Yes, its the simple things that are glaringly absent and veer JMP away from being wholly recommendable. I went looking for this (or a clickable equivalent) and came empty. Seems this is what I want to do for incomplete set designs and ranked order values but need to do some transformations first of the columns. ... View more

Hi Julian,    Would you please repost your CLR Formula Columns Add-in? I was assigned a new computer at work and lost all my previous addins.   PS- I couldn't find it posted in it's own post... just the link here that you posted previously.   Thanks, marxx ... View more

Hi MJ,    I am getting an error message when I try this addin. It looks like it is not recognizing my installation of R. Would you be able to help figure out how to get your addin to recognize my R installation if that is indeed the issue?   I am including a screenshot showing that R is open but not being recognized, and a screenshot of my R install location (not program files) and also  copying some of the error message below.   This looks like a very exciting tool and I am hoping to use it. I've previously found t-sne in R to be useful and it would be of great value to be able to do this right in JMP. Any help you might provide is greatly appreciated.   Thanks!   Screenshots of error and open R instance, then screenshot of R install location   Error code   " An installation of R cannot be found on this system. JMP R support requires R version 2.9.1 or higher in access or evaluation of 'Glue' , write2lastRun( pb2, _addinPath_ ); algr = cbb << get selected(); Print( "Got algr!" ); Try( dim1 = dimBx1 << get; per1 = perBx1 << get; iter1 = iterBx1 << get; ); Try( dim2 = dimBx2 << get; per2 = perBx2 << get; iter2 = iterBx2 << get; dist = distbox << get; ); Print( "Got parameters!" ); Try( predictor = selectedX << getitems ); If( Length( predictor ) < 1, Throw( "Please specify Predictors" ) ); Try( labelY = selectedY << getitems ); If( N Items( labelY ) > 0, labelY1 = labelY[1]; grphVars = Eval Insert( "X( :Y2 ), Y( :Y1 ), Color( :^labelY1^ ) " ); , labelY1 = ""; grphVars = "X( :Y2 ), Y( :Y1 )"; ***** Text Truncated *****"     ... View more

Hi Yves,    Thanks very much, I was able to "//" those lines (although they were like row #188 or so in the extracted script) and get to the next window.   It shows the original data ... However, there seem to be two (independent?) issues that prevent from using the program further.   In the first issue, no bins show up in the initial presentaiton of the plot when the window opens.   When I try to slide the "Binning adjustment" slider I get the following JMP Alert pop-up error message: "y must have only 1 column"   Please note that I can click at a point on the slider scale other than where the diamond is at, and after I click OK on the error message pop up described above, it will show the bin points. I can click elsewhere on the slider and (after the error message appears and is dismissed with an OK) it will adjust the binning, but it will not slide.   The second thing seems to be that the GUI will not plot "OLS fit line" of either original or binned data. I can check the boxes and the checks will appear but no line of fit appears. However, please note- the "Binned fit" R-square and Number of Obs does change, but no line appears in the plot.   The log throws this message when the OLS fit line is checked: invalid subscript (must be number or list of numbers) 51002 times in access or evaluation of 'Subscript' , betas[/*###*/2]   Would you have any tips on progressing through these?   Thanks much, marxx   ... View more

That video was awesome, very explanatory. Thank you much yvesprairie.   To make this comparable, instead of using my data I used the "Growth" sample data that comes with JMP, and I followed your suggestion to use the extracted JSL script directly by copy-pasting it into the Growth Data Set instead of running as an addin.   Unfortunately, still nothing happened when I clicked "OK" after the first dialogue where we enter the X and Y variables.    I tried it in debugging mode, and this is the error message that popped up:   Matrices dimensions do not conform, 72 by 1 and 72 by 2 in access or evaluation of 'Subtract' , ym -  /*###*/axm * lsbetas/*###*/   I tried to google this error and couldn't find much other than it appears that the matrices are of different sizes, but since there are the same number of rows for the only two columns of data in the Growth Sample Data I couldn;t understand how this could be.   Any help you could provide would be greatly appreciated.   Thanks! marxx ... View more

Thank you yvesprairie, will do! 🙂 ... View more

Wonderful! I am often looking for a way to dart away from the screen, so will follow your advice and cruise around while I let it spin for a bit.   Much appreciated, marxx ... View more

 Thank you for the reply yvesprairie,    I will watch the video in a bit when it becomes available (looks like it's loading now) and try to run the emebedded JSL directly, then circle back here. And, sorry I forgot to mention I am actually running Pro as well.    Thanks again for the followup, looks like a very cool add in... I use quite a bit of bivariate continuous fits and am eager to get the samples binned in this manner.   Thanks! marxx  ... View more

Thanks for sharing Tarik and the followup Karen, I will be interestred also in this working with larger data sets when that is available.   Thanks, marxx ... View more

Hi michael, Thank you for sharing. When I try to run the addin with a single coninuous variable I receive the following error message followed by a string of my data values and the program does not complete. Would you be able to provide any insight on what this error message means or what I am doing wrong?   "argument should be character in access or evaluation of 'Length' , Bad Argument( [truncated list of my values for the variable in each observation is shown here] ***** Text Truncated *****"   Thanks in advance, marxx   ... View more

Thank you very much yvesprairie... Would you be able to help, or anyone else who has successfully used the add-in?   I am trying the addin now but am not getting any window or results or interactive GUI after putting continuous variables in both X and Y fields of the initial pop-up window and clicking OK. The initial pop-up window with X and Y variable entry fields disappears but nothing shows up in it's place and no columns are created. I am on Windows 7 Enterprise running JMP 13.2.1 64bit.   Thanks you in advance, marxx ... View more

Thank you Chris, I have done so now and hope that it gets traction.   Much appreciated, marxx ... View more

Two years later. No responses?   PERMANOVA and ANOSIM are workhorses of the microbiome field. They need to be in JMP. ... View more

Hi Julian, I tested the JMP CLR Add In versus a 6 component composition that I had created manually... And the add-in you produced matched all the columns that had been manually produced. I really appreciate it!    Thanks so much! Marxx   [Edit: Looks like screenshot image can't be included, but it works]. [image: Inline image 1] ... View more

Hi Julian, Many thanks for this add-in. It's enormously helpful for analysis of compositional data. Much appreciated!   However, to analyze compositional data in a multivariate manner we need to convert row-wise "counts" to Aitchison's 'centered log ratio' (CLR) for all the columns that are components of the composition (e.g. all the columns that are included in the "percent of total" calculation).   It's very laborious to do this manually in JMP (although we do it for small compositions), and for work with gene transcript or microbiome sequencing data it is not even feasible.   The equation is simple, its just the natural log of the ratio of a given component over the *geometric* mean of all the components of the composition. Thus, for a 3 part composition (A, B, C) A is transformed as: LN(A/((A*B*C)^0.33)); B as LN(B/((A*B*C)^0.33))   and so on for C.   Unfortunately I am not fluent in the scripting (yet)... Would you be able to create a version of the 'Percent of Total' Add In that could instead produce columns of CLR transformed values for the composition?     Particularly, with subcompositional coherence, we are constantly having to make several new different subcompositions on an ongoing basis. If we have a 100 component microbe composition, we might produce 10 or so different subcompositions each having a different set of columns included in the subcomposition... It would be extraordinarily helpful to multi-select columns and produce the CLR transformations.   Thanks much! ... View more