---
title: "PDF Data Extractor (PDE)"
author: "Erik Stricker "
date: "`r Sys.Date()`"
output: 
  rmarkdown::html_document:
    toc: true
vignette: >
  %\VignetteIndexEntry{PDE}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

------------

## Description
PDE is a R package that easily extracts information and tables from PDF files. The `PDE_analyzer_i()` performs the sentence and table extraction while the included `PDE_reader_i()` allows the user-friendly visualization and quick-processing of the obtained results.

------------

## Installation
Install the dependent packages
```R
install.packages("tcltk2")    # Install the dependent package tcltk2
```

The package requires the Xpdf command line tools by Glyph & Cog, LLC. Please download and install the Xpdf command line tools 4.2 from the following website onto your local disk: https://github.com/erikstricker/PDE/tree/master/inst/examples/bin
(https://github.com/erikstricker/PDE/tree/master/inst/examples/bin). Alternatively, the following command can be used to install the correct Xpdf command line tools:  

```R
PDE_install_Xpdftools4.02()    # Download and install the Xpdf command line tools
PDE_check_Xpdf_install()        # Check if all required XPDF tools are installed correctly
```

Install the package through CRAN
```R
install.packages("PDE", dependencies = TRUE)
```  

or choose the location where you downloaded latest PDE_\*.\*.\*.tar.gz and install it from a local
path.  

```R
filename <- file.choose()     # Choose the location where you downloaded the latest PDE_*.*.*.tar.gz
install.packages(filename,  type="source", repos=NULL)
```

**NOTE: The PDE package was tested on Microsoft Windows, Mac and Linux machines. Major differences include the visual appearance of the interfaces and the directory structures, but all functions are preserved.**

------------

## Execution
The PDE analyzer can be accessed through different functions which are outlined below.
```R
PDE_analyzer()
PDE_analyzer_i()
PDE_extr_data_from_pdfs()
PDE_pdfs2table()
PDE_pdfs2table_searchandfilter()
PDE_pdfs2txt_searchandfilter()
```

The PDE reader is only available as an interactive user interface requiring the R package **tcltk2**.
```R
PDE_reader_i()
```
**NOTE: For problem solution concerning a potential error when starting `PDE_analyzer_i()` or `PDE_reader_i()` on Mac see [Troubleshoot] - [Error when starting interactive user interface on Mac (failed to allocate tcl font)].**

## Quick guide to get started

### PDE_analyzer_i()
1. Run
```R
library("PDE")
PDE_analyzer_i()
```
```{r, out.width = "50%", fig.align = "center", echo = FALSE}
knitr::include_graphics("scrnshots/Screenshot_PDE_analyzer_user_interface_empty_mac.png")
```
<center>
`PDE_analyzer_i()` user interface on Mac
</center></br>

2. This should open a user interface. 
3. Fill out the form from top to bottom (standard parameters are preselected).    
4. The filled form can and should be saved as a TSV file at any time. This can be done by clicking the **Save form as tsv** button at the top, center of the form.    
**NOTE: Choose an empty folder or create a new one as the output directory, since analyses create at least a number of files equal to the number of PDF files analyzed.**

------------

### PDE_reader_i()
```{r, out.width = "50%", fig.align = "center", echo = FALSE}
knitr::include_graphics("scrnshots/Screenshot_PDE_reader_user_interface_empty_linux.png")
```
<center>
`PDE_reader_i()` user interface on Linux
</center></br>  
  
1. Run
```R
library("PDE")
PDE_reader_i()
```
2. This should open a user interface. 

3. Load either a sentence analysis file or a folder with such files.  
**NOTE: Analysis files refer to the files created by the PDE_analyzer_i() which contain "txt+-" in their name.**  

4. The user can browse through all analysis files in the folder to get an overview over the data.

5. Additional functions can be enabled by loading the PDF folder as well as the TSV file used for analysis.  
**NOTE: Flagging and marking changes filenames but can be reversed in the program at any time.**  

------------

## Parameters

### PDE_analyzer_i()
**NOTE: Arguments for the R function `PDE_extr_data_from_pdfs()` are listed below each description:**
`argument`

1. Run
```R
library("PDE")
PDE_analyzer_i()
```

#### Choose the locations for the required files:
```{r, out.width = "100%", fig.align = "center", echo = FALSE}
knitr::include_graphics("scrnshots/Screenshot_PDE_analyzer_user_interface.choose_variables_empty.png")
```
<center>
`PDE_analyzer_i()` user interface - Choose the locations for the required files
</center></br> 
  
1. **Load form from tsv** OR **Save form as tsv**: The filled form can and should be saved as a TSV file at any time, accordingly the saved parameters can be loaded from saved TSV files.

2. **Reset form**: This will clear all fields and variables.

#### Input/Output:
```{r, out.width = "100%", fig.align = "center", echo = FALSE}
knitr::include_graphics("scrnshots/Screenshot_PDE_analyzer_user_interface_empty_win.png")
```
<center>
`PDE_analyzer_i()` user interface - Input/Output
</center></br> 
  
1. **Select PDF folder**: Open a folder with PDF files you want to analyze. For the analysis, all PDF files in the folder and subfolders will be analyzed.  
or  
**Load PDF files**: Select one or more PDF files you want to analyze (use Ctrl and/or Shift to select multiple). Multiple PDF files will be separated by ; without a space.  
Argument for `PDE_extr_data_from_pdfs()`: `pdfs`

2. **Select output folder**: All analysis files will be created inside of this folder; therefore,
choose an empty folder or create a new one as output directory, since analyses create at
least a number of files equal to the amount of PDF files analyzed. If no output folder
is chosen, the results will be saved in the R working directory.  
Argument for `PDE_extr_data_from_pdfs()`: `out`
or
**Open output folder**: To have a look at the output files or generally the contents of the output folder click here. The dialog will open the output folder with the standard file explorer.

3. **Choose the output format**: The resulting analyses files can either be generated as
comma-separated values files (.csv) or tab-separated values files (.tsv), with the former
being easier to open and save in Microsoft Excel, while the later leads to less
errors when opening in Microsoft Excel (as tabs are rare in texts). Depending on the operational 
system the output file are opened in, it is recommended to choose the Microsoft Windows 
(WINDOWS-1252), Mac (macintosh) or Linux (UTF-8) encoding.  
Argument for `PDE_extr_data_from_pdfs()`: `out.table.format`

4. **Adjust options in the tabs above**: For available options see below.

5. **Start analysis**: When pressing the "Start analysis" button processing through the `PDE_analyzer_i()` will begin and the button will change to "Pause analysis". Pausing of the analysis is generally delayed until the processing of the current files is finished. While paused the button will change to "Resume analysis". At any time the analysis can be aborted by pressing "Stop analysis". In addition to the analysis output files in the folders a summary file titled `PDE_analyzer_word_stats.csv` will be generated with search word and filter word statistics.

5. **Close session**: The `PDE_analyzer_i()` can be closed with this button. While analysis is running the processing can be aborted by pressing this button which will carry the caption "Stop analysis".

#### Search Words:
```{r, out.width = "100%", fig.align = "center", echo = FALSE}
knitr::include_graphics("scrnshots/Screenshot_PDE_analyzer_user_interface.search_words_empty.png")
```
<center>
`PDE_analyzer_i()` user interface - Search Words
</center></br> 

1. **Choose what to extract**: The PDE analyzer has 2 main functions A] PDF2TXT (extract sentences from pdf) and B] PDF2TABLE (table of PDF to excel file) which can be combined or executed separately. Each function can be combined with filters and search words. 
A file with the sentences carrying the search words will have the name format: `[search words]txt+-[context][PDF file name]` in the corresponding subfolder.
Tables will be named: `[PDF file name][number of table][table heading]`.  
Argument for `PDE_extr_data_from_pdfs()`: `whattoextr`  

2. **Search words?**: The algorithm can either extract \sentences, tables, or sentences and tables
with one of the search words present. If the "tables" only analysis was chosen, the algorithm 
can also extract all tables detected in the paper (choose this option here). In the later 
case, the search words field should remain empty. 

3. **Save table by category**: If search word categories are added and table extraction is
selected, the extracted tables can be saved in different sub-folders according to the category
of the detected search word.
Arguments for `PDE_extr_data_from_pdfs()`: `save.tab.by.category`

4. **Search words**: Type in the list of search words separated by ";" without spaces in
between. Additionally, search word categories can be added by including the category
name before the first search word of each category surrounded by "%:" and ":%",
e.g., %:category:%first search word. For each category word counts will be summarized in the
PDE_analyzer_word_stats.csv file.
Arguments for `PDE_extr_data_from_pdfs()`: `search.words` and  `search.word.categories`

5. **Search words case sensitive**: E.g., for "Word", if "no" was chosen then "word",
"WORD", "Word", etc., will be detected, if "yes" was chosen only "Word" will be detected.  
Argument for `PDE_extr_data_from_pdfs()`: `ignore.case.sw`

6. **Regex**: When checked search words will follow the regex rules 
(see https://github.com/erikstricker/PDE/blob/master/inst/examples/cheatsheets/regex.pdf
(https://github.com/erikstricker/PDE/blob/master/inst/examples/cheatsheets/regex.pdf)).
Argument for `PDE_extr_data_from_pdfs()`: `regex.sw`

7. **Number of sentences before and after**: When 0 is chosen, only the sentence with
the search word is extracted. If any number n is chosen, n number of sentences before
and n number of sentences after the sentence with the search word will be extracted. A
sentence is currently defined by starting and ending with a "." (period with a subsequent
space).    
Argument for `PDE_extr_data_from_pdfs()`: `context`

8. **Evaluate abbreviations?**: If "yes" was chosen, all abbreviations that were used in the
PDF documents for the search words will be saved and then replace by `abbreviation (search word)$*`, 
e.g., `MTX` will be replaced by `MTX (Methotrexate)$*`. In addition
plural of the abbreviations, i.e., the abbreviation with an "s" at the end will be replaced
accordingly as well.  
Argument for `PDE_extr_data_from_pdfs()`: `eval.abbrevs`

#### Filter Words:
```{r, out.width = "100%", fig.align = "center", echo = FALSE}
knitr::include_graphics("scrnshots/Screenshot_PDE_analyzer_user_interface.filter_words_empty.png")
```
<center>
`PDE_analyzer_i()` user interface - Filter Words
</center></br> 

1. **Filter words?**: In some cases, only articles of a certain topic should be analyzed. Filterwords provide a way to analyze only articles which carry words from a list at least n times.  

2. **Filter words**: Type in the list of filter words separated by ";" without spaces in between.
A hit will be counted every time a word from the list is detected in the article.  
Argument for `PDE_extr_data_from_pdfs()`: `filter.words`

3. **Regex**: When checked filter words will follow the regex rules 
(see https://github.com/erikstricker/PDE/blob/master/inst/examples/cheatsheets/regex.pdf
(https://github.com/erikstricker/PDE/blob/master/inst/examples/cheatsheets/regex.pdf)).
Argument for `PDE_extr_data_from_pdfs()`: `regex.fw`

4. **Filter words case sensitive**: E.g., for "Word", if "no" was chosen then "word",
"WORD", "Word", etc., will be detected, if "yes" was chosen only "Word" will be detected.  
Argument for `PDE_extr_data_from_pdfs()`: `ignore.case.fw`

5. **Filter word times**: This represents the minimum number of hits described above
which has to be detected for a paper to be further analyzed. If the threshold is not met,
a documentation file can be exported if selected in the documentation section. The 
filter word threshold can either be an abolute number or a percentage.    
Argument for `PDE_extr_data_from_pdfs()`: `filter.word.times`

6. **Copy/move PDF files**: If filter words are used in the analyses, the processed 
PDF files can either be copied (`cpy`) or moved (`mv`) into the /pdf/ subfolder
of the output folder.
Argument for `PDE_extr_data_from_pdfs()`: `cpy_mv`

#### Parameters:
```{r, out.width = "100%", fig.align = "center", echo = FALSE}
knitr::include_graphics("scrnshots/Screenshot_PDE_analyzer_user_interface.parameters_empty.png")
```
<center>
`PDE_analyzer_i()` user interface - Parameters
</center></br> 
  
1. **Enter table headings**: Standard scientific articles have their tables labeled with "TABLE",
"TAB", "Table" or "table" plus number and are detected accordingly. If a table
is expected to have a different heading, it should be typed in this field. For multiple
different heading use ";" without extra spaces.  
Argument for `PDE_extr_data_from_pdfs()`: `table.heading.words`

2. **Table heading case sensitive**: E.g., for "HEADING", if "no" was chosen then "HEADING",
"heading", "Heading", etc., will be detected, if "yes" was chosen only "HEADING"
will be detected.  
Argument for `PDE_extr_data_from_pdfs()`: `ignore.case.th`

3. **Column pixel deviation**: For some tables the heading is slightly indented which would make the algorithm assume it was a separated column. With the column pixel deviation the size of indention which would be considered the same column can be adjusted.  
Argument for `PDE_extr_data_from_pdfs()`: `dev_x`

4. **Row pixel deviation**: For some tables elements even though in the same row can have slightly different vertical coordiates.
With the row pixel deviation the variation of vertical coordinates which would be considered the same row can be adjusted. It can
be either a number or set to dynamic detection [9999], in which case the font size is used to detect which words are in the same
row.   
Argument for `PDE_extr_data_from_pdfs()`: `dev_y`

#### Documentation/Debugging:
```{r, out.width = "100%", fig.align = "center", echo = FALSE}
knitr::include_graphics("scrnshots/Screenshot_PDE_analyzer_user_interface.docus_empty.png")
```
<center>
`PDE_analyzer_i()` user interface - Documentation/Debugging
</center></br> 
  
1. **Table values in file**: When "tables" detection/export was chosen, this option will be relevant. For "yes", a separate file with the headings of all tables, their relative location in the generated HTML and TXT files, as well as information if search words were found will be generated. The files will start with "htmltablelines", "txttablelines", "keeplayouttablelines" followed by the PDF file name and can be found in `html.docu`, `txt.docu`, `keeptxt.docu` subfolders.  
Argument for `PDE_extr_data_from_pdfs()`: `write.table.locations`

2. **Export tables with problems**: For "yes", if a table was detected in a PDF file but is an image or cannot be read, the page with the table with be exported as a portable network graphics (PNG) file. The documentation file will have the name format: `[PDF name]page[page number]w.table-[page number].png`  
Argument for `PDE_extr_data_from_pdfs()`: `exp.nondetc.tabs`

3. **Table documentation files?**: For "yes", if search words are used for table detection and no search words were found in the tables of a PDF file, a file will be created with the PDF name followed by "no.table.w.search.words" in the folder with the name `no_tab_w_sw`.  
Argument for `PDE_extr_data_from_pdfs()`: `write.tab.doc.file`

4. **Sentence documentation file?**: For "yes", if no search words were found in the sentences of a pdf, a file will be created with the PDF file name followed by "no.txt.w.search.words" in the `no_txt_w_sw` folder. If the PDF file is empty, a file will be created with the PDF file name followed by "non-readable" in the `nr` folder. Files that were filtered out using the filterwords will lead to the creation of a file with the PDF name followed by "no.txt.w.filter.words" in the `excl_by_fw` folder.  
Argument for `PDE_extr_data_from_pdfs()`: `write.txt.doc.file`

5. **Keep intermediate files**: The program generates a txt, keeplayouttxt and HTML
copy of the PDF file, which will be deleted if intermediate files deletion is chosen. In
case, this option was chosen accidentally, the user has two options to delete the .txt and
.html file. 1) Slow & easy option: Rerun the analysis with this option being yes. 2)
Quick and slightly more complicated option: Open the file explorer and search for
`*.txt` and `*.html` in the PDF folder. Then select all files and folders of the search result and press delete. Keeping the intermediate files will set the `delete` to `FALSE.`
Argument for `PDE_extr_data_from_pdfs()`: `delete`

------------

### PDE_reader_i()
```{r, out.width = "75%", fig.align = "center", echo = FALSE}
knitr::include_graphics("scrnshots/Screenshot_PDE_reader_user_interface_empty_win.png")
```
<center>
`PDE_reader_i()` user interface on Microsoft Windows
</center></br> 
  
1. Run
```R
library("PDE")
PDE_reader_i()
```

2. This should open a user interface, e.g., a window with feather icon in task bar.

```{r, out.width = "100%", fig.align = "center", echo = FALSE}
knitr::include_graphics("scrnshots/Screenshot_PDE_reader_user_interface.open_empty.png")
```
<center>
`PDE_reader_i()` user interface - Load and open
</center></br> 
  
3. Load either a sentence analysis file or a folder with such files. The table shown in the center of the application is writable, editable and copyable, but changes will not be saved in the original file.  
**NOTE: Analysis files refer to the files created by the PDE analyzer which contain "txt+-" in their name.**  

    * **Open analysis file**: Loading a single file will be quick and open the selected file in the reader. The file will also be added into the memory of the program until the program is closed. All other analysis files in the folder will be shown under "Jump to file:".  

    * **Load analysis folder**: This will load all analysis files into the memory. For larger number of files, the progress bar on the top right will indicate the progress and indicate when the program can be accessed again. All files will be shown under "Jump to file:" and are quickly accessible, since they are in the memory.  

4. **Save memory to file**: The table and all tables that are currently displayed by the
`PDE_reader_i()` during a session are saved into the memory of the program, enabling
quick browsing through the tables with minimal loading time. Since the memory is reset
anytime the program closes, the memory can be saved into a .RData file to prevent long
loading times during later sessions.  

5. **Load memory from file**: Tables that were saved into the memory during earlier sessions can be loaded into the program from a corresponding .RData file.  

6. **Reset form**: The form and memory can be emptied with this button.  

7. **On/off**: This button enables switching between search word highlighting in case an appropriate TSV file is loaded (see **Load TSV file**). The button shows the current state of highlighting. The search word is found between &#x02588;&#x025B6; and &#x025C4;&#x02588;.  

8. **Load all**: The options **Load TSV file** and **Open analysis file** will only save the already displayed tables into the memory. To shorten loading times all analysis files in the current folder as well as their search word highlighted tables can be loaded into the memory with this button. This will load the tables with and without highlighting to allow rapid switching between the two. The green bar on the top right will display the progress.  
**NOTE: In the case of high numbers of search words or analysis files this step can take a long time (e.g., 1500 analysis files + 400 search words -> 1.5 h). For this reason, saving the memory to a file once the files are loaded is recommended.**  

9. **Load TSV file**: Search words used for the analysis can be highlighted by loading the TSV parameter file used for the analysis. The highlighting can be turned off and on and search words are indicated in the table by &#x02588;&#x025B6;-`[search word]`-&#x025C4;&#x02588;.   

10. **Load PDF folder**: The analyzed PDF file can be loaded into the reader by loading the PDF folder with the corresponding files. The PDF file name will show to the left of the **Open current pdf** button below the load PDF folder row.  

11. **Open current pdf**: If a PDF file analyzed is detected in the PDF folder, pressing
the button will open the PDF file in the system default PDF viewer.  

12. **Extract tables**: This button allows the user to extract all tables from the current PDF file converting them into an Excel compatible format. Extraction parameters such as pixel deviation between columns (see `PDE_analyzer_i()` §3) are derived from the TSV file chosen for search word highlighting. The extraction of the tables usually takes a few seconds, and, after extraction, the destination folder (same as analysis file folder) of the extracted tables is opened.  
**NOTE: The table extraction only works when PDF file and TSV files are available.**  

13. **Jump to file**: This check box lists all analysis files in the chosen folder. When choosing
a file from the list, the reader jumps to the respective table. This will happen with a
slight delay if the files are not already loaded in the memory (see **Open analysis file**, **Load analysis folder**).  

```{r, out.width = "100%", fig.align = "center", echo = FALSE}
knitr::include_graphics("scrnshots/Screenshot_PDE_reader_user_interface.display_empty.png")
```
<center>
`PDE_reader_i()` user interface - Table display
</center></br> 
  
14. **Font size**: The font size of all buttons, the labels and the table can be increased (**+**), decreased (**-**) or reset (**o**) located above the table.  

15. **hotkey mode**: There are 4 different hotkey modes, which allow the use of the buttons of a keyboard to quickly navigate through files. The hotkeys for each mode are as follows and can be changed by clicking on the botton on the right of the hotkey mode label:
  
|                       | **standard**     | **one hand** | **one hand & standard (oh+std)** | **no hotkey** |
|-----------------------|------------------|--------------|----------------------------------|---------------|
| **previous**          | n or left arrow  | j or a       | j or a or n or left arrow        | none          |
| **next**              | p or right arrow | l or d       | l or d or p or right arrow       | none          |
| **scroll table down** | down arrow       | k or s       | k or s or down arrow             | none          |
| **scroll table up**   | up arrow         | i or s       | i or s or up arrow               | none          |
| **flag file**         | f                | h or f       | h or f                           | none          |
| **x mark file**       | x                | space        | space or x                       | none          |
| **unmark file**       | u                | u or e       | u or e                           | none          |
| **open pdf**          | o                | o or q       | o or q                           | none          |
  
16. **Wrap**: When choosing this option, located on the right above the table, the text in the central table will have line breaks to be fully visible. This will prevent in some occasions the resizing of the window. To prevent this issue, choose "don't wrap" while resizing and activate resizing afterwards, again. In case the table does not fit vertically inside the window, either the scroll bar can be used to show different rows of the table.  

17. **Sentence number**: If sentences surrounding the sentence with the search word were extracted by the `PDE_analyzer_i()` (i.e., `context > 0`), the number of sentences displayed can be decreased (**-**), increased (**+**), or reset (**o**). When changing this setting, the sentences with the search word will always be displayed.  

18. **Show txtcontent only**: Generally, the analysis file includes information about the page and paragraphs where the sentences were extracted from. When selecting **Show txtcontent only**, only the sentences without the positional information is displayed.  

19. **Show original text (abbreviations collapsed)**: If the analysis abbreviations were
replaced in the format ABBREVIATION -> ABBREVIATION (search word)\$\* (i.e.,
eval.abbrev = TRUE), then the original text can be restored by using this setting.
This setting will also lead to the disappearance of some search words, as only the
abbreviations remain.

```{r, out.width = "100%", fig.align = "center", echo = FALSE}
knitr::include_graphics("scrnshots/Screenshot_PDE_reader_user_interface.browse_and_mark_empty.png")
```
<center>
`PDE_reader_i()` user interface - Browse and mark
</center></br> 
  
20. **Prev** and **Next**: Using these buttons the user can quickly browse through the different tables in the analysis folder.

21. **Flag file**: Using this button can either **Mark analysis file only**, **Mark PDF only** or **Mark analysis file & PDF**. The reader will rename the corresponding file adding a "!\_" to the beginning of its name.

22. **X mark file**: Using this button can either **Mark analysis file only**, **Mark PDF only** or **Mark analysis file & PDF**. The reader will rename the corresponding file adding a "x\_" to the beginning of its name.

23. **Unmark file**: Using this button can either **Unmark analysis file only**, **Unmark PDF only** or **Unmark analysis file & PDF**. The reader will remove and existing "!\_" or "x\_" at the beginning of the file name.  
**NOTE: Flagging and marking changes filenames but can be reversed in the program at any time.**

------------

## Troubleshoot

This section covers common errors we encountered when testing the package including their solution.

### Error when starting interactive user interface on Mac (failed to allocate tcl font)

#### Step of error occurence:  
`PDE_analyzer_i()`  
or  
`PDE_reader_i()`  

#### Error:  
```
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") :
[tcl] failed to allocate font due to internal system font engine problem.
```  

#### Solution:  
1) Install the latest version of XQuartz on your Mac.

If that does note work:

1) Press the Ctrl+Alt+T key to open the terminal.  
2) Type the following command: `echo 'export PATH=$PATH:/path/to/pdftotext' >> ~/.bashrc`
3) Close the terminal.  
4) Press the Ctrl+Alt+T key to open the terminal, again.  
5) Close the terminal, again.  

------------

## Example

### Process Methotrexate articles with the PDE_analyzer_i()

1. Run
```R
library("PDE")
PDE_analyzer_i()
```
2. This should open a user interface, e.g., a window with feather icon in task bar. 

```{r, out.width = "75%", fig.align = "center", echo = FALSE}
knitr::include_graphics("scrnshots/Screenshot_PDE_analyzer_user_interface_MTX_example.png")
```
<center>
`PDE_analyzer_i()` user interface
</center></br> 
  
All files for example can be found in the installation folder `examples`. The folder can be located by running the following code in the R console:
```R
system.file(package = "PDE")
```

#### Alternative to step-by-step selection: Load form from TSV

1. **Load form from TSV**: Alternatively, all parameters can be loaded from the file with
the name `PDE_parameters_v1.0_all_files+-0.tsv` found in the subfolder `examples/tsvs/`.
Then continue with **Start the PDE analyzer**.

#### Step-by-step selection of the parameters

##### Input/Output:
```{r, out.width = "100%", fig.align = "center", echo = FALSE}
knitr::include_graphics("scrnshots/Screenshot_PDE_analyzer_user_interface_MTX_example.png")
```
<center>
`PDE_analyzer_i()` user interface - Input/Output
</center></br> 
  
1. **Select PDF folder**: Open the folder with the pdfs. For the this example, 3 PDF files downloaded from PubMed using `(methotrexate) NOT Review[Publication Type]` as well as 1 erroneous (`99999999_x.pdf`) and 1 empty file (`00000000_x.pdf`) are in the following folder: 
```
examples/Methotrexate/
``` 
The file names indicate the PMIDs. In addition, negative controls are marked with an
"_x" and the files which include tables with the search words are marked with an "_!" (this
naming system is specifically chosen for the example, but generally analyses files are 
not restricted to any particular naming system other than no two files should have the
same name).  
or   
**Load PDF files**: Select the 5 PDF files to analyze (use Ctrl and/or Shift to select
multiple).  
```
examples/Methotrexate/29973177_!.pdf
examples/Methotrexate/31083238_!.pdf
examples/Methotrexate/31261533_x.pdf
examples/Methotrexate/00000000_x.pdf
examples/Methotrexate/99999999_x.pdf
```

2. **Select output folder**: The files created by the `PDE_analyzer_i()` should be identical to the files found in `examples/MTX_output`. Any output folder can be chosen for the example analysis but the following folder is recommended for direct comparison:     
```
examples/MTX_output_test
```

3. **Choose output format**: For the example analysis, the tab separated values format was chosen:
```
.tsv
```
##### Search words:
```{r, out.width = "100%", fig.align = "center", echo = FALSE}
knitr::include_graphics("scrnshots/Screenshot_PDE_analyzer_user_interface.search_words_MTX_example.png")
```
<center>
`PDE_analyzer_i()` user interface - Search words tab filled for MTX example
</center></br> 

1. **Choose what to extract**: For the example, the analyzer will extract sentences and tables with the keywords. Accordingly, the option `both` should be chosen.

2. **Search words?**: The search words were used to extract all Methotrexate relevant information.
```
yes
```

3. **Search words**: The list of search words includes all aliases of Methotrexate.
The search words are only separated by semicolons (no spaces for separation). 
```
(M|m)ethotrexate;(T|t)rexal;(R|r)heumatrex;(O|o)trexup
```

4. **Regex**: For the search words an exemplary regular expression was used. The vertical line 
in the parenthesis indicates with the upper case OR lower case first letter.
```
TRUE
```

5. **Search words case sensitive**: As explained above, the search words are case-sentive due to an abbreviation being included.
```
yes
```

6. **Number of sentences before and after**: For simplicity reasons, only the sentences with the search words were extracted.   
```
0
```

7. **Evaluate abbreviations?**: Abbreviations of Methotrexate such as MTX should also be detected in the document.
```
yes
```
##### Filter words:
```{r, out.width = "100%", fig.align = "center", echo = FALSE}
knitr::include_graphics("scrnshots/Screenshot_PDE_analyzer_user_interface.filter_words_MTX_example.png")
```
<center>
`PDE_analyzer_i()` user interface - Filter words tab filled for MTX example
</center></br> 

1. **Filter words?**: For this analysis, filter words were used to only analyze articles with case-control data.
```
yes 
```

2. **Filter words**: These words should be found at a high frequency in case-control papers. The filter words are only separated by semicolons (no spaces for separation).
```
cohort;case-control;group;study population;study participants 
```

3. **Regex**: The filter words do not include any regular expressions.
```
FALSE
```

4. **Filter words case sensitive**: Since it does not matter if a word is found capitalized at the beginning of a sentence, in a heading or within a sentence the search is not case-sensitive.
```
no
```

5. **Filter word times**: Kept at standard value of 20. Negative controls included an average of 2.4 times the filter words (despite showing a higher number of filter words `31261533_x.pdf` did not include controls classifying it as a case-control study). The case-control papers displayed on average 55 times the filter words.
```
20
```

5. **Copy/move**: For this example the PDF files stay in their respective pdf folder.
```
no copy/move
```

##### Parameters:
```{r, out.width = "100%", fig.align = "center", echo = FALSE}
knitr::include_graphics("scrnshots/Screenshot_PDE_analyzer_user_interface.parameters_MTX_example.png")
```
<center>
`PDE_analyzer_i()` user interface - Parameters tab filled for MTX example
</center></br> 
  
1. **Enter table headings**: For most scientific papers, this option is not necessary to be
populated as is of greater use in extracting tables from non-journal articles. Accordingly,
for the example the field was left empty.
```
[blank] 
```

2. **Table heading case sensitive**: Irrelevant, as table heading was left blank.

3. **Column pixel deviation**: Kept at standard value of 20. This ensured that despite the indentation each cell value still gets sorted in the correct column instead of creating additional columns.
```
20 
```

4. **Row pixel deviation**: Kept at standard value of 9999, which indicates dynamic detection. Dynamic detection uses the font size used to detect which words are in the same row.
```
9999 
```

##### Documentation:
```{r, out.width = "100%", fig.align = "center", echo = FALSE}
knitr::include_graphics("scrnshots/Screenshot_PDE_analyzer_user_interface.docus_MTX_example.png")
```
<center>
`PDE_analyzer_i()` user interface - Documentation tab filled for MTX example
</center></br> 
  
1. **Table values in file**: This option is commonly not necessary to be selected. Nonetheless,
it helps to identify if the PDE detects the tables and, if yes, if they are exported.
When comparing the files starting with the PDF file name followed by "htmltablelines",
"txttablelines", "keeplayouttablelines", it can be observed that all detected tables contained
at least one of the search words.
```
yes
```

2. **Export tables with problems**: This is recommended to capture all tables, even if
the program cannot detect the table content. This applies especially, for older articles
with scanned tables.
```
yes
```

3. **Table documentation files?**: For completeness of the example, "yes" was chosen.
Generally, it is safe to assume that papers without a file being created were sorted out
due to a lack of search words or filter words. 
```
yes
```

4. **Sentence documentation file?**: For reasoning see **Table documentation files?**. Again, for completeness of the example, "yes" was chosen. This option does not influence the creation of the `[id]_is_secured.txt` file in the
secured folder.
```
yes
```

5. **Keep intermediate files**: This option is primarly for debugging. Having access to
the .txt and .html files will allow the identification of undetected tables/sentences or
conversion issues.  
```
no
```

```{r, out.width = "100%", fig.align = "center", echo = FALSE}
knitr::include_graphics("scrnshots/Screenshot_PDE_analyzer_user_interface.start_MTX_example.png")
```
<center>
`PDE_analyzer_i()` user interface - Start analysis
</center></br> 

#### Start analysis

Start analysis: During the analysis, the progress bar indicates the number of files analyzed,
while the drop down menu and the R console display status updates:
```
Following file is processing: '00000000_x.pdf'
00000000_x.pdf has no readable content
Analysis of '00000000_x.pdf' complete.
Following file is processing: '29973177_!.pdf'
58 filter word(s) were detected in 29973177_!.pdf.
4 table(s) with search words found in '29973177_!.pdf'.
43 sentences with search words were found in '29973177_!.pdf'.
Analysis of '29973177_!.pdf' complete.
Following file is processing: '31261533_x.pdf'
'31261533_x.pdf' was filtered out due to a lack of the filter words. 9 filter word(s) were detected
Analysis of '31261533_x.pdf' complete.
Following file is processing: '99999999_x.pdf'
99999999_x is most likely secured and cannot be processed!
Analysis of '99999999_x.pdf' complete.
Analyses are complete.
```
As mentioned above, the resulting files should be identical to the files found in `examples/MTX_output/.` The file `PDE_analyzer_word_stats.csv` contains search word and filter word statistics.

------------

### Visualize extracted Methotrexate data with the PDE_reader_i()
```{r, out.width = "75%", fig.align = "center", echo = FALSE}
knitr::include_graphics("scrnshots/Screenshot_PDE_reader_user_interface_MTX.png")
```
<center>
`PDE_reader_i()` user interface
</center></br> 
  
1. To open the PDE\_reader\_i() run:
```R
library("PDE")
PDE_reader_i()
```
```{r, out.width = "100%", fig.align = "center", echo = FALSE}
knitr::include_graphics("scrnshots/Screenshot_PDE_reader_user_interface_empty_win.png")
```
<center>
`PDE_reader_i()` user interface in Windows
</center></br>
2. This should open a user interface, e.g., a window with feather icon in task bar.

```{r, out.width = "100%", fig.align = "center", echo = FALSE}
knitr::include_graphics("scrnshots/Screenshot_PDE_reader_user_interface_MTX_Open_analysis_file.png")
```
<center>
`PDE_reader_i()` user interface - Load and open
</center></br>
3. Load either a sentence analysis file such as `31083238_!_txt+-0__M_m_ethotrexate,_T_t_rexal,_R....csv` or the whole folder folder with such files, e.g., `examples/MTX_output`.   
**NOTE: All files with "txt+-" in their name can be browsed.**  

* **Open analysis file**: Loading a single file will be quick and will open the selected
file in the reader.  

* **Load analysis folder**: This will load all analysis files into the memory. For larger
number of files, the progress bar on the top right will indicate the progress and
indicate when the program can be accessed again. All files will be shown under
Jump to file and are quickly accessible, since they are in the memory.  

```{r, out.width = "100%", fig.align = "center", echo = FALSE}
knitr::include_graphics("scrnshots/Screenshot_PDE_reader_user_interface_MTX_load_tsv.png")
```
<center>
`PDE_reader_i()` user interface - Load TSV for highlighting
</center></br>

4. **Load TSV file**: Open the TSV file such as `PDE_parameters_v1.0_all_files+-0.tsv` in the folder `examples/tsvs/` to highlight the search words in following way: &#x02588;&#x025B6;-`[search word]`-&#x025C4;&#x02588;. 

5. **On/off**: Search word highlighting can be turned off and on using this button. This will load the tables with and without highlighting to allow rapid switching between the two.  

6. **Load all**: To speed up browsing, press this button. It might take a second to load all analysis files. 

```{r, out.width = "100%", fig.align = "center", echo = FALSE}
knitr::include_graphics("scrnshots/Screenshot_PDE_reader_user_interface_MTX_load_pdfs.png")
```
<center>
`PDE_reader_i()` user interface - Load PDF folder
</center></br>

 
7. **Load PDF folder**: To enable the **Open current pdf** as well as **Extract tables** button load the PDF folder into the reader, i.e. `examples/Methotrexate`.  

```{r, out.width = "100%", fig.align = "center", echo = FALSE}
knitr::include_graphics("scrnshots/Screenshot_PDE_reader_user_interface_MTX_open_pdf.png")
```
<center>
`PDE_reader_i()` user interface - Open PDF or extract table
</center></br>

8. The name of the current PDF file will show to the left of the **Open current pdf** button below the load PDF folder row.

9. **Open current PDF**: To quickly open the PDF file in the default PDF viewer, click this button.  

10. **Extract tables**: For the example we extracted all tables from the detected PDF (since each table had either the word `Methotrexate` or `MTX` in it). You can still press the button though to watch the program extract all tables into a new subfolder names `extracted_tables` which can be found in the PDF folder.
**NOTE: The table extraction only works when PDF file and TSV files are available.**  

```{r, out.width = "100%", fig.align = "center", echo = FALSE}
knitr::include_graphics("scrnshots/Screenshot_PDE_reader_user_interface_MTX_jump_to.png")
```
<center>
`PDE_reader_i()` user interface - Jump to files
</center></br> 

11. **Jump to file**: Instead of going from one file to the next you can also quickly jump to a file through the drop down menu.  

```{r, out.width = "75%", fig.align = "center", echo = FALSE}
knitr::include_graphics("scrnshots/Screenshot_PDE_reader_user_interface_MTX_table-sentence.png")
```
<center>
`PDE_reader_i()` user interface - Table display with one sentence before and after less
</center></br> 
  
12. **Sentence number**: When choosing a analysis file with `txt+-1` or higher the number of senten displayed can be decreased (**-**), increased (**+**), or reset (**o**). When changing this setting, the sentences with the search word will always be displayed.  

```{r, out.width = "75%", fig.align = "center", echo = FALSE}
knitr::include_graphics("scrnshots/Screenshot_PDE_reader_user_interface_MTX_show_txtcontent_only.png")
```
<center>
`PDE_reader_i()` user interface - Table display with text content only
</center></br> 
  
13. **Show txtcontent only**: When selecting **Show txtcontent only**, only the sentences/text without the positional information is displayed.  

```{r, out.width = "75%", fig.align = "center", echo = FALSE}
knitr::include_graphics("scrnshots/Screenshot_PDE_reader_user_interface_MTX_show_original_text.png")
```
<center>
`PDE_reader_i()` user interface - Table display without abbreviations replaced
</center></br> 
  
14. **Show original text (abbreviations collapsed)**: Choosing this setting will restore the orginial sentences by replacing `ABBREVIATION (search word)$*` with `ABBREVIATION`, e.g., `MTX (Methotrexate)$*` with `MTX`.  

```{r, out.width = "100%", fig.align = "center", echo = FALSE}
knitr::include_graphics("scrnshots/Screenshot_PDE_reader_user_interface_MTX_browse.png")
```
<center>
`PDE_reader_i()` user interface - Browse and mark
</center></br> 
  
15. **Prev** and **Next**: Using these buttons the user can quickly browse through the different tables in the analysis folder.

16. **Flag file**: Using this button can either **Mark analysis file only**, **Mark PDF only** or **Mark analysis file & pdf**. The reader will rename the corresponding file adding a "!\_" to the beginning of its name. This is how `31083238_!.pdf` was generated.
**NOTE: Make sure you have selected the file type (analysis file +- PDF file) which you want to mark.**  

17. **X mark file**: Using this button can either **Mark analysis file only**, **Mark PDF only** or **Mark analysis file & pdf**. The reader will rename the corresponding file adding a "x\_" to the beginning of its name. You can try this option for the files like `31083238_!.pdf`.

18. **Unmark file**: Using this button can either **Unmark analysis file only**, **Unmark PDF only** or **Unmark analysis file & pdf**. The reader will remove and existing "!\_" or "x\_" at the beginning of the file name. You can take off the mark from `31083238_!.pdf`. 
**NOTE: Flagging and marking changes filenames but can be reversed in the program at any time.**

You are at the end of this small example tutorial and should be a pro in literature search now!

```{r, out.width = "100%", fig.align = "center", echo = FALSE}
knitr::include_graphics("scrnshots/Screenshot_PDE_reader_user_interface_MTX.png")
```
<center>
`PDE_reader_i()` user interface
</center></br> 