Re: [R] An important question about running MCMC

On Thu, Dec 13, 2012 at 3:22 AM, Chenyi Pan cp...@virginia.edu wrote: Dear officer I have a question concerning running R when I am doing my research. Can you help me to figure that out? I am now running a MCMC iteration in the R program. But it is always stucked in some loop. This cause big

[R] remove NA in df results in NA, NA.1 ... rows

Good morning! I have the following data frame (df): X.outer Y.outer X.PAD1 Y.PAD1 X.PAD2 Y.PAD2 X.PAD3 Y.PAD3 X.PAD4 Y.PAD4 73 574690.0 179740.0 574690.2 179740.0 574618.3 179650 574729.2 179674 574747.1 179598 74 574680.6 179737.0 574693.4 179740.0 574719.0 179688 574831.8

[R] how to aggregate the data ?

HI, now I have dataset: Product Price_LC.1 Price_LC.2 Price_elasticity.1 Price_elasticity.2 Mean_Price Mean_Price_elasticity Trade_Price_Band Country 1 100 357580.1 527483.6 -4.1498383 -2.8459564 473934.0

Re: [R] remove NA in df results in NA, NA.1 ... rows

Hi Raphael, see below. I have the following data frame (df): ... df2 X.PAD2 Y.PAD2 73 574618.3 179650 74 574719.0 179688 75 574719.0 179688 76 574723.5 179678 77 574724.9 179673 78 574747.1 179598 79 574641.8 179570 80 574639.6 179573 81 574618.3 179650 82 NA NA 83 NA

Re: [R] remove NA in df results in NA, NA.1 ... rows

df2 - df2[!is.na(df2),] isn't doing what you want it to do because df2 is a data.frame and not a vector to solve your problem, review http://stackoverflow.com/questions/4862178/r-remove-rows-with-nas-in-data-frame On Thu, Dec 13, 2012 at 3:20 AM, raphael.fel...@art.admin.ch wrote: Good

[R] How to aggregate the dataset?

HI, I want to transform the following dataset Product Price_LC.1 Price_LC.2 Price_elasticity.1 Price_elasticity.2 Mean_Price Mean_Price_elasticity Trade_Price_Band Country 100 35 52 -4.14 -2.84 47 -3.69

Re: [R] remove NA in df results in NA, NA.1 ... rows

is.na(df2) is not doing what you think it is doing. Perhaps you should read ?na.omit. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#.

Re: [R] create a color palette with custom ranges between colors

Thank you Nicole! I did it with the color.palette function in the link you gave me. I added then in my levelplot function a sequence with at: at=seq(-40,40,1) And it works quite good. Thanks again Nicole. Merci à toi aussi pascal, et vive le CRC ainsi que le grand C. C. ! ;) --

Re: [R] possible bug in function 'mclapply' of package parallel

Mailing list ate the attachment. Can you send it plain text (if short) or post it somewhere online? Michael On Dec 13, 2012, at 1:54 AM, Asis Hallab asis.hal...@gmail.com wrote: Dear parallel users and developers, I might have encountered a bug in the function 'mclapply' of package

[R] how to aggregate the dataset

HI, Sorry for messing up.. I want to transform the following dataset: product min_price max_price mean_price country price_band 11 34 50 40 VN 0-300 22 10 30 15 VN 0-300 Into:

Re: [R] how to aggregate the dataset

Really sorry for messing up. I want to transform: product min_price max_price mean_price country price_band 11 34 50 40 VN 0-300 2210 30

Re: [R] How do you use agrep inside a loop

Thank you all it worked after I checked for length of agrep's result :) On Tue, Dec 11, 2012 at 6:11 PM, Rui Barradas ruipbarra...@sapo.pt wrote: Hello, Inline. Em 11-12-2012 12:04, surekha nagabhushan escreveu: Rui, I have initialized it...doesn't seem to help... result_vector -

Re: [R] how to aggregate the dataset

Hello, maybe something like this? range - with(dat, paste0([, min_price, ,, max_price, ])) dat2 - with(dat, data.frame(product = product, VN = mean_price, range = range, price_band = price_band)) Unless it's a printing problem and you really want the range below VN. Hope this helps, Rui

Re: [R] Running MCMC in R

Why don't you use one of the existing MCMC packages. There are many to choose from... On Wed, Dec 12, 2012 at 10:49 PM, Chenyi Pan cp...@virginia.edu wrote: Dear all I am now running a MCMC iteration in the R program. But it is always stucked in some loop. This cause big problems for my

[R] max_prepared_stmt_count exceeded using RODBC + 64-bit win7

Hi I am running R2.15.2 64-bit on Windows 7, using RODBC 1.3-6, MySQL5.5.20, MySQL Connector 5.5.2 - these are the latest 64-bit versions AFAIK. sqlQuery and sqlSave work fin as expected, but in a long session with a few sqlSave() calls, I get an error, for example: Error in sqlSave(channel =

[R] Installing Packages from a Local Repository

Hi everyone, I've followed the instructions from R-Admin Section 6.6 for creating a local repository. I've modified my Rprofile.site file to add the local repository to my repos, but I haven't been able to successfully install my package from the repo. Here's the code that I've run.

Re: [R] neural net

Thanks for your reply. I have compared my data with some other which works and I cannot see the difference... The structure of my data is shown below: str(data) 'data.frame': 19 obs. of 7 variables: $ drug: Factor w/ 19 levels A,B,C,D,..: 1 2 3 4 5 6 7 8 9 10 ... $ param1 : int 111

[R] How to create multiple country's data into multiple sheets of one excel

HI, I have large dataset of many countries. I have written the program to run through each country to generate one output for each country. I want to put the output like this: one sheet has output for one country. How do I achieve it by r. I have tried this: library(xlsx) write.xlsx(nnn,

Re: [R] remove NA in df results in NA, NA.1 ... rows

You can use complete.cases: df - df[complete.cases(df), ] On Thu, Dec 13, 2012 at 3:20 AM, raphael.fel...@art.admin.ch wrote: Good morning! I have the following data frame (df): X.outer Y.outer X.PAD1 Y.PAD1 X.PAD2 Y.PAD2 X.PAD3 Y.PAD3 X.PAD4 Y.PAD4 73 574690.0 179740.0

Re: [R] How to create multiple country's data into multiple sheets of one excel

use append = TRUE inside your write.xlsx() function On Thu, Dec 13, 2012 at 7:52 AM, Tammy Ma metal_lical...@live.com wrote: HI, I have large dataset of many countries. I have written the program to run through each country to generate one output for each country. I want to put the

Re: [R] How to create multiple country's data into multiple sheets of one excel

I use the XLConnect package to write out multiple sheets to an Excel workbook On Thu, Dec 13, 2012 at 7:52 AM, Tammy Ma metal_lical...@live.com wrote: HI, I have large dataset of many countries. I have written the program to run through each country to generate one output for each country.

Re: [R] VarimpAUC in Party Package

Error: could not find function varimpAUC Was this function NOT included in the Windows binary I downloaded and installed? Which windows binary are you talking about? The R installer, the Party .zip or something else? S Ellison

Re: [R] Running MCMC in R

?try ?tryCatch (if the suggestion to use an MCMC package does not fix your problem). -- Bert On Wed, Dec 12, 2012 at 7:49 PM, Chenyi Pan cp...@virginia.edu wrote: Dear all I am now running a MCMC iteration in the R program. But it is always stucked in some loop. This cause big problems for

[R] Webinar: Advances in Gradient Boosting: the Power of Post-Processing. TOMORROW, 10-11 a.m., PST

Webinar: Advances in Gradient Boosting: the Power of Post-Processing TOMORROW: December 14, 10-11 a.m., PST Webinar Registration: http://2.salford-systems.com/gradientboosting-and-post-processing/ Course Outline: I. Gradient Boosting and Post-Processing: o What is missing from Gradient

Re: [R] Running MCMC in R

I am now running a MCMC iteration in the R program. But it is always stucked in some loop. I never like it when folk just say Please read and follow the posting guide referenced in every R help email but ... please, read and follow the posting guide referenced in every R help email if you

[R] abline of an lm fit not correct

Hello fellow R-users,   I’m stuck with something i think is pretty stupid, but i can’t find out where i’m wrong, and it’s turning me crazy!   I am doing a very simple linear regression with Northing/Easting data, then I plot the data as well as the regression line :  

Re: [R] abline of an lm fit not correct

You don't provide a reproducible example, but my first guess is that the print method is rounding what appears on the screen, so you aren't actually using the slope and intercept. See ?print.default and the digits argument under ?options for more. Why do you need to copy and paste the

[R] Pairwise deletion in a linear regression and in a GLM ?

Dear useRs, In a thesis, I found a mention of the use of pairwise deletion in linear regression and GLM (binomial family). The author said that he has used R to do the statistics, but I did not find the option allowing pairwise deletion in both lm and glm functions. Is there somewhere a package

[R] recursion depth limitations

Hello List, I am aware that one can set with recursion depth 'options(expressions = #)', but it has 500K limit. Why do we have a 500K limit on this? While some algorithms are only solvable feasibility with recursion and 500K sounds not too much i.e. graph algorithms for example dependency trees

Re: [R] Pairwise deletion in a linear regression and in a GLM ?

Hi Arnaud, A quick help search of lm or glm tells you that 'the factory-fresh default is na.omit'. If you then look up 'na.omit', you'll read that it 'returns the object with incomplete cases removed'. So, pairwise deletion is the default option in both lm and glm. On a related note, it goes

[R] How to select a subset data to do a barplot in ggplot2

Hi,everybody I have a dataframe like this FID IID STATUS 14621live 14628dead 24631live 24632live 24633live 24634live 64675live 64679dead 104716dead 104719live 104721dead 114726live 114728

Re: [R] remove NA in df results in NA, NA.1 ... rows

Hi, You could use either: ?na.omit() #the option was already suggested #or df2[complete.cases(df2),] #In this case, this should also work sapply(df2,function(x) x[!is.na(x)]) #or  apply(df2,2,function(x) x[!is.na(x)]) #If the NAs are not in the same rows, then the ouptut will be a list with

Re: [R] how to aggregate the dataset

Hi, You could try this: dat3-read.table(text= product min_price  max_price mean_price country  price_band 11  34  50  40    VN    0-300 22  10  30  15    VN    0-300 ,sep=,header=TRUE,stringsAsFactors=FALSE)

[R] Repeat elements of matrix based on vector counts

I have two dataframes (df) that share a column header (plot.id). In the 1st df, plot.id records are repeated a variable number of times based on the number of trees monitored within each plot. The 2nd df only has a single record for each plot.id, and contains a variable named load that is

[R] How do I make a loop to extract a column from multiple lists and then bind them together to make a new matrix?

Hi! I am new to looping and R in general; and I have sent wy to much time on this one problem and am about a hair away from doing it manually for the next two days. So, there is a package that while calculating the statistic creates lists (that look like matrices) in the background. Each

Re: [R] Running MCMC in R

And if by stuck you mean taking too long a time you can generate an error at a given time limit by using setTimeLimit() and tryCatch() or try() can catch that error. E.g. timeOut - function (expr, cpu = Inf, elapsed = Inf) { setTimeLimit(cpu = cpu, elapsed = elapsed, transient =

Re: [R] Pairwise deletion in a linear regression and in a GLM ?

Hi Jose, To my perception na.omit is different from a pairwise deletion. With na.omit, you omit totally that case if there is a missing value for one of the variable you consider in the model. In the pairwise deletion, the case with some missing value is kept and values that are not missing are

Re: [R] Repeat elements of matrix based on vector counts

Hi Sarah, If I understand your requirements correctly, the easiest thing to do is approach it from a different direction: df3a - merge(df1, df2) But you can also use rep for this simple example because plot.id in df2 is sorted: nindex - table(df1$plot.id) df3b - df2[rep(1:length(nindex),

Re: [R] Repeat elements of matrix based on vector counts

Hello, Something like this? rep(df2$load, table(df1$plot.id)) Hope this helps, Rui Barradas Em 13-12-2012 14:15, Sarah Haas escreveu: I have two dataframes (df) that share a column header (plot.id). In the 1st df, plot.id records are repeated a variable number of times based on the number

Re: [R] Repeat elements of matrix based on vector counts

Hi, Try ?merge() or ?join() from library(plyr) res-merge(df1,df2,by=plot.id)  head(res,6) #  plot.id tree.tag load #1   plot1  111   17 #2   plot1  112   17 #3   plot1  113   17 #4   plot2  222    6 #5   plot2  223    6 #6   plot3  333   24 A.K - Original Message

Re: [R] Pairwise deletion in a linear regression and in a GLM ?

Sorry, Arnaud, I misinterpreted the question. There isn't a built-in option in lm or glm to run pairwise deletion, but in the 'psych' package you can run regressions on covariance matrices rather than on raw data. So, first, you can obtain a covariance matrix by cov() with the option

Re: [R] Pairwise deletion in a linear regression and in a GLM ?

Thanks Jose, but I doubt that the author of these analysis used such a complex approach. Arnaud 2012/12/13 Jose Iparraguirre jose.iparragui...@ageuk.org.uk Sorry, Arnaud, I misinterpreted the question. There isn’t a built-in option in lm or glm to run pairwise deletion, but in the

[R] subsetting time series

Hello, my series of dates look like [1] 2012-05-30 18:30:00 UTC 2012-05-30 19:30:00 UTC [3] 2012-05-30 20:30:00 UTC 2012-05-30 21:30:00 UTC [5] 2012-05-30 22:30:00 UTC 2012-05-30 23:30:00 UTC [7] 2012-05-31 00:30:00 UTC 2012-05-31 01:30:00 UTC [9] 2012-05-31 02:30:00 UTC 2012-05-31

Re: [R] [R-sig-hpc] recursion depth limitations

On Dec 13, 2012, at 10:45 AM, Suzen, Mehmet wrote: Hello List, I am aware that one can set with recursion depth 'options(expressions = #)', but it has 500K limit. Why do we have a 500K limit on this? Because it's far beyond what you can handle without changing a lot of other things. 500k

Re: [R] How to select a subset data to do a barplot in ggplot2

Hi, May be this: p-ggplot(subset(dat1,STATUS!=nosperm),aes(x=FID))  p+geom_bar(aes(x=factor(FID),y=..count..,fill=STATUS)) A.K. - Original Message - From: Yao He yao.h.1...@gmail.com To: r-help@r-project.org Cc: Sent: Thursday, December 13, 2012 7:38 AM Subject: [R] How to select a

Re: [R] subsetting time series

Is this a one off or not? Why not do it manually? If you need to write a function some example data would be helpful. On Thu, Dec 13, 2012 at 10:52 AM, m p mzp3...@gmail.com wrote: Hello, my series of dates look like [1] 2012-05-30 18:30:00 UTC 2012-05-30 19:30:00 UTC [3] 2012-05-30

Re: [R] subsetting time series

On Dec 13, 2012, at 8:52 AM, m p wrote: Hello, my series of dates look like [1] 2012-05-30 18:30:00 UTC 2012-05-30 19:30:00 UTC [3] 2012-05-30 20:30:00 UTC 2012-05-30 21:30:00 UTC [5] 2012-05-30 22:30:00 UTC 2012-05-30 23:30:00 UTC [7] 2012-05-31 00:30:00 UTC 2012-05-31 01:30:00 UTC [9]

Re: [R] More efficient use of reshape?

On Dec 13, 2012, at 9:16 AM, Nathan Miller wrote: Hi all, I have played a bit with the reshape package and function along with melt and cast, but I feel I still don't have a good handle on how to use them efficiently. Below I have included a application of reshape that is rather clunky

Re: [R] More efficient use of reshape?

Sorry David, In my attempt to simplify example and just include the code I felt was necessary I left out the loading of ggplot2, which then imports reshape2, and which was actually used in the code I provided. Sorry to the mistake and my misunderstanding of where the reshape function was coming

[R] CPOS from cwhmisc package not found

Hi: I wonder if anyone can help me about cpos function not found error: : path.package(cwhmisc, quiet = FALSE) [1] C:/Users/slee/Documents/R/win-library/2.15/cwhmisc So I have package cwhmisc where there is cpos function. But I got error: cpos(ab,b,1) Error: could not find function cpos Then I

Re: [R] subsetting time series

Hi, Try this: seq1-seq(from=as.POSIXct(2012-05-30 18:30:00,tz=UTC),to=as.POSIXct(2012-05-31 02:30:00,tz=UTC),by=1 hour) seq2-seq(from=as.POSIXct(2012-05-31 00:30:00,tz=UTC),to=as.POSIXct(2012-05-31 08:30:00,tz=UTC),by=1 hour) seq3-seq(from=as.POSIXct(2012-05-31

Re: [R] abline of an lm fit not correct

Easting and northing data uses numbers requiring more digits than R's default of 7. In all the years I've used R, the only time I've needed to adjust the default digits is with easting and northing data. Try something like options(digits = 11) HTH On Thu, 13-Dec-2012 at 03:22PM +,

Re: [R] How do I make a loop to extract a column from multiple lists and then bind them together to make a new matrix?

Try this ... MDD.mean.s10 - sapply(MC_MDD.noNA$results, function(x) x[[2]][, 7]) Jean On Thu, Dec 13, 2012 at 8:31 AM, Corinne Lapare corinnelap...@gmail.comwrote: Hi! I am new to looping and R in general; and I have sent wy to much time on this one problem and am about a hair away

Re: [R] subsetting time series

Thats works perfectly, thanks a lot, Mark On Thu, Dec 13, 2012 at 11:34 AM, arun smartpink...@yahoo.com wrote: Hi, Try this: seq1-seq(from=as.POSIXct(2012-05-30 18:30:00,tz=UTC),to=as.POSIXct(2012-05-31 02:30:00,tz=UTC),by=1 hour) seq2-seq(from=as.POSIXct(2012-05-31

[R] Available Memory

I have a large database on sql Server 2012 Developers edition,  Windows 7 ultimate edition, some of my tables are as large as 10GB, I am running R15.2 with a 64-bit build I have been connecting fine to the database and extracting info.  but  it seams this was the first time I tried to pull a

Re: [R] CPOS from cwhmisc package not found

On Dec 13, 2012, at 10:56 AM, Shirley Lee wrote: Hi: I wonder if anyone can help me about cpos function not found error: : path.package(cwhmisc, quiet = FALSE) [1] C:/Users/slee/Documents/ R/win-library/2.15/cwhmisc So I have package cwhmisc where there is cpos function. But I got error:

Re: [R] [R-sig-hpc] recursion depth limitations

On 13 December 2012 17:52, Simon Urbanek simon.urba...@r-project.org wrote: Because it's far beyond what you can handle without changing a lot of other things. 500k expressions will require at least about 320Mb of stack (!) in the eval() chain alone -- compare that to the 8Mb stack size which

[R] changing character strings with hash marks

Hi R users, I am quite new to R and I don't know how to deal with this (surely) easy issue. I need to replace words in sentences with as many hash marks as the number of characters per each word, as in the following example: Mary plays football # Any suggestion about the

Re: [R] changing character strings with hash marks

On 13.12.2012 22:30, simona mancini wrote: Hi R users, I am quite new to R and I don't know how to deal with this (surely) easy issue. I need to replace words in sentences with as many hash marks as the number of characters per each word, as in the following example: Mary plays football

Re: [R] changing character strings with hash marks

Simona: If you intend to work with text, you need to learn about regular expressions. There are many tutorials on this topic on the web. Go search. Then learn about how R handles them via: ?regex ## at the R prompt Then ask your question more clearly, although by this time you'll probably have

Re: [R] [R-sig-hpc] recursion depth limitations

Hello. Inline. Em 13-12-2012 21:31, Suzen, Mehmet escreveu: On 13 December 2012 17:52, Simon Urbanek simon.urba...@r-project.org wrote: Because it's far beyond what you can handle without changing a lot of other things. 500k expressions will require at least about 320Mb of stack (!) in the

[R] replace parenthetical phrases in a string

R-helpers, I have a vector of character strings in which I would like to replace each parenthetical phrase with a single space, . For example if I start with x, I would like to end up with y. x - c(My toast=bog(keep=3 no=4) and eggs(er34)omit=32, dogs have ears, cats have tails (and ears,

Re: [R] replace parenthetical phrases in a string

My apologies. I sent too soon! I did a bit more digging, and found a solution on the R-help archives. y - gsub( *\\([^)]*\\) *, , x) Jean On Thu, Dec 13, 2012 at 4:53 PM, Adams, Jean jvad...@usgs.gov wrote: R-helpers, I have a vector of character strings in which I would like to replace

[R] duplicated.data.frame() and POSIXct with DST shift

Hi, I encountered the behavior, that the duplicated method for data.frames gives false positives if there are columns of class POSIXct with a clock shift from DST to standard time. time - as.POSIXct(2012-10-28 02:00, tz=Europe/Vienna) + c(0, 60*60) time [1] 2012-10-28 02:00:00 CEST 2012-10-28

Re: [R] changing character strings with hash marks

Hi, You could also use: gsub(\\w,#,Mary plays football) #[1] # #or gsub([A-Za-z], #, Mary plays football) A.K. - Original Message - From: Uwe Ligges lig...@statistik.tu-dortmund.de To: simona mancini mancinisim...@yahoo.it Cc: r-help@r-project.org r-help@r-project.org

[R] Combined Marimekko/heatmap

Hi all, I'm trying to figure out a way to create a data graphic that I haven't ever seen an example of before, but hopefully there's an R package out there for it. The idea is to essentially create a heatmap, but to allow each column and/or row to be a different width, rather than having

Re: [R] neural net

Hi Thanks for your reply. I have compared my data with some other which works and I cannot see the difference... The structure of my data is shown below: str(data) 'data.frame': 19 obs. of 7 variables: $ drug: Factor w/ 19 levels A,B,C,D,..: 1 2 3 4 5 6 7 8 9 10 ... $ param1 :

Re: [R] duplicated.data.frame() and POSIXct with DST shift

On Dec 13, 2012, at 1:43 PM, Tobias Gauster wrote: Hi, I encountered the behavior, that the duplicated method for data.frames gives false positives if there are columns of class POSIXct with a clock shift from DST to standard time. time - as.POSIXct(2012-10-28 02:00, tz=Europe/Vienna) +

Re: [R] How to select a subset data to do a barplot in ggplot2

Hi: The simplest way to do it is to modify the input data frame by taking out the records not having status live or dead and then redefining the factor in the new data frame to get rid of the removed levels. Calling your input data frame DF rather than data, DF - structure(list(FID = c(1L, 1L,

[R] How can I read the following complicated table

Hello, I have a table (in a txt file) which look like this: Monday 12 78 89 Tuesday 34 44 67 Wednesday 78 98 2 Thursday 34 55 4 Then the table repeats Monday , Tuesday, ... followed by several numbers My goal is to read values after the table. My problem is a little more complicated,

Re: [R] duplicated.data.frame() and POSIXct with DST shift

On Dec 13, 2012, at 5:01 PM, David Winsemius wrote: On Dec 13, 2012, at 1:43 PM, Tobias Gauster wrote: Hi, I encountered the behavior, that the duplicated method for data.frames gives false positives if there are columns of class POSIXct with a clock shift from DST to standard time.

Re: [R] How can I read the following complicated table

What have you tried so far that did not work, and what do you want the result of your reading the text file look like? What is store somewhere? Why does myDF - read.table( myData.txt ) which gives you myDF V1 V2 V3 V4 1Monday 12 78 89 2 Tuesday 34 44 67 3 Wednesday 78 98 2

Re: [R] replace parenthetical phrases in a string

Hi, I guess there are some problems with spaces in this solution.  y [1] My toast=bog  and eggs omit=32 dogs have ears    [3] cats have tails   gsub( *\\([^)]*\\) *, , x) #[1] My toast=bogand eggsomit=32 dogs have ears #[3] cats have tails   You could

Re: [R] neural net

Hi, I tried your dataset.  I couldn't reproduce the Error: message.  Instead, mydata-read.table(text= drug param1 param2 param3 param4 param5 class A 111 15 125 40 0.5 1 B 347 13 280 55 3 2 C 335 9 119 89 -40 1 D 477 37 75 2 0 1 E 863 24 180 10 5 2 F 737 28 150 15 6 2 G 390 63 167 12 0 3 H 209 93

Re: [R] How can I read the following complicated table

Hi, If it is a dataframe with four columns. dat1-read.table(text= Monday 12 78 89 Tuesday 34 44 67 Wednesday 78 98 2 Thursday 34 55 4 Friday 14 25 13 Monday 18 75 56 Tuesday 28 42 65 ,header=FALSE,stringsAsFactors=FALSE) dat1Mon-dat1[,-1][dat1[,1]==Monday,] #rows with first column Monday