Rmarkdown error

[tomassilveira]

Hi everyone,

I am trying to run an rmarkdown document similar to the one we did on clustering but get the following error :

rmarkdown::render("INSEADAnalytics-master/INSEADAnalytics-master/CourseSessions/Homicides_project/Final_Project_v2TS.Rmd")
processing file: Final_Project_v2TS.Rmd
Installing package into 'C:/Users/tomas/Documents/R/win-library/3.5'
(as 'lib' is unspecified)
trying URL 'https://cran.r-project.org/src/contrib/Archive/networkD3/networkD3_0.2.13.tar.gz'
Content type 'application/x-gzip' length 107647 bytes (105 KB)
downloaded 105 KB

• installing source package 'networkD3' ...
  ** package 'networkD3' successfully unpacked and MD5 sums checked
  ** R
  ** data
  *** moving datasets to lazyload DB
  ** inst
  ** byte-compile and prepare package for lazy loading
  ** help
  *** installing help indices
  converting help for package 'networkD3'
  finding HTML links ... done
  JS html
  finding level-2 HTML links ... done

  MisLinks html
  MisNodes html
  SchoolsJournals html
  as.radialNetwork html
  chordNetwork html
  dendroNetwork html
  diagonalNetwork html
  forceNetwork html
  igraph_to_networkD3 html
  networkD3-package html
  networkD3-shiny html
  radialNetwork html
  sankeyNetwork html
  saveNetwork html
  simpleNetwork html
  ** building package indices
  ** testing if installed package can be loaded
  *** arch - i386
  *** arch - x64

• DONE (networkD3)
  In R CMD INSTALL
  Quitting from lines 174-175 (Final_Project_v2TS.Rmd)
  Error in quantile.default(r, 0.25) :
  missing values and NaN's not allowed if 'na.rm' is FALSE
  In addition: Warning messages:
  1: In block_exec(params) : failed to tidy R code in chunk
  reason: Error in loadNamespace(name) : there is no package called 'formatR'

2: In block_exec(params) : failed to tidy R code in chunk
reason: Error in loadNamespace(name) : there is no package called 'formatR'

Anyone had the same issue/would be willing to help?

Tomas

[tomassilveira]

The error seems to be coming from this line of code :

iprint.df(round(my_summary(ProjectDataFactor), 2))

[Antoine-Engerand]

Hi Tomas. Maybe this website can help for the tidy R error: https://yihui.name/formatr/
For the first one, there may be NA or NaN values in your data. That's what the message seems to indicate. I hope it helps! ;)

[tomassilveira]

Thank you Antoine! Indeed, there was a problem with some NA values. Slowly progressing :)

[cynthiadandrea]

I am also trying to do the same thing, but am getting a different style of error: "Error in quantile.default(r, 0.25) :
missing values and NaN's not allowed if 'na.rm' is FALSE "

[tomassilveira]

Seems to be in the same line you are having a problem, and also due to NA values.

Have you checked the ProjectData_Initial file to see if you have any NAs?

[cynthiadandrea]

I do. I tried using the below to fix it, but it doesnt seem to work.
fixNAs<-function(data_frame){

Define reactions to NAs

integer_reac<-0
factor_reac<-"FIXED_NA"
character_reac<-"FIXED_NA"
date_reac<-as.Date("1900-01-01")

[tomassilveira]

Here is how we did. Perhaps it will work with you :

rawdata$Perpetrator.Age[rawdata$Perpetrator.Age=="NA"] = 0
rawdata$Victim.Age[rawdata$Victim.Age=="NA"] = 0
rawdata$Victim.Age[rawdata$Victim.Age=="NA"] = 0

The first line for instance is basically saying : if column Perpetrator.Age in rawdata is equal to "NA", then turn it equal to 0. With just one line you solve the problem of an entire column