Hi Vincent,
https://cran.r-project.org/web/packages/radiant/index.html
Karim

how can i get radiant for 3.4? When I try to install radiant on my ubuntu server, I get this message

package ‘radiant’ is not available (for R version 3.2.4 Revised)

• Gather and Spread in Data > Transform
• Poisson (with offset option)
• Marginals for probit
• Conjoint market simulation and estimation for multiple respondents
• etc.

README.md has a merge conflict in lines 96-108.

Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
namespace ‘nlme’ 3.1-122 is already loaded, but >= 3.1.123 is required
In addition: Warning message:
package ‘radiant’ was built under R version 3.2.4
Error: package or namespace load failed for ‘radiant’

I downloaded nlme and it still isnt working.. got any ideas as to why?

Thanks!

Btw, good job!

I saw @vnijs share a link to a radiant session that was part of a bug report. I clicked the link, moved to a different tab, and now the original link goes to my new tab.

It could be useful if the URL was ...?SSUID=blahblahblah&update=0 which would tell radiant to just bring me to the same point as that session, but not record any further actions.

I noticed this when I was trying out Radiant on a Digital Ocean shiny server. In the Code and Report tabs, messages come up indicating that code and rmd files are not evaluated when Radiant is running on a server.

I was able to find where these flags are in the code base, but had some difficulty finding comments or documentation on why this is disabled.

Can I get these features to work on a server simply by commenting out the !r_local statements?

Is there any unexpected behaviour I should look for when I do this?

The shiny app on shinyapps.io does not start, but throws the following error:

Error in function_list[k] : could not find function "sshhr"
Calls: local ... eval -> _fseq -> freduce -> withVisible ->
Execution halted

Hi Vincent,
I have not changed anything since one month in manage.R file. But today I got this error
I'am using S4Vectors 0.6.1.
The same error is also in tranform panel.
Any suggestion?
Thanks
Karim

error in evaluating the argument 'x' in selecting a method for function 'slice': Error in .Call2("Rle_constructor", values, lengths, check, 0L, PACKAGE = "S4Vectors") :
Rle of type 'list' is not supported

I'm attempting to install Radiant from GitHub using devtools. I'm getting the following error, however:

** preparing package for lazy loading
Error : object ‘print.arrange’ is not exported by 'namespace:gridExtra'
ERROR: lazy loading failed for package ‘radiant’

I'm using R 3.2.1. Thanks!

• Drew

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.cross_tabs
> ### Title: Plot method for the cross_tabs function
> ### Aliases: plot.cross_tabs
> 
> ### ** Examples
> 
> result <- cross_tabs("newspaper", "Income", "Newspaper")
> plot(result, ct_check = c("observed","expected","chi_sq"))
Error in gather_.data.frame(., "variable", "values") : 
  argument "gather_cols" is missing, with no default
Calls: plot ... _fseq -> freduce -> withVisible -> <Anonymous> -> sshhr
Execution halted

Any ideas?

Hi,
In actual version we can save dtree as pdf or ps using actionLink function.
If I am right, dtree plot uses mermaid library from DiagrammeR package and It is not the same process to save diagrammeR plot compared the standard plots that use plot_downloader function (as in Visualize panel).
It is not yet clear for me, how plot_downloader captures plot_name from current plot. If it is possible to have simple example.

Any suggestion to use plot_downloader with DiagrammeR mermaid or grViz plots?
Thanks
Karim

The probability calculator function for Uniform dist in file radiant/R/prob_calc.R , line 958 has a typo

stdev <- (max-min)^2 / 12  

should be

stdev <- (max-min)^2 / sqrt(12)

install.packages("radiant", repos = "http://vnijs.github.io/radiant_miniCRAN/", type = "binary")
Installing package into ‘C:/Users/epcil_000/Documents/R/win-library/3.2’
(as ‘lib’ is unspecified)

package ‘radiant’ is available as a source package but not as a binary

Warning message:
package ‘radiant’ is not available (as a binary package for R version 3.2.2)

Hi Dr Vincent,
I would like to combine data frames. Before that, I need to add a column for every df with a class.
for example I would like to add new column named 'Origin' :
diamonds$Origin = 'Africa' (all rows have 'Africa')
I used Transform > create but I can't add a character/factor as variable.

diamonds$Origin = 'Africa'
Origin = rep('Africa',nrow(diamonds)
Origin = rep(’Africa’,3000)

How to?
Thanks

I am facing issue in installing dependency - data.tree. Here is the complete log:

also installing the dependency ‘data.tree’
trying URL 'http://vnijs.github.io/radiant_miniCRAN/src/contrib/data.tree_0.1.9.tar.gz'

Content type 'application/octet-stream' length 898890 bytes (877 KB)

downloaded 877 KB

• installing source package ‘data.tree’ ...
  ** R
  ** data
  ** demo
  ** inst
  ** preparing package for lazy loading
  Error in R6Class("Node", lock_objects = FALSE, public = list(parent = NULL, :
  unused argument (lock_objects = FALSE)
  Error : unable to load R code in package ‘data.tree’
  ERROR: lazy loading failed for package ‘data.tree’
• removing ‘/home/bolaka/R/x86_64-pc-linux-gnu-library/3.2/data.tree’
  Warning in install.packages :
  installation of package ‘data.tree’ had non-zero exit status
  ERROR: dependency ‘data.tree’ is not available for package ‘radiant’
• removing ‘/home/bolaka/R/x86_64-pc-linux-gnu-library/3.2/radiant’
  Warning in install.packages :
  installation of package ‘radiant’ had non-zero exit status

First, thanks a lot for this great tool offering a great GUI for non R user.

I began to test it few days ago and I realized that the visualize function was not really behaving how I would have like or how ggplot2 is.

Here an example with the diamonds dataset :

visualize(dataset = "diamonds", xvar = "clarity", yvar = "carat", type = "line", color = "color")

If I then modify just a bit the visualize function to have the same behavior than ggplot2:

I would really appreciate to have such possibility with radiant. I may not understand all the potential problem that my modification would do but I ask you to consider it :)

Here the changes :

else if (type == "line") {
    itt <- 1
    for (i in xvar) {
        for (j in yvar) {
            if (color == "none") {
              if (is.factor(dat[[i]])) {
                tbv <- if (is.null(byvar)) 
                  i
                else c(i, byvar)
                tmp <- dat %>% group_by_(.dots = tbv) %>% 
                  select_(j) %>% summarise_each(funs(mean))
                plot_list[[itt]] <- ggplot(tmp, aes_string(x = i, 
                  y = j)) + geom_point() + geom_line(aes(group = 1))
              }
              else {
                plot_list[[itt]] <- ggplot(dat, aes_string(x = i, 
                  y = j)) + geom_line()
              }
            }
            else {
              if (is.factor(dat[[i]])) {
                tbv <- if (is.null(byvar)) 
                  i
                else c(i, byvar)
                print(tbv)
                tmp <- dat %>% group_by_(.dots = tbv) %>% 
                  select_(j, color) %>% summarise_each(funs(mean))

Original code:

                    plot_list[[itt]] <- ggplot(tmp, aes_string(x = i, 
                      y = j, color = color)) + geom_point() + 
                      geom_line(aes(group = 1))

New code:

                    plot_list[[itt]] <- ggplot(tmp, aes_string(x = i, 
                      y = j, color = color, group=color)) + geom_point() + 
                      geom_line()

              }
              else {

Original code :

                    plot_list[[itt]] <- ggplot(dat, aes_string(x = i, 
                      y = j, color = color)) + geom_line()

New code:

                    plot_list[[itt]] <- ggplot(dat, aes_string(x = i, 
                      y = j, color = color, group=color)) + geom_line()

              }
            }

            if ("log_x" %in% axes) 
              plot_list[[itt]] <- plot_list[[itt]] + xlab(paste("log", 
                i))
            if ("log_y" %in% axes) 
              plot_list[[itt]] <- plot_list[[itt]] + ylab(paste("log", 
                j))
            itt <- itt + 1
        }
    }
}

Helo

I download your application and try to run it locally on my computer
everything just work fine the first time i start the application
the problem is when i refresh the browser the ui only reload the navigation bar.

if i restart the R session, everything is loading properly.
but if i refresh the browser again, the ui will not reload anymore.

i am using shiny 0.10.0, and R 3.1.0

the warning message in R console are as follows:
Warning in addResourcePath("figures", "tools/help/figures/") :
Overriding existing prefix figures => C:\Users\Asus\Documents\R\shiny\fastedit\tools\help\figures
Shiny URLs starting with /figures will mapped to C:\Users\Asus\Documents\R\shiny\radiant-master\inst\marketing\tools\help\figures\

thank you

Hi vnijs,
First many thanks for building such a wonderful shiny app!
One little thought: I think claiming file encoding explicitly by adding encoding = "UTF-8" to the source() function will allow your code to be more portable to people working on windows and using languages other than English. Without it, most non-ascii characters in the sourced file will not display correctly.

When you do facet density plots add an option yo normalize the density between 0-1. This makes comparison of density plots lot easier

anyway to do that?

visualize(dataset = "W", xvar = "NumberOfPeople", yvar = "Sentiment", bins = 4, alpha = 0.54, data_filter = "Belong", custom = TRUE)+
theme(axis.text = element_text(size = 24)

)

I tried col, color, colour as a regular paramters, according tothe function, it should just be color...

any thoughts?

Error when trying to run Radiant:
I see this in the browser (chrome)
ERROR: path[1]="/www/MathJax/": No such file or directory

i see this on the command line

radiant("marketing")

Listening on http://127.0.0.1:7160
Error in normalizePath(directoryPath, mustWork = TRUE) :
path[1]="/www/MathJax/": No such file or directory
Error in normalizePath(directoryPath, mustWork = TRUE) :
path[1]="/www/MathJax/": No such file or directory

Info:
RStudio
Version 0.99.465 – © 2009-2015 RStudio, Inc.

R.Version()
$platform
[1] "x86_64-apple-darwin13.4.0"

$arch
[1] "x86_64"

$os
[1] "darwin13.4.0"

$system
[1] "x86_64, darwin13.4.0"

$status
[1] ""

$major
[1] "3"

$minor
[1] "2.1"

$year
[1] "2015"

$month
[1] "06"

$day
[1] "18"

$svn rev
[1] "68531"

$language
[1] "R"

$version.string
[1] "R version 3.2.1 (2015-06-18)"

$nickname
[1] "World-Famous Astronaut"

packageVersion("radiant")
[1] ‘0.1.83’

Hi,
suddenly, I had this error message:

shiny::runApp('inst/base')
Listening on http://127.0.0.1:7767
Error in readRDS(fn) : error reading from connection
ERROR: [on_request_read] connection reset by peer
ERROR: [on_request_read] connection reset by peer

When there is no old r_state, r_data, r_session, .RData file and .Rhistory, I can't run my radiant fork.
Any Suggestion?
Thanks

ls()
 [1] "clusterProfilesEnv" "DOSEEnv"            "GOSemSimEnv"        "ICEnv"              "js_head"            "nav_ui"             "r_encoding"         "r_functions"        "r_help"            
[10] "r_local"            "r_path"             "r_pkgs"             "r_sessions"         "SemSimCache"        "shared_ui"          "withMathJax"       

sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.5 (Yosemite)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
 [1] stats4    parallel  tcltk     stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] XML_3.98-1.3           RCurl_1.95-4.7         bitops_1.0-6           clusterProfiler_2.2.3  DOSE_2.6.4             org.Hs.eg.db_3.1.2     RSQLite_1.0.0          DBI_0.3.1             
 [9] AnnotationFuncs_1.18.0 AnnotationDbi_1.30.1   GenomeInfoDb_1.4.1     IRanges_2.2.5          S4Vectors_0.6.1        geNetClassifier_1.8.0  minet_3.26.0           EBarrays_2.32.0       
[17] lattice_0.20-33        Biobase_2.28.0         BiocGenerics_0.14.0    DT_0.1.28              metabologram_0.1       coffeewheel_0.1        cgdsr_1.2.5            scales_0.3.0          
[25] yaml_2.1.13            data.tree_0.2.1        shinyAce_0.2.1         rmarkdown_0.8          readr_0.1.1            htmlwidgets_0.5        broom_0.3.7            dplyr_0.4.3           
[33] tidyr_0.3.1            magrittr_1.5           pryr_0.1.2             ggdendro_0.1-17        ggplot2_1.0.1          lubridate_1.3.3        knitr_1.11             AlgDesign_1.1-7.3     
[41] wordcloud_2.5          RColorBrewer_1.1-2     psych_1.5.8            GPArotation_2014.11-1  gridExtra_2.0.0        car_2.1-0              DiagrammeR_0.7         shiny_0.12.2          

loaded via a namespace (and not attached):
 [1] nlme_3.1-122       pbkrtest_0.4-2     httr_1.0.0         tools_3.2.1        R6_2.1.1           lazyeval_0.1.10    mgcv_1.8-7         colorspace_1.2-6   nnet_7.3-11        mnormt_1.5-3      
[11] quantreg_5.19      SparseM_1.7        slam_0.1-32        stringr_1.0.0      digest_0.6.8       minqa_1.2.4        XVector_0.8.0      MathJaxR_0.11      htmltools_0.2.6    lme4_1.1-9        
[21] rstudioapi_0.3.1   jsonlite_0.9.17    GOSemSim_1.26.0    R.oo_1.19.0        GO.db_3.1.2        Matrix_1.2-2       Rcpp_0.12.1        munsell_0.4.2      proto_0.3-10       R.methodsS3_1.7.0 
[31] stringi_0.5-5      zlibbioc_1.14.0    MASS_7.3-44        plyr_1.8.3         qvalue_2.0.0       grid_3.2.1         DO.db_2.9          Biostrings_2.36.1  splines_3.2.1      KEGGREST_1.8.0    
[41] igraph_1.0.1       reshape2_1.4.1     codetools_0.2-14   png_0.1-7          nloptr_1.0.4       httpuv_1.3.3       MatrixModels_0.4-1 gtable_0.1.2       assertthat_0.1     mime_0.4          
[51] xtable_1.7-4       e1071_1.6-7        class_7.3-14       memoise_0.2.1      cluster_2.0.3     

After I installed the radiant and clicked the radiant.bat(marketing) , the cmd windows showed the message as follows:
Listening on http://127.0.0.1:4444
Error in eval(substitute(expr), envir, enclos) :
corrupt 'grouped_df', contains 70 rows, and 168 rows in groups
Error in eval(substitute(expr), envir, enclos) :
corrupt 'grouped_df', contains 70 rows, and 168 rows in groups
Error in eval(substitute(expr), envir, enclos) :
corrupt 'grouped_df', contains 70 rows, and 168 rows in groups

Cloning this repository is very painful because of the previous Mini-Cran inclusion.

I would suggest you use the bfg to clean the repo history of all archive files.

The following reduced the radiant directory size from over 700M to 61M on my machine.

alias bfg=java -jar bfg-1.12.3.jar
bfg -D '*.{gz,tgz,zip}' radiant
cd radiant && git reflog expire --expire=now --all && git gc --prune=now --aggressive

Is it possible to run radiant from shiny server?
Thanks

Is there any possibility to add more GUI component to the Radiant with some code or loading packages.

For example, Rcmdr: Extending the R Commander by “Plug-In” Packages.

HI Vincent,
I installed the last version V0.2.40.
I note in Visualize sidebar, the dropdown variables are missing (also explore panel).
The new checkbox(Line, Loess, Jitter) are visible only once.
Maybe these news features are in progress..
Thanks
Karim

I get the message above when clicking on the Explore tab in the diamond dataset. I am running Radiant within a shiny server (inst/base) directory using a checked-out version of the master branch. My shiny server logfile shows:

Listening on http://127.0.0.1:60101
Error in eval(substitute(expr), envir, enclos) :
  could not find function "nmissing"
Error: could not find function "nmissing"
Execution halted

The logfile shows all packages loading correctly. Any help would be appreciated.

Hi,
I expect that the previous version of pivotr_ui is the future for complexe data visualisation. it makes free the choice of variables and the plot style (treemap...). the user is free to combine variables depending of its data to get significant view.
I did not note the advantages of the last version of pivotr_ui.

https://github.com/vnijs/radiant/blob/8462695ef30df38fccacc2564dea2d038c842fc3/inst/base/tools/help/figures/pivotr.png

When I pick the Visualize option to start plotting I dont see the dropdown list of variables. I can see then in the view and other options though. I have the latest version of Radiant, Rstudio and R.
-Lakshmi

Hi,
I did not used any example data. I just checked "clipboard" to paste some thing. The default data is diamonds.

Dear Dr Vincent,

Using this link, the clipboard works correctly .
When I use actual R version
library('radiant')
radiant('quant')

or R devel from GitHub.

shiny::runApp('inst/quant')

The text area does not appear and when I clic on "paste data", the R session aborted with this message:
incompatible final line found by readTableHeader on 'pbpaste'

Thanks for help,
Karim

Radiant fails (produces errors) on loading R Data (".rda") file. Full issue report in PDF format is available here: https://github.com/abnova/test/blob/master/Radiant_LoadData_Error_Report_081214.pdf. Please let me know, if you need more information on this issue.

Hi,
how can I check programmatically if my new object exists or not under r_data.

I tested:

 exists('Mydatase', envir=.GlobalEnv)
 exists(r_data[['Mydatase']], envir=.GlobalEnv)
not_available('Mydatase')

Thanks

Hi Dr Vincent,
Transform > Remove missing value delete row with at less one blank.
If I have some missing value in different lines I expect to loose a lot of data.
How can I replace blank by NA

df[df==""]  <- NA

Thanks

Hi again Vincent,

Sorry to bother you again. I was trying to teach validation analysis to my students, and although all students set the seed to a specific value (111), students got two different results on different computers. I thought it was related to Windows vs. MacOS or 32bits vs. 64bits but these two factors were not the issue.

It would be great if you can check this to see what might be the issue. Last year when I ran the same analysis, all 170+ students got similar results.

Best
Koushyar

Hi Vincent,

I don't understand why in Radiant when the "center" option is used for linear regression, the estimated intercept is 0. Using the Diamonds dataset, when I use the transform tab to meancenter the independent variables, the estimated intercept is different than 0 (see image below).

I am guessing that the "center" option also meancenters the DV. In that case, the explanation on website should change to reflect that:

If possible, could you update the "center" option so that it only centers the explanatory variables? Or perhaps add a new option.

Thanks

While exploring the chi-squared distribution i stumbled across that radiant displays the mean of chi squared distribution as DOF (degrees of freedom) +1, where as it should be DOF +2. The graph however shows the mean and mode correctly .

Hi,
I lost my sync fork when I changed the name of my repository.
I added a new upstream

git remote add upstream https://github.com/vnijs/radiant.git
git fetch upstream

The second command replaced my fork by radiant and I can't merge master/upstream

git merge upstream/master

Is there a way to compare and merge again my fork with radiant?
Thanks

First, thanks for creating such a great tool. The problem I'm running into with decision trees is that the costs from previous branches don't seem to be inherited at all. Also the terminal payoff doesn't seem to be taking cost into account. I see that you may have created a fix for this but it doesn't seem to be implemented.

• Alyssa

not really an issue, but a neat logo or some sort of branding would be nice for this thing :)

I am refering to it in my school presentation for my masters and all I have to go by is "Radiant"... I might put a picture of a diamon or something :)

I waited a bit to post this until I checked on multiple browsers and multiple systems, but I cannot get the filter-cuntion to work.

Everytime, I check the box to apply a filter (anywhere within the marketing instance, either on the "pure" r-side nor on the "batch"-side with "win_launcher()") the field for entering the condition is displayed, but nothing within it is actually applied to the data. And I mean really nothing!

I am no experienced programmer nor did I have the time to dig into the potential source of this but I hope that this blunt description may help a little.

Tested systems: W7 64bit, one with all admin rights, one with totally restricted rights. Everywhere, all functions worked but the filter.

Browsers: Firefix 37.0.2, Chrome 42.0.2311.135 and IE11 (newest version)

Maybe I am just not seeing the obvious, but I don't know....

In README.md, the instructions say to do this:

install_github('shiny', 'wch', ref='hidden-state')

But this is no longer necessary. The fixes have been incorporated into rstudio/master.

Sadly it won't work for me:

> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)

locale:
[1] de_DE.UTF-8/de_DE.UTF-8/de_DE.UTF-8/C/de_DE.UTF-8/de_DE.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] shiny_0.10.1

loaded via a namespace (and not attached):
[1] bitops_1.0-6    caTools_1.17.1  digest_0.6.4    htmltools_0.2.6 httpuv_1.3.0    Rcpp_0.11.3     RJSONIO_1.3-0  
[8] tools_3.1.2     xtable_1.7-4   

Just pulled the latest master, and get the error above when executing runApp() inside inst/base. This seems to stop radiant from executing entirely. I have run the
install.packages("radiant", repos = "http://vnijs.github.io/radiant_miniCRAN/") command already.

I've seen this type of error before when some library needs tk -- is there a new dependency?

Dear Dr Vincent,
I notice that row names are not supported in the default version.
I am trying to make visible the row names in Manage/View panel and combine two different data frames (do not have the same column names) by row names.
for example in View.R file it is enough to change rownames = TRUE in line 148 and 50.
But with 'Manage' panel is not the same format of table.
1- How can I make visible row names in Manage and Combine panels?
Thanks
Karim

Hello, I downloaded a .zip archive of your application via the GitHub page, and I kept getting errors about an invalid path in the addResourcePath("figures", "../base/tools/help/figures/") line in global.R for your base application. I saw that there was no figures subdirectory in the base/tools/help area, so I created a base/tools/help/figures subdirectory and then the application ran successfully. In case other users encounter this error when running your base application I wanted to make you aware of this. The other two applications (marketing and quant) have the figures subdirectory present.

When click the download button on View page, it gives the error "slice condition does not evaluate to an integer or numeric vector. " Other download buttons have similar issues.

Dear Dr Vincent,
To avoid github depends, I have to bundle MathJaxR to my radiantFork.
I copied

MathJaxR/inst/MathJax to radiantFork/inst/MathJax

MathJax/R/withMathJax.R to radiantFork/R/withMathJax.R

I changed the two global.R files :

if (r_local) {
  addResourcePath("MathJax", file.path(system.file(package = "radiantFork"), "MathJax/"))
  withMathJax <- radiantFork::withMathJaxR
}

and I removed MathJaxR depends from description files and imports from /R files.
There isn't

importFrom(MathJaxR withMathJaxR)

in namespace. but there is

export(withMathJax)

When I build my radiantFork, I have always the Warning message of the MathJaxR depends

* checking for file bioCancer/DESCRIPTION ... OK
* preparing bioCancer:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
      -----------------------------------
* installing *source* package bioCancer ...
** R
** data
*** moving datasets to lazyload DB
Warning: namespace MathJaxR is not available and has been replaced
by .GlobalEnv when processing object withMathJax
Loading required package: DBI

I removed radiantFork/build folder.
I removed dependencies.R file.
I searched for all files in package that have 'MathJaxR' string using bash/regex.
I removed .Rdata and Rhistory hidden files

Only withMathJax.R and global.R have 'withMathJax' string.

please, have you an idea from where the dependency of MathJaxR always exists?
Thanks