[R] Help with knitr pkg

Wed Jul 18 18:33:55 CEST 2018

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}}