[R] latin hypercube sampling

Hi all, I am attempting to use latin hypercube sampling to sample different variable functions in a series of simultaneous differential equations. There is very little code online about lhs or clhs, so from different other help threads I have seen, it seems I need to create a probability density

Re: [R] cumulative sum by group and under some criteria

Hi, Thanks. I tried this code below, why does expanded dataset 'res1' has m1=3 and n1=3 , dataset 'd3' doesn't have m1=3, n1=3.   d3-structure(list(m1 = c(2, 3, 2), n1 = c(2, 2, 3), cterm1_P0L = c(0.9025, 0.857375, 0.9025), cterm1_P1L = c(0.64, 0.512, 0.64), cterm1_P0H = c(0.9025, 0.9025,

Re: [R] cumulative sum by group and under some criteria

Hi, If you don't want the m1=3, n1=3 combination in the final dataset: library(plyr) res2- join(res1,d3,by=c(m1,n1),type=inner) tail(res2) #    m1 n1 x1 y1 m n x y cterm1_P0L cterm1_P1L cterm1_P0H cterm1_P1H #235  3  2  2  1 5 4 3 1   0.857375  0.512 0.9025   0.64 #236  3  2  2  1 5 4

Re: [R] How to do a backward calculation for each record in a dataset

Hi everyone, From your helps of giving me several ideas, eventually I can solve the posted problem. Here is the R code. It can be done by applying the uniroot.all to the data frame together with the proper form of equation (slightly modification of the original equation). #Generate the sample

[R] recode data according to quantile breaks

Dear R-List, I would like to recode my data according to quantile breaks, i.e. all data within the range of 0%-25% should get a 1, 25%-50% a 2 etc. Is there a nice way to do this with all columns in a dataframe. e.g. df-

Re: [R] creating a new variable.

Hello, Try the following. levels - c(democrat, republican, other) dem - c(1,1,1,1,0,0,0,0) rep - c(1,1,1,0,0,0,0,0) other - c(1,0,0,0,0,0,0,0) party - factor(rep(levels, c(sum(dem), sum(rep), sum(other party Hope this helps, Rui Barradas Em 19-02-2013 00:01, Nicole Ford escreveu:

Re: [R] recode data according to quantile breaks

Hi Alain, The following should get you started: apply(df[,-1], 2, function(x) cut(x, breaks = quantile(x), include.lowest = TRUE, labels = 1:4)) Check ?cut and ?apply for more information. HTH, Jorge.- On Tue, Feb 19, 2013 at 9:01 PM, D. Alain wrote: Dear R-List, I would like to recode

Re: [R] foreach loop, stata equivalent

Hi Nelissa I hope the answers from Joshua and Milan helped you figure out a good solution. So basically in R you have two big parallel packages, the parallel/snow described by Joshua, or the foreach one. If you would be to use foreach, you would need probably a nested loop, which is described in

[R] introducing jitter in overlapping graphs using ggplots (plotmeans). Also sciplot.

Hi, I want to plot means with standard deviations of Total Nitrogen (TN) across 4 stations (S1-S4) and over 3 years (2007-2009). I want this plot in one panel. I do not want medians (bwplot, boxplot). I have tried a few different packages and it seems that ggplots with plotmeans was the

Re: [R] mtext unicode failure

On 19/02/2013, r-help-requ...@r-project.org r-help-requ...@r-project.org wrote: -- Message: 22 Subject: Re: [R] mtext unicode failure On 18/02/2013 14:15, e-letter wrote: Readers, How to solve this unicode input error please? On what system, in what locale?

Re: [R] foreach loop, stata equivalent

On 18.02.2013 13:39, Jamora, Nelissa wrote: Hi! I'm a recent convert from Stata, so forgive my ignorance. In Stata, I can write foreach loops (example below) foreach var of varlist p1-p14 { foreach y of varlist p15-p269 { reg `var' `y' } } It's looping p1-p15, p1-p16,

[R] Using lm to estimate a parameter?

Hi, I have a data with three variables (X,Y,Z) and I have an equation as Z=X/(1+L*X/Y) where L is a constant which need to be estimated from data. How should I write the formula in lm or is it possible to fit a linear model in this case? Thanks! Hallen [[alternative HTML version

Re: [R] Uplift modeling with R ?

Thank you Bert but i already stumbled upon that kind of article (especially those of Radcliffe, the precursor). I'm looking for something more pratical, if not a package, a piece of code i coud use in R.  But maybe, it's a good opportunity for me to work on my developer's skills ;-). Bye.

Re: [R] Random number generator used in 'runif'

2013/2/18 Daniel Nordlund djnordl...@frontier.com: -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Mauricio Zambrano-Bigiarini Sent: Monday, February 18, 2013 1:33 AM To: r-help@r-project.org Subject: [R] Random number

Re: [R] latin hypercube sampling

Aimee Kopolow alj27 at georgetown.edu writes: Hi all, I am attempting to use latin hypercube sampling to sample different variable functions in a series of simultaneous differential equations. There is very little code online about lhs or clhs, so from different other help threads I have

Re: [R] R nls results different from those of Excel ??

This thread unfortunately pushes a number of buttons: - Excel computing a model by linearization which fits to residual = log(data) - log(model) rather than wanted_residual = data - model The COBB.RES example in my (freely available but rather dated) book at

Re: [R] Using lm to estimate a parameter?

On 19.02.2013 11:23, hellen wrote: Hi, I have a data with three variables (X,Y,Z) and I have an equation as Z=X/(1+L*X/Y) where L is a constant which need to be estimated from data. How should I write the formula in lm or is it possible to fit a linear model in this case? Neither, it is

Re: [R] compare posterior samples from R2OpenBugs and R function bugs{R2WinBUGS}

On 18.02.2013 05:24, Jia Liu wrote: Hi all, I used both OpenBugs and R function bugs{R2WinBUGS} to run a linear mixed effects model based on the same data set and initial values. I got the same summary statistics but different posterior samples. However, if I order these two sets of samples,

Re: [R] Getting WinBUGS Leuk example to work from R using R2winBUGS

On 17.02.2013 08:47, Andy Cox wrote: I am trying to learn to use winBUGS from R, I have experience with R. I have managed to successfully run a simple example from R with no problems. I have been trying to run the Leuk: Survival from winBUGS examples Volume 1. I have managed to run this from

Re: [R] Using lm to estimate a parameter?

Uwe Ligges ligges at statistik.tu-dortmund.de writes: On 19.02.2013 11:23, hellen wrote: Hi, I have a data with three variables (X,Y,Z) and I have an equation as Z=X/(1+L*X/Y) where L is a constant which need to be estimated from data. How should I write the formula in lm or is it

Re: [R] R nls results different from those of Excel ??

Jeff Newmiller jdnewmil at dcn.davis.ca.us writes: Excel definitely does not use nonlinear least squares fitting for power curve fitting. It uses linear LS fitting of the logs of x and y. There should be no surprise in the OP's observation. May I be allowed to say that the general comments

[R] Cramer von Mises test for a discrete distribution

Hi,   I'm trying to carry out Cramer von Mises tests between pairs of vectors belonging to a discrete distribution (concretely frequencies from 0 to 200). However, the program crashes in the attempt. The problem seems to be that these vectors only have positive integer numbers (+ zero). When I

Re: [R] introducing jitter in overlapping graphs using ggplots (plotmeans). Also sciplot.

Hi Anna, A small point -- there is no package called ggplots. There is a package called gplots and one called ggplot2, which in earlier form was called ggplot. To see what is happening I believe we need some sample data from the three data files or some mock-up data that matches your actual

Re: [R] R nls results different from those of Excel ??

I use Excel regularly, and do not consider this a slam... it is a fact. I am aware of Solver, but the query was about trend lines generated by Excel. In general it is possible to do arbitrarily complex computations with a four function calculator, but we don't describe that as something the

Re: [R] How to do a backward calculation for each record in a dataset

On 19-02-2013, at 09:55, Prakasit Singkateera asltjoey.rs...@gmail.com wrote: Hi everyone, From your helps of giving me several ideas, eventually I can solve the posted problem. Here is the R code. It can be done by applying the uniroot.all to the data frame together with the proper form

Re: [R] Quantiles of a subset of data

bradleyd wrote Excuse the request from an R novice! I have a data frame (DATA) that has two numeric columns (YEAR and DAY) and 4000 rows. For each YEAR I need to determine the 10% and 90% quantiles of DAY. I'm sure this is easy enough, but I am a new to this. quantile(DATA$DAY,c(0.1,0.9))

Re: [R] data format

Hi, Try this: el- read.csv(el.csv,header=TRUE,sep=\t,stringsAsFactors=FALSE)  elsplit- split(el,el$st)   datetrial-data.frame(date1=seq.Date(as.Date(1930.1.1,format=%Y.%m.%d),as.Date(2010.12.31,format=%Y.%m.%d),by=day)) elsplit1- lapply(elsplit,function(x)

[R] calcMin

I tried to use calcMin with a function that uses a number of ... arguments (all args from resid on) besides the vector of parameters being fit. Same idea as optim, nlm, nlminb for which this form of ... syntax works. But with calcMin I get an error regarding unused arguments. No partial matches to

Re: [R] cumulative sum by group and under some criteria

Hello, The expansion was based on the unique values of m1 and n1 in dataset d3.  I guess that is the way it works for expansion. I am not sure what kind of results you are expecting.  Even the code that you provided will also give the combination of m1=3 and n1=3.  As I mentioned in the

[R] e1071::svm train model based on balanced accuracy

Hey For classification I use the svm from package e1071. Since I have unbalanced data sets I would like to train the model based on balanced accuracy not on just accuracy. I couldn't find an option in the svm function to do so. Does anyone know if it is possible to tell the svm which kind of

Re: [R] Quantiles of a subset of data

bradleyd wrote Thanks for your help Pete. I can almost get it to work with; by(day,year,quantile) but this only gives me 0% 25% 50% 75% 100%, not the ones I'm looking for, 10% and 90%. I have tried; by(day,year,quantile(c(0.1, 0.9))) but this is rejected by Error in FUN(X[[1L]],

[R] Any R package to do the harmonic analysis

Hi R Users, I was wondering if there is any R package available to do the harmonic analysis of tide. Any suggestion is highly appreciated. Janesh [[alternative HTML version deleted]] __ R-help@r-project.org mailing list

Re: [R] Cramer von Mises test for a discrete distribution

On Tue, Feb 19, 2013 at 2:49 PM, Santiago Guallar sgual...@yahoo.com wrote: Hi, I'm trying to carry out Cramer von Mises tests between pairs of vectors belonging to a discrete distribution (concretely frequencies from 0 to 200). However, the program crashes in the attempt. The problem seems

[R] Converting the data in year month day hour and minutes to date

Hi , I am trying to convert the date as factor to date using as.date function in R. I have the date in the following format 2008-01-01 02:30 I tried to use the following command : as.Date(mydata$Date, format=%y-%m-%d ) Can somebody help me with this ? I was able to convert the

[R] calculating seconds

Dear R People: I'm looking at some data which has the time in seconds since 1992/10/8, 15:15:42.5 Are there any functions currently available to translate this or should I just do my own? I figured that I'd check first. Thanks, Erin -- Erin Hodgess Associate Professor Department of Computer

Re: [R] cumulative sum by group and under some criteria

Hi,Another thing you could do will be to use ?paste() #for example. #d3 dataset  paste(d3$m1,d3$n1) #[1] 2 2 3 2 2 3 #then you use that instead of unique(d3$m1), unique(d3$n1) in the loop. I didn't try it.  But, that is one possibility. You still didn't show me the results you expected in the

Re: [R] cumulative sum by group and under some criteria

Hi, Try this: res1- do.call(rbind,lapply(paste(d3$m1,d3$n1),function(m1) do.call(rbind,lapply(0:(as.numeric(substr(m1,1,1))-1),function(x1) do.call(rbind,lapply(0:(as.numeric(substr(m1,3,3))-1),function(y1)

Re: [R] calculating seconds

On 19.02.2013 18:52, Erin Hodgess wrote: Dear R People: I'm looking at some data which has the time in seconds since 1992/10/8, 15:15:42.5 Just ask R to strptime(1992/10/8,15:15:42.5, %Y/%m/%d,%H:%M:%OS) + NumberOfSeconds and you get the actual date after the given amount of

Re: [R] Converting the data in year month day hour and minutes to date

On 19.02.2013 18:47, Janesh Devkota wrote: Hi , I am trying to convert the date as factor to date using as.date function in R. I have the date in the following format 2008-01-01 02:30 I tried to use the following command : as.Date(mydata$Date, format=%y-%m-%d ) Can somebody help me

Re: [R] Converting the data in year month day hour and minutes to date

jdbaba wrote Hi , I am trying to convert the date as factor to date using as.date function in R. I have the date in the following format 2008-01-01 02:30 I tried to use the following command : as.Date(mydata$Date, format=%y-%m-%d ) Can somebody help me with this

Re: [R] calculating seconds

Your subject line says you want to calculate seconds... the body of your message says you want to translate seconds (to something unspecified). I am not sure how we are supposed to respond. Can you give us a short example of what you have and what you want using R syntax?

Re: [R] Converting the data in year month day hour and minutes to date

Hello, Try the following. x - 2008-01-01 02:30 as.POSIXct(x, format = %Y-%m-%d %H:%M) Hope this helps, Rui Barradas Em 19-02-2013 17:47, Janesh Devkota escreveu: Hi , I am trying to convert the date as factor to date using as.date function in R. I have the date in the following format

Re: [R] Converting the data in year month day hour and minutes to date

It is possible to squeeze a square peg into a round hole, but often you will not be satisfied with the result. Date is for... surprise, dates. You may want to use the chron package or the POSIXct type. The R Journal of June 2004 (Volume 4/1) R Help Desk column is recommended reading.

Re: [R] Quantiles of a subset of data

bradleyd wrote That does it, thanks. Do you think you help me a little bit further? I actually have 4 columns, YEAR, DAY, TEMP , and IBI. They are all numeric. I need to calculate the average TEMP and IBI values between the 10% and 90% quantiles for each YEAR. The code *

Re: [R] recode data according to quantile breaks

HI Alain, Try this: df.breaks-data.frame(id=df[,1],sapply(df[,-1],function(x) findInterval(x,quantile(x),rightmost.closed=TRUE)),stringsAsFactors=FALSE) df.breaks #   id a b c #1 x01 1 1 1 #2 x02 1 1 1 #3 x03 2 2 2 #4 x04 3 3 3 #5 x05 4 4 4 #6 x06 4 4 4 A.K. - Original Message - From:

Re: [R] Converting the data in year month day hour and minutes to date

You need to convert the factor to character. as.Date( as.character(mydata$Date), %Y-%m-%d) should do it. John Kane Kingston ON Canada -Original Message- From: janesh.devk...@gmail.com Sent: Tue, 19 Feb 2013 11:47:04 -0600 To: r-help@r-project.org Subject: [R] Converting the data

[R] make a list with names with s/lapply

Hello, I open some files in a directory and get a list. open.list - sapply (namen, function (x) {file - list.files (ddir, pattern=x, full.names=TRUE) # namen is vector and each element detects a special file to open file - read.table (file)

Re: [R] introducing jitter in overlapping graphs using ggplots (plotmeans). Also sciplot.

On 02/19/2013 10:38 PM, Anna Zakrisson wrote: Hi, I want to plot means with standard deviations of Total Nitrogen (TN) across 4 stations (S1-S4) and over 3 years (2007-2009). I want this plot in one panel. I do not want medians (bwplot, boxplot). ... Hi Anna, From your description, the

Re: [R] make a list with names with s/lapply

Hello, I'm not sure I understabd, but if the names are in 'namen' then the following might do what you want. names(open.list) - namen Hope this helps, Rui Barradas Em 19-02-2013 18:09, Hermann Norpois escreveu: Hello, I open some files in a directory and get a list. open.list - sapply

Re: [R] Quantiles of a subset of data

bradleyd wrote Thanks Pete. The TRIM argument in the MEAN function tells me how to trim off decimal points, but I am lost as to how to append the mean values of TEMP and IBI between the 10% and 90% quantiles of DAY in each YEAR. DAY is the julian date that an event occurred in certain

[R] CARET. Relationship between data splitting trainControl

I have carefully read the CARET documentation at: http://caret.r-forge.r-project.org/training.html, the vignettes, and everything is quite clear (the examples on the website help a lot!), but I am still a confused about the relationship between two arguments to trainControl: method index and the

Re: [R] cumulative sum by group and under some criteria

this is the data I expected suppose that I have a dataset 'd' m1 n1A B C D 1 2 2 0.9025000.640 0.90250.64 2 3 2 0.8573750.512 0.90250.64 I want to add x1 (from 0 to m1), y1(from 0 to n1), m (range from m1+2 to 7-n1), n(from n1+2 to

Re: [R] cumulative sum by group and under some criteria

Hi, suppose that I have a dataset 'd'    m1  n1    A B C D 1  2  2   0.902500    0.640   0.9025    0.64 2  3  2   0.857375    0.512   0.9025    0.64 I want to add  x1 (from 0 to m1), y1(from 0 to n1), m (range from m1+2 to 7-n1), n(from n1+2 to 9-m), x (x1 to x1+m-m1),

[R] Help reshaping a dataset with multiple tuples per row

I have a dataset which contains several multi-column measurement sets per row. Col 1 identifies patient: Col1Col2Col3 Col 4Col 5 Col 6 Col7 ... Patient Treatment Outcome Advice Treatment Outcome Advice P1 T1 O1

Re: [R] Help reshaping a dataset with multiple tuples per row

Hi, Try this: dat1- read.table(text= Patient  Treatment Outcome  Advice Treatment  Outcome  Advice P1    T1  O1  A1    T2    O2  A2 ,sep=,header=TRUE,stringsAsFactors=FALSE) names(dat1)[-1]-paste(gsub(\\..*,,names(dat1)[-1]),_,rep(1:2,each=3),sep=)  

[R] Seeing Global Workspace and dealing with attach and detach

Hi, When writing a script, I often start with: library(ISwR) attach(thuesen) Then write some more code, testing it as I write to see if it runs. Then, at the end, a final: detach(thuesen) However, what happens is that I often get errors, which cause an attach, but no subsequent detach. Now,

Re: [R] Any R package to do the harmonic analysis

Have a look thru the Time Series task view... http://cran.r-project.org/web/views/TimeSeries.html -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Janesh Devkota Sent: Wednesday, 20 February 2013 5:52a To: r-help@r-project.org

Re: [R] Seeing Global Workspace and dealing with attach and detach

In general, creating variables while attached leads to problems such as you describe. Normally the recommendation is to avoid the use of attach and detach entirely in favor of explicit reference to the data frame using [[]], [,], $, and the data= argument supported by many functions.

Re: [R] reading data

Hi, Try this: files-paste(MSMS_,23,PepInfo.txt,sep=) read.data-function(x) {names(x)-gsub(^(.*)\\/.*,\\1,x); lapply(x,function(y) read.table(y,header=TRUE,sep = \t,stringsAsFactors=FALSE,fill=TRUE))}

Re: [R] Seeing Global Workspace and dealing with attach and detach

Jeff Newmiller jdnewmil at dcn.davis.ca.us writes: In general, creating variables while attached leads to problems such as you describe. Normally the recommendation is to avoid the use of attach and detach entirely in favor of explicit reference to the data frame using [[]], [,], $, and the

[R] Why R simulation gives same random results?

Hi, list I am doing 100,000 iterations of Bayesian simulations. What I did is I split it into 4 different R sessions, each one runs 25,000 iteration. But two of the sessions gave the simulation result. I did not use any set.seed(). What is going on here? Thanks, Mike [[alternative

[R] 'gmm' package: How to pass controls to a numerical solver used in the gmm() function?

Hello -- The question I have is about the gmm() function from the 'gmm' package (v. 1.4-5). The manual accompanying the package says that the gmm() function is programmed to use either of four numerical solvers -- optim, optimize, constrOptim, or nlminb -- for the minimization of the GMM

Re: [R] lattice 3x3 plot: force common y-limits accross rows and align x-axes

Duncan and Bert, Thank you very much for your help with my question.  It's very much appreciated. I used your suggestions to get the plot I needed: * 3x3 lattice of dotplots, * x-limits are the same for all panels, * y-limits and y-ticks in each row are the same, * y-limits and

Re: [R] 'gmm' package: How to pass controls to a numerical solver used in the gmm() function?

On Feb 19, 2013, at 5:25 PM, Malikov, Emir wrote: Hello -- The question I have is about the gmm() function from the 'gmm' package (v. 1.4-5). The manual accompanying the package says that the gmm() function is programmed to use either of four numerical solvers -- optim, optimize,

Re: [R] Problems with line types in plots saved as PDF files

Hi, On Tue, Feb 19, 2013 at 7:09 PM, Ian Renner ian_ren...@yahoo.com wrote: Hi, I am trying to save a plot as a PDF with different line types. In the example below, R displays the plot correctly with 2 curves in solid lines, 2 curves in dashed lines and 1 curve as a dotted line. However,

Re: [R] Problems with line types in plots saved as PDF files

Hi Ista, I'm using Adobe Reader XI. It's good to hear that the plot was produced correctly and that it is Adobe that is failing to represent it properly. Thanks! Ian From: Ista Zahn istaz...@gmail.com Cc: r-help@r-project.org r-help@r-project.org Sent:

Re: [R] How to do a backward calculation for each record in a dataset

Hi Berend, Your method is really much better. Thank you very much. (Yes I also forgot to add the $root at the end.) Best, Prakasit On Tue, Feb 19, 2013 at 10:51 PM, Berend Hasselman b...@xs4all.nl wrote: On 19-02-2013, at 09:55, Prakasit Singkateera asltjoey.rs...@gmail.com wrote: Hi

Re: [R] Problems with line types in plots saved as PDF files

On Tue, Feb 19, 2013 at 10:20 PM, Ian Renner ian_ren...@yahoo.com wrote: Hi Ista, I'm using Adobe Reader XI. It's good to hear that the plot was produced correctly and that it is Adobe that is failing to represent it properly. Right, well I just installed acroread (adobe reader for linux) and

Re: [R] Problems with line types in plots saved as PDF files

Hi, I also see the expected lines on your pdf file with Evince (3.2.1) using poppler/cairo (0.18.0). Regards, Pascal Le 20/02/2013 09:09, Ian Renner a écrit : Hi, I am trying to save a plot as a PDF with different line types. In the example below, R displays the plot correctly with 2

Re: [R] Problems with line types in plots saved as PDF files

On Feb 19, 2013, at 7:40 PM, Ista Zahn wrote: On Tue, Feb 19, 2013 at 10:20 PM, Ian Renner ian_ren...@yahoo.com wrote: Hi Ista, I'm using Adobe Reader XI. It's good to hear that the plot was produced correctly and that it is Adobe that is failing to represent it properly. Right, well I

Re: [R] Problems with line types in plots saved as PDF files

Ian No differences with Adobe X with the following windows(6,6) #pdf(file = TestPlot.pdf, 6, 6) #{ plot(b, l, type = l, ylim = c(y.min, y.max), lwd = 2, xlab = expression(beta), ylab = , col = green, yaxt = n, xaxt = n) points(b, p, type = l, lty = dotted, lwd = 2, col = red) points(b,

[R] generate variable y to produce excess zero in ZIP analysis

Dear Mr/Mrs I am Lili Puspita Rahayu, student from magister third level of Statistics in Bogor Agriculture University. Mr/ Mrs, now I'm analyzing the Zero inflated Poisson (ZIP), which is a solution of the Poisson regression where the response variable (Y) has zero excess. ZIP now I was doing

Re: [R] compare posterior samples from R2OpenBugs and R function bugs{R2WinBUGS}

On Tue, Feb 19, 2013 at 7:18 AM, Uwe Ligges lig...@statistik.tu-dortmund.de wrote: On 18.02.2013 05:24, Jia Liu wrote: Hi all, I used both OpenBugs and R function bugs{R2WinBUGS} to run a linear mixed effects model based on the same data set and initial values. I got the same summary