I'm trying to create a PDF with headers from rmarkdown. I'm reading in a large text file, and I want to print out this PDF using headers. I can easily read in and print to the PDF with desired formatting, minus the headers, using
```{r comment='', echo=FALSE}
cat(readLines("blah.txt", encoding="UTF-8"), sep="/n")
```
However, I can't get rmarkdown to evaluate '#' in my text, which creates headers. I've inserted the '#' into different sections of the .txt file where I want to create a header, but it doesn't evaluate the hashtag.
Does anyone know how to get rmarkdown to evaluate the '#' as a header without messing up the formatting of the text file as I already have it?
RMarkdown recognizes # ...-headers only if there is an empty line before. So what you need is simply to use one more line-break \n (note the back-slashes).
```{r comment='', echo=FALSE, results='asis'}
cat(readLines("blah.txt", encoding="UTF-8"), sep="\n\n")
```
Note, that you may want to add results='asis' in the R-junk.
Related
I have two pdf documents, both in same layout with different information. The problem is:
I can read one perfectly but the other one the data is unrecognizable.
This is an example which I can read perfectly, download here:
from_pdf = camelot.read_pdf('2019_05_2.pdf', flavor='stream', strict=False)
df_pdf = from_pdf[0].df
camelot.plot(from_pdf[0], kind='text').show()
print(from_pdf[0].parsing_report)
This is the dataframe as expected:
This is an example which after I read, the information is unrecognizable, download here:
from_pdf = camelot.read_pdf('2020_04_2.pdf', flavor='stream', strict=False)
df_pdf = from_pdf[0].df
camelot.plot(from_pdf[0], kind='text').show()
print(from_pdf[0].parsing_report)
This is the dataframe with unrecognizable information:
I don't understand what I have done wrong and why the same code doesn't work for both files. I need some help, thanks.
The problem: malformed PDF
Simply, the problem is that your second PDF is malformed / corrupted. It doesn't contain correct font information, so it is impossible to extract text from your PDF as is. It is a known and difficult problem (see this question).
You can check this by trying to open the PDF with Google Docs.
Google Docs tries to extract the text and this is the result:.
Possible solutions
If you want to extract the text, you can print the document to an image-based PDF and perform an OCR text extraction.
However, Camelot does not currently support image-based PDFs, so it is not possible to extract the table.
If you have no way to recover a well-formed PDF, you could try this strategy:
print PDF to an image-based PDF
add a good text layer to your image-based PDF (using OCRmyPDF)
try using Camelot to extract tables
I thought it would be a good idea to write a longer report/protocol using bookdown since it's more comfortable to have one file per topic to write in instead of just one RMarkdown document with everything. Now I'm faced with the problem of sharing this document - the HTML looks best (except for wide tables being cut off) but is difficult to send via e-mail to a supervisor for example. I also can't expect anyone to be able to open the ePub format on their computer, so PDF would be the easiest choice. Now my problems:
My chapter headings are pretty long, which doesn't matter in HTML but they don't fit the page headers in the PDF document. In LaTeX I could define a short title for that, can I do that in bookdown as well?
I include figure files using knitr::include_graphics() inside of code chunks, so I generate the caption via the chunk options. For some figures, I can't avoid having an underscore in the caption, but that does not work out in LaTeX. Is there a way to escape the underscore that actually works (preferrably for HTML and PDF at the same time)? My LaTeX output looks like this after rendering:
\textbackslash{}begin\{figure\}
\includegraphics[width=0.6\linewidth,height=0.6\textheight]{figures/0165_HMMER} \textbackslash{}caption\{Output of HMMER for PA\_0165\}\label{fig:0165}
\textbackslash{}end\{figure\}
Edit
MWE showing that the problem is an underscore in combination with out.height (or width) in percent:
---
title: "MWE FigCap"
author: "LilithElina"
date: "19 Februar 2020"
output: pdf_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## R Markdown
This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.
When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
```{r cars}
summary(cars)
```
## Including Plots
You can also embed plots, for example:
```{r pressure, echo=FALSE, fig.cap="This is a nice figure caption", out.height='40%'}
plot(pressure)
```
Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.
```{r pressure2, echo=FALSE, fig.cap="This is a not nice figure_caption", out.height='40%'}
plot(pressure)
```
Concerning shorter headings: pandoc, which is used for the markdown to LaTeX conversion, does not offer a "shorter heading". You can do that yourself, though:
# Really long chaper heading
\markboth{\thechapter~short heading}{}
[...]
## Really long section heading
\markright{\thesection~short heading}
This assumes a document class with chapters and sections.
Concerning the underscore in the figure caption: For me it works for both PDF and HTML to escape the underscore:
```{r pressure2, echo=FALSE, fig.cap="This is a not nice figure\\_caption", out.height='40%'}
plot(pressure)
```
In a pre-build event, a batch file is executed to combine multiple SQL files into a single one.
It is done using this command :
COPY %#ProjectDir%\Migrations\*.sql %#ProjectDir%ContinuousDeployment\AllFilesMergedTogether.sql
Everything appear to work fine but somehow the result give an incorrect syntaxe error.
After two hours of investigation, it turn out the issue is caused by an invisible character that remain invisible even with notepad++.
Using an online website, the character has been spotted and is U+FEFF has shown in following image.
Here are the two input scripts.
PRINT 'Script1'
PRINT 'Script2'
Here is the output given by the copy command.
PRINT 'Script1'
PRINT 'Script2'
Additional info :
Batch file is encoded with UTF-8
Input files are encoded with UTF-8-BOM
Output file is encoded with UTF-8-BOM.
I'm not sure it is possible to change the encoding output of command copy.
I've tried and failed.
What should be done to eradicate this extremely frustrating parasitic character?
It has turned out that changing encoding of input files to ANSI does fix the issue.
No more pesky character(s).
Also, doing so does change the encoding of the result file to UTF-8 instead of UTF-8-BOM which is great I believe.
Encoding can be changed using Notepad++ as show in following picture.
I am referring to this Suppress automatic figure numbering in pdf output with r markdown/knitr
which I don't think was answered fully.
Essentially, I am using knitr::spin and rmarkdown to produce word, pdf and html documents.
For word, there appears to be no numbering when one puts in
+fig.1, fig.cap = "Figure name"
You only get an output Figure name in the caption.
To solve that, I used captioner class.
figs = captioner("Figure")
That works fine for word
But I am not faced with rewriting the script for pdf document as the caption turns up as figure 1: figure 1: The name
I am using knitr::spin to actually generate the RMD document for forward outputs in word and pdf.
I am not sure I can use hooks in knitr::spin, as I have tried it as advertised but can't get it to work.
I also tried
header-includes: \usepackage{caption} \usepackage{float}
\captionsetup[table]{labelformat=empty}
\captionsetup[figure]{labelformat=empty}
as suggested somehere to surpress the prefix for pdf but I get errors from pandoc. It uses pdf2latex.
I am not sure how one would query the output format in knitr::spin to actually produce different actions for different formats which could be a solution although cumbersome.
Thank you so much for your help from a novice.
I had lots of data in a .rtf file(having usernames and passwords).How can I fetch that data into a table. I'm using sqlite3.
I had created a "userDatabase.sql" in that I had created a table "usersList" having fields "username","password". I want to get the list of data in the "list.rtf" file in to my table "usersList". Please help me .
Thanks in advance.
Praveena.
I would write a little parser. Re-save the .rtf as a txt-file and assume it look like this:
user1:pass1
user2:pass2
user5:pass5
Now do this (in your code):
open the .txt file (NSString -stringWithContentsOfFile:usedEncoding:error:)
read line by line
for each line, fetch user and password (NSArray -componentsSeparatedByString)
store user/password into your DB
Best,
Christian
Edit: for parsing excel-sheets I recommend export as CSV file and then do the same
Parsing RTF files is mostly trivial. They're actually text, not binary (like doc pdf etc).
Last I used it, I remember the file format wasn't too difficult either.
Example:
{\rtf1\ansi\ansicpg1252\deff0\deflang1033{\fonttbl{\f0\fnil\fcharset0 Calibri;}}
{\*\generator Msftedit 5.41.21.2510;}\viewkind4\uc1\pard\sa200\sl276\slmult1\lang9\f0\fs22 Username Password\par
Username2 Password2\par
UsernameN PasswordN\par
}
Do a regular expression match to get the last { ... } part. By sure to match { not \{.
Next, parse the text as you want, but keep in mind that:
everything starting with a \ is escaped, I would write a little function to unescape the text
the special identifier \par is for a new line
there are other special identifiers, such as \b which toggles bolding text
the color change identifier, \cfN changes the text color according to the color table defined in the file header. You would want to ignore this identifier since we're talking about plain text.