Re: [R] R CMD methods and ggplot2 advice

Dear Glenn, Suppose this function test - function(df){ ggplot(df, aes(x = gp, y = y)) + geom_point() } Then R CMD check will consider gp and y as global variables since they are undefined. Because R CMD check cannot detect that gp and y will be extracted from df by ggplot2. Possible

Re: [R] Help on Histogram ~ Barplot

HI Jim, Thanks for the help however R throws an error when i create a var tot_mon_wt- tot_mon_wt-by(mwlc$MFST_WT,mwlc$Month,sum). It gives me an error = Error in Summary.factor(c(1L, 1L), na.rm = FALSE) : ‘sum’ not meaningful for factors Not sure what this error refers to. Thank you, Shivi

[R] Help on Histogram ~ Barplot

Hello All, I need help on creating a histogram for one of my data. The data is as below (sample): MFST_WT Hours PROCESS Month Weekday Day of the Month 6,828 13 INBOUND Mar Fri13 2,504 16 INBOUND Mar Fri27 20

Re: [R] Remove entry with sensitive information from history

Hi David, thanks, but the function has to work from an R shell, I have no graphical server in my remote machines. On Wed, May 27, 2015 at 9:45 AM, David Winsemius dwinsem...@comcast.net wrote: On May 27, 2015, at 12:29 AM, Luca Cerone wrote: Hi everybody, in one of my packages I store

Re: [R] Remove entry with sensitive information from history

On 27/05/2015 09:17, Luca Cerone wrote: Hi David, thanks, but the function has to work from an R shell, I have no graphical server in my remote machines. My suggestion was going to be to use readline() to read the passwords. Ideally one would use a custom reader from stdin which did not echo,

Re: [R] Find and replace backslashes XXXX

On 26/05/2015 9:56 PM, Ista Zahn wrote: Escape the backslash with another backslash, i.e., gsub(\\,/,X:\\Classes\\TT\\Automation, fixed = TRUE) ... and note that if you want to use a regular expression (i.e. fixed = FALSE), you would need another level of escaping, i.e.

Re: [R] Find and replace backslashes XXXX

Since the character looks like a Windows file path, you could use normalizePath() instead of gsub(). normalizePath(X:\\Classes\\TT\\Automation, winslash = /, mustWork = FALSE) ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie

Re: [R] Identifying peak periods of observations in circular yearly data

Hi Daisy, You face a problem similar to one with which I have grappled in different fields. The year is designed for the northern hemisphere, beginning and ending in less productive biologic states in those regions. I have previously argued that since the calendar year is an arbitrary progression,

Re: [R] Remove entry with sensitive information from history

To answer your question on filtering the command-line history: You can use savehistory()/loadhistory() to rewrite the history, but like all other solutions/suggestions, it's not guaranteed to work everywhere. Example: filterhistory - function(filter) { stopifnot(is.function(filter)) hf -

Re: [R] Help on Histogram ~ Barplot

Hi Shivi82, My suggestion is that the error concerned a mismatch between the number of labels and the number of bars. More seriously, you seem to want to sum the values of weight (MFST_WT) within each month. So: tot_mon_wt-by(mwlc$MFST_WT,mwlc$Month,sum) barplot(tot_mon_wt, names.arg =

Re: [R] Problem merging data frames and duplicates

y has unequal n's . There are 6 states and 7 loci. It is safer to submit data in the dput() form. See ?dput for information. John Kane Kingston ON Canada -Original Message- From: burbrink...@gmail.com Sent: Tue, 26 May 2015 20:12:55 -0400 To: r-help@r-project.org Subject: [R]

Re: [R] Logistic regression R and Stata grouping variable

You were not completely clear, but it appears that you have data where each subject has results from 8 trials, as a pair of variables is changed. If that is correct, then you want to have a variance that corrects for the repeated measures. In R the glm command handles the simple case but not

Re: [R] Doubts on Forecasting

I doubt if there is enough information in your email to let anyone really comment. Have a look at Reproducibility : http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example and http://adv-r.had.co.nz/Reproducibility.html for some suggestions on how to frame a

Re: [R] Help on Histogram ~ Barplot

On 27/05/2015 11:56, Shivi82 wrote: HI Jim, Thanks for the help however R throws an error when i create a var tot_mon_wt- tot_mon_wt-by(mwlc$MFST_WT,mwlc$Month,sum). It gives me an error = Error in Summary.factor(c(1L, 1L), na.rm = FALSE) : ‘sum’ not meaningful for factors Not sure what

Re: [R] Problem with comparing multiple data sets

Hi Mohammad, I went back and reread your original statement of the problem about and I think I kinda grasp it. It is actually quite clear and I misunderstood it completely. At the moment I have no idea how to approach it. As Jim Lemon said, it looks easy but may not be. I'll go back and

[R] Doubts on Forecasting

Hello Team. I have one doubts on Forecasting I have the 2 years of data by month wise i need to find 3rd year Value based on the past 2 years value if we using forecasting trend value coming i want to find the exact value please help Thanks and Regards Venkatesan [[alternative HTML

Re: [R] Find and replace backslashes XXXX

On 27/05/2015 8:55 AM, Dan Abner wrote: Hi Ista, Is there no way to not escape the backslash in the pathway? You don't need to escape it if you read it from a file, get it from list.files(), etc. You only need to escape it if you are writing a literal string in R code. Duncan Murdoch The

Re: [R] Printing with Header no of observations

I am not totally clear on the header question but would something like ?head help here? It will show a certain number of rows of data with headers included . I think the default is 6 rows but if all you want to do is check names and a bit of data something like head(xx, 2) works nicely. RE

[R] Printing with Header no of observations

HI Team, A quick question. When I used the print option in R to see the output of my syntax I do not see the headers or column names. Is there a way to see the headers in the print. Also as most of the datasets we work today have huge number of observations but when I print it only shows a

Re: [R] Find and replace backslashes XXXX

Hi Ista, Is there no way to not escape the backslash in the pathway? The pathway is going to change and will become very long and I need to do this programmatically. Beside, escaping the backslash defeats the purpose of using gsub. If I could do this manually each and every time, I would change

[R] pls - No variable selection

I am attempting to use mixOmics' pls() on a problem with 16 rows and 27 columns. When I run pls I get the message No variable selection. I have included a small problem below that produces this message. What am I doing wrong? Any help is appreciated. #= Begin small reproducible sample

Re: [R] pls - No variable selection

Hi Barry, I looked at the source code for pls quickly and couldn't find where/why this message is being printed. Maybe an undocumented behavior? I would ask the package maintainer. It doesn't look like a warning - just that there was no variable selection. HTH, Stephen On Wed, May 27, 2015 at

Re: [R] About performance of R

On May 27, 2015, at 8:00 AM, Suman wrote: Hi there, Now that R has grown up with a vibrant community. It's no 1 statistical package used by scientists. It's graphics capabilities are amazing. Now it's time to provide native support in R core for distributed and parallel computing for

[R] About performance of R

Hi there, Now that R has grown up with a vibrant community. It's no 1 statistical package used by scientists. It's graphics capabilities are amazing. Now it's time to provide native support in R core for distributed and parallel computing for high performance in massive datasets. And may be

[R] Simulating a time series with a given spectrum

Hi All: Is there a routine in R that allows me to simulate a time series that has a given spectrum? I have looked at the R Time Series Task view, and have done a web search also, including an article to appear in the handbook of statistics on time series in R, but I don’t see anything

[R] use of writePNG() in a multiplot OR rasterImage() size control in a multiplot

Dear All, I am trying to plot several things in a multiplot using par(mfrow...) AND add a pre-existing png file to that plot. I have found 2 options of doing this in the web: writePNG() and another fix using rasterImage(). writePNG(): the option using writePNG() does not add the

Re: [R] Identifying peak periods of observations in circular yearly data

You can use package circular for this. You have to convert 1-366 to 1-360 by dividing the days by 366 and multiplying by 360 and converting the results back to days by adding 360 if the value is 0 and dividing by 360 and multiplying by 366: library(circular) degrees - obsDay/366*360 #

Re: [R] Problem with comparing multiple data sets

Thanks John, I really hope it can be answered. Yes all 3 data sets have the same items. On Wed, May 27, 2015 at 9:32 AM, John Kane jrkrid...@inbox.com wrote: Thanks Mohammad. The data appear to have come through just fine. This probably means you can ignore some of the questions I just sent

Re: [R] About performance of R

Did you consider the amount of code your suggestions would break? -- Bert Bert Gunter Genentech Nonclinical Biostatistics (650) 467-7374 Data is not information. Information is not knowledge. And knowledge is certainly not wisdom. Clifford Stoll On Wed, May 27, 2015 at 8:00 AM, Suman

Re: [R] Simulating a time series with a given spectrum

On 27/05/2015 16:54, Roy Mendelssohn - NOAA Federal wrote: Hi All: Is there a routine in R that allows me to simulate a time series that has a given spectrum? I have looked at the R Time Series Task view, and have done a web search also, including an article to appear in the handbook of

Re: [R] Problem with comparing multiple data sets

Hi Mohammad, My mantra for the day is Plain Text, Plain Text. A bas HTML. And I really need to get out of here. I have not found a solution but is this a bit more like what you want? #=== dat1 - structure(list(class.1 = c(0L, 0L, 0L, 0L, 0L, 0L,

Re: [R] Problem merging data frames and duplicates

I have figured out a cheesy work around since these problems have to do with not having unique identifiers for the States: 1) Append a unique identifier to each state such that both AR becomes ARa and ARb 2) run the normal merge(x,y,by=1, all=T) 3) Use subst to cut the appended identifiers.

Re: [R] Problem merging data frames and duplicates

Interesting solutions. Thanks guys! On Wed, May 27, 2015 at 9:27 AM, William Michels w...@caa.columbia.edu wrote: Hi Frank! Ok, bind columns together in a state-wise fashion, allowing for state duplicates. Below (maybe cheesy) uses the state abbreviations state.abb in the datasets package.

Re: [R] Problem with comparing multiple data sets

Thanks Mohammad. The data appear to have come through just fine. This probably means you can ignore some of the questions I just sent you -- our emails are crossing. I probably will not get a chance to look at this til this afternoon (10:25 here now). We can hope someone with more skill than

[R] Getting a cdf equal to 1 from a variable kernel density estimation

When I integrate the variable kernel density estimation of a sample from -inf to inf, I should get 1. But it is not what I get with my code below. I find a value higher than 2. How can I fix this? n-1000 df - data.frame(x=unlist(lapply(1, function(i) rnorm(n, 0,sd=1

Re: [R] Problem merging data frames and duplicates

Thanks Bill, However, unique(merge(x, y, by = 1, all=T)) is giving me: state locus.x locus.y 1 AR 5 2 2 AR 5 3 3 AR 6 2 4 AR 6 3 5 IL 1 1 9 LA 2 NA 11MS 3 NA 12MS 4 NA

Re: [R] Problem with comparing multiple data sets

I was wondering about the layout of each of your data sets. I cobbled together what I think is the most likely scenarios. My bet is the data sets most closely resemble my data set 4 in structure. Am I correct? I dropped the other two columns in your data layout as likely to be immaterial to

Re: [R] Problem merging data frames and duplicates

Hi Frank! Ok, bind columns together in a state-wise fashion, allowing for state duplicates. Below (maybe cheesy) uses the state abbreviations state.abb in the datasets package. Also uses two functions rbind.na and cbind.na, available from Andrej-Nikolai Spiess' website at:

[R] Estimating Four Parameters with nls in R

Hello all! I am trying to estimate four parameters of a model (mu, sigma, theta and lambda) for a subset of data (snapshot given below). I have tried to do this using the nls package in R but I kept getting error messages (Error in numericDeriv(form[[3L]], names(ind), env) : --AND-- Missing

Re: [R] Identifying peak periods of observations in circular yearly data

Thanks for the advice Jim. I did actually play around with this idea, but for some bird species (emu) the beginning of the breeding season is actually January while for others it is in July or at other times. Breeding seasons can be driven by dry season or temperatures, so although there are

Re: [R] Problem with comparing multiple data sets

Hi John, I created the original data set with dput . This time I only loaded 50 values for each data set (dat1, dat2, dat3). About your question, all 0,1 and 2 are indicator of a specific class. The task is to compare 3 independent classification of a certain term and and determine the actual

Re: [R] Simulating a time series with a given spectrum

Thanks, I will look at that. -Roy On May 27, 2015, at 9:15 AM, Prof Brian Ripley rip...@stats.ox.ac.uk wrote: On 27/05/2015 16:54, Roy Mendelssohn - NOAA Federal wrote: Hi All: Is there a routine in R that allows me to simulate a time series that has a given spectrum? I have looked

Re: [R] Help on Histogram ~ Barplot

On May 27, 2015, at 2:28 AM, Shivi82 wrote: Hello All, I need help on creating a histogram for one of my data. The data is as below (sample): MFST_WT Hours PROCESS Month Weekday Day of the Month 6,828 13 INBOUND Mar Fri13 2,504 16

Re: [R] About performance of R

a) Base R already includes the parallel package. Deciding to use more than one processor for a particular computation is a very high level decision that can require knowledge of computing time cost, importance of other tasks on the system, and interdependence of computation results. It is not a

Re: [R] Problem merging data frames and duplicates

Notes: 1. You can get output for all states (alphabetically) by pre-merging data with states.abb: a1 - merge(state.abb, x, by= 1, all.x=T) b1 - merge(state.abb, y, by= 1, all.x=T) colnames(a1) - c(state, locus) colnames(b1) - c(state, locus) by.states1(a1,b1) 2. In my previous post (based on

[R] Issue with 95% CI using MASS{confint}

I am trying to run a nonlinear model looking at seasonal abundance of plants with the following limitations: fit.nls.s-nls(S_a~beta+m*time+alpha*sin(w*time+phi), data= xy, start=list(beta=2.1, m=0, alpha=2, phi = 1, w = 1), upper=list(beta=inf, m=inf,

[R] Collinearity? Cannot get logisticRidge{ridge} to work

I am currently working on a health care related project using R. I am learning R while working on data analysis. Below is the part of the data in which i am encountering a problem. Case#Sex Therapy1 Therapy2 Outcome 1 male no no

[R] Double Hierarchical Generalized Linear Models

I am new modeling and I am trying to analyse my data using the package Double Hierarchical Generalized Linear Models. However, I always get the same sort of error: Error in z %*% v_h : non-conformable arguments. I think that this error indicates that the matrices are created with

[R] information_request

Good Morning, I'm an italian student of Statistics. I'd like to know how to obtain the source code of summary() function, because I'm building a new model in R, and I would like to implement a summary function similar to that used for linear models. How can I obtain the source code? Thank you in

Re: [R] Problem with comparing multiple data sets

Ok. so I read about the (modeest) package that gives the results that I am looking for (most repeated value). I modified the data frame a little and moved the text to the first column. This is the data frame with all 3 possible classes for each term. =

Re: [R] About performance of R

On 27/05/2015 11:00 AM, Suman wrote: Hi there, Now that R has grown up with a vibrant community. It's no 1 statistical package used by scientists. It's graphics capabilities are amazing. Now it's time to provide native support in R core for distributed and parallel computing for high

Re: [R] information_request

Start R and then type: summary.lm David L. Carlson Department of Anthropology Texas AM University -Original Message- From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Carmine Apice Sent: Wednesday, May 27, 2015 11:24 AM To: r-help@r-project.org Subject: [R]

Re: [R] Collinearity? Cannot get logisticRidge{ridge} to work

On May 27, 2015, at 10:10 AM, Kengo Inagaki wrote: I am currently working on a health care related project using R. I am learning R while working on data analysis. Below is the part of the data in which i am encountering a problem. Case#Sex Therapy1 Therapy2

Re: [R] Problem with comparing multiple data sets

Save the result of the apply() function: Out - apply(df[ ,2:length(df)], 1, mfv) Then there are several options: Approximately what you asked for data.frame(Out) t(t(Out)) More typing but exactly what you asked for cat(paste0([, 1:length(Out), ] , Out), sep=\n) David L. Carlson Department of

Re: [R] Problem with comparing multiple data sets

Thanks David it worked ! One more thing. I hope it's not complicated. Is it also possible to display the terms for each row next to it? for example: [1] #dac2 [2] #dac0 [3] #dac1 ... On Wed, May 27, 2015 at 2:18 PM, David L Carlson dcarl...@tamu.edu wrote: Save the result of

Re: [R] Issue with 95% CI using MASS{confint}

On 27/05/2015 4:08 PM, Jennifer Sweatman wrote: I am trying to run a nonlinear model looking at seasonal abundance of plants with the following limitations: fit.nls.s-nls(S_a~beta+m*time+alpha*sin(w*time+phi), data= xy, start=list(beta=2.1, m=0, alpha=2,

[R] Multivariate Kernel Regression : Nadaraya-Watson or Gasser-Muller methods

Hi R-users, Can anybody kindly inform me which package I need to install in RStudio to run *Multivariate Kernel Regressions* (preferably,Gasser-Muller or Nadaraya-Watson) ? I am getting only univariate set-ups in the online resources, I need multivariate (i.e. multiple regressors). Thanks and

Re: [R] Collinearity? Cannot get logisticRidge{ridge} to work

Thank you very much for your rapid response. I sincerely appreciate your input. I am sorry for sending the previous email in HTML format. with(a, table(Sex, Therapy1) ) shows the following. Therapy1 Sex no yes female 6 7 male7 5 with(a, table(Sex, Outcome) ) and

Re: [R] Collinearity? Cannot get logisticRidge{ridge} to work

I did not understand complete separation quite well.. Thank you very much for clarification. Kengo 2015-05-27 17:03 GMT-05:00 David Winsemius dwinsem...@comcast.net: On May 27, 2015, at 3:00 PM, Kengo Inagaki wrote: Here is the result- with(a, table(Sex, Therapy1, Outcome) ) , , Outcome

Re: [R] Problem with comparing multiple data sets

cat(paste0([, 1:length(Out), ] #dac , Out), sep=\n) David From: Mohammad Alimohammadi [mailto:mxalimoha...@ualr.edu] Sent: Wednesday, May 27, 2015 2:29 PM To: David L Carlson; r-help@r-project.org Subject: Re: [R] Problem with comparing multiple data sets Thanks David it worked ! One more

Re: [R] Simulating a time series with a given spectrum

On Thu, May 28, 2015 at 12:54 AM, Roy Mendelssohn - NOAA Federal roy.mendelss...@noaa.gov wrote: Hi All: Is there a routine in R that allows me to simulate a time series that has a given spectrum? I have looked at the R Time Series Task view, and have done a web search also, including an

[R] Really stuck with the nls function!! It's Urgent !!

Greetings, I'm trying to use the nls function in my statistics project but I'm really finding lot of difficulties. I have a function called apinene_modele_prediction that calculates the estimations: library(expm); #exp of a matrixapinene_modele_prediction - function(t,theta)

Re: [R] Collinearity? Cannot get logisticRidge{ridge} to work

Here is the result- with(a, table(Sex, Therapy1, Outcome) ) , , Outcome = Alive Therapy1 Sex no yes female 0 4 male4 5 , , Outcome = Death Therapy1 Sex no yes female 6 3 male3 0 2015-05-27 16:57 GMT-05:00 David Winsemius

[R] Using lapply when there are dependencies

Hi all, Let's say I have a vector: vv-c(1,2,3) And suppose I have a function f(a,b), which is a function of 2 scalar inputs. I would like to evaluate this function separately for each element of the vv vector while the second input to f( ) will be the previous output from f( ). So, the

Re: [R] Double Hierarchical Generalized Linear Models

On May 27, 2015, at 10:00 AM, Mariana Velasque wrote: I am new modeling and I am trying to analyse my data using the package Double Hierarchical Generalized Linear Models. However, I always get the same sort of error: Error in z %*% v_h : non-conformable arguments. It means the either

[R] Problem with particular file in XML package?

I have been attempting to install the R devtools package at work. The version of R is 3.1.2 (Pumpkin Helmet). However, the installation of devtools fails because devtools depends on rversions which in turn depends upon the XML package (XML_3.98-1.1.tar.gz), and the XML package is not importing

Re: [R] Getting a cdf equal to 1 from a variable kernel density estimation

On 5/27/2015 2:43 AM, Lionel Delmas wrote: When I integrate the variable kernel density estimation of a sample from -inf to inf, I should get 1. But it is not what I get with my code below. I find a value higher than 2. How can I fix this? n-1000 df - data.frame(x=unlist(lapply(1, function(i)

Re: [R] Collinearity? Cannot get logisticRidge{ridge} to work

On May 27, 2015, at 2:49 PM, Kengo Inagaki wrote: Thank you very much for your rapid response. I sincerely appreciate your input. I am sorry for sending the previous email in HTML format. with(a, table(Sex, Therapy1) ) shows the following. Therapy1 Sex no yes female

Re: [R] Collinearity? Cannot get logisticRidge{ridge} to work

On May 27, 2015, at 3:00 PM, Kengo Inagaki wrote: Here is the result- with(a, table(Sex, Therapy1, Outcome) ) , , Outcome = Alive Therapy1 Sex no yes female 0 4 male4 5 , , Outcome = Death Therapy1 Sex no yes female 6 3 male3 0

[R] Remove entry with sensitive information from history

Hi everybody, in one of my packages I store encrypted password. If the user has to change the password in use she can run: update_password(old_password, new_password) The problem is that the commands ends up in the .Rhistory file. Is there any way I can avoid this? Any suggestion about it?

Re: [R] Retrieving data from nested lists

On May 26, 2015, at 3:59 PM, blue honour via R-help wrote: Dear R users, I have a question regarding retrieving data from nested lists. To illustrate, here is an example input: d1-data.table(v1=c(3,4),v2=c(2,5))

Re: [R] X11 font problem

On 27/05/2015 02:12, Renato Rivera wrote: Hi I have this problem and do not know how to solve it, I'm new to R R version 2.15.0 (2012-03-30) That is a very old version of R: the posting guide asked you to update before posting. Copyright (C) 2012 The R Foundation for Statistical Computing

Re: [R] Remove entry with sensitive information from history

On May 27, 2015, at 12:29 AM, Luca Cerone wrote: Hi everybody, in one of my packages I store encrypted password. If the user has to change the password in use she can run: update_password(old_password, new_password) The problem is that the commands ends up in the .Rhistory file.

Re: [R] Problem merging data frames and duplicates

Hi Frank, It looks like you're very close. I think you want: unique(merge(x, y, by = 1, all=T)) Gabor Grothendieck's sqldf package is very useful if you're more comfortable with SQL-type syntax, see: https://github.com/ggrothendieck/sqldf Best Regards, William (Bill) Michels, Ph.D. On

[R] Identifying peak periods of observations in circular yearly data

Greetings, I am trying to identify at which point during the year 80% of bird breeding observations are. typically I would answer a question like this by finding the median or quartiles but how do I deal with situations where the 80% of the is from day 285 through day 366 (leap year) and extends