Sorry forgot to keep the rest of the group in the loop - Luca ---------- Forwarded message ---------- From: Luca Meyer <lucam1...@gmail.com> Date: 2015-03-22 16:27 GMT+01:00 Subject: Re: [R] Joining two datasets - recursive procedure? To: Bert Gunter <gunter.ber...@gene.com>
Hi Bert, That is exactly what I am trying to achieve. Please notice that negative v4 values are allowed. I have done a similar task in the past manually by recursively alterating v4 distribution across v3 categories within fix each v1&v2 combination so I am quite positive it can be achieved but honestly I took me forever to do it manually and since this is likely to be an exercise I need to repeat from time to time I wish I could learn how to do it programmatically.... Thanks again for any further suggestion you might have, Luca 2015-03-22 16:05 GMT+01:00 Bert Gunter <gunter.ber...@gene.com>: > Oh, wait a minute ... > > You still want the marginals for the other columns to be as originally? > > If so, then this is impossible in general as the sum of all the values > must be what they were originally and you cannot therefore choose your > values for V3 arbitrarily. > > Or at least, that seems to be what you are trying to do. > > -- Bert > > Bert Gunter > Genentech Nonclinical Biostatistics > (650) 467-7374 > > "Data is not information. Information is not knowledge. And knowledge > is certainly not wisdom." > Clifford Stoll > > > > > On Sun, Mar 22, 2015 at 7:55 AM, Bert Gunter <bgun...@gene.com> wrote: > > I would have thought that this is straightforward given my previous > email... > > > > Just set z to what you want -- e,g, all B values to 29/number of B's, > > and all C values to 2.567/number of C's (etc. for more categories). > > > > A slick but sort of cheat way to do this programmatically -- in the > > sense that it relies on the implementation of factor() rather than its > > API -- is: > > > > y <- f1$v3 ## to simplify the notation; could be done using with() > > z <- (c(29,2.567)/table(y))[c(y)] > > > > Then proceed to z1 as I previously described > > > > -- Bert > > > > > > Bert Gunter > > Genentech Nonclinical Biostatistics > > (650) 467-7374 > > > > "Data is not information. Information is not knowledge. And knowledge > > is certainly not wisdom." > > Clifford Stoll > > > > > > > > > > On Sun, Mar 22, 2015 at 2:00 AM, Luca Meyer <lucam1...@gmail.com> wrote: > >> Hi Bert, hello R-experts, > >> > >> I am close to a solution but I still need one hint w.r.t. the following > >> procedure (available also from > >> https://www.dropbox.com/s/qhmpkkrejjkpbkx/sample_code.txt?dl=0) > >> > >> rm(list=ls()) > >> > >> # this is (an extract of) the INPUT file I have: > >> f1 <- structure(list(v1 = c("A", "A", "A", "A", "A", "A", "B", "B", "B", > >> "B", "B", "B"), v2 = c("A", "B", "C", "A", "B", "C", "A", "B", "C", "A", > >> "B", "C"), v3 = c("B", "B", "B", "C", "C", "C", "B", "B", "B", "C", "C", > >> "C"), v4 = c(18.18530, 3.43806,0.00273, 1.42917, 1.05786, 0.00042, > 2.37232, > >> 3.01835, 0, 1.13430, 0.92872, 0)), .Names = c("v1", "v2", "v3", "v4"), > class > >> = "data.frame", row.names = c(2L, 9L, 11L, 41L, 48L, 50L, 158L, 165L, > 167L, > >> 197L, 204L, 206L)) > >> > >> # this is the procedure that Bert suggested (slightly adjusted): > >> z <- rnorm(nrow(f1)) ## or anything you want > >> z1 <- round(with(f1,v4 + z -ave(z,v1,v2,FUN=mean)), digits=5) > >> aggregate(v4~v1*v2,f1,sum) > >> aggregate(z1~v1*v2,f1,sum) > >> aggregate(v4~v3,f1,sum) > >> aggregate(z1~v3,f1,sum) > >> > >> My question to you is: how can I set z so that I can obtain specific > values > >> for z1-v4 in the v3 aggregation? > >> In other words, how can I configure the procedure so that e.g. B=29 and > >> C=2.56723 after running the procedure: > >> aggregate(z1~v3,f1,sum) > >> > >> Thank you, > >> > >> Luca > >> > >> PS: to avoid any doubts you might have about who I am the following is > my > >> web page: http://lucameyer.wordpress.com/ > >> > >> > >> 2015-03-21 18:13 GMT+01:00 Bert Gunter <gunter.ber...@gene.com>: > >>> > >>> ... or cleaner: > >>> > >>> z1 <- with(f1,v4 + z -ave(z,v1,v2,FUN=mean)) > >>> > >>> > >>> Just for curiosity, was this homework? (in which case I should > >>> probably have not provided you an answer -- that is, assuming that I > >>> HAVE provided an answer). > >>> > >>> Cheers, > >>> Bert > >>> > >>> Bert Gunter > >>> Genentech Nonclinical Biostatistics > >>> (650) 467-7374 > >>> > >>> "Data is not information. Information is not knowledge. And knowledge > >>> is certainly not wisdom." > >>> Clifford Stoll > >>> > >>> > >>> > >>> > >>> On Sat, Mar 21, 2015 at 7:53 AM, Bert Gunter <bgun...@gene.com> wrote: > >>> > z <- rnorm(nrow(f1)) ## or anything you want > >>> > z1 <- f1$v4 + z - with(f1,ave(z,v1,v2,FUN=mean)) > >>> > > >>> > > >>> > aggregate(v4~v1,f1,sum) > >>> > aggregate(z1~v1,f1,sum) > >>> > aggregate(v4~v2,f1,sum) > >>> > aggregate(z1~v2,f1,sum) > >>> > aggregate(v4~v3,f1,sum) > >>> > aggregate(z1~v3,f1,sum) > >>> > > >>> > > >>> > Cheers, > >>> > Bert > >>> > > >>> > Bert Gunter > >>> > Genentech Nonclinical Biostatistics > >>> > (650) 467-7374 > >>> > > >>> > "Data is not information. Information is not knowledge. And knowledge > >>> > is certainly not wisdom." > >>> > Clifford Stoll > >>> > > >>> > > >>> > > >>> > > >>> > On Sat, Mar 21, 2015 at 6:49 AM, Luca Meyer <lucam1...@gmail.com> > wrote: > >>> >> Hi Bert, > >>> >> > >>> >> Thank you for your message. I am looking into ave() and tapply() as > you > >>> >> suggested but at the same time I have prepared a example of input > and > >>> >> output > >>> >> files, just in case you or someone else would like to make an > attempt > >>> >> to > >>> >> generate a code that goes from input to output. > >>> >> > >>> >> Please see below or download it from > >>> >> https://www.dropbox.com/s/qhmpkkrejjkpbkx/sample_code.txt?dl=0 > >>> >> > >>> >> # this is (an extract of) the INPUT file I have: > >>> >> f1 <- structure(list(v1 = c("A", "A", "A", "A", "A", "A", "B", "B", > >>> >> "B", "B", "B", "B"), v2 = c("A", "B", "C", "A", "B", "C", "A", > >>> >> "B", "C", "A", "B", "C"), v3 = c("B", "B", "B", "C", "C", "C", > >>> >> "B", "B", "B", "C", "C", "C"), v4 = c(18.18530, 3.43806,0.00273, > >>> >> 1.42917, > >>> >> 1.05786, 0.00042, 2.37232, 3.01835, 0, 1.13430, 0.92872, > >>> >> 0)), .Names = c("v1", "v2", "v3", "v4"), class = "data.frame", > >>> >> row.names = > >>> >> c(2L, > >>> >> 9L, 11L, 41L, 48L, 50L, 158L, 165L, 167L, 197L, 204L, 206L)) > >>> >> > >>> >> # this is (an extract of) the OUTPUT file I would like to obtain: > >>> >> f2 <- structure(list(v1 = c("A", "A", "A", "A", "A", "A", "B", "B", > >>> >> "B", "B", "B", "B"), v2 = c("A", "B", "C", "A", "B", "C", "A", > >>> >> "B", "C", "A", "B", "C"), v3 = c("B", "B", "B", "C", "C", "C", > >>> >> "B", "B", "B", "C", "C", "C"), v4 = c(17.83529, 3.43806,0.00295, > >>> >> 1.77918, > >>> >> 1.05786, 0.0002, 2.37232, 3.01835, 0, 1.13430, 0.92872, > >>> >> 0)), .Names = c("v1", "v2", "v3", "v4"), class = "data.frame", > >>> >> row.names = > >>> >> c(2L, > >>> >> 9L, 11L, 41L, 48L, 50L, 158L, 165L, 167L, 197L, 204L, 206L)) > >>> >> > >>> >> # please notice that while the aggregated v4 on v3 has changed … > >>> >> aggregate(f1[,c("v4")],list(f1$v3),sum) > >>> >> aggregate(f2[,c("v4")],list(f2$v3),sum) > >>> >> > >>> >> # … the aggregated v4 over v1xv2 has remained unchanged: > >>> >> aggregate(f1[,c("v4")],list(f1$v1,f1$v2),sum) > >>> >> aggregate(f2[,c("v4")],list(f2$v1,f2$v2),sum) > >>> >> > >>> >> Thank you very much in advance for your assitance. > >>> >> > >>> >> Luca > >>> >> > >>> >> 2015-03-21 13:18 GMT+01:00 Bert Gunter <gunter.ber...@gene.com>: > >>> >>> > >>> >>> 1. Still not sure what you mean, but maybe look at ?ave and > ?tapply, > >>> >>> for which ave() is a wrapper. > >>> >>> > >>> >>> 2. You still need to heed the rest of Jeff's advice. > >>> >>> > >>> >>> Cheers, > >>> >>> Bert > >>> >>> > >>> >>> Bert Gunter > >>> >>> Genentech Nonclinical Biostatistics > >>> >>> (650) 467-7374 > >>> >>> > >>> >>> "Data is not information. Information is not knowledge. And > knowledge > >>> >>> is certainly not wisdom." > >>> >>> Clifford Stoll > >>> >>> > >>> >>> > >>> >>> > >>> >>> > >>> >>> On Sat, Mar 21, 2015 at 4:53 AM, Luca Meyer <lucam1...@gmail.com> > >>> >>> wrote: > >>> >>> > Hi Jeff & other R-experts, > >>> >>> > > >>> >>> > Thank you for your note. I have tried myself to solve the issue > >>> >>> > without > >>> >>> > success. > >>> >>> > > >>> >>> > Following your suggestion, I am providing a sample of the > dataset I > >>> >>> > am > >>> >>> > using below (also downloadble in plain text from > >>> >>> > https://www.dropbox.com/s/qhmpkkrejjkpbkx/sample_code.txt?dl=0): > >>> >>> > > >>> >>> > #this is an extract of the overall dataset (n=1200 cases) > >>> >>> > f1 <- structure(list(v1 = c("A", "A", "A", "A", "A", "A", "B", > "B", > >>> >>> > "B", "B", "B", "B"), v2 = c("A", "B", "C", "A", "B", "C", "A", > >>> >>> > "B", "C", "A", "B", "C"), v3 = c("B", "B", "B", "C", "C", "C", > >>> >>> > "B", "B", "B", "C", "C", "C"), v4 = c(18.1853007621835, > >>> >>> > 3.43806581506388, > >>> >>> > 0.002733567617055, 1.42917483425029, 1.05786640463504, > >>> >>> > 0.000420548864162308, > >>> >>> > 2.37232740842861, 3.01835841813241, 0, 1.13430282139936, > >>> >>> > 0.928725667117666, > >>> >>> > 0)), .Names = c("v1", "v2", "v3", "v4"), class = "data.frame", > >>> >>> > row.names > >>> >>> > = > >>> >>> > c(2L, > >>> >>> > 9L, 11L, 41L, 48L, 50L, 158L, 165L, 167L, 197L, 204L, 206L)) > >>> >>> > > >>> >>> > I need to find a automated procedure that allows me to adjust v3 > >>> >>> > marginals > >>> >>> > while maintaining v1xv2 marginals unchanged. > >>> >>> > > >>> >>> > That is: modify the v4 values you can find by running: > >>> >>> > > >>> >>> > aggregate(f1[,c("v4")],list(f1$v3),sum) > >>> >>> > > >>> >>> > while maintaining costant the values you can find by running: > >>> >>> > > >>> >>> > aggregate(f1[,c("v4")],list(f1$v1,f1$v2),sum) > >>> >>> > > >>> >>> > Now does it make sense? > >>> >>> > > >>> >>> > Please notice I have tried to build some syntax that tries to > modify > >>> >>> > values > >>> >>> > within each v1xv2 combination by computing sum of v4, row > percentage > >>> >>> > in > >>> >>> > terms of v4, and there is where my effort is blocked. Not really > >>> >>> > sure > >>> >>> > how I > >>> >>> > should proceed. Any suggestion? > >>> >>> > > >>> >>> > Thanks, > >>> >>> > > >>> >>> > Luca > >>> >>> > > >>> >>> > > >>> >>> > 2015-03-19 2:38 GMT+01:00 Jeff Newmiller < > jdnew...@dcn.davis.ca.us>: > >>> >>> > > >>> >>> >> I don't understand your description. The standard practice on > this > >>> >>> >> list > >>> >>> >> is > >>> >>> >> to provide a reproducible R example [1] of the kind of data you > are > >>> >>> >> working > >>> >>> >> with (and any code you have tried) to go along with your > >>> >>> >> description. > >>> >>> >> In > >>> >>> >> this case, that would be two dputs of your input data frames > and a > >>> >>> >> dput > >>> >>> >> of > >>> >>> >> an output data frame (generated by hand from your input data > >>> >>> >> frame). > >>> >>> >> (Probably best to not use the full number of input values just > to > >>> >>> >> keep > >>> >>> >> the > >>> >>> >> size down.) We could then make an attempt to generate code that > >>> >>> >> goes > >>> >>> >> from > >>> >>> >> input to output. > >>> >>> >> > >>> >>> >> Of course, if you post that hard work using HTML then it will > get > >>> >>> >> corrupted (much like the text below from your earlier emails) > and > >>> >>> >> we > >>> >>> >> won't > >>> >>> >> be able to use it. Please learn to post from your email software > >>> >>> >> using > >>> >>> >> plain text when corresponding with this mailing list. > >>> >>> >> > >>> >>> >> [1] > >>> >>> >> > >>> >>> >> > >>> >>> >> > http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example > >>> >>> >> > >>> >>> >> > >>> >>> >> > --------------------------------------------------------------------------- > >>> >>> >> Jeff Newmiller The ..... > ..... Go > >>> >>> >> Live... > >>> >>> >> DCN:<jdnew...@dcn.davis.ca.us> Basics: ##.#. ##.#. > >>> >>> >> Live > >>> >>> >> Go... > >>> >>> >> Live: OO#.. Dead: OO#.. > >>> >>> >> Playing > >>> >>> >> Research Engineer (Solar/Batteries O.O#. #.O#. > >>> >>> >> with > >>> >>> >> /Software/Embedded Controllers) .OO#. .OO#. > >>> >>> >> rocks...1k > >>> >>> >> > >>> >>> >> > >>> >>> >> > --------------------------------------------------------------------------- > >>> >>> >> Sent from my phone. Please excuse my brevity. > >>> >>> >> > >>> >>> >> On March 18, 2015 9:05:37 AM PDT, Luca Meyer < > lucam1...@gmail.com> > >>> >>> >> wrote: > >>> >>> >> >Thanks for you input Michael, > >>> >>> >> > > >>> >>> >> >The continuous variable I have measures quantities (down to the > >>> >>> >> > 3rd > >>> >>> >> >decimal level) so unfortunately are not frequencies. > >>> >>> >> > > >>> >>> >> >Any more specific suggestions on how that could be tackled? > >>> >>> >> > > >>> >>> >> >Thanks & kind regards, > >>> >>> >> > > >>> >>> >> >Luca > >>> >>> >> > > >>> >>> >> > > >>> >>> >> >=== > >>> >>> >> > > >>> >>> >> >Michael Friendly wrote: > >>> >>> >> >I'm not sure I understand completely what you want to do, but > >>> >>> >> >if the data were frequencies, it sounds like task for fitting a > >>> >>> >> >loglinear model with the model formula > >>> >>> >> > > >>> >>> >> >~ V1*V2 + V3 > >>> >>> >> > > >>> >>> >> >On 3/18/2015 2:17 AM, Luca Meyer wrote: > >>> >>> >> >>* Hello, > >>> >>> >> >*>>* I am facing a quite challenging task (at least to me) and > I > >>> >>> >> > was > >>> >>> >> >wondering > >>> >>> >> >*>* if someone could advise how R could assist me to speed the > >>> >>> >> > task > >>> >>> >> > up. > >>> >>> >> >*>>* I am dealing with a dataset with 3 discrete variables and > one > >>> >>> >> >continuous > >>> >>> >> >*>* variable. The discrete variables are: > >>> >>> >> >*>>* V1: 8 modalities > >>> >>> >> >*>* V2: 13 modalities > >>> >>> >> >*>* V3: 13 modalities > >>> >>> >> >*>>* The continuous variable V4 is a decimal number always > greater > >>> >>> >> > than > >>> >>> >> >zero in > >>> >>> >> >*>* the marginals of each of the 3 variables but it is > sometimes > >>> >>> >> > equal > >>> >>> >> >to zero > >>> >>> >> >*>* (and sometimes negative) in the joint tables. > >>> >>> >> >*>>* I have got 2 files: > >>> >>> >> >*>>* => one with distribution of all possible combinations of > >>> >>> >> > V1xV2 > >>> >>> >> >(some of > >>> >>> >> >*>* which are zero or neagtive) and > >>> >>> >> >*>* => one with the marginal distribution of V3. > >>> >>> >> >*>>* I am trying to build the long and narrow dataset V1xV2xV3 > in > >>> >>> >> > such > >>> >>> >> >a way > >>> >>> >> >*>* that each V1xV2 cell does not get modified and V3 fits as > >>> >>> >> > closely > >>> >>> >> >as > >>> >>> >> >*>* possible to its marginal distribution. Does it make sense? > >>> >>> >> >*>>* To be even more specific, my 2 input files look like the > >>> >>> >> >following. > >>> >>> >> >*>>* FILE 1 > >>> >>> >> >*>* V1,V2,V4 > >>> >>> >> >*>* A, A, 24.251 > >>> >>> >> >*>* A, B, 1.065 > >>> >>> >> >*>* (...) > >>> >>> >> >*>* B, C, 0.294 > >>> >>> >> >*>* B, D, 2.731 > >>> >>> >> >*>* (...) > >>> >>> >> >*>* H, L, 0.345 > >>> >>> >> >*>* H, M, 0.000 > >>> >>> >> >*>>* FILE 2 > >>> >>> >> >*>* V3, V4 > >>> >>> >> >*>* A, 1.575 > >>> >>> >> >*>* B, 4.294 > >>> >>> >> >*>* C, 10.044 > >>> >>> >> >*>* (...) > >>> >>> >> >*>* L, 5.123 > >>> >>> >> >*>* M, 3.334 > >>> >>> >> >*>>* What I need to achieve is a file such as the following > >>> >>> >> >*>>* FILE 3 > >>> >>> >> >*>* V1, V2, V3, V4 > >>> >>> >> >*>* A, A, A, ??? > >>> >>> >> >*>* A, A, B, ??? > >>> >>> >> >*>* (...) > >>> >>> >> >*>* D, D, E, ??? > >>> >>> >> >*>* D, D, F, ??? > >>> >>> >> >*>* (...) > >>> >>> >> >*>* H, M, L, ??? > >>> >>> >> >*>* H, M, M, ??? > >>> >>> >> >*>>* Please notice that FILE 3 need to be such that if I > aggregate > >>> >>> >> > on > >>> >>> >> >V1+V2 I > >>> >>> >> >*>* recover exactly FILE 1 and that if I aggregate on V3 I can > >>> >>> >> > recover > >>> >>> >> >a file > >>> >>> >> >*>* as close as possible to FILE 3 (ideally the same file). > >>> >>> >> >*>>* Can anyone suggest how I could do that with R? > >>> >>> >> >*>>* Thank you very much indeed for any assistance you are > able to > >>> >>> >> >provide. > >>> >>> >> >*>>* Kind regards, > >>> >>> >> >*>>* Luca* > >>> >>> >> > > >>> >>> >> > [[alternative HTML version deleted]] > >>> >>> >> > > >>> >>> >> >______________________________________________ > >>> >>> >> >R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, > see > >>> >>> >> >https://stat.ethz.ch/mailman/listinfo/r-help > >>> >>> >> >PLEASE do read the posting guide > >>> >>> >> >http://www.R-project.org/posting-guide.html > >>> >>> >> >and provide commented, minimal, self-contained, reproducible > code. > >>> >>> >> > >>> >>> >> > >>> >>> > > >>> >>> > [[alternative HTML version deleted]] > >>> >>> > > >>> >>> > ______________________________________________ > >>> >>> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, > see > >>> >>> > https://stat.ethz.ch/mailman/listinfo/r-help > >>> >>> > PLEASE do read the posting guide > >>> >>> > http://www.R-project.org/posting-guide.html > >>> >>> > and provide commented, minimal, self-contained, reproducible > code. > >>> >> > >>> >> > >> > >> > [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
