[R] Help with use RMarkdown and knitr in an rdm output to word.doc

Sun Apr 7 15:05:23 CEST 2019

The kable_styling function in your code does not appear in the example docx howto, so no, they are not the same.

Bill, at some point you have to stop depending on copying snippets from blogs and read the function documentation, especially the arguments and values sections. The docs for the kable_styling function specifically mention only HTML and LaTeX that I warned you about. It has to generate pure markdown to be converted to docx.

Also, you probably shouldn't use the results='asis' chunk setting in most cases for docx output.

For example, if you read the help page for the rmarkdown::word_document function you should find a keep_md argument. Rmarkdown uses the YAML to setup the call to this function so you can write

output:
    word_document:
        keep_md: yes

for the purpose of looking at the raw markdown after knitr is done processing chunks. Applied to your code with the kable_styling function, you should see an extra md output file as it looks just before being converted to docx, with a bunch of HTML code in the md file where that chunk used to be. This would be fine if the final destination was a web browser, but not for converting to word. If you remove that function then the md file should have a plain markdown table... you can tell because it is much simpler to read than the html in raw form is.

Note that markdown is intentionally simple... there is a lot that you cannot convey through it about appearance. You are shackling yourself to a lower standard of appearance by using it. I inevitably have to manually reformat the results if I share the file for further editing. If that is unacceptable for your case then consider using the officer package... but your finalfit package won't play well with that.

On April 7, 2019 3:07:53 AM PDT, Bill Poling <Bill.Poling using zelis.com> wrote:
>Thanks Jeff, yes well I have followed the Harrison tutorial and my
>chunks are the same as his examples which appear to work fine for him?
>I am stymied.
>
>#https://www.datasurg.net/2018/05/22/finalfit-knitr-and-r-markdown-for-quick-results/
>
>I will keep working on it though, many thanks.
>
>WHP
>
>
>
>
>From: Jeff Newmiller <jdnewmil using dcn.davis.ca.us>
>Sent: Saturday, April 6, 2019 6:51 PM
>To: Bill Poling <Bill.Poling using zelis.com>; r-help using r-project.org; r-help
>(r-help using r-project.org) <r-help using r-project.org>
>Subject: RE: [R] Help with use RMarkdown and knitr in an rdm output to
>word.doc
>
>Read the help files for the functions in each code block that are
>actually producing output that will be displayed. One of them is not
>compatible with docx file output.
>
>On April 6, 2019 2:44:55 PM PDT, Bill Poling
><mailto:Bill.Poling using zelis.com> wrote:
>>Thank you Jeff, I am so darn close, I solve one problem and another
>>emerges!
>>
>>However, I realized that back in July when I made my first and, up
>>until this weekend, only attempt at this I was following the original
>>url that was reposted by R-Bloggers that I mentioned in my original
>>post earlier.
>>#https://www.datasurg.net/2018/05/16/elegant-regression-results-tables-and-plots-the-finalfit-package/
>>
>>Low and behold realized I had asked the author (Ewen Harrison with
>>DataSurg) these questions back then in the comments, UGH!
>>But since I ditched the idea in frustrationback then and I did not
>>follow-up I hadn't realized the author created a companion url for
>this
>>very topic, how to get from .Rmd to word/PDF etc..
>>
>>I located his companion reference url to the original.
>>
>>#https://www.datasurg.net/2018/05/22/finalfit-knitr-and-r-markdown-for-quick-results/
>>
>>So following his further instructions I have made more progress,
>>however, as I mention above the final document remains elusive.
>>
>>SO I did some further googling and perused these sites as well
>>
>>#https://rmarkdown.rstudio.com/articles_docx.html
>>#https://ourcodingclub.github.io/2016/11/24/rmarkdown-1.html
>>
>>Between the companion url of Harrison and
>>https://rmarkdown.rstudio.com/articles_docx.html I have almost got it.
>>
>>---
>>title: "AutoDist Analysis"
>>author: "WHP"
>>date: "4/6/2018"
>>output:
>> word_document:
>> reference_docx: word-styles-reference-01.docx
>>
>>---
>>```{r setup, include=FALSE}
>># Load data into global environment.
>>library(finalfit)
>>library(dplyr)
>>library(knitr)
>>library(kableExtra)
>>load("C:/WHP/Revenue Development Products//BRA
>>AutoDistribution/Test1.rda")
>>```
>>
>>## Table 1 - Associations between Autodist Yes/No and other
>explanatory
>>variables
>>```{r table1, echo = FALSE, results='asis'}
>>kable(table1, row.names=FALSE, align=c("l", "l", "r", "r", "r", "r"),
>>booktabs=TRUE)
>>```
>>
>>## Table 2 - Logistic regression table
>>```{r table2, echo = FALSE, results='asis'}
>>kable(table2, row.names=FALSE, align=c("l", "l", "r", "r", "r", "r"),
>>booktabs=TRUE) %>%
>>kable_styling(font_size=8)
>>```
>>
>>## Figure 1 - Odds Ratio Plot
>>```{r figure1, echo = FALSE, warning=FALSE, message=FALSE,
>>fig.width=10}
>>tmp %>%
>> or_plot(dependent, explanatory)
>>
>>However, now the issue is:
>>"Error: Functions that produce HTML output found in document targeting
>>docx output.
>>Please change the output type of this document to HTML. Alternatively,
>>you can allow
>>HTML output in non-HTML formats by adding this option to the YAML
>>front-matter of
>>your rmarkdown file:
>> always_allow_html: yes
>>Note however that the HTML output will not be visible in non-HTML
>>formats.
>>Execution halted"
>>
>>This is confusing as heck, however, I tried adding that to the YAML
>but
>>I get the same error
>>---
>>title: "AutoDist Analysis"
>>author: "WHP"
>>date: "4/6/2018"
>>output:
>> word_document:
>> reference_docx: word-styles-reference-01.docx
>> always_allow_html: yes
>>---
>>
>>SO needless to say am really disappointed!
>>
>>Whole Saturday on this, sheesh!
>>
>>Thanks for listening
>>
>>WHP
>>
>>
>>From: Jeff Newmiller <mailto:jdnewmil using dcn.davis.ca.us>
>>Sent: Saturday, April 6, 2019 2:25 PM
>>To: Bill Poling <mailto:Bill.Poling using zelis.com>;
>mailto:r-help using r-project.org; r-help
>>(mailto:r-help using r-project.org) <mailto:r-help using r-project.org>
>>Subject: RE: [R] Help with use RMarkdown and knitr in an rdm output to
>>word.doc
>>
>>Maybe you need to format the data frame as markdown before it gets
>>displayed.
>>
>>tmp %>%
>>summary_factorlist(dependent, explanatory, p=TRUE,
>>add_dependent_label=TRUE) %>%
>>knitr::kable()
>>
>>You can also tune how the columns are formatted a bit with arguments
>to
>>the kable function.
>>
>>On April 6, 2019 10:58:53 AM PDT, Bill Poling
>><mailto:Bill.Poling using zelis.com> wrote:
>>>Hello Jeff,as always, thank you for your response.
>>>
>>>Yes .Rmd, and here I thought I was being so thorough about providing
>>as
>>>much detail as possible, my apologies.
>>>
>>>I have an open .Rmd file from the File ->New File menu in RStudio, so
>>I
>>>think that part is correct.
>>>
>>>My code is this.
>>>---
>>>title: "AutoDist Analysis"
>>>author: "WHP"
>>>date: "April 6, 2019"
>>>output:
>>> word_document: default
>>> ---
>>>
>>>```{r ElegantRegress, include = FALSE}
>>>knitr::opts_chunk$set(echo = FALSE)
>>>```
>>>```{r global_options, include=FALSE}
>>>knitr::opts_chunk$set(echo=FALSE, warning=FALSE,
>>>message=FALSE,align=c("l", "l", "r", "r", "r", "r"))
>>>```
>>>
>>>```{r message=FALSE,warning=FALSE}
>>>library(finalfit)
>>>library(dplyr)
>>>library(knitr)
>>>library(memisc)
>>>load("C:/WHP/Revenue Development Products//BRA
>>>AutoDistribution/Autodist RegTests V1.RData")
>>>setwd("C:/WHP/Revenue Development Products/BRA AutoDistribution")
>>>```
>>>
>>>```{r echo=FALSE, results='asis'}
>>>explanatory = c("TBCat","ClaimType","drgcode2","typeofbillid2")
>>>dependent = "Autodist2"
>>>tmp %>% summary_factorlist(dependent, explanatory, p=TRUE,
>>>add_dependent_label=TRUE)
>>>```
>>>
>>>I do get a word.doc file output from the above code (attachment did
>>>not survive the communication as you mentioned) however, it is not in
>>>the format described in the tutorial.
>>>Here is the output I do get:
>>>
>>>AutoDist Analysis
>>>WHP
>>>
>>>April 6, 2019
>>>
>>>Dependent: Autodist2 No Yes p 5 TBCat 1 6257 (96.6) 222 (3.4) <0.001
>6
>>>2 5780 (89.1) 709 (10.9)
>>>7 3 5424 (83.9) 1042 (16.1)
>>>8 4 5324 (82.2) 1156 (17.8)
>>>9 5 5120 (79.0) 1360 (21.0)
>>>10 6 5158 (79.6) 1322 (20.4)
>>>11 7 5022 (77.5) 1459 (22.5)
>>>12 8 5081 (78.4) 1398 (21.6)
>>>13 9 4905 (75.7) 1575 (24.3)
>>>14 10 5011 (77.3) 1469 (22.7)
>>>1 ClaimType 1 48113 (80.6) 11566 (19.4) <0.001 2 2 4969 (97.1) 146
>>>(2.9)
>>>3 drgcode2 FALSE 41015 (80.8) 9734 (19.2) <0.001 4 TRUE 12067 (85.9)
>>>1978 (14.1)
>>>15 typeofbillid2 FALSE 4560 (90.3) 490 (9.7) <0.001 16 TRUE 48522
>>>(81.2) 11222 (18.8)
>>>
>>>I will revisit the links you provide once again.
>>>I have tried to find my problem solution in these earlier.
>>>Not surprisingly given the breadth and depth of information these
>>links
>>>provide I have probably overlooked something nuanced yet highly
>>>important to the formatting issue I am having.
>>>
>>>Once again thank you for your response Sir.
>>>
>>>WHP
>>>
>>>
>>>From: Jeff Newmiller <mailto:jdnewmil using dcn.davis.ca.us>
>>>Sent: Saturday, April 6, 2019 10:42 AM
>>>To: mailto:r-help using r-project.org; Bill Poling
>><mailto:Bill.Poling using zelis.com>; r-help
>>>(mailto:r-help using r-project.org) <mailto:r-help using r-project.org>
>>>Subject: Re: [R] Help with use RMarkdown and knitr in an rdm output
>to
>>>word.doc
>>>
>>>No surprise, the attachments did not come through. There are a
>limited
>>>few MIME types that are allowed, but most email programs don't let
>you
>>>have direct control over that, making embedding your entire
>>>reproducible plain-text example in the main body of the email the
>most
>>>sure path to successful communication on this mailing list.
>>>
>>>I did skim through what you wrote below, scratching my head over what
>>>"rdm" was, until it dawned on me that you might mean a file with an
>>>".Rmd" extension (are-mark-down) and that failing to use the correct
>>>extension might have something to do with your failure.
>>>
>>>Anyway, the topic on this mailing list is the R language, and
>>>contributed packages are (according to the Posting Guide) technically
>>>supposed to have support resources of their own [2] listed in their
>>>DESCRIPTION files [1]. I think the "how it works" discussion there
>>>could be useful in clarifying which other packages rmarkdown is using
>>>and which functions you might find useful documentation about. They
>>>also have a community forum over there I think.
>>>
>>>FWIW my own experience with rmarkdown has been that that most of its
>>>power comes from augmenting it with other packages, and those
>packages
>>>are often very specific to which final output format you are using.
>>The
>>>Word output format is much less extensively supported than HTML or
>PDF
>>>(via LaTeX) are. Don't fall into the trap of using HTML or LaTeX
>>>features when generating Word output.
>>>
>>>[1] https://cran.r-project.org/web/packages/rmarkdown/index.html
>>>[2] https://rmarkdown.rstudio.com
>>>
>>>On April 6, 2019 6:42:01 AM PDT, Bill Poling
>>><mailto:Bill.Poling using zelis.com> wrote:
>>>>Hello:
>>>>
>>>>#sessionInfo()
>>>>#R version 3.5.3 (2019-03-11)
>>>>#Platform: x86_64-w64-mingw32/x64 (64-bit)
>>>>#Running under: Windows >= 8 x64 (build 9200)
>>>>
>>>>#I have been struggling with learning how to use RMarkdown and knitr
>>>in
>>>>an rdm while following this tutorial using my own data.
>>>>#I Tried many months ago to self-teach but it drove me nuts,
>however,
>>>I
>>>>am now at a point where it is essential I get this figured out.
>>>>
>>>>#The tutorial
>>>>#https://www.r-bloggers.com/elegant-regression-results-tables-and-plots-in-r-the-finalfit-package/
>>>>
>>>>#I have googled and googled but cannot solve the problem of "how to
>>>get
>>>>my rdm output" word doc to look like the tutorial examples.
>>>>
>>>>#Many googles
>>>>#https://stackoverflow.com/questions/20060370/in-rstudio-is-there-a-way-to-specify-a-fig-path-for-all-figures-for-this-file
>>>>#https://rstudio.github.io/distill/figures.html
>>>>#https://kbroman.org/knitr_knutshell/pages/Rmarkdown.html
>>>>
>>>>#And the list goes on. UGH!
>>>>
>>>>#I attach my rmd code and the word doc output, hopefully they get
>>>>through. Please let me know, and if not how I might improvise
>please.
>>>>
>>>>#Here is the basic procedure from the tutorial which runs fine into
>>>the
>>>>console, however, I am trying to output it with the suggested
>>>>formatting in the tutorial
>>>>explanatory = c("TBCat","ClaimType","drgcode2","typeofbillid2")
>>>>dependent = "Autodist2"
>>>>tmp %>%
>>>>summary_factorlist(dependent, explanatory, p=TRUE,
>>>>add_dependent_label=TRUE)
>>>>
>>>>#Here is a sample of my data.
>>>>
>>>>#I am sure there are also basic formatting inconsistencies or
>>>>redundancies in the rdm and would appreciate any advice or
>suggestion
>>>>for that as well, happy Saturday.
>>>>
>>>>sample <- tmp %>% slice(1:35)
>>>>> dput(sample)
>>>>structure(list(Autodist2 = structure(c(2L, 2L, 2L, 2L, 2L, 2L,
>>>>2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
>>>>2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L), .Label =
>c("No",
>>>>"Yes"), class = "factor"), TBCat = structure(c(4L, 10L, 6L, 8L,
>>>>9L, 4L, 6L, 8L, 4L, 8L, 5L, 10L, 9L, 6L, 7L, 4L, 3L, 8L, 7L,
>>>>4L, 10L, 7L, 8L, 8L, 7L, 4L, 10L, 9L, 3L, 4L, 9L, 8L, 5L, 2L,
>>>>8L), .Label = c("1", "2", "3", "4", "5", "6", "7", "8", "9",
>>>>"10"), class = "factor"), RestictedPayorID = structure(c(2L,
>>>>2L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 1L, 1L,
>>>>1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 2L, 1L, 1L, 2L, 1L,
>>>>2L, 2L), .Label = c("FALSE", "TRUE"), class = "factor"), ClaimType =
>>>>structure(c(1L,
>>>>1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
>>>>1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
>>>>1L, 1L), .Label = c("1", "2"), class = "factor"),
>>>>ClaimStatus_Non_Acceptance = structure(c(1L,
>>>>1L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
>>>>2L, 2L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 1L, 1L, 2L,
>>>>1L, 1L), .Label = c("0", "1"), class = "factor"),
>>ClaimStatus_Accepted
>>>>= structure(c(2L,
>>>>2L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
>>>>1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 1L,
>>>>2L, 2L), .Label = c("0", "1"), class = "factor"), ClaimManagerID3 =
>>>>structure(c(2L,
>>>>1L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 1L,
>>>>2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 2L, 2L, 2L,
>>>>2L, 1L), .Label = c("FALSE", "TRUE"), class = "factor"),
>>>>ClaimStatus_In_Process = structure(c(1L,
>>>>1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
>>>>1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
>>>>1L, 1L), .Label = c("0", "1"), class = "factor"), Appeals2 =
>>>>structure(c(2L,
>>>>2L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 1L,
>>>>1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
>>>>2L, 1L), .Label = c("FALSE", "TRUE"), class = "factor"), drgcode2 =
>>>>structure(c(1L,
>>>>1L, 1L, 1L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 1L,
>>>>2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 1L, 2L, 1L, 1L, 1L, 2L,
>>>>1L, 1L), .Label = c("FALSE", "TRUE"), class = "factor"), edi2 =
>>>>structure(c(1L,
>>>>2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L,
>>>>2L, 2L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 1L, 2L,
>>>>2L, 1L), .Label = c("FALSE", "TRUE"), class = "factor"),
>>typeofbillid2
>>>>= structure(c(2L,
>>>>2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
>>>>2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
>>>>2L, 2L), .Label = c("FALSE", "TRUE"), class = "factor"),
>>>>ExternalNetworkID2 = structure(c(1L,
>>>>1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
>>>>1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
>>>>1L, 1L), .Label = c("FALSE", "TRUE"), class = "factor"),
>>>>AdjustmentType2 = structure(c(2L,
>>>>2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 2L,
>>>>2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
>>>>2L, 2L), .Label = c("FALSE", "TRUE"), class = "factor"),
>>>>CustomEOPLanguage2 = structure(c(2L,
>>>>2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 2L,
>>>>2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
>>>>2L, 2L), .Label = c("FALSE", "TRUE"), class = "factor")), row.names
>=
>>>>c(NA,
>>>>-35L), class = "data.frame")
>>>>
>>>>
>>>>
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