Re: [R] Using apply

Indeed. But perhaps it's also worth noting that if such statistics are calculated as implementations of (e.g. anova) formulae still found (sadly) in many statistics texts, then they shouldn't be calculated at all. Rather, the appropriate matrix methods (e.g. QR decompositions ) built into R -- man

Re: [R] Using apply

It should be said that for many basic statistics, there are faster functions than apply, for example here you want sum = colSums(x) As already said, for sum of squares you would do colSums(x^2). Many useful functions of this kind are implemented in package matrixStats. Once you install it, eithe

Re: [R] Using apply

> s2 <- apply(x*x, 2, sum) > s2 [1] 55 330 Jim Holtman Data Munger Guru What is the problem that you are trying to solve? Tell me what you want to do, not how you want to do it. On Tue, Oct 30, 2018 at 10:28 PM Steven Yen wrote: > > I need help with "apply". Below, I have no problem getting the

[R] Using apply

I need help with "apply". Below, I have no problem getting the column sums. 1. How do I get the sum of squares? 2. In general, where do I look up these functions? Thanks. x<-matrix(1:10,nrow=5); x sum <- apply(x,2,sum); sum [[alternative HTML version deleted]]

Re: [R] Using apply function to merge list of data frames

; -Original Message- >> From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of >Naresh >> Gurbuxani >> Sent: 25 July 2018 07:17 >> To: R-help@r-project.org >> Subject: [R] Using apply function to merge list of data frames >> >> I ha

Re: [R] Using apply function to merge list of data frames

xpected results. S Ellison > -Original Message- > From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Naresh > Gurbuxani > Sent: 25 July 2018 07:17 > To: R-help@r-project.org > Subject: [R] Using apply function to merge list of data frames > > I have

Re: [R] Using apply function to merge list of data frames

> On 25 Jul 2018, at 08:17, Naresh Gurbuxani > wrote: > > I have a list whose components are data frames. My goal is to construct a > data frame by merging all the list components. Is it possible to achieve > this using apply and without a for loop, as used below? > > Thanks, > Naresh >

Re: [R] using apply

3,]31 # [4,]32 David L Carlson Department of Anthropology Texas A&M University College Station, TX 77843-4352 -Original Message- From: R-help On Behalf Of Ulrik Stervbo Sent: Wednesday, May 2, 2018 3:49 PM To: Neha Aggarwal

Re: [R] using apply

Hi Neha, Perhaps merge() from base or join from dplyr is what you are looking for. data. table could also be interesting. Hth Ulrik On Wed, 2 May 2018, 21:28 Neha Aggarwal, wrote: > Hi > > I have 3 dataframes, a,b,c with 0/1 values...i have to check a condition > for dataframe a and b and the

[R] using apply

Hi I have 3 dataframes, a,b,c with 0/1 values...i have to check a condition for dataframe a and b and then input the rows ids to datframe c . In the if condition, I AND the 2 rows of from a and b and then see if the result is equal to one of them. I have done this using a for loop, however, it ta

Re: [R] Using apply on a three dimensional matrix and passing multiple arguments to user defined function

ilto:justin%20peter%20%3cjustin.pe...@usq.edu.au%3e>> CC: r-help@r-project.org mailto:%22r-h...@r-project.org%22%20%3cr-h...@r-project.org%3e>> Subject: Re: [R] Using apply on a three dimensional matrix and passing multiple arguments to user defined function Date: Wed, 7 Sep 2016 1

Re: [R] Using apply on a three dimensional matrix and passing multiple arguments to user defined function

Hi, Jean's example with lapply works fine. However, if you still want to use apply, I think this works. One observation first. You were passing c(1,2) as second argument to apply, in your code. And that is what makes you have lots of NAs as a result, since your function is being applied twice,

Re: [R] Using apply on a three dimensional matrix and passing multiple arguments to user defined function

Should be working, so the devil is in the details you are not showing. Please provide a reproducible (self-contained) example [1] and post in plain text rather than HTML formatted email to avoid code corruption. [1] http://adv-r.had.co.nz/Reproducibility.html -- Sent from my phone. Please excu

Re: [R] Using apply on a three dimensional matrix and passing multiple arguments to user defined function

Justin, I don't think you can get the apply() function to return an array. You could use lapply() instead, and then use simplify2array() to convert the list of matrices to an array. Also, in your mask() function you don't need the which() and you should return the x. See my example with toy dat

[R] Using apply on a three dimensional matrix and passing multiple arguments to user defined function

Dear R-user, I have a three-dimensional matrix of atmospheric data. The first two dimensions are spatial (lon and lat) and the third is time, such that dim(data) <- c(nlon,nlat,ntime) I wish to apply a land sea mask data which is a matrix of "0" and "1" if dim(nlon,nlat) dim(lsmask) <- c(nlon

Re: [R] using apply to a data frame

> On Apr 7, 2016, at 1:25 PM, John Sorkin wrote: > > > ‪‪I would like to apply a function, fract, to the columns of a > dataframe. I tried the following > apply(data5NonEventEpochs,2,fract) > but, no surprise it did not work as apply works on matrices not data > frames. As Bert pointed out yo

Re: [R] using apply to a data frame

Use lapply or sapply. A data frame is also a list with each component representing one column; lapply/sapply will apply the function to each column. Peter On Thu, Apr 7, 2016 at 1:25 PM, John Sorkin wrote: > > ‪‪I would like to apply a function, fract, to the columns of a > dataframe. I tried th

Re: [R] using apply to a data frame

Inline. -- Bert Bert Gunter On Thu, Apr 7, 2016 at 1:25 PM, John Sorkin wrote: > > ‪‪I would like to apply a function, fract, to the columns of a > dataframe. I tried the following > apply(data5NonEventEpochs,2,fract) > but, no surprise it did not work as apply works on matrices not data > fr

Re: [R] using apply to a data frame

Dear John, Try using sapply(data5NonEventEpochs, fract) HTH Best, Luisfo Chiroque PhD Student IMDEA Networks Institute http://fourier.networks.imdea.org/people/~luis_nunez/ > El 7 abr 2016, a las 23:25, John Sorkin > escribió: >

[R] using apply to a data frame

‪‪I would like to apply a function, fract, to the columns of a dataframe. I tried the following apply(data5NonEventEpochs,2,fract) but, no surprise it did not work as apply works on matrices not data frames. How can I apply a fuction to the columns of a data frame? (I can't covert data5NonEventsE

Re: [R] Using apply() with functions I wrote

: r-help@r-project.org Subject: [R] Using apply() with functions I wrote Hello! Does apply() not work with customized functions? Here is a simple example: AddSeven<-function(n){n+7} AddSeven(3) [1] 10 M<-matrix(nrow=2,ncol=2,data=c(1,2,3,4),byrow=TRUE)

Re: [R] Using apply() with functions I wrote

Ugghh... Sorry for bothering you all!! (Yes, I analyzed the data for my ecology M.S. project with R, but I wasted countless hours committing silly mistakes like this.) On Thu, Jul 24, 2014 at 4:11 PM, Bert Gunter wrote: > ummm R is case sensitive! "fun" != "FUN" > > (Have you gone throug

Re: [R] Using apply() with functions I wrote

ummm R is case sensitive! "fun" != "FUN" (Have you gone through any R tutorials yet? If not, please do so before posting further). Cheers, Bert Bert Gunter Genentech Nonclinical Biostatistics (650) 467-7374 "Data is not information. Information is not knowledge. And knowledge is certainly n

[R] Using apply() with functions I wrote

Hello! Does apply() not work with customized functions? Here is a simple example: AddSeven<-function(n){n+7} AddSeven(3) [1] 10 M<-matrix(nrow=2,ncol=2,data=c(1,2,3,4),byrow=TRUE) M [,1] [,2] [1,]12 [2,]34 apply(x=M,margin

Re: [R] Using apply with more than one matrix

t; From: arun [mailto:smartpink...@yahoo.com] >> Sent: Thursday, May 01, 2014 6:24 AM >> To: R. Help >> Cc: Waichler, Scott R >> Subject: Re: [R] Using apply with more than one matrix >> >> Hi, >> Sorry, a typo in the previous function: >> -

Re: [R] Using apply with more than one matrix

and how I can bring in the operation on a1.  This doesn't > work: > > evaluate <- function(idx) { >   ind.not.na <- which(!is.na(a1[idx,])) ]))  # doesn't work; improper > indexing for a1 >   if(length(ind.not.na) > 0) { >     return(condition1*(a1[idx,ind.

Re: [R] Using apply with more than one matrix

> > Sapply or mapply may work, I haven't used these much and will try to > learn better how to use them. Your use of sapply looks good; but I'm > trying to understand if and how I can bring in the operation on a1. This > doesn't work: > > > > evaluate <- function(idx) { > > ind.not.na <- which(!

Re: [R] Using apply with more than one matrix

ing for a1   if(length(ind.not.na) > 0) {     return(condition1*(a1[idx,ind.not.na[1]] + m2[idx]))  # doesn't work; improper indexing for a1   } } vec <- sapply(seq(length(m2)), evaluate) Scott Waichler > -Original Message----- > From: David Winsemius [mailto:dwinsem...@comcas

Re: [R] Using apply with more than one matrix

] + m2[idx]))  # doesn't work; improper indexing for a1   } } vec <- sapply(seq(length(m2)), evaluate) Scott Waichler > -Original Message- > From: David Winsemius [mailto:dwinsem...@comcast.net] > Sent: Wednesday, April 30, 2014 8:46 PM > To: Waichler, Scott R > Cc: Bert Gunt

Re: [R] Using apply with more than one matrix

Scott Waichler > >> -----Original Message- >> From: David Winsemius [mailto:dwinsem...@comcast.net] >> Sent: Wednesday, April 30, 2014 8:46 PM >> To: Waichler, Scott R >> Cc: Bert Gunter; r-help@r-project.org >> Subject: Re: [R] Using apply with more th

Re: [R] Using apply with more than one matrix

Sent: Wednesday, April 30, 2014 8:46 PM > To: Waichler, Scott R > Cc: Bert Gunter; r-help@r-project.org > Subject: Re: [R] Using apply with more than one matrix > > > On Apr 30, 2014, at 6:03 PM, Waichler, Scott R wrote: > > > Here is a working example with no random parts.

Re: [R] Using apply with more than one matrix

On Apr 30, 2014, at 6:03 PM, Waichler, Scott R wrote: > Here is a working example with no random parts. Thanks for your patience and > if I'm still off the mark with my presentation I'll drop the matter. > > v <- c(NA, 1.5, NA, NA, > NA, 1.1, 0.5, NA, > NA, 1.3, 0.4, 0.9) > a1 <-

Re: [R] Using apply with more than one matrix

Try ?mapply Description: 'mapply' is a multivariate version of 'sapply'. 'mapply' applies 'FUN' to the first elements of each ... argument, the second elements, the third elements, and so on. Arguments are recycled if necessary. Rich On Wed, Apr 30, 2014 at 9:03 PM, Waich

Re: [R] Using apply with more than one matrix

Here is a working example with no random parts. Thanks for your patience and if I'm still off the mark with my presentation I'll drop the matter. v <- c(NA, 1.5, NA, NA, NA, 1.1, 0.5, NA, NA, 1.3, 0.4, 0.9) a1 <- array(v, dim=c(2,2,3)) m1 <- matrix(c(NA, 1.5, 2.1, NA), ncol=2, by

Re: [R] Using apply with more than one matrix

etter test might be to specify set.seed() to give a reproducible example. -- David. > > Scott Waichler > > > >> -Original Message- >> From: Bert Gunter [mailto:gunter.ber...@gene.com] >> Sent: Wednesday, April 30, 2014 12:18 PM >> To: Waichl

Re: [R] Using apply with more than one matrix

n1[i,j] && length(ind.not.na) > 0) { ans[i,j] <- a1[i,j,ind.not.na[1]] + m2[i,j] } } } Scott Waichler > -Original Message- > From: Bert Gunter [mailto:gunter.ber...@gene.com] > Sent: Wednesday, April 30, 2014 12:18 PM > To: Waichler, Scott R > Cc: r-he

Re: [R] Using apply with more than one matrix

Scott: Your problem specification is rather vague: What do you mean by "use"? In general, matrices are merely vectors with a dim attribute, so if you can do what you want with them as vectors, then that will work for them as matrices. For example: > m1<- matrix(1:6, nr=3) > m2 <- matrix(11:16, n

Re: [R] Using apply with more than one matrix

Hi Scott, You could set up a three-dimensional array and then use apply on the desired dimension (MARGIN in apply language). HTH! Many thanks, Ranjan On Wed, 30 Apr 2014 17:54:48 + "Waichler, Scott R" wrote: > Hi, > > I want to apply a custom function to all the elements of one matrix.

[R] Using apply with more than one matrix

Hi, I want to apply a custom function to all the elements of one matrix. The function uses the value in the same i,j in a second matrix. How can I use apply() or similar function to avoid nested loops in i and j? Thanks, Scott Waichler Pacific Northwest National Laboratory Richland, WA, USA

Re: [R] Using apply function

Is this what you want: > random <- expand.grid(R1 = 1:5, R2 = -(1:5)) > result <- cbind(F1 = 10, F2 = 100, random) > > result F1 F2 R1 R2 1 10 100 1 -1 2 10 100 2 -1 3 10 100 3 -1 4 10 100 4 -1 5 10 100 5 -1 6 10 100 1 -2 7 10 100 2 -2 8 10 100 3 -2 9 10 100 4 -2 10 10 100

[R] Using apply function

Hi all R-users, I'm trying to using apply function to input a range of values into a function I wrote. I wrote a function with 4 information needed. I would like to make 2 of them fixed and the other 2 random (but with specified values). I would like to replicate the function 1 times. I wa

Re: [R] using 'apply' to apply princomp to an array of datasets

Thank you, Rui! This is incredibly helpful -- anonymous functions are new to me, and I appreciate being shown how useful they are. Best regards, David On Wed, Dec 12, 2012 at 10:12 AM, Rui Barradas wrote: > Hello, > > As for the first question try > > scoreset <- lapply(pcl, function(x) x$scor

Re: [R] using 'apply' to apply princomp to an array of datasets

Hello, As for the first question try scoreset <- lapply(pcl, function(x) x$scores[, 1]) do.call(cbind, scoreset) As for the second question, you want to know which columns in 'datasets' have NA's? colidx <- apply(datasets, 2, function(x) any(is.na(x))) datasets[, colidx] # These have NA's

Re: [R] using 'apply' to apply princomp to an array of datasets

Sorry, I just realized I didn't send the message below in plain text. -David Romano On Wed, Dec 12, 2012 at 9:14 AM, David Romano wrote: > > Hi everyone, > > Suppose I have a 3D array of datasets, where say dimension 1 corresponds > to cases, dimension 2 to datasets, and dimension 3 to observatio

[R] using 'apply' to apply princomp to an array of datasets

Hi everyone, Suppose I have a 3D array of datasets, where say dimension 1 corresponds to cases, dimension 2 to datasets, and dimension 3 to observations within a dataset. As an example, suppose I do the following: > x <- sample(1:20, 48, replace=TRUE) > datasets <- array(x, dim=c(4,3,2)) Here,

Re: [R] Using "apply" instead of "for" loop / multithreading

That worked better because of vectorization, but isn't multithreaded. To have this resource look at plyr package. On Mon, Nov 12, 2012 at 9:08 PM, Charles D. wrote: > it works really faster ! > thank you > > > > -- > View this message in context: > http://r.789695.n4.nabble.com/Using-apply-inst

Re: [R] Using "apply" instead of "for" loop / multithreading

it works really faster ! thank you -- View this message in context: http://r.789695.n4.nabble.com/Using-apply-instead-of-for-loop-multithreading-tp4649326p4649346.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org

Re: [R] Using "apply" instead of "for" loop / multithreading

Since you did not provide sample data (use dput instead of posting links to 'jpg' files), you can probably do it without loops: k=resp[,5] CO2umol <- resp[,6]*((Press*infoch[k,11]*1e-6)/(R*(resp[,7]+273.15))) CO2v <- CO2umol/(infoch[k,10]) CO2s <- CO2umol/(infoch[k,9] On Mon, Nov 12, 2012 at 12:3

[R] Using "apply" instead of "for" loop / multithreading

Hello , I'm new to R and don't really understand how to use the function "apply" instead of a "for loop", particularly for a function with multiple entries. I have a big data file and would like to apply a function in multi thread to accelerate the processus. I have a data frame containing values

Re: [R] using apply with sparse matrix from package Matrix

On Tue, Sep 4, 2012 at 10:58 AM, Martin Maechler wrote: >> Jennifer Lyon >> on Fri, 31 Aug 2012 17:22:57 -0600 writes: > > > Hi: > > I was trying to use apply on a sparse matrix from package Matrix, > > and I get the error: > > > Error in asMethod(object) : > > Cho

Re: [R] using apply with sparse matrix from package Matrix

> Jennifer Lyon > on Fri, 31 Aug 2012 17:22:57 -0600 writes: > Hi: > I was trying to use apply on a sparse matrix from package Matrix, > and I get the error: > Error in asMethod(object) : > Cholmod error 'problem too large' at file ../Core/cholmod_dense.c, line 1

[R] using apply with sparse matrix from package Matrix

Hi: I was trying to use apply on a sparse matrix from package Matrix, and I get the error: Error in asMethod(object) : Cholmod error 'problem too large' at file ../Core/cholmod_dense.c, line 106 Is there a way to apply a function to all the rows without bumping into this problem? Here is a si

Re: [R] Using apply() with a function involving ode()

Dear Berend, Yes, the wnv.sim function should have included "wnv.model" instead of "wnv.incubation." Sorry for the typo. Although I had inspected the expand.grid() object, I had not connected the error with a naming problem. Thanks so much for the help! The function works perfectly. Sin

Re: [R] Using apply() with a function involving ode()

See inline comments. On 25-04-2012, at 08:40, Adam Zeilinger wrote: > Hello, > > I am trying to get the output from the numerical simulation of a system of > ordinary differential equations for a range of values for three parameters. > I am using the ode() function (deSolve package) to run t

[R] Using apply() with a function involving ode()

Hello, I am trying to get the output from the numerical simulation of a system of ordinary differential equations for a range of values for three parameters. I am using the ode() function (deSolve package) to run the numerical simulation and apply() to run the simulation function for each se

Re: [R] using apply function and storing output

On Fri, Oct 15, 2010 at 6:46 AM, David A. wrote: > > Thanks Dennis, > > I don't think it was a problem of not feeding in a function for rollapply(), > because I was using mean() and my co.var() function in the FUN argument. > The key part seems to be the transformation that zoo() does to the matr

Re: [R] using apply function and storing output

atrix, the rollapply() function now works fine. Thanks again David Date: Fri, 15 Oct 2010 03:00:27 -0700 Subject: Re: [R] using apply function and storing output From: djmu...@gmail.com To: dasol...@hotmail.com CC: r-help@r-project.org Hi: You need to give a function for rollapply() to

Re: [R] using apply function and storing output

eated function... > > > xxx<-rollapply(ord_raw_filt.df,3,FUN=co.var,by=3) > Error in UseMethod("rollapply") : > no applicable method for 'rollapply' applied to an object of class > "c('matrix', 'integer', 'numeric')

Re: [R] using apply function and storing output

ed function... > xxx<-rollapply(ord_raw_filt.df,3,FUN=co.var,by=3) Error in UseMethod("rollapply") : no applicable method for 'rollapply' applied to an object of class "c('matrix', 'integer', 'numeric')" Can you help me with the error?

Re: [R] using apply function and storing output

one efficient way to do this, avoiding loops, is using the rowsum() function, e.g., mat <- matrix(rnorm(1710*244), 1710, 244) id <- rep(seq_len(570), each = 3) means <- rowsum(mat, id, FALSE) / 3 Regarding the second part of your question, indeed a "gold" rule of efficient R programming when

Re: [R] using apply function and storing output

Hi: Look into the rollmean() function in package zoo. HTH, Dennis On Fri, Oct 15, 2010 at 12:34 AM, David A. wrote: > > Hi list, > > I have a 1710x244 matrix of numerical values and I would like to calculate > the mean of every group of three consecutive values per column to obtain a > new mat

[R] using apply function and storing output

Hi list, I have a 1710x244 matrix of numerical values and I would like to calculate the mean of every group of three consecutive values per column to obtain a new matrix of 570x244. I could get it done using a for loop but how can I do that using apply functions? In addition to this, do I hav

Re: [R] Using apply for logical conditions

Wow, Thanks for all the excellent (and fast) responses. That's really helped. Sorry I didn't supply a cut and paste-able example (noted for future reference) but your examples caught the essence of my problem. I ended up opting for the apply any solution. But I'll bear the Reduce function in m

Re: [R] Using apply for logical conditions

Just for fun, here are another couple of versions that work for data frames. For Reduce with "|" do.call(pmax,c(mydata,na.rm=TRUE)) >0 and for "&" do.call(pmin,c(mydata,na.rm=TRUE)) >0  Cheers, Bert Gunter Genentech Nonclinical Biostatistics On Mon, Aug 2, 2010 at 2:28 PM, Joshua Wiley wr

Re: [R] Using apply for logical conditions

Reduce() is really amazingly fast! Even with a much larger number of columns, it is still in the same ballpark (and much more readable): > boolean <- c(TRUE, rep(FALSE,10^3)) > a<-matrix(sample(boolean, 10^7, replace = TRUE),10^4,10^3) > b<-data.frame(a) > system.time({opt4 <- rowSums(a, na.rm =

Re: [R] Using apply for logical conditions

On Mon, Aug 2, 2010 at 2:08 PM, Michael Lachmann wrote: > > Reduce() is much nicer, but I usually use > > rowSums(A) > 0 for 'or', and > rowSums(A) == ncols for 'and'. > > Which works slightly faster. For the sake of my own curiosity, I compared several of these options, but in case others are in

Re: [R] Using apply for logical conditions

Yes, you must do the conversion. The reason is that Reduce requires its argument x, to be a vector; and a matrix is seen a vector obtained by columnwise concatenation. e.g. > Reduce("+",matrix(1:6,nr=3)) [1] 21 > Reduce("+",1:6) [1] 21 The data frame is seen as a list with elements the columns of

Re: [R] Using apply for logical conditions

Reduce() is much nicer, but I usually use rowSums(A) > 0 for 'or', and rowSums(A) == ncols for 'and'. Which works slightly faster. I noticed, though, that Reduce() doesn't work on matrices. Is there an alternative for matrices, or do you have to convert the matrix first to a data.frame, and the

Re: [R] Using apply for logical conditions

In addition to Reduce(), you can take a look at ?any for '|' and ?all for '&'. Josh On Mon, Aug 2, 2010 at 1:43 PM, Allan Engelhardt wrote: > `|` is a binary operator which is why the apply will not work.  See > > help("Reduce") > > For example, > > set.seed(1) > data <- data.frame(A = runif(10)

Re: [R] Using apply for logical conditions

Alastair wrote: Hi, I've got some boolean data in a data.frame in the form: XYZA B C [1] T TFT F F [2] F TTF F F . . . What I want to do is create a new column which is the logical disjunction of several of the columns. Just like: new.

Re: [R] Using apply for logical conditions

`|` is a binary operator which is why the apply will not work. See help("Reduce") For example, set.seed(1) data <- data.frame(A = runif(10) > 0.5, B = runif(10) > 0.5, C = runif(10) > 0.5) Reduce(`|`, data) # [1] TRUE FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE Hope this helps.

[R] Using apply for logical conditions

Hi, I've got some boolean data in a data.frame in the form: XYZA B C [1] T TFT F F [2] F TTF F F . . . What I want to do is create a new column which is the logical disjunction of several of the columns. Just like: new.column <- data$X |

Re: [R] Using apply function on duplicates in a data.frame

Thanks a lot. All the three approaches work for me! On Sun, Jan 31, 2010 at 10:43 PM, hadley wickham wrote: > On Sun, Jan 31, 2010 at 5:05 PM, Sunny Srivastava > wrote: > > Dear R-Helpers, > > I have a data.frame (df) and the head of data.frame looks like > > > > ProbeUID ControlType Pr

Re: [R] Using apply function on duplicates in a data.frame

On Sun, Jan 31, 2010 at 5:05 PM, Sunny Srivastava wrote: > Dear R-Helpers, > I have a data.frame (df) and the head of data.frame looks like > >     ProbeUID ControlType     ProbeName GeneName SystematicName > 1665     1577           0 pSysX_50_22_1 pSysX_50       pSysX_50 > 5422     5147          

Re: [R] Using apply function on duplicates in a data.frame

On Jan 31, 2010, at 6:05 PM, Sunny Srivastava wrote: Dear R-Helpers, I have a data.frame (df) and the head of data.frame looks like ProbeUID ControlType ProbeName GeneName SystematicName 1665 1577 0 pSysX_50_22_1 pSysX_50 pSysX_50 5422 5147 0 pSysX_49

[R] Using apply function on duplicates in a data.frame

Dear R-Helpers, I have a data.frame (df) and the head of data.frame looks like ProbeUID ControlType ProbeName GeneName SystematicName 1665 1577 0 pSysX_50_22_1 pSysX_50 pSysX_50 5422 5147 0 pSysX_49_8_1 pSysX_49 pSysX_49 4042 3843 0 p

Re: [R] Using apply() and scale() in combination

nd case. You can, of course, transpose the result using t(). HTH . Peter Alspach > -Original Message- > From: r-help-boun...@r-project.org > [mailto:r-help-boun...@r-project.org] On Behalf Of Armin Raznahan > Sent: Tuesday, 19 May 2009 9:44 a.m. > To: r-help@r-project

[R] Using apply() and scale() in combination

Hello I am an R newbie, and am coming against a couple of problems when I try and apply the scale function across all the rows of a matrix. - #I have a matrix "dt_l". > str(dt_l) num [1:40962, 1:885] 3.04 4.1 3.4 3.58 3.77 ... #I want to convert the values in each row

Re: [R] Using apply to get group means

That is precisely the reason for the existence of the ave function. Using Wickham's example: > x1 <- rep(c("A", "B", "C"), 3) > x2 <- c(rep(1, 3), rep(2, 3), 1, 2, 1) > x3 <- c(1, 2, 3, 4, 5, 6, 2, 6, 4) > df <- data.frame(x1, x2, x3) > df$grpx3 <- ave(df$x3, list(x1,x2)) > df x1 x2 x3 grpx

Re: [R] Using apply to get group means

Sorry, there was a mistake in the previous mail: Domenico Vistocco wrote: A different solution (using aggregate for the table of means and merge for adding it to the dataframe): x1<-rep(c("A","B","C"),3) x2<-c(rep(1,3),rep(2,3),1,2,1) x3<-c(1,2,3,4,5,6,2,6,4) x<-data.frame(x1,x2,x3) #here usi

Re: [R] Using apply to get group means

A different solution (using aggregate for the table of means and merge for adding it to the dataframe): x1<-rep(c("A","B","C"),3) x2<-c(rep(1,3),rep(2,3),1,2,1) x3<-c(1,2,3,4,5,6,2,6,4) x<-data.frame(x1,x2,x3) #here using data.frame the x1 variable is directly converted to factor x3means <-

Re: [R] Using apply to get group means

On Tue, Mar 31, 2009 at 11:31 AM, baptiste auguie wrote: > Not exactly the output you asked for, but perhaps you can consider, > > library(doBy) >> summaryBy(x3~x2+x1,data=x,FUN=mean) >> >>  x2 x1 x3.mean >> 1  1  A     1.5 >> 2  1  B     2.0 >> 3  1  C     3.5 >> 4  2  A     4.0 >> 5  2  B     5.

Re: [R] Using apply to get group means

Not exactly the output you asked for, but perhaps you can consider, library(doBy) > summaryBy(x3~x2+x1,data=x,FUN=mean) x2 x1 x3.mean 1 1 A 1.5 2 1 B 2.0 3 1 C 3.5 4 2 A 4.0 5 2 B 5.5 6 2 C 6.0 the plyr package also provides similar functionality, as do t

[R] Using apply to get group means

Hi all, I'm trying to improve my R skills and make my programming more efficient and succinct. I can solve the following question, but wonder if there's a better way to do it: I'm trying to calculate mean by several variables and then put this back into the original data set as a new variable

Re: [R] Using apply to generate matrix from rows?

Dear Stephan, Try this: do.call(rbind,lapply(1:2,function(x) matrix(u[x,]%*%t(u[x,]),ncol=ncol(u HTH, Jorge On Mon, Jan 19, 2009 at 12:39 PM, Stephan Lindner wrote: > Dear all, > > > I have a simple question which I unfortunately do not seem to be able > to solve myself. I have a (NxK) ma

Re: [R] Using apply to generate matrix from rows?

Try this: matrix(apply(u, 1, tcrossprod), nr = nrow(u)*ncol(u), byrow = T) On Mon, Jan 19, 2009 at 3:39 PM, Stephan Lindner wrote: > Dear all, > > > I have a simple question which I unfortunately do not seem to be able > to solve myself. I have a (NxK) matrix and want to generate a new > matrix

[R] Using apply to generate matrix from rows?

Dear all, I have a simple question which I unfortunately do not seem to be able to solve myself. I have a (NxK) matrix and want to generate a new matrix by multiplying each row with itself such that the new matrix has dimension ((N*K)xK) (or better, generate an array with dimension (K,K,N)). I tr

[R] Using apply for two datasets

It depends on how the data are arranged ## x<-matrix(c(1,2,3,2,8,2,4,5,6),nrow=3) y<-matrix(c(10,2,13,0,8,4,4.2,5.2,6.2),nrow=3) q<-mapply(t.test,as.data.frame(x),as.data.frame(y)) q ## The ith column of q contain the results of applying t.te

Re: [R] Using apply for two datasets

; to test by column and > > mapply(t.test,as.data.frame(t(myData1)),as.data.frame(t(myData2))) > > > to test by row? > > > - Original Message > From: Gang Chen > To: Henrique Dallazuanna > Cc: r-h...@stat.math.ethz.ch > Sent: Tuesday, January 6, 2009 10

Re: [R] Using apply for two datasets

Dallazuanna Cc: r-h...@stat.math.ethz.ch Sent: Tuesday, January 6, 2009 10:10:44 AM Subject: Re: [R] Using apply for two datasets Thanks a lot for the quick help! mapply() seems promising. However, mapply(t.test, myData1, myData2) would not work, so how can I specify the margin in mapply() which function

Re: [R] Using apply for two datasets

Hi Gang, Perhaps this post might be useful in this case. Please take a special lookat Gábor Csárdi's reply. http://www.nabble.com/apply,-t-test-and-p-values-to20012292.html#a20012292 HTH, Jorge On Tue, Jan 6, 2009 at 1:10 PM, Gang Chen wrote: > Thanks a lot for the quick help! > > mapply() s

Re: [R] Using apply for two datasets

Thanks a lot for the quick help! mapply() seems promising. However, mapply(t.test, myData1, myData2) would not work, so how can I specify the margin in mapply() which function t.test() will be applied over? For example, I specify the 2nd dimension (column) in apply(myData1, 2, t.test) to run one-s

Re: [R] Using apply for two datasets

I think that you can use mapply for this. On Tue, Jan 6, 2009 at 3:24 PM, Gang Chen wrote: > I can run one-sample t-test on an array, for example a matrix myData1, > with the following > > apply(myData1, 2, t.test) > > Is there a similar fashion using apply() or something else to run > 2-sample

[R] Using apply for two datasets

I can run one-sample t-test on an array, for example a matrix myData1, with the following apply(myData1, 2, t.test) Is there a similar fashion using apply() or something else to run 2-sample t-test with datasets from two groups, myData1 and myData2, without looping? TIA, Gang __

Re: [R] using apply to loop

On 2007-12-21, Louis Martin <[EMAIL PROTECTED]> wrote: > Hi, > > I am running the following loop, but it takes hours to run as n is big. Is > there any way "apply" can be used? Thanks. > ### Start > nclass <- dim(data)[[2]] - 1 > z <- matrix(0, ncol = nclass, nrow = nclass) > n <- dim(

Re: [R] using apply to loop [SEC=UNCLASSIFIED]

From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Louis Martin Sent: Friday, 21 December 2007 11:37 AM To: R-help@r-project.org Subject: [R] using apply to loop Hi, I am running the following loop, but it takes hours to run as n is big. Is there any way "apply" can be u

[R] using apply to loop

Hi, I am running the following loop, but it takes hours to run as n is big. Is there any way "apply" can be used? Thanks. ### Start nclass <- dim(data)[[2]] - 1 z <- matrix(0, ncol = nclass, nrow = nclass) n <- dim(data)[[1]] x <- c(1:nclass) # loop starts for(loop in 1:n) {