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