[R] Help with knitr pkg
Rainer Hurling
rhur||n @end|ng |rom gwdg@de
Thu Jul 19 09:44:33 CEST 2018
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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