Help with knitr pkg

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Help with knitr pkg

Bill Poling
Hi,
I worked through this excellent tutorial:
#Elegant regression results tables and plots in R: the finalfit package
https://www.r-bloggers.com/elegant-regression-results-tables-and-plots-in-r-the-finalfit-package/



Now I am applying it to my own data.

In the tutorial there is mention of:

# Tables can be knitted to PDF, Word or html documents. We do this in
# RStudio from a .Rmd document. Example chunk:
#   ```{r, echo = FALSE, results='asis'}
# knitr::kable(example_table, row.names=FALSE,
#              align=c("l", "l", "r", "r", "r", "r"))
# ```

I am having a difficult time understanding how this works?

I have read through the help:

?knitr
#"This function takes an input file, extracts the R code in it according to a list of patterns, evaluates the code and writes the output in another file.
#It can also tangle R source code from the input document (purl() is a wrapper to knit(..., tangle = TRUE)).
#The knitr.purl.inline option can be used to also tangle the code of inline expressions (disabled by default)."

install.packages("knitr")
library(knitr)
?knit
?stitch
install.packages("stitch")#package 'stitch' is not available (for R version 3.5.1)
?spin
install.packages("spin") #package 'spin' is not available (for R version 3.5.1)Warning in install.packages :  Perhaps you meant 'SPIn' ?

I have also looked at the github and knitr author's links

https://github.com/yihui/knitr

https://yihui.name/knitr/demo/stitch/

https://github.com/yihui/knitr/blob/master/inst/examples/knitr-spin.Rmd


If I understand this correctly I have to have a template already in place as the input object, is that correct? How would I construct this it that is so?

I also tried writing out directly to pdf and png with no success.

#pdf("c:/WHP/Appeals/OutputPDFs/EX&DE V1.pdf")
#png("c:/WHP/Appeals/OutputPDFs/EX&DE V1.png")
#opts_chunk$set(fig.path = "c:/WHP/Appeals/OutputPDFs/EX&DE V1.pdf") <--I don't even understand what this does, poached it from one of the google sites I have been reviewing and tried to make it work?

#This is the script I would like the output placed in PDF
explanatory = c("claimStatusId", "AgeCat", "PatientGender", "PayorID")
dependent = "AppealOverturned" # Appeals Status
appdf1DT2 %>%
  summary_factorlist(dependent, explanatory, p=TRUE, add_dependent_label=TRUE)

#dev.off()


str(appdf1DT2)
# Classes 'data.table' and 'data.frame':   3983 obs. of  21 variables:
#   $ ClaimServiceID   : Factor w/ 3983 levels "51318639","51318640",..: 1 2 4 3 5 12 6 8 7 9 ...
# $ LineNumber       : Factor w/ 140 levels "1","2","3","4",..: 1 2 4 3 5 7 1 3 2 4 ...
# $ claimStatusId    : Factor w/ 2 levels "2","3": 2 2 2 2 2 1 1 1 1 1 ...
# $ PatientGender    : Factor w/ 3 levels "F","M","UNK": 2 2 2 2 2 1 1 1 1 1 ...
# $ PayorID          : Factor w/ 19 levels "000","234","239",..: 1 1 1 1 1 1 1 1 1 1 ...
# $ AppealID         : Factor w/ 512 levels "79765","116998",..: 1 1 1 1 1 2 2 2 2 2 ...
# $ ZipCode          : Factor w/ 223 levels "2155","3037",..: 72 72 72 72 72 102 102 102 102 102 ...
# $ EditID           : Factor w/ 21 levels "","0","001X",..: 2 12 8 12 8 8 2 8 12 8 ...
# $ CurrentBilled    : num  14394 14394 14394 14394 14394 ...
# $ ClaimLineSavings : num  0 0 0 0 0 ...
# $ StatusChangeMo   : Factor w/ 7 levels "2018-01","2018-02",..: 4 4 4 4 4 4 4 4 4 4 ...
# $ Grouping         : Factor w/ 9 levels "","Agencies",..: 4 4 4 4 4 4 4 4 4 4 ...
# $ AppealOverturned : Factor w/ 2 levels "1","2": 2 2 2 2 2 1 1 1 1 1 ...
# $ PrimaryDX        : Factor w/ 360 levels "","8442","912",..: 2 2 2 2 2 171 171 171 171 171 ...
# $ RevCodeCats      : Factor w/ 41 levels "AdminStorProcBlProd",..: 2 2 18 2 18 18 2 2 2 18 ...
# $ AgeCat           : Factor w/ 9 levels "[0-5]","[11-20]",..: 4 4 4 4 4 8 8 8 8 8 ...
# $ ClaimLevelSavings: num  0 0 0 0 0 ...
# - attr(*, ".internal.selfref")=<externalptr>

head(appdf1DT2)
   ClaimServiceID LineNumber claimStatusId PatientGender PayorID ProviderID AppealID ZipCode        TIN EditID
1:       51318639          1             3             M     000     149385    79765              33904      0
2:       51318640          2             3             M     000     149385    79765              33904    022
3:       51318642          4             3             M     000     149385    79765              33904   00504
4:       51318641          3             3             M     000     149385    79765              33904     022
5:       51318643          5             3             M     000     149385    79765              33904   00504
6:       85833537          7             2             F     000    3240182   116998              46635   00504
   CurrentBilled ClaimLineSavings StatusChangeMo                                 Grouping AppealOverturned PrimaryDX        RevCodeCats
1:      14394.08                0        2018-04  Ambulatory Health Care Facilities                2      8442        AmbSurgCare
2:      14394.08                0        2018-04  Ambulatory Health Care Facilities                2      8442        AmbSurgCare
3:      14394.08                0        2018-04  Ambulatory Health Care Facilities                2      8442 MedSurgSuppandDevs
4:      14394.08                0        2018-04  Ambulatory Health Care Facilities                2      8442        AmbSurgCare
5:      14394.08                0        2018-04  Ambulatory Health Care Facilities                2      8442 MedSurgSuppandDevs
6:      23472.92                0        2018-04  Ambulatory Health Care Facilities                1     M1712 MedSurgSuppandDevs
    AgeCat ClaimLevelSavings
1: [31-40]              0.00
2: [31-40]              0.00
3: [31-40]              0.00
4: [31-40]              0.00
5: [31-40]              0.00
6: [61-70]            296.25


Maybe I am in over my head in this pursuit given my novice status with R, however, any direction would be appreciated.

Thank you.

WHP

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Re: Help with knitr pkg

Rainer Hurling
Hi Bill,

Am 18.07.18 um 18:33 schrieb Bill Poling:

> Hi,
> I worked through this excellent tutorial:
> #Elegant regression results tables and plots in R: the finalfit package
> https://www.r-bloggers.com/elegant-regression-results-tables-and-plots-in-r-the-finalfit-package/
>
>
>
> Now I am applying it to my own data.
>
> In the tutorial there is mention of:
>
> # Tables can be knitted to PDF, Word or html documents. We do this in
> # RStudio from a .Rmd document. Example chunk:
> #   ```{r, echo = FALSE, results='asis'}
> # knitr::kable(example_table, row.names=FALSE,
> #              align=c("l", "l", "r", "r", "r", "r"))
> # ```
>
> I am having a difficult time understanding how this works?
>
> I have read through the help:
>
> ?knitr
> #"This function takes an input file, extracts the R code in it according to a list of patterns, evaluates the code and writes the output in another file.
> #It can also tangle R source code from the input document (purl() is a wrapper to knit(..., tangle = TRUE)).
> #The knitr.purl.inline option can be used to also tangle the code of inline expressions (disabled by default)."
>
> install.packages("knitr")
> library(knitr)
> ?knit
> ?stitch
> install.packages("stitch")#package 'stitch' is not available (for R version 3.5.1)
> ?spin
> install.packages("spin") #package 'spin' is not available (for R version 3.5.1)Warning in install.packages :  Perhaps you meant 'SPIn' ?
>
> I have also looked at the github and knitr author's links
>
> https://github.com/yihui/knitr
>
> https://yihui.name/knitr/demo/stitch/
>
> https://github.com/yihui/knitr/blob/master/inst/examples/knitr-spin.Rmd
>
>
> If I understand this correctly I have to have a template already in place as the input object, is that correct? How would I construct this it that is so?
>
> I also tried writing out directly to pdf and png with no success.
>
> #pdf("c:/WHP/Appeals/OutputPDFs/EX&DE V1.pdf")
> #png("c:/WHP/Appeals/OutputPDFs/EX&DE V1.png")
> #opts_chunk$set(fig.path = "c:/WHP/Appeals/OutputPDFs/EX&DE V1.pdf") <--I don't even understand what this does, poached it from one of the google sites I have been reviewing and tried to make it work?
>
> #This is the script I would like the output placed in PDF
> explanatory = c("claimStatusId", "AgeCat", "PatientGender", "PayorID")
> dependent = "AppealOverturned" # Appeals Status
> appdf1DT2 %>%
>    summary_factorlist(dependent, explanatory, p=TRUE, add_dependent_label=TRUE)
>
> #dev.off()
>
>
> str(appdf1DT2)
> # Classes 'data.table' and 'data.frame':   3983 obs. of  21 variables:
> #   $ ClaimServiceID   : Factor w/ 3983 levels "51318639","51318640",..: 1 2 4 3 5 12 6 8 7 9 ...
> # $ LineNumber       : Factor w/ 140 levels "1","2","3","4",..: 1 2 4 3 5 7 1 3 2 4 ...
> # $ claimStatusId    : Factor w/ 2 levels "2","3": 2 2 2 2 2 1 1 1 1 1 ...
> # $ PatientGender    : Factor w/ 3 levels "F","M","UNK": 2 2 2 2 2 1 1 1 1 1 ...
> # $ PayorID          : Factor w/ 19 levels "000","234","239",..: 1 1 1 1 1 1 1 1 1 1 ...
> # $ AppealID         : Factor w/ 512 levels "79765","116998",..: 1 1 1 1 1 2 2 2 2 2 ...
> # $ ZipCode          : Factor w/ 223 levels "2155","3037",..: 72 72 72 72 72 102 102 102 102 102 ...
> # $ EditID           : Factor w/ 21 levels "","0","001X",..: 2 12 8 12 8 8 2 8 12 8 ...
> # $ CurrentBilled    : num  14394 14394 14394 14394 14394 ...
> # $ ClaimLineSavings : num  0 0 0 0 0 ...
> # $ StatusChangeMo   : Factor w/ 7 levels "2018-01","2018-02",..: 4 4 4 4 4 4 4 4 4 4 ...
> # $ Grouping         : Factor w/ 9 levels "","Agencies",..: 4 4 4 4 4 4 4 4 4 4 ...
> # $ AppealOverturned : Factor w/ 2 levels "1","2": 2 2 2 2 2 1 1 1 1 1 ...
> # $ PrimaryDX        : Factor w/ 360 levels "","8442","912",..: 2 2 2 2 2 171 171 171 171 171 ...
> # $ RevCodeCats      : Factor w/ 41 levels "AdminStorProcBlProd",..: 2 2 18 2 18 18 2 2 2 18 ...
> # $ AgeCat           : Factor w/ 9 levels "[0-5]","[11-20]",..: 4 4 4 4 4 8 8 8 8 8 ...
> # $ ClaimLevelSavings: num  0 0 0 0 0 ...
> # - attr(*, ".internal.selfref")=<externalptr>
>
> head(appdf1DT2)
>     ClaimServiceID LineNumber claimStatusId PatientGender PayorID ProviderID AppealID ZipCode        TIN EditID
> 1:       51318639          1             3             M     000     149385    79765              33904      0
> 2:       51318640          2             3             M     000     149385    79765              33904    022
> 3:       51318642          4             3             M     000     149385    79765              33904   00504
> 4:       51318641          3             3             M     000     149385    79765              33904     022
> 5:       51318643          5             3             M     000     149385    79765              33904   00504
> 6:       85833537          7             2             F     000    3240182   116998              46635   00504
>     CurrentBilled ClaimLineSavings StatusChangeMo                                 Grouping AppealOverturned PrimaryDX        RevCodeCats
> 1:      14394.08                0        2018-04  Ambulatory Health Care Facilities                2      8442        AmbSurgCare
> 2:      14394.08                0        2018-04  Ambulatory Health Care Facilities                2      8442        AmbSurgCare
> 3:      14394.08                0        2018-04  Ambulatory Health Care Facilities                2      8442 MedSurgSuppandDevs
> 4:      14394.08                0        2018-04  Ambulatory Health Care Facilities                2      8442        AmbSurgCare
> 5:      14394.08                0        2018-04  Ambulatory Health Care Facilities                2      8442 MedSurgSuppandDevs
> 6:      23472.92                0        2018-04  Ambulatory Health Care Facilities                1     M1712 MedSurgSuppandDevs
>      AgeCat ClaimLevelSavings
> 1: [31-40]              0.00
> 2: [31-40]              0.00
> 3: [31-40]              0.00
> 4: [31-40]              0.00
> 5: [31-40]              0.00
> 6: [61-70]            296.25
>
>
> Maybe I am in over my head in this pursuit given my novice status with R, however, any direction would be appreciated.
>
> Thank you.
>
> WHP
>
> Confidentiality Notice This message is sent from Zelis. ...{{dropped:15}}
>


Not sure, if I get you right. Seems, that you use knitr:: and code
chunks without the necessary context?

Please have a look at https://rmarkdown.rstudio.com/ to get a more
general understanding about using knitr within RMarkdown context.

HTH,
Rainer Hurling

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Re: Help with knitr pkg

Thierry Onkelinx
In reply to this post by Bill Poling
Dear Bill,

It seems like you are looking at the wrong help files. The code in the
tutorial uses the package::function() syntax. So knitr::kable()
translates into use the function kable() from the knitr package. The
help file you are looking for is ?kable (when knitr is loaded) or
?knitr::kable (when knitr is not loaded).

Best regards,

ir. Thierry Onkelinx
Statisticus / Statistician

Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE
AND FOREST
Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
[hidden email]
Havenlaan 88 bus 73, 1000 Brussel
www.inbo.be

///////////////////////////////////////////////////////////////////////////////////////////
To call in the statistician after the experiment is done may be no
more than asking him to perform a post-mortem examination: he may be
able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does
not ensure that a reasonable answer can be extracted from a given body
of data. ~ John Tukey
///////////////////////////////////////////////////////////////////////////////////////////




2018-07-18 18:33 GMT+02:00 Bill Poling <[hidden email]>:

> Hi,
> I worked through this excellent tutorial:
> #Elegant regression results tables and plots in R: the finalfit package
> https://www.r-bloggers.com/elegant-regression-results-tables-and-plots-in-r-the-finalfit-package/
>
>
>
> Now I am applying it to my own data.
>
> In the tutorial there is mention of:
>
> # Tables can be knitted to PDF, Word or html documents. We do this in
> # RStudio from a .Rmd document. Example chunk:
> #   ```{r, echo = FALSE, results='asis'}
> # knitr::kable(example_table, row.names=FALSE,
> #              align=c("l", "l", "r", "r", "r", "r"))
> # ```
>
> I am having a difficult time understanding how this works?
>
> I have read through the help:
>
> ?knitr
> #"This function takes an input file, extracts the R code in it according to a list of patterns, evaluates the code and writes the output in another file.
> #It can also tangle R source code from the input document (purl() is a wrapper to knit(..., tangle = TRUE)).
> #The knitr.purl.inline option can be used to also tangle the code of inline expressions (disabled by default)."
>
> install.packages("knitr")
> library(knitr)
> ?knit
> ?stitch
> install.packages("stitch")#package 'stitch' is not available (for R version 3.5.1)
> ?spin
> install.packages("spin") #package 'spin' is not available (for R version 3.5.1)Warning in install.packages :  Perhaps you meant 'SPIn' ?
>
> I have also looked at the github and knitr author's links
>
> https://github.com/yihui/knitr
>
> https://yihui.name/knitr/demo/stitch/
>
> https://github.com/yihui/knitr/blob/master/inst/examples/knitr-spin.Rmd
>
>
> If I understand this correctly I have to have a template already in place as the input object, is that correct? How would I construct this it that is so?
>
> I also tried writing out directly to pdf and png with no success.
>
> #pdf("c:/WHP/Appeals/OutputPDFs/EX&DE V1.pdf")
> #png("c:/WHP/Appeals/OutputPDFs/EX&DE V1.png")
> #opts_chunk$set(fig.path = "c:/WHP/Appeals/OutputPDFs/EX&DE V1.pdf") <--I don't even understand what this does, poached it from one of the google sites I have been reviewing and tried to make it work?
>
> #This is the script I would like the output placed in PDF
> explanatory = c("claimStatusId", "AgeCat", "PatientGender", "PayorID")
> dependent = "AppealOverturned" # Appeals Status
> appdf1DT2 %>%
>   summary_factorlist(dependent, explanatory, p=TRUE, add_dependent_label=TRUE)
>
> #dev.off()
>
>
> str(appdf1DT2)
> # Classes 'data.table' and 'data.frame':   3983 obs. of  21 variables:
> #   $ ClaimServiceID   : Factor w/ 3983 levels "51318639","51318640",..: 1 2 4 3 5 12 6 8 7 9 ...
> # $ LineNumber       : Factor w/ 140 levels "1","2","3","4",..: 1 2 4 3 5 7 1 3 2 4 ...
> # $ claimStatusId    : Factor w/ 2 levels "2","3": 2 2 2 2 2 1 1 1 1 1 ...
> # $ PatientGender    : Factor w/ 3 levels "F","M","UNK": 2 2 2 2 2 1 1 1 1 1 ...
> # $ PayorID          : Factor w/ 19 levels "000","234","239",..: 1 1 1 1 1 1 1 1 1 1 ...
> # $ AppealID         : Factor w/ 512 levels "79765","116998",..: 1 1 1 1 1 2 2 2 2 2 ...
> # $ ZipCode          : Factor w/ 223 levels "2155","3037",..: 72 72 72 72 72 102 102 102 102 102 ...
> # $ EditID           : Factor w/ 21 levels "","0","001X",..: 2 12 8 12 8 8 2 8 12 8 ...
> # $ CurrentBilled    : num  14394 14394 14394 14394 14394 ...
> # $ ClaimLineSavings : num  0 0 0 0 0 ...
> # $ StatusChangeMo   : Factor w/ 7 levels "2018-01","2018-02",..: 4 4 4 4 4 4 4 4 4 4 ...
> # $ Grouping         : Factor w/ 9 levels "","Agencies",..: 4 4 4 4 4 4 4 4 4 4 ...
> # $ AppealOverturned : Factor w/ 2 levels "1","2": 2 2 2 2 2 1 1 1 1 1 ...
> # $ PrimaryDX        : Factor w/ 360 levels "","8442","912",..: 2 2 2 2 2 171 171 171 171 171 ...
> # $ RevCodeCats      : Factor w/ 41 levels "AdminStorProcBlProd",..: 2 2 18 2 18 18 2 2 2 18 ...
> # $ AgeCat           : Factor w/ 9 levels "[0-5]","[11-20]",..: 4 4 4 4 4 8 8 8 8 8 ...
> # $ ClaimLevelSavings: num  0 0 0 0 0 ...
> # - attr(*, ".internal.selfref")=<externalptr>
>
> head(appdf1DT2)
>    ClaimServiceID LineNumber claimStatusId PatientGender PayorID ProviderID AppealID ZipCode        TIN EditID
> 1:       51318639          1             3             M     000     149385    79765              33904      0
> 2:       51318640          2             3             M     000     149385    79765              33904    022
> 3:       51318642          4             3             M     000     149385    79765              33904   00504
> 4:       51318641          3             3             M     000     149385    79765              33904     022
> 5:       51318643          5             3             M     000     149385    79765              33904   00504
> 6:       85833537          7             2             F     000    3240182   116998              46635   00504
>    CurrentBilled ClaimLineSavings StatusChangeMo                                 Grouping AppealOverturned PrimaryDX        RevCodeCats
> 1:      14394.08                0        2018-04  Ambulatory Health Care Facilities                2      8442        AmbSurgCare
> 2:      14394.08                0        2018-04  Ambulatory Health Care Facilities                2      8442        AmbSurgCare
> 3:      14394.08                0        2018-04  Ambulatory Health Care Facilities                2      8442 MedSurgSuppandDevs
> 4:      14394.08                0        2018-04  Ambulatory Health Care Facilities                2      8442        AmbSurgCare
> 5:      14394.08                0        2018-04  Ambulatory Health Care Facilities                2      8442 MedSurgSuppandDevs
> 6:      23472.92                0        2018-04  Ambulatory Health Care Facilities                1     M1712 MedSurgSuppandDevs
>     AgeCat ClaimLevelSavings
> 1: [31-40]              0.00
> 2: [31-40]              0.00
> 3: [31-40]              0.00
> 4: [31-40]              0.00
> 5: [31-40]              0.00
> 6: [61-70]            296.25
>
>
> Maybe I am in over my head in this pursuit given my novice status with R, however, any direction would be appreciated.
>
> Thank you.
>
> WHP
>
> Confidentiality Notice This message is sent from Zelis. ...{{dropped:15}}
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> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
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Re: Help with knitr pkg

Bill Poling
In reply to this post by Rainer Hurling
Hi Rainer:

Thank you I will have a look at the link you provide.
As I mentioned,
“#opts_chunk$set(fig.path = "c:/WHP/Appeals/OutputPDFs/EX&DE V1.pdf") <--I don't even understand what this does, poached it from one of the google sites I have been reviewing and tried to make it work?”

Hopefully your reference has an example I can follow, will let you know, cheers.

WHP


>>Not sure, if I get you right. Seems, that you use knitr:: and code
chunks without the necessary context?

Please have a look at https://rmarkdown.rstudio.com/<https://rmarkdown.rstudio.com/> to get a more
general understanding about using knitr within RMarkdown context.<<<<



From: Rainer Hurling <[hidden email]>
Sent: Thursday, July 19, 2018 3:45 AM
To: Bill Poling <[hidden email]>
Cc: r-help ([hidden email]) <[hidden email]>
Subject: Re: [R] Help with knitr pkg

Hi Bill,

Am 18.07.18 um 18:33 schrieb Bill Poling:

> Hi,
> I worked through this excellent tutorial:
> #Elegant regression results tables and plots in R: the finalfit package
> https://www.r-bloggers.com/elegant-regression-results-tables-and-plots-in-r-the-finalfit-package/<https://www.r-bloggers.com/elegant-regression-results-tables-and-plots-in-r-the-finalfit-package/>
>
>
>
> Now I am applying it to my own data.
>
> In the tutorial there is mention of:
>
> # Tables can be knitted to PDF, Word or html documents. We do this in
> # RStudio from a .Rmd document. Example chunk:
> # ```{r, echo = FALSE, results='asis'}
> # knitr::kable(example_table, row.names=FALSE,
> # align=c("l", "l", "r", "r", "r", "r"))
> # ```
>
> I am having a difficult time understanding how this works?
>
> I have read through the help:
>
> ?knitr
> #"This function takes an input file, extracts the R code in it according to a list of patterns, evaluates the code and writes the output in another file.
> #It can also tangle R source code from the input document (purl() is a wrapper to knit(..., tangle = TRUE)).
> #The knitr.purl.inline option can be used to also tangle the code of inline expressions (disabled by default)."
>
> install.packages("knitr")
> library(knitr)
> ?knit
> ?stitch
> install.packages("stitch")#package 'stitch' is not available (for R version 3.5.1)
> ?spin
> install.packages("spin") #package 'spin' is not available (for R version 3.5.1)Warning in install.packages : Perhaps you meant 'SPIn' ?
>
> I have also looked at the github and knitr author's links
>
> https://github.com/yihui/knitr<https://github.com/yihui/knitr>
>
> https://yihui.name/knitr/demo/stitch/<https://yihui.name/knitr/demo/stitch/>
>
> https://github.com/yihui/knitr/blob/master/inst/examples/knitr-spin.Rmd<https://github.com/yihui/knitr/blob/master/inst/examples/knitr-spin.Rmd>
>
>
> If I understand this correctly I have to have a template already in place as the input object, is that correct? How would I construct this it that is so?
>
> I also tried writing out directly to pdf and png with no success.
>
> #pdf("c:/WHP/Appeals/OutputPDFs/EX&DE V1.pdf")
> #png("c:/WHP/Appeals/OutputPDFs/EX&DE V1.png")
> #opts_chunk$set(fig.path = "c:/WHP/Appeals/OutputPDFs/EX&DE V1.pdf") <--I don't even understand what this does, poached it from one of the google sites I have been reviewing and tried to make it work?
>
> #This is the script I would like the output placed in PDF
> explanatory = c("claimStatusId", "AgeCat", "PatientGender", "PayorID")
> dependent = "AppealOverturned" # Appeals Status
> appdf1DT2 %>%
> summary_factorlist(dependent, explanatory, p=TRUE, add_dependent_label=TRUE)
>
> #dev.off()
>
>
> str(appdf1DT2)
> # Classes 'data.table' and 'data.frame': 3983 obs. of 21 variables:
> # $ ClaimServiceID : Factor w/ 3983 levels "51318639","51318640",..: 1 2 4 3 5 12 6 8 7 9 ...
> # $ LineNumber : Factor w/ 140 levels "1","2","3","4",..: 1 2 4 3 5 7 1 3 2 4 ...
> # $ claimStatusId : Factor w/ 2 levels "2","3": 2 2 2 2 2 1 1 1 1 1 ...
> # $ PatientGender : Factor w/ 3 levels "F","M","UNK": 2 2 2 2 2 1 1 1 1 1 ...
> # $ PayorID : Factor w/ 19 levels "000","234","239",..: 1 1 1 1 1 1 1 1 1 1 ...
> # $ AppealID : Factor w/ 512 levels "79765","116998",..: 1 1 1 1 1 2 2 2 2 2 ...
> # $ ZipCode : Factor w/ 223 levels "2155","3037",..: 72 72 72 72 72 102 102 102 102 102 ...
> # $ EditID : Factor w/ 21 levels "","0","001X",..: 2 12 8 12 8 8 2 8 12 8 ...
> # $ CurrentBilled : num 14394 14394 14394 14394 14394 ...
> # $ ClaimLineSavings : num 0 0 0 0 0 ...
> # $ StatusChangeMo : Factor w/ 7 levels "2018-01","2018-02",..: 4 4 4 4 4 4 4 4 4 4 ...
> # $ Grouping : Factor w/ 9 levels "","Agencies",..: 4 4 4 4 4 4 4 4 4 4 ...
> # $ AppealOverturned : Factor w/ 2 levels "1","2": 2 2 2 2 2 1 1 1 1 1 ...
> # $ PrimaryDX : Factor w/ 360 levels "","8442","912",..: 2 2 2 2 2 171 171 171 171 171 ...
> # $ RevCodeCats : Factor w/ 41 levels "AdminStorProcBlProd",..: 2 2 18 2 18 18 2 2 2 18 ...
> # $ AgeCat : Factor w/ 9 levels "[0-5]","[11-20]",..: 4 4 4 4 4 8 8 8 8 8 ...
> # $ ClaimLevelSavings: num 0 0 0 0 0 ...
> # - attr(*, ".internal.selfref")=<externalptr>
>
> head(appdf1DT2)
> ClaimServiceID LineNumber claimStatusId PatientGender PayorID ProviderID AppealID ZipCode TIN EditID
> 1: 51318639 1 3 M 000 149385 79765 33904 0
> 2: 51318640 2 3 M 000 149385 79765 33904 022
> 3: 51318642 4 3 M 000 149385 79765 33904 00504
> 4: 51318641 3 3 M 000 149385 79765 33904 022
> 5: 51318643 5 3 M 000 149385 79765 33904 00504
> 6: 85833537 7 2 F 000 3240182 116998 46635 00504
> CurrentBilled ClaimLineSavings StatusChangeMo Grouping AppealOverturned PrimaryDX RevCodeCats
> 1: 14394.08 0 2018-04 Ambulatory Health Care Facilities 2 8442 AmbSurgCare
> 2: 14394.08 0 2018-04 Ambulatory Health Care Facilities 2 8442 AmbSurgCare
> 3: 14394.08 0 2018-04 Ambulatory Health Care Facilities 2 8442 MedSurgSuppandDevs
> 4: 14394.08 0 2018-04 Ambulatory Health Care Facilities 2 8442 AmbSurgCare
> 5: 14394.08 0 2018-04 Ambulatory Health Care Facilities 2 8442 MedSurgSuppandDevs
> 6: 23472.92 0 2018-04 Ambulatory Health Care Facilities 1 M1712 MedSurgSuppandDevs
> AgeCat ClaimLevelSavings
> 1: [31-40] 0.00
> 2: [31-40] 0.00
> 3: [31-40] 0.00
> 4: [31-40] 0.00
> 5: [31-40] 0.00
> 6: [61-70] 296.25
>
>
> Maybe I am in over my head in this pursuit given my novice status with R, however, any direction would be appreciated.
>
> Thank you.
>
> WHP
>
> Confidentiality Notice This message is sent from Zelis. ...{{dropped:15}}
>


Not sure, if I get you right. Seems, that you use knitr:: and code
chunks without the necessary context?

Please have a look at https://rmarkdown.rstudio.com/<https://rmarkdown.rstudio.com/> to get a more
general understanding about using knitr within RMarkdown context.

HTH,
Rainer Hurling

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______________________________________________
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.