwidth}{ssbb} 
\hline & & \multicolumn{2}{c}{\textbf{GDP}} \\ 
 & & \textbf{Fulfilled} & \textbf{Not fulfilled} \\ 
 \hline \\ 
 \multirow{2}{*}{\textbf{Population}} & \textbf{Fulfilled} & 
 AGO (1990, 1992), FRA (1993), GBR (1997) & BEN (1996, 1999), FRA (1999), GBR (1993), RWA (1992, 1994)\\  
 \\ \hline \\ 
 & \textbf{Not fulfilled} &  BEN (1997), RWA (1990) & AGO (1991), BEN (1995, 1998), FRA (1996), GBR (1991, 1995, 1999), RWA (1991, 1993, 1995)\\  \hline \\ 
 \end{tabularx} 
 \end{table} 
```
</details>

<p align="center">
<img src='ex3.png' height="200"/>
</p>

`overview_latex` further allows more specifications such as the font size or a a label. 
```{r, eval = FALSE}
overview_latex(obj = output_table,
               fontsize = "scriptsize",
               label = "tab:overview")
```

With ```save_out = TRUE``` the function exports the output as a ```.tex``` file and stores it on the device.

```{r, eval = FALSE}
overview_latex(
  obj = output_table,
  save_out = TRUE,
  file_path = "SET-YOUR-PATH/output.tex"
)
```

# Visual overview

## `overview_plot`

In addition to tables, `overviewR` also provides plots to illustrate the structure of your data. 
`overview_plot` illustrates the information that is generated in `overview_table` in a ggplot graphic. All scope objects (e.g., countries) are listed on the y-axis where horizontal lines indicate the coverage across the entire time frame of the data (x-axis). This helps to spot gaps in the data for specific scope objects and outlines at what time point they occur. 

```{r, out.width = '50%', fig.align='center'}
data(toydata)
overview_plot(dat = toydata, id = ccode, time = year)
```

The results are sorted alphabetically by default. The order can also be reversed by setting `asc` to `FALSE`.

```{r, out.width = '50%', fig.align='center'}
overview_plot(
  dat = toydata,
  id = ccode,
  time = year,
  asc = FALSE
)
```

There is also an option to color the time lines conditionally. Here, we introduce a dummy variable that indicates whether the year was before 1995 or not. We use this dummy to color the time lines using the `color` argument.

```{r, out.width = '50%', fig.align='center', include = TRUE, results = TRUE, message = FALSE, warning=FALSE}
library(overviewR) # Easily Extracting Information About Your Data
library(magrittr) # A Forward-Pipe Operator for R

# Code whether a year was before 1995
toydata <- toydata %>%
  dplyr::mutate(before = ifelse(year < 1995, 1, 0))

# Plot using the `color` argument
overview_plot(
  dat = toydata,
  id = ccode,
  time = year,
  color = before
)
```


The development version also allows to change the dot size using the `dot_size` argument. The default is "2".
  
```{r, out.width = '50%', fig.align='center', include = TRUE, results = TRUE, message = FALSE, warning=FALSE}
# Plot using the `color` argument
overview_plot(
  dat = toydata,
  id = ccode,
  time = year,
  dot_size = 5
)
```

If you want to change the color in your plot, follow `ggplot2`'s layering logic and add a new layer to it. 

```{r, out.width = '50%', fig.align='center', include = TRUE, results = TRUE, message = FALSE, warning=FALSE}
library(ggplot2)

overview_plot(
  dat = toydata,
  id = ccode,
  time = year
) + ggplot2::scale_color_brewer(palette="Dark2")
```

## `overview_crossplot`

To visualize also the cross table, `overview_crossplot` does the job. 

```{r, out.width = '50%', fig.align='center', include = TRUE, results = TRUE, message = FALSE, warning=FALSE}
overview_crossplot(
  toydata,
  id = ccode,
  time = year,
  cond1 = gdp,
  cond2 = population,
  threshold1 = 25000,
  threshold2 = 27000,
  color = TRUE,
  label = TRUE
)
```


## `overview_heat`

`overview_heat` takes a closer look at the time and scope conditions by visualizing the data coverage for each time and scope combination in a ggplot heat map. This function is best explained using an example. Suppose you have a dataset with monthly data for different countries and want to know if data is available for each country in every month. `overview_heat` intuitively does this by plotting a heat map where each cell indicates the coverage for that specific combination of time and scope (e,g., country-year). As illustrated below, the darker the cell is, the more coverage it has. The plot also indicates the relative or absolute coverage of each cell. For instance, Angola ("AGO") in 1991 shows the coverage of 75%. This means that of all potential 12 months of coverage (12 months for one year), only 9 are covered.

For this purpose, we first artificially reduced the `toydata`.

```{r, include = TRUE}
toydata_red <- toydata[-sample(seq_len(nrow(toydata)), 64), ]
```

```{r, out.width = '50%', fig.align='center'}
overview_heat(toydata_red,
              ccode,
              year,
              perc = TRUE,
              exp_total = 12)
```


## `overview_na`

`overview_na` is a simple function that provides information about the content of all variables in your data, not only the time and scope conditions. It returns a horizontal ggplot bar plot that indicates the amount of missing data (NAs) for each variable (on the y-axis). You can choose whether to display the relative amount of NAs for each variable in percentage (the default) or the total number of NAs. 

For this purpose, we first artificially reduced our `toydata`.

```{r, include=TRUE}
toydata_with_na <- toydata %>%
  dplyr::mutate(
    year = ifelse(year < 1992, NA, year),
    month = ifelse(month %in% c("Jan", "Jun", "Aug"), NA, month),
    gdp = ifelse(gdp < 20000, NA, gdp)
  )
```

```{r, out.width = '50%', fig.align='center'}
overview_na(toydata_with_na)
```

```{r, out.width = '50%', fig.align='center'}
overview_na(toydata_with_na, perc = FALSE)
```

## `overview_overlap`

This function allows to compare two data sets. We are currently working on an extended version that allows comparing >2 data sets. 
  
  At the current development stage, the function works as follows:
  
```{r, out.width = '50%', fig.align='center', eval = TRUE}
library(dplyr)

# Subset one data set for comparison
toydata2 <- toydata %>% dplyr::filter(year > 1992)

overview_overlap(
  dat1 = toydata,
  dat2 = toydata2,
  dat1_id = ccode,
  dat2_id = ccode,
  plot_type = "bar" # This is the default
)
```

  
  Or a Venn diagram
```{r_venn, out.width = '50%', fig.align='center', eval = TRUE}
overview_overlap(
  dat1 = toydata,
  dat2 = toydata2,
  dat1_id = ccode,
  dat2_id = ccode,
  plot_type = "venn"
)
```


## Customizing plots: `ggplot2`

The plot functions are fully `ggplot2` based. While a theme is pre-defined, this can easily be overwritten.

A classical `ggplot2` theme alternative
```{r, out.width = '50%', fig.align='center'}
library(ggplot2) # Create Elegant Data Visualisations 
                 # Using the Grammar of Graphics

overview_na(toydata_with_na) +
  ggplot2::theme_minimal()
```

# Compatibilities with other packages 

## Workflow: `tidyverse`

All functions are further easily accessible using a common `tidyverse` workflow. Here are just three examples -- the possibilities are endless.

Using a filter function
```{r, out.width = '50%', fig.align='center'}
library(dplyr) # A Grammar of Data Manipulation # A Grammar of Data Manipulation

toydata_with_na %>%
  dplyr::filter(year > 1993) %>%
  overview_na()
```

Using mutate to generate meaningful country names
```{r, out.width = '50%', fig.align='center'}
library(countrycode) # Convert Country Names and Country Codes
library(dplyr) # A Grammar of Data Manipulation # A Grammar of Data Manipulation

toydata %>%
  # Transform the country code (ISO3 character code) into a country name using
  # the `countrycode` package
  dplyr::mutate(country =
                  countrycode::countrycode(ccode, "iso3c", "country.name")) %>%
  overview_plot(id = country, time = year)
```

Using different `overviewR` functions after each other to generate a workflow
```{r, eval = FALSE}
# Produces a printable LaTeX output
toydata %>%
  overview_tab(id = ccode, time = year) %>%
  overview_latex()
```

```
% Overview table generated in R version 4.0.2 (2020-06-22) using overviewR 
% Table created on 2020-12-30
\begin{table}[ht] 
 \centering 
 \caption{Time and scope of the sample} 
\label{tab:tab1} 

\begin{tabular}{ll} 
 \hline 
Sample & Time frame \\ 
\hline 
 AGO & 1990 - 1992 \\ 
 BEN & 1995 - 1999 \\ 
 FRA & 1993, 1996, 1999 \\ 
 GBR & 1991, 1993, 1995, 1997, 1999 \\ 
 RWA & 1990 - 1995 \\ 
 \hline 
 \end{tabular} 
 \end{table} 
```

## Presenting tables: `flextable`, `xtable`, and `kable`
The outputs of `overview_tab` and `overview_crosstab` are also compatible with other functions such as [`xtable`](https://CRAN.R-project.org/package=xtable), [`flextable`](https://CRAN.R-project.org/package=flextable), or [`kable`](https://bookdown.org/yihui/rmarkdown-cookbook/kable.html) from [`knitr`](https://yihui.org/knitr/).

Two examples are shown below:

```{r, eval=FALSE}
library(flextable) # not installed on this machine
table_output <- qflextable(output_table)
table_output <-
  set_header_labels(table_output,
                    ccode = "Countries",
                    time_frame = "Time frame")
set_table_properties(table_output,
                     width = .4,
                     layout = "autofit")
```

```{r, echo=FALSE, include=FALSE}
output_table <-
  data.frame(
    ccode = c("RWA", "AGO", "BEN", "GBR", "FRA"),
    time_frame = c(
      "1990-1995",
      "1990-1992",
      "1995-1999",
      "1991, 1993, 1995, 1997, 1999",
      "1993, 1996, 1999"
    )
  )
```

```{r}
library(knitr) # A General-Purpose Package for Dynamic Report Generation in R
knitr::kable(output_table)
```


A classical `ggplot2` theme alternative
```{r, out.width = '50%', fig.align='center'}
library(ggplot2) # Create Elegant Data Visualisations Using the
# Grammar of Graphics

overview_na(toydata_with_na) +
  ggplot2::theme_minimal()
```


## Extensions

If you wish to compare two data sets using `overview_tab`, this is not (yet) implemented in `overviewR` but there is currently a workaround. 

```{r, eval=TRUE}
library(overviewR)
library(dplyr)
library(xtable)

# Load data
data(toydata)

# Restrict the data so that we have something to compare :-)
toydata_res <- toydata %>%
  dplyr::filter(year > 1992)

# Generate two overview_tab objects
dat1 <- overview_tab(toydata, id = ccode, time = year)
dat2 <- overview_tab(toydata_res, id = ccode, time = year)

# And now we use full_join to combine both
dat_full <- dat1 %>%
  dplyr::full_join(dat2, by = "ccode") %>%
  dplyr::rename(time_dat1 = time_frame.x,
                time_dat2 = time_frame.y)
```

Having a look at the output, we see that this is exactly what we wanted to have:
```{r, eval=FALSE}
head(dat_full)
```
```
#> # A tibble: 5 x 3
#> # Groups:   ccode [5]
#>   ccode time_dat1                    time_dat2             
#>   <chr> <chr>                        <chr>                 
#> 1 AGO   1990 - 1992                  <NA>                  
#> 2 BEN   1995 - 1999                  1995 - 1999           
#> 3 FRA   1993, 1996, 1999             1993, 1996, 1999      
#> 4 GBR   1991, 1993, 1995, 1997, 1999 1993, 1995, 1997, 1999
#> 5 RWA   1990 - 1995                  1993 - 1995
```

`overview_latex` cannot handle this object (yet), so we use `xtable` instead which gives us the LaTeX output.

```{r, eval=FALSE}
print(xtable(dat_full), include.rownames = FALSE)
```

```
% latex table generated in R 4.0.2 by xtable 1.8-4 package
% Tue Feb 16 18:20:51 2021
\begin{table}[ht]
\centering
\begin{tabular}{lll}
  \hline
ccode & time\_dat1 & time\_dat2 \\ 
  \hline
AGO & 1990 - 1992 &  \\ 
  BEN & 1995 - 1999 & 1995 - 1999 \\ 
  FRA & 1993, 1996, 1999 & 1993, 1996, 1999 \\ 
  GBR & 1991, 1993, 1995, 1997, 1999 & 1993, 1995, 1997, 1999 \\ 
  RWA & 1990 - 1995 & 1993 - 1995 \\ 
   \hline
\end{tabular}
\end{table}
```

</details>

<p align="center">
<img src='extension1.png' height="150"/>
</p>

