[R] How to use AUC metric in caret

Hello everyone I am using nested resampling in caret (5-fold outer and bootstrap inner resampling) and by default, it shows the "Accuracy" metric. How can I use it for the ROC/AUC metric? My code is: d=readARFF("apns.arff") index <- createDataPartition(d$isKilled , p = .70,list = FALSE) tr <-

Re: [R] How to use contour plot?

On Tue, 16 Nov 2021 09:45:34 +0100 Luigi Marongiu wrote: > contour(df$X, df$Y, df$Z) contour() works on matrices (sometimes called "wide format" data). Z must be a numeric matrix, X must be a numeric vector with length(X) == nrow(Z), and Y must be a numeric vector with length(Y) == ncol(Z).

Re: [R] How to use contour plot?

On 16/11/2021 3:45 a.m., Luigi Marongiu wrote: Hello, I have a dataframe with 3 values and that I would like to plot with contour: ``` head(df) Y X Z 1 0.0008094667 50 1 2 0.0012360955 50 1 3 0.0016627243 50 1 4 0.0020893531 50 1 5

[R] How to use contour plot?

Hello, I have a dataframe with 3 values and that I would like to plot with contour: ``` > head(df) Y X Z 1 0.0008094667 50 1 2 0.0012360955 50 1 3 0.0016627243 50 1 4 0.0020893531 50 1 5 0.0025159819 50 1 6 0.0029426108 50 1 >

Re: [R] How to use ifelse without invoking warnings

Dear Ravi, I have uploaded on GitHub a version which handles also constant values instead of functions. Regarding named arguments: this is actually handled automatically as well: eval.by.formula((x > 5 & x %% 2) ~ (x <= 5) ~ ., FUN, y=2, x) # [1]  1  4  9 16 25  6 14  8 18 10

Re: [R] How to use ifelse without invoking warnings

Dear Ravi, I wrote a small replacement for ifelse() which avoids such unnecessary evaluations (it bothered me a few times as well - so I decided to try a small replacement). ### Example: x = 1:10 FUN = list(); FUN[[1]] = function(x, y) x*y; FUN[[2]] = function(x, y) x^2; FUN[[3]] =

Re: [R] How to use ifelse without invoking warnings

yes; tmp[!test] <- no[!test]; tmp) , possibly extended to handle missing values in 'test'. Best, -Deepayan > Thanks & Best regards, > Ravi > > From: John Fox > Sent: Thursday, October 7, 2021 2:00 PM > To: Ravi Varadhan > Cc:

Re: [R] How to use ifelse without invoking warnings

his behavior. > >Thanks & Best regards, >Ravi > >From: John Fox >Sent: Thursday, October 7, 2021 2:00 PM >To: Ravi Varadhan >Cc: R-Help >Subject: Re: [R] How to use ifelse without invoking warnings > > > External Email

Re: [R] How to use ifelse without invoking warnings

i Varadhan via R-help Sent: Friday, October 8, 2021 8:22 AMiu To: John Fox l Cc: R-Help Subject: Re: [R] How to use ifelse without invoking warnings Thank you to Bert, Sarah, and John. I did consider suppressing warnings, but I felt that there must be a more principled approach. While John's so

Re: [R] How to use ifelse without invoking warnings

Ravi From: John Fox Sent: Thursday, October 7, 2021 2:00 PM To: Ravi Varadhan Cc: R-Help Subject: Re: [R] How to use ifelse without invoking warnings External Email - Use Caution Dear Ravi, It's already been suggested that you could disable warnings, but th

Re: [R] How to use ifelse without invoking warnings

arguments. Best, John Thanks & Best regards, Ravi *From:* John Fox *Sent:* Thursday, October 7, 2021 2:00 PM *To:* Ravi Varadhan *Cc:* R-Help *Subject:* Re: [R] How to use ifelse without invoking warn

Re: [R] How to use ifelse without invoking warnings

Dear Ravi, It's already been suggested that you could disable warnings, but that's risky in case there's a warning that you didn't anticipate. Here's a different approach: > kk <- k[k >= -1 & k <= n] > ans <- numeric(length(k)) > ans[k > n] <- 1 > ans[k >= -1 & k <= n] <- pbeta(p, kk + 1, n

Re: [R] How to use ifelse without invoking warnings

Bert's approach is much less risky! On Thu, Oct 7, 2021 at 1:37 PM Bert Gunter wrote: > > ?suppressWarnings > > > p <- .05 > > k <- c(-1.2,-0.5, 1.5, 10.4) > > n <- 10 > > > > ans <- ifelse (k >= -1 & k <= n, pbeta(p,k+1,n-k,lower.tail=FALSE), > ifelse (k < -1, 0, 1) ) > Warning message: > In

Re: [R] How to use ifelse without invoking warnings

If you are positive the warnings don't matter for your application, you can disable them: see ?options for details of warn. But that can be dangerous, so be careful! Sarah On Thu, Oct 7, 2021 at 1:21 PM Ravi Varadhan via R-help wrote: > > Hi, > I would like to execute the following vectorized

Re: [R] How to use ifelse without invoking warnings

?suppressWarnings > p <- .05 > k <- c(-1.2,-0.5, 1.5, 10.4) > n <- 10 > > ans <- ifelse (k >= -1 & k <= n, pbeta(p,k+1,n-k,lower.tail=FALSE), ifelse (k < -1, 0, 1) ) Warning message: In pbeta(p, k + 1, n - k, lower.tail = FALSE) : NaNs produced > > suppressWarnings(ans <- ifelse (k >= -1 & k <=

[R] How to use ifelse without invoking warnings

Hi, I would like to execute the following vectorized calculation: ans <- ifelse (k >= -1 & k <= n, pbeta(p, k+1, n-k, lower.tail = FALSE), ifelse (k < -1, 0, 1) ) For example: > k <- c(-1.2,-0.5, 1.5, 10.4) > n <- 10 > ans <- ifelse (k >= -1 & k <= n, pbeta(p,k+1,n-k,lower.tail=FALSE),

Re: [R] How to use R for Speech to text conversion

Whether you use RStudio is up to you... the heavy lifting would be done by R anyway. I am not a STT person, but TensorFlow was recently released on CRAN [1] so there may be more opportunities for R users to make headway in this area. [1] https://tensorflow.rstudio.com/installation/ On October

Re: [R] How to use R for Speech to text conversion

Have you checked here: https://cran.r-project.org/web/views/NaturalLanguageProcessing.html Speech to text is a very complex, specialized task requiring, I would expect, a lot of IP. It would not surprise me if you have to resort to big time, specialized software products with or without R.

Re: [R] How to use R for Speech to text conversion

I am also interested in this. Maybe a start: https://voice.mozilla.org/ -Original Message- To: r-help@r-project.org Subject: *SPAM* [R] How to use R for Speech to text conversion Hi Iam a newbie to NLP and I would like to get some directions on how to convert speech

[R] How to use R for Speech to text conversion

Hi Iam a newbie to NLP and I would like to get some directions on how to convert speech file to text Google search leads me to using GoogleLanguageR Package and API's but these need payments to be made for Google. Can someone suggest ways in which I can do the speech to text conversion in R

Re: [R] How to use mle2 function?

The basic problem is that holling() is not a (negative) loglikelihood function. nll() _is_ a negative loglikelihood, but it is not clear for what. You appear to be very confused as to what a likelihood even is (what is k? apparently your response variable? Then how can it be a scalar if X is a

Re: [R] How to use mle2 function?

Addendum: the optimization actually got a worse outcome than the original eyeball estimation: ``` actual <- c(8, 24, 39, 63, 89, 115, 153, 196, 242, 287, 344, 408, 473, 546, 619, 705, 794, 891, 999, 1096, 1242, 1363, 1506, 1648, 1753, 1851,

Re: [R] How to use mle2 function?

No, I got the same. I reckon the problem is with X: this was I scalar, I was providing a vector with the actual values. Ho can mle2 optimize without knowing what are the actual data? and what values should I give for X? Thank you On Tue, Jun 30, 2020 at 2:06 PM Eric Berger wrote: > > I have no

Re: [R] How to use mle2 function?

I have no problem with the following code: library(bbmle) holling <- function( a, b, x ) { a*x^2 / (b^2 + x^2) } A=3261 B=10 X=30 foo <- mle2( minuslogl=holling, start=list(a=A,b=B,x=X) ) foo # Call: # mle2(minuslogl = holling, start = list(a = A, b = B, x = X)) # Coefficients: #a

Re: [R] How to use mle2 function?

Sorry for the typo, but I have the same error if using b instead of h: ``` > O = mle2(minuslogl = holling, start = list(a = A, b = B)) > Error in minuslogl(a = 3261, b = 10) : argument "x" is missing, with no default # let's add x X = c(8, 24, 39, 63, 89, 115, 153, 196, 242, 287,

Re: [R] How to use mle2 function?

Hi Luigi, I took a quick look. First error: You wrote O = mle2(minuslogl = holling, start = list(a = A, h = B, x = X)) it should be b=B (h is not an argument of holling()) The error message gave very precise information! Second error: You wrote O = mle2(minuslogl = nll, start = list(a = A, h =

[R] How to use mle2 function?

Hello, I would like to optimize the function: ``` holling = function(a, b, x) { y = (a * x^2) / (b^2 + x^2) return(y) } ``` I am trying to use the function mle2 from bbmle, but how do I need to feed the data? If I give `holling` as function to be optimized, passing the starting values for `a`,

[R] How to use msaPrettyPrint in memory efficient mode?

Hello, I have an alignment made with the package MSA. I installed latex on my ubuntu machine with `sudo apt-get install texlive-full` but I could not find the package texshade that is mentioned in the MSA's manual. When I run msaPrettyPrint I get: ``` Multiple alignment written to temporary file

Re: [R] How to use R0 package?

Because the dates might not be consecutive. Or in ISO format. On May 22, 2020 7:38:17 PM PDT, Jim Lemon wrote: >So what if you treat a nuisance as a feature and import your dates as >factors? as.numeric(dates) would have the correct structure or am I, >as usual, missing something? > >Jim > >On

Re: [R] How to use R0 package?

So what if you treat a nuisance as a feature and import your dates as factors? as.numeric(dates) would have the correct structure or am I, as usual, missing something? Jim On Sat, May 23, 2020 at 1:00 AM Jeff Newmiller wrote: > > This is getting off-topic here but R0 is a mathematical parameter

Re: [R] How to use R0 package?

This is getting off-topic here but R0 is a mathematical parameter unrelated to calendar dates. It arises when analyzing case counts (integers) as a function of the numerical measure of time since some non-trivial number of cases has occurred (conventionally this measure is in days).. dta$days

Re: [R] How to use R0 package?

Hi, you should be able to convert your date variables to integers (usually viewed as the elapse between 1970/01/01 and today) by using date conversion to integers: TODAY="2020-05-22" as.Date(TODAY) [1] "2020-05-22" > as.integer(as.Date(TODAY)) [1] 18404 Doing the same with your reference dates

Re: [R] How to use R0 package?

class(length(x1)) "integer" Your problem is thinking that begin=1 means you are passing begin as an integer. class(1) "numeric" class(1L) "integer" You should pass: begin=1L, end=length(x1) Best, Eric On Fri, May 22, 2020 at 3:31 PM Luigi Marongiu wrote: > > In theory, it works > ``` > > R0

Re: [R] How to use R0 package?

In theory, it works ``` > R0 = estimate.R(x1, t=d1, GT=mGT, begin=1, end=117, methods="EG",pop.size=pop, nsim=N) >R0 Reproduction number estimate using Exponential Growth method. R : 0.7425278[ 0.7409297 , 0.7441229 ] ``` but I am not happy because 1. I have to use numbers

Re: [R] How to use R0 package?

Hi Luigi, I am not familiar with the R0 package but I took a quick look. The example in the documentation sets begin and end to integers. Try setting begin = 1, end = 121 and see if that works. HTH, Eric On Fri, May 22, 2020 at 1:17 PM Luigi Marongiu wrote: > > Hello, > I am trying ot get the

[R] How to use R0 package?

Hello, I am trying ot get the R0 from the incidence data from China for the COVID-19. I set the following: ``` library("R0") x1 <- c(259, 457, 688, 769, 1771, 1459, 1737, 1981, 2099, 2589, 2825, 3235, 3884, 3694, 3143, 3385, 2652, 2973, 2467, 2015, 14108, 5090, 2641,

Re: [R] How to use pakcage R0

R0 = estimate.R(germany_vect, mGT, begin=germany_vect[1], end=germany_vect[length(germany_vect)], methods="EG", pop.size=pop_de, nsim=100) Error in begin.nb:end.nb : argument of length 0 germany_vect[1] 1 184 germany_vect[length(germany_vect)] 57 488 ``` What might be the problem

[R] How to use pakcage R0

Dear all, I have been trying to use the package R0 https://www.rdocumentation.org/packages/R0/versions/1.2-6/topics/estimate.R but the manual is not so rich of words. The example given is based on the named vector Germany.1918 ``` > library("R0") > data(Germany.1918) > Germany.1918 1918-09-29

Re: [R] How to use preProcess in Caret?

Hello there, Yes, I'd tried scale as well. I mean, I could do my preprocessing separately and it was working fine. I was just wondering how preProcess argument in train function works. As far as I know, when preProcess argument is set, it normalizes inputs but not outputs. Then I've figured we

Re: [R] How to use preProcess in Caret?

Hello, Have you tried alternative methods of pre-processing your data, such as simply calling scale()? What is the effect on convergence, for both the caret package and and the neuralnet package? There's an example using scale() with the neuralnet package at the link below:

[R] How to use preProcess in Caret?

Hello there, I am using caret and neuralnet to train a neural network to predict times table. I am using 'backprop' algorithm for neuralnet to experiment and learn. Before using caret, I've trained a neuralnet without using caret, I've normalized my input & outputs using preProcess with 'range'

Re: [R] how to use a matrix as an index to another matrix?

No loops necessary. Use array indexing (see ?"[", of course -- the section on matrices and arrays) set.seed(123) A <- matrix(sample(1:10), nrow = 5) B <- matrix(c(sample(1:5), sample(1:5)), nrow =5, byrow = FALSE) ## The following could be a 1-liner, but I broke it out for clarity. ix <-

Re: [R] how to use a matrix as an index to another matrix?

Hi Jinsong, In such a case I think explicit loop IS the most elegant solution. for(i in 1:2) A[,i] <- A[,i][B[,i]] Linus On Fri, 11 Oct 2019 at 11:44, Jinsong Zhao wrote: > > Hi there, > > I have two matrices, A and B. The columns of B is the index of the > corresponding columns of A. I hope

Re: [R] how to use a matrix as an index to another matrix?

A matrix can be subset by another 2-column matrix, where the first column is the row index and the second column the column index. So idx = matrix(c(B, col(B)), ncol = 2) A[] <- A[idx] Martin Morgan On 10/11/19, 6:31 AM, "R-help on behalf of Eric Berger" wrote: Here is one way A <-

Re: [R] how to use a matrix as an index to another matrix?

Here is one way A <- sapply(1:ncol(A), function(i) {A[,i][B[,i]]}) On Fri, Oct 11, 2019 at 12:44 PM Jinsong Zhao wrote: > Hi there, > > I have two matrices, A and B. The columns of B is the index of the > corresponding columns of A. I hope to rearrange of A by B. A minimal > example is

[R] how to use a matrix as an index to another matrix?

Hi there, I have two matrices, A and B. The columns of B is the index of the corresponding columns of A. I hope to rearrange of A by B. A minimal example is following: > set.seed(123) > A <- matrix(sample(1:10), nrow = 5) > B <- matrix(c(sample(1:5), sample(1:5)), nrow =5, byrow = FALSE) > A

Re: [R] How to use Conda with R + RStudio Server

Solution: https://github.com/grst/rstudio-server-conda It works. [[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

Re: [R] How to use breaks argument in hist() function correctly?

> When I had breaks = 18, I get total number of cells as 16, which is > same when I put breaks = 20 > > In the 2nd case I was expecting total number of cells (i.e. bars) as > 20 i.e. if I understand the documentation correctly I should expect > total number of cells (bars) should be same as breaks

Re: [R] How to use breaks argument in hist() function correctly?

Hi Cristofer, If you just ask for a number of breaks, you will get what "hist" thinks you should. Try this or something similar: hist(x,breaks=seq(min(x),max(x),length.out=21)) Jim On Wed, Sep 18, 2019 at 8:55 PM Christofer Bogaso wrote: > > Hi, > > I have a numerical vector as below > > x =

[R] How to use breaks argument in hist() function correctly?

Hi, I have a numerical vector as below x = c(92958.2014593977, -379826.025677203, 881937.411562002, 25761.5278163719, -11837.158273897, 48450.8089746788, -415505.62910869, -168462.98512054, 328504.255373387, -298966.051027528, 237133.794811816, -49610.1148173768, -92459.1170329526,

Re: [R] How to use Conda with R + RStudio Server

You may get a response here (including my poorly-informed one) but this is off topic (_do read the Posting Guide_) so you are basically barking into the darkness here. You should be asking in the RStudio community forum. As far as I am aware you have to run your RSS in a single environment, so

[R] How to use Conda with R + RStudio Server

Dear R-help Mailing List: For reproducibility, I want to use Conda + R (IRkernel), which will allow me to have within the same machine different "environments", with different versions of R installed, and specific package versions:

Re: [R] How to use depmix for HMM with intial parameters

> On 20 Sep 2017, at 11:14, niharika singhal > wrote: > > Hello, > > I have initial parameters for HMM model and I want to use depmixS4 package. > The parameters are in the form > > intial_prob_matrix=matrix(c(0.07614213, 0.45177665, 0.47208122), nrow=1, >

[R] How to use depmix for HMM with intial parameters

Hello, I have initial parameters for HMM model and I want to use depmixS4 package. The parameters are in the form intial_prob_matrix=matrix(c(0.07614213, 0.45177665, 0.47208122), nrow=1, ncol=3, byrow = TRUE) transition_matrix=matrix(c(0.4667,0.4667,0.0667,

Re: [R] How to use getSymbols() to get annual data

On 01/09/2017 7:37 PM, Yingrui Liu wrote: Dear Sir/Madam, How to use getSymbols() to get annual data? For example, I need the annual stock price of APPLE from the year 2000 to 2016. How to write the command? I only know how to get the daily data. It is:

Re: [R] How to use getSymbols() to get annual data

Reading ?getSymbols, why do think you can get yearly data if the src -- "yahoo" by default -- only contains daily data? And if you can get the daily data, why can't you just pick a day from each year to make it yearly? Note: I'm not a quantmod user, so apologies if I just don't get it. Cheers,

Re: [R] How to use getSymbols() to get annual data

I suppose that might depend what you mean by "annual data". ?yearlyReturn or ### library(quantmod) #> Loading required package: xts #> Loading required package: zoo #> #> Attaching package: 'zoo' #> The following objects are masked from 'package:base': #> #> as.Date, as.Date.numeric #>

[R] How to use getSymbols() to get annual data

Dear Sir/Madam, How to use getSymbols() to get annual data? For example, I need the annual stock price of APPLE from the year 2000 to 2016. How to write the command? I only know how to get the daily data. It is: getSymbols("AAPL",from="2000-01-01",to="2016-12-31") Thank you very much.

Re: [R] How to use apply() to fill matrix by rows or columns?

I was using OS X native R editor. I would imagine that editor is as simple and native as it gets. But, if it's truly native, why would Gmail think of my code chunk so differently. I'm just throwing it out there! I can always remove format in Gmail after pasting as a precaution. :) On Fri,

Re: [R] How to use apply() to fill matrix by rows or columns?

I am pretty sure it is not RStudio that is converting it to html... it is Gmail... but many email programs seem to do this these days so that people can send Wingdings symbols to their lolz pals, with no thought of the damage done to computer code examples. -- Sent from my phone. Please

Re: [R] How to use apply() to fill matrix by rows or columns?

Thanks for letting me know. That line does look familiar. It's interesting how I simply copy and paste from R editor can result in HTML format. On Fri, Feb 24, 2017 at 9:16 PM, Jeff Newmiller wrote: > There is a little button near the bottom of the Gmail editing box

Re: [R] How to use apply() to fill matrix by rows or columns?

There is a little button near the bottom of the Gmail editing box that switches to plain text. We can immediately tell because of the [[alternative HTML version deleted]] line when we receive it, and sometimes it loses all of the line breaks or has extra asterisks mixed in. You can look in the

Re: [R] How to use apply() to fill matrix by rows or columns?

I suppose for loop will suffice. I simply copy & paste the code from R editor. From my email, it looks plain. Is there a way to tell? On Fri, Feb 24, 2017 at 8:50 PM, Jeff Newmiller wrote: > The apply function is one of many alienate ways to write a loop. It is not >

Re: [R] How to use apply() to fill matrix by rows or columns?

The apply function is one of many alienate ways to write a loop. It is not appreciably more efficient in cpu time than a for loop. Your example creates the numbers in the loop... does your actual data get created in a loop? If so then your original code should be perfectly serviceable. If not

Re: [R] How to use apply() to fill matrix by rows or columns?

In theory, I am generating from group 5 groups of random numbers, each group has 3 samples. Isn't apply() the replacement of loops? On Fri, Feb 24, 2017 at 8:23 PM, Jeff Newmiller wrote: > What is wrong with > > dat <- matrix(rnorm(15), nrow=5, ncol = 3) > > ? > > And

Re: [R] How to use apply() to fill matrix by rows or columns?

What is wrong with dat <- matrix(rnorm(15), nrow=5, ncol = 3) ? And what is this "no loop drama" you refer to? I use loops frequently to loop around large memory gobbling chunks of code. -- Sent from my phone. Please excuse my brevity. On February 24, 2017 5:02:46 PM PST, C W

[R] How to use apply() to fill matrix by rows or columns?

Dear R, I wanted to simulate a 5 by 3 matrix which fills up by either rows or columns? I started with the following filling the matrix by rows, dat <- matrix(NA, nrow=5, ncol = 3) for(i in 1:5){ dat[i, ] <- rnorm(3) } But, R is known for no loop drama. Any suggestions? Thanks!

Re: [R] how to use vector of values to change row order of a heatmap

eans(x, na.rm = na.rm). If either is NA, no reordering will be done for the corresponding side. Cheers Petr > -Original Message- > From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Fix Ace via > R-help > Sent: Monday, November 21, 2016 9:14 PM > To: r-help@r-p

[R] how to use vector of values to change row order of a heatmap

Hello, there, R document for heatmap says that Rowv could be a vector of values to specify the row order. However, I couldn't figure out how to apply it. A simple example here:> b=as.data.frame(matrix(c(3,4,5,8,9,10,13,14,15,27,19,20),3,4)) > b   V1 V2 V3 V4 1  3  8 13 27 2  4  9 14 19 3  5 10

[R] how to use vector of values to change row order of a heatmap

Hello, there, R document for heatmap says that Rowv could be a vector of values to specify the row order. However, I couldn't figure out how to apply it. A simple example here:> b=as.data.frame(matrix(c(3,4,5,8,9,10,13,14,15,27,19,20),3,4)) > b   V1 V2 V3 V4 1  3  8 13 27 2  4  9 14 19 3  5 10

[R] how to use the fontchooser tcl tk widget ?

hello all r users, somebody has a example how to use fontchooser widget? I haven't success in my try :-( Thanks Cleber > library( tcltk ) # in R-devel, > tclVersion() [1] "8.6.4" > tclvalue( tcl('tk::fontchooser', 'show', command='' ) ) Error in (function (name, pos = -1L, envir =

Re: [R] How to use predict() so that one retains the rows that they're associated with?

om: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Richard M. Heiberger Sent: Thursday, October 20, 2016 8:05 AM To: mviljamaa Cc: r-help Subject: Re: [R] How to use predict() so that one retains the rows that they're associated with? I believe you have missing values and therefore you n

Re: [R] How to use predict() so that one retains the rows that they're associated with?

I believe you have missing values and therefore you need to use the argument glm(formula, data, na.action=na.exclude, ...) ?na.exclude The relevant line is when 'na.exclude' is used the residuals and predictions are padded to the correct length by inserting 'NA's for cases

Re: [R] How to use predict() so that one retains the rows that they're associated with?

ject.org] On Behalf Of mviljamaa > Sent: Thursday, October 20, 2016 1:40 PM > To: r-help@r-project.org > Subject: [R] How to use predict() so that one retains the rows that they're > associated with? > > I'm using predict() for my glm() logistic model, but I'm having trouble > rel

Re: [R] How to use predict() so that one retains the rows that they're associated with?

Some more context would help here but here goes anyway. You should have a vector of predictions with length equal to the number of rows in your original data-set so you can just use cbind. If that is not true check the documentation for the correct setting of na.action. If you used newdata =

[R] How to use predict() so that one retains the rows that they're associated with?

I'm using predict() for my glm() logistic model, but I'm having trouble relating the predicted results to the rows that produced them. I want to be able to plot predictions along some categorical variables. So what can I do in order to get predicted values but also know what variable values

Re: [R] how to use 97.5%, 2.5% values of parameters for next calculation

> On Oct 6, 2016, at 7:07 AM, abhishek pandey > wrote: > > Sent from RediffmailNG on Android > > From: abhishek pandeyabhishekpandey_1...@rediffmail.com > Sent:Thu, 06 Oct 2016 13:24:39 +0530 > To: r-help-ow...@r-project.org > Subject: how to use 97.5%,2.5%

[R] How to use fuzzy_partition with fuzzy_trapezoid

Hello, guys! I tried to do that: > teste = fuzzy_partition( varnames = c( "a", "b" ), FUN = fuzzy_trapezoid, > corners = c( 0, 1, 2, 3), corners = c(4, 5, 6, 7)) Error in FUN(i, ...) : argumento formal "corners" corresponde a múltiplos argumentos especificados So, how can I use

[R] How to use seas()

Dear all, I am trying to run the seas() function. In doing so, I need an object of class "ts". I tried to generate an ts object using the ts() function but it does not work. Does anyone have an idea how to generate an ts object. In addition, I get the error that there are too many observations

Re: [R] how to use AND in grepl

Please try to read my earlier comments. In the absence of a proper example with expected output I think what you are trying to achieve is: # create a sample dataframe df <- data.frame(Command=c("_localize_PD", "_localize_tre_t2", "_abdomen_t1_seq", "knee_pd_t1_localize", "pd_local_abdomen_t2"))

Re: [R] how to use AND in grepl

On Mon, May 2, 2016 at 1:01 PM, ch.elahe via R-help wrote: > I just changed all the names in Command to lowercase, then this > str_extract works fine for "pd" and "t2", but not for "PDT2". Do you have > any idea how I can bring PDT2 also in str_extract? > Looking at

Re: [R] how to use AND in grepl

I just changed all the names in Command to lowercase, then this str_extract works fine for "pd" and "t2", but not for "PDT2". Do you have any idea how I can bring PDT2 also in str_extract? On Monday, May 2, 2016 9:16 AM, Tom Wright wrote: The first thing I notice here

Re: [R] how to use AND in grepl

The first thing I notice here is that your first two subset statements are searching in an object named Command, not the column df$Command. I'm not at all sure what you are trying to achieve with the str_extract process but it is looking for the exact string 'PDT2' the vectors / dataframe formed

Re: [R] how to use AND in grepl

Yes it works, but let me explain what I am going to do. I extract all the names I want and then create a new column out of them for my plot. This is he whole thing I do: PD=subset(df,grepl("pd",Command)) //extract names in Command with only "pd" t2=subset(df,grepl("t2",Command)) //extract

Re: [R] how to use AND in grepl

Sorry for the missed braces earlier. I was typing on a phone, not the best place to conjugate regular expressions. Using the example you provided: > df=data.frame(Command=c("_localize_PD", "_localize_tre_t2", "_abdomen_t1_seq", "knee_pd_t1_localize", "pd_local_abdomen_t2")) >

Re: [R] how to use AND in grepl

Thanks Peter, you were right, the exact grepl is grepl("(.*t2.*pd.*)|(.*pd.*t2.*)",df$Command), but it does not change anything in Command, when I check the size of it by sum(grepl("(.*t2.*pd.*)|(.*pd.*t2.*)",df$Command)) the result is 0, but I am sure that the size is not 0. It seems that

Re: [R] how to use AND in grepl

On 02 May 2016, at 12:43 , ch.elahe via R-help wrote: > Thanks for your reply tom. After using > Subset(df,grepl("(.*t2.*pd.*)|(.*pd.*t2.*)"),df$Command) I get this error: > Argument "x" is missing, with no default. Actually I don't know how to fix > this. Do you have

Re: [R] how to use AND in grepl

Thanks for your reply tom. After using Subset(df,grepl("(.*t2.*pd.*)|(.*pd.*t2.*)"),df$Command) I get this error: Argument "x" is missing, with no default. Actually I don't know how to fix this. Do you have any idea? Thanks, Elahe On Saturday, April 30, 2016 7:35 PM, Tom Wright

Re: [R] how to use AND in grepl

Actually not sure my previous answer does what you wanted. Using your approach: t2pd=subset(df,grepl("t2",df$Command) & grepl("pd",df$Command)) Should work. I think the regex pattern you are looking for is: Subset(df,grepl("(.* t2.*pd.* )|(.* pd.* t2.*)",df$Command) On Sat, Apr 30, 2016,

Re: [R] how to use AND in grepl

subset(df,grepl("t2|pd",x$Command)) On Sat, Apr 30, 2016 at 2:38 PM, ch.elahe via R-help wrote: > Hi all, > > I have one factor variable in my df and I want to extract the names from > it which contain both "t2" and "pd": > > 'data.frame': 36919 obs. of 162 variables >

Re: [R] how to use AND in grepl

Your code looks fine to me. What did t2pd look like? I tried reproducing the problem in R-3.2.4(Revised) and everything worked (although the output of str() looked a bit different - perhaps you have an old version of R) > df <- data.frame(TE=1:10, TR=101:110,

[R] how to use AND in grepl

Hi all, I have one factor variable in my df and I want to extract the names from it which contain both "t2" and "pd": 'data.frame': 36919 obs. of 162 variables $TE:int 38,41,11,52,48,75,. $TR:int 100,210,548,546,. $Command :factor

Re: [R] how to use vectorization instead of for loop

> > > From: ruipbarra...@sapo.pt <ruipbarra...@sapo.pt> > > Sent: Monday, March 21, 2016 11:50 AM > > To: Stephen HK WONG > > Cc: r-help@r-project.org > > Subject: Re: [R] how to use vectorization instead of for loop &g

Re: [R] how to use vectorization instead of for loop

rom: ruipbarra...@sapo.pt <ruipbarra...@sapo.pt> > Sent: Monday, March 21, 2016 11:50 AM > To: Stephen HK WONG > Cc: r-help@r-project.org > Subject: Re: [R] how to use vectorization instead of for loop > > Hello, > > I've renamed your dataframe to 'dat'. Since ?ifelse i

Re: [R] how to use vectorization instead of for loop

ifelse ? Thanks. From: ruipbarra...@sapo.pt <ruipbarra...@sapo.pt> Sent: Monday, March 21, 2016 11:50 AM To: Stephen HK WONG Cc: r-help@r-project.org Subject: Re: [R] how to use vectorization instead of for loop Hello, I've renamed your dataframe to 'dat'. Since ?ifelse is vectorized, try

[R] how to use vectorization instead of for loop

Dear All, I have a dataframe like below but with many thousands rows, structure(list(gene_id = structure(1:6, .Label = c("0610005C13Rik", "0610007P14Rik", "0610009B22Rik", "0610009L18Rik", "0610009O20Rik", "0610010B08Rik,OTTMUSG0016609"), class = "factor"), log2.fold_change. = c(0.0114463,

Re: [R] how to use vectorization instead of for loop

Hello, I've renamed your dataframe to 'dat'. Since ?ifelse is vectorized, try dat[, 4] <- ifelse(dat[, 2] > 0, 1 * (1/dat[,3]), -1* (1/dat[,3])) Oh, and why do you multiply by 1 and by -1? It would simply be 1/dat[,3] and -1/dat[,3]. Hope this helps, Rui Barradas Quoting Stephen HK WONG

Re: [R] How to use compare.linkage in RecordLinkage package -- unexpected output

Problem resolved. I confused the true matching status and the probabilistic record linkage results. Anders Alexandersson andersa...@gmail.com On Thu, Jan 28, 2016 at 9:48 AM, Anders Alexandersson wrote: > I am using the compare.linkage function in the RecordLinkage

[R] How to use compare.linkage in RecordLinkage package -- unexpected output

I am using the compare.linkage function in the RecordLinkage package, and getting a result I know is wrong, so I know I'm misunderstanding something. I am using R 3.2.3 for x64 Windows. I am very familar with Stata but not so much with R. I can create record pairs from the blocking fields but all

[R] How to use compare.linkage in RecordLinkage package -- unexpected output

I am using the compare.linkage function in the RecordLinkage package, and getting a result I know is wrong, so I know I'm misunderstanding something. I am using R 3.2.3 for x64 Windows. I am very familar with Stata but not so much with R. I can create record pairs from the blocking fields but all

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