[R] FW: Completing Unordered Categorical missing variables using package mi
Hello all, A perhaps simple question. I am trying to complete unordered categorical missing data using mi package. There are two variables with missing data: Mat and Use. The problem is that the Use has several categories and somehow this means I can't plot the results as I get this error. Any idea how to fix the problem? Any help much appreciated, Best, Ioanna new-read(Sample.csv) new$Use-factor(new$Use) MissingData - missing_data.frame(new) MissingData - change(MissingData, y = DS, what = type, to = ordered-categorical) # STEP 3: look deeper summary(MissingData) summary(MissingData@patterns) show(MissingData) hist(MissingData) # STEP 4: impute ## Not run: IMPsample - mi(MissingData) #STEP5: diagnostics Plot(IMPsample) Error in `rownames-`(`*tmp*`, value = c(Oc11, Oc12, Oc13, Oc14, : length of 'dimnames' [1] not equal to array extent Data new DS Use Material SurfaceIM 31237 3 Oc22 Wood 95.710401 3.148 48947 1 Oc19 Wood 124.427200 1.762 7038 5 Oc11 Wood 142.113800 1.890 8150 3 Oc32Steel 70.709451 2.530 43471 1 Oc19 NA3.609650 1.597 24815 5 Oc11 Wood 121.541500 3.638 8683 2 Oc11 Wood 80.341550 2.242 47303 1 Oc39 NA 19.018000 1.410 27467 5 Oc11 Wood 86.799050 3.782 35026 2 Oc11 Wood 113.185700 2.565 50635 5 Oc19 NA 28.169550 3.887 9459 2 Oc11 Wood 40.825350 1.779 14042 2 Oc13Steel 36.233100 4.293 17393 3 Oc11 Wood 56.069700 2.833 21157 5 Oc11 Wood 89.254700 4.958 42345 2 Oc19 NA2.973600 0.468 4372 5 Oc11 Wood7.872750 3.950 16654 5 Oc11 Wood 75.315600 6.395 47335 1 Oc19 NA 14.564400 1.781 49609 5 Oc19 NA 17.249000 3.545 4973 5 Oc19 Wood 28.511699 3.243 44784 2 Oc19 NA4.473000 2.328 29581 5 Oc11 Wood 96.884250 4.378 31949 3 Oc11 Wood 126.996500 3.225 7352 5 Oc11 Wood 71.905200 3.430 43139 1 Oc19 NA 133.573551 1.849 43350 2 Oc19 NA3.739350 1.205 11592 2 Oc11 Wood 72.146800 2.906 33767 3 Oc11 Wood 91.578001 2.905 51748 5 Oc39 NA9.108800 3.138 21160 5 Oc12 Wood 100.677100 4.268 34390 2 Oc12 Wood 120.401199 1.603 23255 5 Oc12 Wood 122.333801 5.557 38414 2 Oc21Steel 69.686100 3.021 48810 3 Oc29 Wood 79.609950 3.670 44611 2 Oc19 NA 15.328000 1.480 17905 3 Oc11 Wood 61.188500 1.857 35509 2 Oc11 Wood 160.180349 2.511 10252 2 Oc11 Wood 94.414799 1.446 47152 2 Oc19 Wood 12.160450 2.285 43221 2 Oc11 Wood 70.796299 1.361 32569 3 Oc11 Wood 97.269300 2.842 5671 5 Oc11 Wood 84.672250 3.050 1157 3 Oc11 Wood 79.297800 2.612 3441 2 Oc11 Wood 112.435650 2.105 36678 5 Oc21 Wood 27.223500 4.017 52241 5 Oc19 Wood3.946150 3.373 4688 5 Oc11 Wood 68.009700 3.766 42933 2 Oc19 Wood3.946801 2.039 31048 5 Oc11 Wood 25.172301 3.633 28660 1 Oc11 Wood 133.387099 1.285 22726 5 Oc12 Wood 216.952900 7.550 22397 5 Oc11 Wood 115.320750 5.825 41008 3 Oc11 Wood 97.253199 1.960 49054 3 Oc21 NA8.542800 1.329 5594 5 Oc41 RC 264.505000 3.185 45379 3 Oc41 Wood 39.357100 2.909 17498 3 Oc11 Wood 45.544750 1.459 1176 5 Oc11 Wood 87.020400 2.750 33055 1 Oc11 Wood 55.777250 1.437 37071 5 Oc32 Wood 201.629599 3.287 53813 5 Oc19 Wood 56.919600 4.322 11037 2 Oc11 Wood 107.886600 1.479 14453 2 Oc11 Wood 106.369949 2.508 3767 1 Oc11 Wood 71.325500 2.012 52303 5 Oc29 NA8.916150 6.092 19706 5 Oc19 Wood 25.936699 6.417 37658 5 Oc14 Wood 65.761651 4.317 26195 1 Oc12 Wood 82.510849 0.835 35808 3 Oc13 Wood 54.798851 2.337 6035 5 Oc12 Wood 286.075700 3.905 33383 3 Oc11 Wood 96.809150 2.560 43497 1 Oc19 NA 13.039000 1.103 41777 5 NA NA 47.153349 2.658 12024 2 Oc11 Wood 19.851000 2.567 39538 1 Oc19 NA 31.996200 2.108 15553 3 Oc19 Wood 197.062201 2.559 31522 3 Oc11 Wood 129.499700 2.906 11916 2 Oc11 Wood 58.358951 2.939 9688 2 Oc11 Wood 106.568201 1.822 1690 3 Oc11 Wood 202.613700 2.290 9773 Oc11 Wood 179.321800 1.987 12410 2 Oc14Steel 108.682100 2.821 52428 5 Oc19 NA 36.041699 6.042 14109 2 Oc21Steel 130.929300 4.178 52769 5 Oc31 Wood 18.525650 2.187 11324 1 Oc11 Wood 94.108351 1.456 12394 2 Oc21 RC 1836.975800 2.415 35991 3 Oc11 Wood 114.716550 2.664 4006 5 Oc39Steel 309.854000 4.041 43404 2 Oc19 RC 27.745400 1.772 12680 1 Oc21 RC 327.789699 2.669 43607 1 Oc29 NA5.812499 2.406 33590 3 Oc11 Wood8.115450 3.183 16230 5 Oc32 Wood 610.293850 6.312 19815 5 Oc11 Wood 89.220350 6.122 4520
Re: [R] Polysomnographic data analysis with R?
Hi Charles, As I don't know what sort of data you are using, I can only guess. If you want to visualize the sleep patterns and events, it is fairly easy to extract these from the sleep example on the EDF format page and display them. sleep_stages-list(labels=c(Sleep stage W, Sleep stage N1, Sleep stage N2, Sleep stage N3, Sleep stage N2, Sleep stage N3, Sleep stage N2), starts=c(0,660,960,1140,1440,1620,1890), ends=c(660,960,1140,1440,1620,1890,1920)) library(plotrix) gantt.chart(sleep_stages,vgridlab=seq(0,2000,by=100), vgridpos=seq(0,2000,by=100),main=Sleep recording, taskcolors=2:5) abline(v=c(660,742,993,1019,1526,1620,1634)) sleep_events-c(Lights off,Turning right side - back, Limb movement R+L leg,Limb movement R leg, Obstructive apnea,Obstructive apnea, Turning back - left side) staxlab(side=1,at=c(660,742,993,1019,1526,1620,1634), labels=sleep_events,pos=0.555, top.line=1,nlines=4,cex=0.7) Jim On Wed, Jun 17, 2015 at 10:15 PM, Charles Novaes de Santana charles.sant...@gmail.com wrote: Dear Jim, Thank you for your response. Yes, it is the European Data Format you mention. Actually we can read the data correctly, but I was wondering if there is any package that can identify different sleep phases automatically based on the data. I supposed such a package does not exist, it is really difficult to automatize the identification of sleep phases based only on data, but I asked here just in case. Thanks for your attention! Best, Charles On 17 June 2015 at 13:46, Jim Lemon drjimle...@gmail.com wrote: Hi Charles, This looks like the European Data Format (EDF and EDF+), which has a complete file specification. If there is no existing R package, it might be possible to write an import function from the specification, something like the functions in the foreign package. Jim On Wed, Jun 17, 2015 at 4:55 AM, Charles Novaes de Santana charles.sant...@gmail.com wrote: Dear all, Do you know if there is any R package or function we can use to analyze polysomnographic data? For example, something that can import an EDF file (or in a different format) and can give some properties of the polysomnographic records like periods of different sleep phases, etc. I looked for it in the web and I didn't find. But maybe I used the wrong key-words. Any help will be much appreciated! Best, Charles -- Um axé! :) -- Charles Novaes de Santana, PhD http://www.imedea.uib-csic.es/~charles [[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 guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Um axé! :) -- Charles Novaes de Santana, PhD http://www.imedea.uib-csic.es/~charles __ 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 guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] help for lay person assisting R user with disability
Good Morning, I am currently working with a disabled R user who is a student here at CMU. The student has both sight and mobility issues. The student has asked for an assistant who is well versed in R to enter data for her, which we are having a hard time finding. I would like information from R developers/users about how/how well R interfaces with Excel (an easier skill set to find!) In your opinion, could it be as easy as uploading data from excel into R? Also, do you know of a way to enlarge the R interface or otherwise assist in making the program accessible to a low vision person? My limited understanding leads me to believe that screen magnifiers like zoom text don't work particularly well. If you have information on that, I would very much appreciate it. Thanks for your help and for bearing with me! Courtney Courtney Bryant, EOS Specialist Equal Opportunity Services, Human Resources Carnegie Mellon University 412-268-3930 | cbry...@andrew.cmu.edu __ 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 guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to round only one df row how to keep 3rd sigdif if zero
Hi You need to distinguish between an object and printing an object on console. When you print an object you can use several options for formating. ?sprintf, ?formatC formatC(t(a), digits=1, format=f) [,1] [,2] [,3] count 1.0 2.0 3.0 rate 16.7 33.3 50.0 Also when you transpose a the result is not data frame but matrix. str(t(a)) num [1:2, 1:3] 1 16.7 2 33.3 3 50 - attr(*, dimnames)=List of 2 ..$ : chr [1:2] count rate ..$ : NULL str(a) 'data.frame': 3 obs. of 2 variables: $ count: num 1 2 3 $ rate : num 16.7 33.3 50 If you used google or other internet search options you would get plenty of results yourself. try formatting numbers R Cheers Petr -Original Message- From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of bcrombie Sent: Thursday, June 18, 2015 3:09 PM To: r-help@r-project.org Subject: [R] How to round only one df row how to keep 3rd sigdif if zero # How do I round only one row of a dataframe? # After transposing a dataframe of counts rates, all values took on the most # of signif digits in the dataset (rates), but I want counts to remain only one digit. # Also, how can I keep 3 significant digits in R when the 3rd is a zero? count - c(1, 2, 3) rate - c(16.7, 33.3, 50.0) a - data.frame(count,rate) a # count rate # 1 1 16.7 # 2 2 33.3 # 3 3 50.0 a - t(a) a # [,1] [,2] [,3] # count 1.0 2.03 # rate 16.7 33.3 50 -- View this message in context: http://r.789695.n4.nabble.com/How-to- round-only-one-df-row-how-to-keep-3rd-sigdif-if-zero-tp4708819.html Sent from the R help mailing list archive at Nabble.com. __ 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 guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. Tento e-mail a jakékoliv k němu připojené dokumenty jsou důvěrné a jsou určeny pouze jeho adresátům. Jestliže jste obdržel(a) tento e-mail omylem, informujte laskavě neprodleně jeho odesílatele. Obsah tohoto emailu i s přílohami a jeho kopie vymažte ze svého systému. Nejste-li zamýšleným adresátem tohoto emailu, nejste oprávněni tento email jakkoliv užívat, rozšiřovat, kopírovat či zveřejňovat. Odesílatel e-mailu neodpovídá za eventuální škodu způsobenou modifikacemi či zpožděním přenosu e-mailu. V případě, že je tento e-mail součástí obchodního jednání: - vyhrazuje si odesílatel právo ukončit kdykoliv jednání o uzavření smlouvy, a to z jakéhokoliv důvodu i bez uvedení důvodu. - a obsahuje-li nabídku, je adresát oprávněn nabídku bezodkladně přijmout; Odesílatel tohoto e-mailu (nabídky) vylučuje přijetí nabídky ze strany příjemce s dodatkem či odchylkou. - trvá odesílatel na tom, že příslušná smlouva je uzavřena teprve výslovným dosažením shody na všech jejích náležitostech. - odesílatel tohoto emailu informuje, že není oprávněn uzavírat za společnost žádné smlouvy s výjimkou případů, kdy k tomu byl písemně zmocněn nebo písemně pověřen a takové pověření nebo plná moc byly adresátovi tohoto emailu případně osobě, kterou adresát zastupuje, předloženy nebo jejich existence je adresátovi či osobě jím zastoupené známá. This e-mail and any documents attached to it may be confidential and are intended only for its intended recipients. If you received this e-mail by mistake, please immediately inform its sender. Delete the contents of this e-mail with all attachments and its copies from your system. If you are not the intended recipient of this e-mail, you are not authorized to use, disseminate, copy or disclose this e-mail in any manner. The sender of this e-mail shall not be liable for any possible damage caused by modifications of the e-mail or by delay with transfer of the email. In case that this e-mail forms part of business dealings: - the sender reserves the right to end negotiations about entering into a contract in any time, for any reason, and without stating any reasoning. - if the e-mail contains an offer, the recipient is entitled to immediately accept such offer; The sender of this e-mail (offer) excludes any acceptance of the offer on the part of the recipient containing any amendment or variation. - the sender insists on that the respective contract is concluded only upon an express mutual agreement on all its aspects. - the sender of this e-mail informs that he/she is not authorized to enter into any contracts on behalf of the company except for cases in which he/she is expressly authorized to do so in writing, and such authorization or power of attorney is submitted to the recipient or the person represented by the recipient, or the existence of such authorization is known to the recipient of the person represented by the recipient. __ R-help@r-project.org mailing
Re: [R] Cross tabulation with top one variable and side as multiple variables
They do not match because xtabs() in R produces a multidimensional array (one dimension for each variable). Looking at your spreadsheet on nabble, it appears that SPSS is just creating 4 crosstabulations with TREND against each of the other variables. That is easily done in R, but for tested code, you need to give us reproducible data using dput(). I get an error using read.spss() on your uploaded file. You should also read some of the extensive free documentation available on R. The ftable() function creates a two dimensional representation of that 5-dimensional array. But your spreadsheet is just a stack of two-dimensional tables. You could get there with the margin.table() function, but unless you really need the 5-dimensional array, you probably want something more like: rowvars - c(AGET, SEXT, EDUCRT, JOBRT) table.lst - lapply(rowvars, function(x) xtabs(~x+TREND)) That would give you a list containing a crosstabulation table between each of the variables and TREND. A spreadsheet with 2000 tables seems a bit unwieldy so you might want to give some thought to what you really want as output. - David L Carlson Department of Anthropology Texas AM University College Station, TX 77840-4352 -Original Message- From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of jagadishpchary Sent: Thursday, June 18, 2015 1:46 AM To: r-help@r-project.org Subject: Re: [R] Cross tabulation with top one variable and side as multiple variables I think my explanation in the post is not giving the full details on the job to be done. Sorry for that. Here is what I am doing.. 1. I have a SPSS data set with more than 2000 variables. However for test purpose I have created a temporary data set with 5 variables which I am reading it to R environment (Attached the test.sav file). 2. There is a variable called “TREND” which has the year data. So all I need to do is cross tabulate the variables with this Trend variable. In SPSS the syntax would be CTABLES /VLABELS VARIABLES =ALL DISPLAY=LABEL /TABLES (AGET +SEXT +EDUCRT +JOBRT ) [COUNT F40.0] by TREND. The final cross tabulation results are placed in the attached excel report with sheet name “Results”. As I am new to R - I tried searching the forums for the cross tabulation with top variable constant and multiple variables as side however I could not find it. Anyhow I tried using the below syntax : Xtabs ( ~ AGET +SEXT +EDUCRT +JOBRT + TREND, data=mydata) summary(~AGET +SEXT +EDUCRT +JOBRT, data= mydata, fun=table) ftable (mydata, row.vars=c(AGET , SEXT , EDUCRT , “JOBRT”), col.vars=TREND) the results are not identical to what I am getting in SPSS Hence I would request to suggest me a R code that helps me in getting the results as shown in the attached excel report with sheet name “Results”. Test.sav http://r.789695.n4.nabble.com/file/n4708799/Test.sav Cross_tabulation.xlsx http://r.789695.n4.nabble.com/file/n4708799/Cross_tabulation.xlsx -- View this message in context: http://r.789695.n4.nabble.com/Cross-tabulation-with-top-one-variable-and-side-as-multiple-variables-tp4708379p4708799.html Sent from the R help mailing list archive at Nabble.com. __ 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 guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ 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 guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] help for lay person assisting R user with disability
You may have people knowledgeable about R there at Carnegie Mellon since it hosts a mirror for R software (one of 18 in the US). As Petr pointed out it is relatively easy to transfer information from an Excel spreadsheet to R by cutting and pasting (the method he suggested is for Windows computers) or by saving the file in a tab delimited or comma separated format so data entry should not be a problem assuming the data are arranged in a consistent format. As for the interface, there are a number of ways of interacting with R, but the default method involves a command window that allows you to type commands. On Windows it is called the R Console and the GUI Preferences option on the Edit menu tab allows you to choose the font, its size, and the number of rows and columns. For example changing the default size of 10 to 24 makes the type and the window larger. If the settings are saved, they should be preserved when the program is restarted. There are also some graphical user interfaces for R that may be easier to use such as R Commander. - David L Carlson Department of Anthropology Texas AM University College Station, TX 77840-4352 -Original Message- From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of PIKAL Petr Sent: Thursday, June 18, 2015 10:04 AM To: Courtney Bryant; r-help@R-project.org Subject: Re: [R] help for lay person assisting R user with disability Hi I believe that others come with more elaborated answers. Probably easiest way how to transfer Excel data to R is: select rectangular area you want to transfer, preferably with sensible header. pres Ctrl-C In R enter command object - read.delim(clipboard) possibly with header or NA options. However this approach is not reproducible (you lose information about data source in .Rhistory), so there are other ways (e.g. through saved CSV file) but they can be more tricky. Cheers Petr -Original Message- From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Courtney Bryant Sent: Thursday, June 18, 2015 4:33 PM To: r-help@R-project.org Subject: [R] help for lay person assisting R user with disability Good Morning, I am currently working with a disabled R user who is a student here at CMU. The student has both sight and mobility issues. The student has asked for an assistant who is well versed in R to enter data for her, which we are having a hard time finding. I would like information from R developers/users about how/how well R interfaces with Excel (an easier skill set to find!) In your opinion, could it be as easy as uploading data from excel into R? Also, do you know of a way to enlarge the R interface or otherwise assist in making the program accessible to a low vision person? My limited understanding leads me to believe that screen magnifiers like zoom text don't work particularly well. If you have information on that, I would very much appreciate it. Thanks for your help and for bearing with me! Courtney Courtney Bryant, EOS Specialist Equal Opportunity Services, Human Resources Carnegie Mellon University 412-268-3930 | cbry...@andrew.cmu.edu __ 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 guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. Tento e-mail a jakékoliv k němu připojené dokumenty jsou důvěrné a jsou určeny pouze jeho adresátům. Jestliže jste obdržel(a) tento e-mail omylem, informujte laskavě neprodleně jeho odesílatele. Obsah tohoto emailu i s přílohami a jeho kopie vymažte ze svého systému. Nejste-li zamýšleným adresátem tohoto emailu, nejste oprávněni tento email jakkoliv užívat, rozšiřovat, kopírovat či zveřejňovat. Odesílatel e-mailu neodpovídá za eventuální škodu způsobenou modifikacemi či zpožděním přenosu e-mailu. V případě, že je tento e-mail součástí obchodního jednání: - vyhrazuje si odesílatel právo ukončit kdykoliv jednání o uzavření smlouvy, a to z jakéhokoliv důvodu i bez uvedení důvodu. - a obsahuje-li nabídku, je adresát oprávněn nabídku bezodkladně přijmout; Odesílatel tohoto e-mailu (nabídky) vylučuje přijetí nabídky ze strany příjemce s dodatkem či odchylkou. - trvá odesílatel na tom, že příslušná smlouva je uzavřena teprve výslovným dosažením shody na všech jejích náležitostech. - odesílatel tohoto emailu informuje, že není oprávněn uzavírat za společnost žádné smlouvy s výjimkou případů, kdy k tomu byl písemně zmocněn nebo písemně pověřen a takové pověření nebo plná moc byly adresátovi tohoto emailu případně osobě, kterou adresát zastupuje, předloženy nebo jejich existence je adresátovi či osobě jím zastoupené známá. This e-mail and any documents attached to it may be confidential and are intended only for its intended
Re: [R] help for lay person assisting R user with disability
On Thu, Jun 18, 2015 at 10:32 AM, Courtney Bryant cbry...@andrew.cmu.edu wrote: Good Morning, I am currently working with a disabled R user who is a student here at CMU. The student has both sight and mobility issues. The student has asked for an assistant who is well versed in R to enter data for her, which we are having a hard time finding. I would like information from R developers/users about how/how well R interfaces with Excel (an easier skill set to find!) In your opinion, could it be as easy as uploading data from excel into R? Also, do you know of a way to enlarge the R interface or otherwise assist in making the program accessible to a low vision person? My limited understanding leads me to believe that screen magnifiers like zoom text don't work particularly well. If you have information on that, I would very much appreciate it. Thanks for your help and for bearing with me! Courtney 1. If the data file is in the form of a rectangular table with rows and columns and the first row is a header row then if, in Excel, it is saved as a .csv file it can be read into R like this: DF - read.csv(/Users/JoeDoe/myspreadsheet.csv) 2. The openxlsx, readxl (and a number of other packages) can alternetely be used to directly read in an xls or xlsx file, e.g. install.packages(readxl) library(readxl) DF - read_excel(/Users/JoeDoe/myspreadsheet.xlsx) 3. The Windows magnifier that comes with Windows does work with R. -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com [[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 guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] adjusted values for CI in a within-subjects design
Dear R-ers,
I am trying to adjust the values of a within-items, within-subjects design
(the experimental conditions are within subjects), to calculate between
subjects confidence intervals (CI). I am following the recommendations from
O'Brien Cousineau (2014; see also Cousineau, 2005; Morey, 2008 for
similar solutions). So, formula is the following.
# formula for corrected CI:
# Y = Xsj - Xj. + X..
# where...
# Xsj = single value of a trial of a time window per participant
# Xj. = participants mean on that conditions across trials
# X.. = overall mean on that condition
# W = sqrt(J/(J-1))*(Y - Y.j) + Y.j
# where...
# J = sqrt(f/(f-1))
# f = total number of measures per subject
# Y.j = mean for a condition across participants
# W = the corrected value from which we can calculate the CI between
subjects.
I've written a code that does that using a dataset of random values (0,1),
but with the same structure that the actual dataset for which I hope to
calculate corrected CI.
fixprop subj trial time
11 11
01 12
11 13
01 14
01 15
01 16
The experiments deliver the time course of an effect (similar to
longitudinal data), meaning, we have N time steps in which the effect is
modulated. I've tested the script with this dummy dataset of 4
participants, 10 items, and 400 time steps, and it works nicely. The tricky
part here is that in the real experiments, we have many more participants,
items and time steps. Thus, the adjustment needs to be done many many
times.
With the dummy dataset the process takes about 6 seconds,
proc.time() - ptm
user system elapsed
4.530.066.03
but when I've added a bit more data (10 participants, 125 trials, 400 time
steps), the scritp takes more than an hour,
proc.time() - ptm
user system elapsed
3483.64 879.31 4456.86
So, I don't even want to try doing this with real data, in which we have
thousands of times steps, and generally over 50 participants (although less
items in general, perhaps 40 or 50).
QUESTION: does anyone know how could I optimize my script, such as it does
not take forever?
Here is the script.
library(doBy)
library(plotrix)
library(matrixStats)
library(doBy)
library(bear)
library(ggplot2)
library(reshape)
rm(list=ls()) # clear memory
setwd (??) # set directory
infile = test.txt#
test.txt is the name of the fixation report
data = read.delim(file=infile, header=T, sep=\t) # load the file
data = data[with(data, order(subj,trial)), ]# data need to
be organized by part, by trials
head(data)
subj = unique(data$subj)
np=length(subj); np # how many participants
trial = unique(data$trial)
nt=length(trial); nt # how many items
timewindows = unique(data$time)
twsn=length(timewindows); twsn # how many time steps
critcoln = 1 #column in which we find the dependent variable
ncoln = 4 #total number of columns of your file
f = 2 #total number of conditions per subject
tm - cbind(rep(c(critcoln:twsn), each=(nt*np)))
newvar - cbind(rep(c((critcoln+ncoln):(critcoln+ncoln)),
each=(nt*np*twsn)))
subj - cbind(rep(1:np, each=nt, times=twsn))
count -cbind(rep(c(1:1), each=(nt*np*twsn)))
X..data = summaryBy(fixprop ~ time, FUN = mean, keep.names=T, data=data)
Xj.data = summaryBy(fixprop ~ subj + time, FUN = mean, keep.names=T,
data=data)
ptm - proc.time()
prev_tw = 0
prev_subj = 0
j = 0
t = 0
for (i in 1:(nrow(data)))
{
curr_tw = tm[i]
curr_subj = subj[i]
if (prev_subj curr_subj)
{j = j + 1}
Y. = data[i,critcoln] - Xj.data[j,3]
if (prev_tw curr_tw)
{t = t + 1}
Y = Y. + X..data[t,2]
data[i,newvar[i]] - Y
prev_tw = curr_tw
prev_subj = curr_subj
}
proc.time() - ptm
colnames(data)[ncoln+1] - 'fixprop_adj'
Y.jdata = summaryBy(fixprop_adj ~ subj + time, FUN = mean, keep.names=T,
data=data)
J = sqrt(f/(f-1)) #correction factor
newvar - cbind(rep(c((critcoln+ncoln+1):(critcoln+ncoln+1)),
each=(nt*np*twsn)))
prev_tw = 0
t = 0
for (i in 1:(nrow(data)))
{
curr_tw = tm[i]
if (prev_tw curr_tw)
{t = t + 1}
W = J*((data[i,ncoln+1]) - Y.jdata[t,3]) + Y.jdata[t,3]
data[i,newvar[i]] - W
prev_tw = curr_tw
}
proc.time() - ptm
colnames(data)[ncoln+2] - 'fixprop_final'
That's all. The processes that really take long are the for loops, I know
loops are not the best, but I couldn't think of a process that can do this
better so far...
Any comments, suggestions, criticisms and questions are welcome...
Cheers,
Ernesto.
[[alternative HTML version deleted]]
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[R] How to round only one df row how to keep 3rd sigdif if zero
# How do I round only one row of a dataframe? # After transposing a dataframe of counts rates, all values took on the most # of signif digits in the dataset (rates), but I want counts to remain only one digit. # Also, how can I keep 3 significant digits in R when the 3rd is a zero? count - c(1, 2, 3) rate - c(16.7, 33.3, 50.0) a - data.frame(count,rate) a # count rate # 1 1 16.7 # 2 2 33.3 # 3 3 50.0 a - t(a) a # [,1] [,2] [,3] # count 1.0 2.03 # rate 16.7 33.3 50 -- View this message in context: http://r.789695.n4.nabble.com/How-to-round-only-one-df-row-how-to-keep-3rd-sigdif-if-zero-tp4708819.html Sent from the R help mailing list archive at Nabble.com. __ 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 guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] help for lay person assisting R user with disability
Hi I believe that others come with more elaborated answers. Probably easiest way how to transfer Excel data to R is: select rectangular area you want to transfer, preferably with sensible header. pres Ctrl-C In R enter command object - read.delim(clipboard) possibly with header or NA options. However this approach is not reproducible (you lose information about data source in .Rhistory), so there are other ways (e.g. through saved CSV file) but they can be more tricky. Cheers Petr -Original Message- From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Courtney Bryant Sent: Thursday, June 18, 2015 4:33 PM To: r-help@R-project.org Subject: [R] help for lay person assisting R user with disability Good Morning, I am currently working with a disabled R user who is a student here at CMU. The student has both sight and mobility issues. The student has asked for an assistant who is well versed in R to enter data for her, which we are having a hard time finding. I would like information from R developers/users about how/how well R interfaces with Excel (an easier skill set to find!) In your opinion, could it be as easy as uploading data from excel into R? Also, do you know of a way to enlarge the R interface or otherwise assist in making the program accessible to a low vision person? My limited understanding leads me to believe that screen magnifiers like zoom text don't work particularly well. If you have information on that, I would very much appreciate it. Thanks for your help and for bearing with me! Courtney Courtney Bryant, EOS Specialist Equal Opportunity Services, Human Resources Carnegie Mellon University 412-268-3930 | cbry...@andrew.cmu.edu __ 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 guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. Tento e-mail a jakékoliv k němu připojené dokumenty jsou důvěrné a jsou určeny pouze jeho adresátům. Jestliže jste obdržel(a) tento e-mail omylem, informujte laskavě neprodleně jeho odesílatele. Obsah tohoto emailu i s přílohami a jeho kopie vymažte ze svého systému. Nejste-li zamýšleným adresátem tohoto emailu, nejste oprávněni tento email jakkoliv užívat, rozšiřovat, kopírovat či zveřejňovat. Odesílatel e-mailu neodpovídá za eventuální škodu způsobenou modifikacemi či zpožděním přenosu e-mailu. V případě, že je tento e-mail součástí obchodního jednání: - vyhrazuje si odesílatel právo ukončit kdykoliv jednání o uzavření smlouvy, a to z jakéhokoliv důvodu i bez uvedení důvodu. - a obsahuje-li nabídku, je adresát oprávněn nabídku bezodkladně přijmout; Odesílatel tohoto e-mailu (nabídky) vylučuje přijetí nabídky ze strany příjemce s dodatkem či odchylkou. - trvá odesílatel na tom, že příslušná smlouva je uzavřena teprve výslovným dosažením shody na všech jejích náležitostech. - odesílatel tohoto emailu informuje, že není oprávněn uzavírat za společnost žádné smlouvy s výjimkou případů, kdy k tomu byl písemně zmocněn nebo písemně pověřen a takové pověření nebo plná moc byly adresátovi tohoto emailu případně osobě, kterou adresát zastupuje, předloženy nebo jejich existence je adresátovi či osobě jím zastoupené známá. This e-mail and any documents attached to it may be confidential and are intended only for its intended recipients. If you received this e-mail by mistake, please immediately inform its sender. Delete the contents of this e-mail with all attachments and its copies from your system. If you are not the intended recipient of this e-mail, you are not authorized to use, disseminate, copy or disclose this e-mail in any manner. The sender of this e-mail shall not be liable for any possible damage caused by modifications of the e-mail or by delay with transfer of the email. In case that this e-mail forms part of business dealings: - the sender reserves the right to end negotiations about entering into a contract in any time, for any reason, and without stating any reasoning. - if the e-mail contains an offer, the recipient is entitled to immediately accept such offer; The sender of this e-mail (offer) excludes any acceptance of the offer on the part of the recipient containing any amendment or variation. - the sender insists on that the respective contract is concluded only upon an express mutual agreement on all its aspects. - the sender of this e-mail informs that he/she is not authorized to enter into any contracts on behalf of the company except for cases in which he/she is expressly authorized to do so in writing, and such authorization or power of attorney is submitted to the recipient or the person represented by the recipient, or the existence of such authorization is known to the recipient of the person represented by the
Re: [R] help for lay person assisting R user with disability
Hi Courtney and John, The RStudio environment mentioned below will not work with speech output (I tried with Window-Eyes awhile ago). Some of my clients use it but I have no experience with it. Since the student is partially sighted, they might be able to customize the environment with big fonts and contrast, I’m just not sure. Using a screen reader like Window-Eyes, the student could use the R GUI environment, although it’s a little frustrating because it doesn’t speak a lot and you need to use the mouse keys a lot. The other option if you have to stick with Windows is to run R at the command prompt, which makes interaction slightly easier but you’d have to figure out how to log the output. What is being recommended for the rest of the students in the class? Ideally, this student’s experience should be as close as possible to the others’. Liz On Jun 18, 2015, at 12:17 PM, John McKown john.archie.mck...@gmail.com wrote: On Thu, Jun 18, 2015 at 9:32 AM, Courtney Bryant cbry...@andrew.cmu.edu wrote: Good Morning, I am currently working with a disabled R user who is a student here at CMU. The student has both sight and mobility issues. The student has asked for an assistant who is well versed in R to enter data for her, which we are having a hard time finding. I would like information from R developers/users about how/how well R interfaces with Excel (an easier skill set to find!) In your opinion, could it be as easy as uploading data from excel into R? Also, do you know of a way to enlarge the R interface or otherwise assist in making the program accessible to a low vision person? My limited understanding leads me to believe that screen magnifiers like zoom text don't work particularly well. If you have information on that, I would very much appreciate it. Thanks for your help and for bearing with me! Courtney I am a bit confused (a normal condition for me). Is the student writing R code or is the student running a application written in R? Also, since you mentioned Excel, I am assuming that the student is using a PC running Windows as opposed to Linux or a Mac. If the student is writing R code, then I'd suggest that your computer support person install Rstudio. It is cost free and can be downloaded here: http://www.rstudio.com/ . The installer can then customize Rstudio to use a really large font, if that would be helpful. Please forgive my lack of knowledge about accessibility issues. If the student has trouble typing (mobility issue?), this likely won't help. Would a speech to text / text to speech interface help instead of a screen magnifier? I know next to nothing about these tools, other than that they exist. === If the student is running an R application (which is what enter data for her implies to me), then any accessibility issues would need to be addressed in the application itself. But I don't understand why a data entry assistant would need any skills in R itself in order to enter data into it. But without knowing more, that's about all that I can say. One thought: CMU has a college teaching electrical and computer engineering. Depending on what that means, perhaps someone from that college (professor, TA, or grad student) could see what your student is doing and perhaps have some insights on how to help. Or is there a computer club on campus where some geeky student might be found? You might look here: http://www.club.cc.cmu.edu/ If these are true geeks (and the web site sounds promising), then a lure of beer pizza would likely be irresistible grin. === For interfacing R with Excel, you might want to look at RExcel here: http://rcom.univie.ac.at/download.html#RExcel . It has a free student version. But is this more for an Excel user who wants to use R for analysis, not an R user wanting to use Excel for data entry. -- Yoda of Borg, we are. Futile, resistance is, yes. Assimilated, you will be. My sister opened a computer store in Hawaii. She sells C shells down by the seashore. If someone tell you that nothing is impossible: Ask him to dribble a football. He's about as useful as a wax frying pan. 10 to the 12th power microphones = 1 Megaphone Maranatha! John McKown [[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 guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Liz Hare, PhD Dog Genetics LLC dogg...@earthlink.net http://www.doggenetics.com http://www.doggenetics.com/ [[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 guide
Re: [R] help for lay person assisting R user with disability
On Thu, Jun 18, 2015 at 9:32 AM, Courtney Bryant cbry...@andrew.cmu.edu wrote: Good Morning, I am currently working with a disabled R user who is a student here at CMU. The student has both sight and mobility issues. The student has asked for an assistant who is well versed in R to enter data for her, which we are having a hard time finding. I would like information from R developers/users about how/how well R interfaces with Excel (an easier skill set to find!) In your opinion, could it be as easy as uploading data from excel into R? Also, do you know of a way to enlarge the R interface or otherwise assist in making the program accessible to a low vision person? My limited understanding leads me to believe that screen magnifiers like zoom text don't work particularly well. If you have information on that, I would very much appreciate it. Thanks for your help and for bearing with me! Courtney I am a bit confused (a normal condition for me). Is the student writing R code or is the student running a application written in R? Also, since you mentioned Excel, I am assuming that the student is using a PC running Windows as opposed to Linux or a Mac. If the student is writing R code, then I'd suggest that your computer support person install Rstudio. It is cost free and can be downloaded here: http://www.rstudio.com/ . The installer can then customize Rstudio to use a really large font, if that would be helpful. Please forgive my lack of knowledge about accessibility issues. If the student has trouble typing (mobility issue?), this likely won't help. Would a speech to text / text to speech interface help instead of a screen magnifier? I know next to nothing about these tools, other than that they exist. === If the student is running an R application (which is what enter data for her implies to me), then any accessibility issues would need to be addressed in the application itself. But I don't understand why a data entry assistant would need any skills in R itself in order to enter data into it. But without knowing more, that's about all that I can say. One thought: CMU has a college teaching electrical and computer engineering. Depending on what that means, perhaps someone from that college (professor, TA, or grad student) could see what your student is doing and perhaps have some insights on how to help. Or is there a computer club on campus where some geeky student might be found? You might look here: http://www.club.cc.cmu.edu/ If these are true geeks (and the web site sounds promising), then a lure of beer pizza would likely be irresistible grin. === For interfacing R with Excel, you might want to look at RExcel here: http://rcom.univie.ac.at/download.html#RExcel . It has a free student version. But is this more for an Excel user who wants to use R for analysis, not an R user wanting to use Excel for data entry. -- Yoda of Borg, we are. Futile, resistance is, yes. Assimilated, you will be. My sister opened a computer store in Hawaii. She sells C shells down by the seashore. If someone tell you that nothing is impossible: Ask him to dribble a football. He's about as useful as a wax frying pan. 10 to the 12th power microphones = 1 Megaphone Maranatha! John McKown [[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 guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Correlation matrix for pearson correlation (r,p,BH(FDR))
The way the sample data is provided is not useful. I have re-built your data,
please find the dput() version below (and pls check whether I got it right...).
This is not my area of competence at all, but from what I see from the help
page is that the expected parameters are, among others:
x A matrix or dataframe
y A second matrix or dataframe __with the same number of rows as x__
I hope that somebody with a better understanding of your intention is able to
pick up from here, with the sample data in useful format.
Rgds,
Rainer
dput( genes )
structure(list(Genes = structure(1:10, .Label = c(KCNAB3, KCNB1,
KCNB2, KERA, KGFLP1, KGFLP2, KHDC1, KHDC1L, KHDC3L,
KHDRBS1), class = factor), Cell.line1 = c(12.02005181, 0.02457449,
0.44791862, 0.06090217, 0.02450101, 0, 0, 2.3189445, 0, 0), Cell.line2 =
c(11.140091,
1.3028535, 0.1060137, 0, 0, 0, 0, 2.8252262, 0, 0), Cell.line3 = c(15.60381163,
0.81538294, 0.09864136, 0.03352993, 0, 0, 0, 5.29099724, 0, 0
), Cell.line4 = c(13.44151596, 0.59318327, 0, 0.03634781, 0,
0, 0, 7.44183228, 0, 0), Cell.line5 = c(25.3716103, 0.15332321,
0, 0.04190912, 0, 0, 0, 1.94629741, 0, 0), Cell.line6 = c(8.12373424,
4.18181234, 0.05857207, 0, 0.02563099, 0, 0, 8.56022436, 0, 0
), Cell.line7 = c(7.67506261, 1.65268403, 0.05945414, 0, 0.03902548,
0, 0, 7.50838343, 0, 0.0308118), Cell.line8 = c(24.43776341,
5.9834632, 0.20733924, 0.07752608, 0, 0, 0, 7.17964645, 0, 0),
Cell.line9 = c(18.33244818, 1.51423807, 0.05830982, 0.01585643,
0, 0, 0, 3.28602729, 0, 0), Cell.line10 = c(9.224225, 0,
0, 16.664245, 0, 0, 0, 0, 3.598534, 2.600173)), .Names = c(Genes,
Cell.line1, Cell.line2, Cell.line3, Cell.line4, Cell.line5,
Cell.line6, Cell.line7, Cell.line8, Cell.line9, Cell.line10
), row.names = c(1, 2, 3, 4, 5, 6, 7, 8, 9,
10), class = data.frame)
dput( features )
structure(list(Cell.line = c(Growth rate, Drug sensitivity
), Cell.line1 = c(NA, 41.33), Cell.line2 = c(NA, 26.76),
Cell.line3 = c(NA, 24.19), Cell.line4 = c(51.41, NA),
Cell.line5 = c(NA_character_, NA_character_), Cell.line6 = c(5.03,
1.40), Cell.line7 = c(6.57, 1.88), Cell.line8 = c(8,
1.33), Cell.line9 = c(1.26, 5.05), Cell.line10 = c(3,
9.12)), .Names = c(Cell.line, Cell.line1, Cell.line2,
Cell.line3, Cell.line4, Cell.line5, Cell.line6, Cell.line7,
Cell.line8, Cell.line9, Cell.line10), row.names = c(NA,
-2L), class = data.frame)
On Thu June 18 2015 10:19:55 Sarah Bazzocco wrote:
This post was called help before, I changed the Subject.
Thanks for the comments.
Here the example: (I have the two lists saved as .csv and I can open them in
R)
Sheet one- Genes (10 genes expression, not binary, meaured in 10 cell lines)
genes
Genes Cell.line1 Cell.line2 Cell.line3 Cell.line4 Cell.line5
1 KCNAB3 12.02005181 11.1400910 15.60381163 13.44151596 25.37161030
2KCNB1 0.02457449 1.3028535 0.81538294 0.59318327 0.15332321
3KCNB2 0.44791862 0.1060137 0.09864136 0. 0.
4 KERA 0.06090217 0.000 0.03352993 0.03634781 0.04190912
5 KGFLP1 0.02450101 0.000 0. 0. 0.
6 KGFLP2 0. 0.000 0. 0. 0.
7KHDC1 0. 0.000 0. 0. 0.
8 KHDC1L 2.31894450 2.8252262 5.29099724 7.44183228 1.94629741
9 KHDC3L 0. 0.000 0. 0. 0.
10 KHDRBS1 0. 0.000 0. 0. 0.
Cell.line6 Cell.line7 Cell.line8 Cell.line9 Cell.line10
1 8.12373424 7.67506261 24.43776341 18.332448189.224225
2 4.18181234 1.65268403 5.98346320 1.514238070.00
3 0.05857207 0.05945414 0.20733924 0.058309820.00
4 0. 0. 0.07752608 0.01585643 16.664245
5 0.02563099 0.03902548 0. 0.0.00
6 0. 0. 0. 0.0.00
7 0. 0. 0. 0.0.00
8 8.56022436 7.50838343 7.17964645 3.286027290.00
9 0. 0. 0. 0.3.598534
10 0. 0.03081180 0. 0.2.600173
Sheet two - features (2 features(Growth rate,drug sensitivity for 10 cell
lines)
features
Cell.line Cell.line1 Cell.line2 Cell.line3 Cell.line4 Cell.line5
1 Growth rate NA NA NA 51.41 NA
2 Drug sensitivity 5.03 6.57 8 1.26 3
Cell.line6 Cell.line7 Cell.line8 Cell.line9 Cell.line10
1 41.33 26.76 24.19 NA NA
2 1.40 1.88 1.33 5.059.12
What I found:
corr.test {psych}
corr.test(x, y = NULL, use =
pairwise,method=pearson,adjust=BH,alpha=.01)
-- I adjusted the original command to what I need (BH insted og holm) and
alpha=.01 insted of 0.05.
I would be very happy, if someone could show me how to use this command, in
particular
Re: [R] How to round only one df row how to keep 3rd sigdif if zero
Thanks for taking the time to share your thoughts, PP. I always extensively google search before resorting to R forum. In my real dataset, not in the example I created for the forum, I had tried converting the matrix to a dataframe but it retained the unwanted format. And, these tables are being used in a report generated with the rtf package, so I have to get the format right for outside the console. Because of another unrelated issue, though, I had to use a different approach to creating the dataframe with counts/rates added, so the issue was circumvented. Cheers. -Original Message- From: PIKAL Petr [mailto:petr.pi...@precheza.cz] Sent: Thursday, June 18, 2015 10:56 AM To: Crombie, Burnette N; r-help@r-project.org Subject: RE: [R] How to round only one df row how to keep 3rd sigdif if zero Hi You need to distinguish between an object and printing an object on console. When you print an object you can use several options for formating. ?sprintf, ?formatC formatC(t(a), digits=1, format=f) [,1] [,2] [,3] count 1.0 2.0 3.0 rate 16.7 33.3 50.0 Also when you transpose a the result is not data frame but matrix. str(t(a)) num [1:2, 1:3] 1 16.7 2 33.3 3 50 - attr(*, dimnames)=List of 2 ..$ : chr [1:2] count rate ..$ : NULL str(a) 'data.frame': 3 obs. of 2 variables: $ count: num 1 2 3 $ rate : num 16.7 33.3 50 If you used google or other internet search options you would get plenty of results yourself. try formatting numbers R Cheers Petr -Original Message- From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of bcrombie Sent: Thursday, June 18, 2015 3:09 PM To: r-help@r-project.org Subject: [R] How to round only one df row how to keep 3rd sigdif if zero # How do I round only one row of a dataframe? # After transposing a dataframe of counts rates, all values took on the most # of signif digits in the dataset (rates), but I want counts to remain only one digit. # Also, how can I keep 3 significant digits in R when the 3rd is a zero? count - c(1, 2, 3) rate - c(16.7, 33.3, 50.0) a - data.frame(count,rate) a # count rate # 1 1 16.7 # 2 2 33.3 # 3 3 50.0 a - t(a) a # [,1] [,2] [,3] # count 1.0 2.03 # rate 16.7 33.3 50 -- View this message in context: http://r.789695.n4.nabble.com/How-to- round-only-one-df-row-how-to-keep-3rd-sigdif-if-zero-tp4708819.html Sent from the R help mailing list archive at Nabble.com. __ 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 guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. Tento e-mail a jakékoliv k němu připojené dokumenty jsou důvěrné a jsou určeny pouze jeho adresátům. Jestliže jste obdržel(a) tento e-mail omylem, informujte laskavě neprodleně jeho odesílatele. Obsah tohoto emailu i s přílohami a jeho kopie vymažte ze svého systému. Nejste-li zamýšleným adresátem tohoto emailu, nejste oprávněni tento email jakkoliv užívat, rozšiřovat, kopírovat či zveřejňovat. Odesílatel e-mailu neodpovídá za eventuální škodu způsobenou modifikacemi či zpožděním přenosu e-mailu. V případě, že je tento e-mail součástí obchodního jednání: - vyhrazuje si odesílatel právo ukončit kdykoliv jednání o uzavření smlouvy, a to z jakéhokoliv důvodu i bez uvedení důvodu. - a obsahuje-li nabídku, je adresát oprávněn nabídku bezodkladně přijmout; Odesílatel tohoto e-mailu (nabídky) vylučuje přijetí nabídky ze strany příjemce s dodatkem či odchylkou. - trvá odesílatel na tom, že příslušná smlouva je uzavřena teprve výslovným dosažením shody na všech jejích náležitostech. - odesílatel tohoto emailu informuje, že není oprávněn uzavírat za společnost žádné smlouvy s výjimkou případů, kdy k tomu byl písemně zmocněn nebo písemně pověřen a takové pověření nebo plná moc byly adresátovi tohoto emailu případně osobě, kterou adresát zastupuje, předloženy nebo jejich existence je adresátovi či osobě jím zastoupené známá. This e-mail and any documents attached to it may be confidential and are intended only for its intended recipients. If you received this e-mail by mistake, please immediately inform its sender. Delete the contents of this e-mail with all attachments and its copies from your system. If you are not the intended recipient of this e-mail, you are not authorized to use, disseminate, copy or disclose this e-mail in any manner. The sender of this e-mail shall not be liable for any possible damage caused by modifications of the e-mail or by delay with transfer of the email. In case that this e-mail forms part of business dealings: - the sender reserves the right to end negotiations about entering into a contract in any time, for any reason, and without stating any reasoning. - if the e-mail contains an
Re: [R] help for lay person assisting R user with disability
Given that neither you nor the student are (skilled?) R users, I think you would do better contacting someone locally for help -- there will be many in the statistics and social sciences departments (among others). There are several R packages that interface with Excel (e.g. RExcel), but it may merely be a matter of reading in text files via R's native facilities (e.g. read.csv ) . A local resource can best help you sort out what would work best in your situation imho. Cheers, Bert Bert Gunter Data is not information. Information is not knowledge. And knowledge is certainly not wisdom. -- Clifford Stoll On Thu, Jun 18, 2015 at 7:32 AM, Courtney Bryant cbry...@andrew.cmu.edu wrote: Good Morning, I am currently working with a disabled R user who is a student here at CMU. The student has both sight and mobility issues. The student has asked for an assistant who is well versed in R to enter data for her, which we are having a hard time finding. I would like information from R developers/users about how/how well R interfaces with Excel (an easier skill set to find!) In your opinion, could it be as easy as uploading data from excel into R? Also, do you know of a way to enlarge the R interface or otherwise assist in making the program accessible to a low vision person? My limited understanding leads me to believe that screen magnifiers like zoom text don't work particularly well. If you have information on that, I would very much appreciate it. Thanks for your help and for bearing with me! Courtney Courtney Bryant, EOS Specialist Equal Opportunity Services, Human Resources Carnegie Mellon University 412-268-3930 | cbry...@andrew.cmu.edu __ 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 guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[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 guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] help for lay person assisting R user with disability
On 18/06/2015 11:32 AM, Courtney Bryant wrote: Good Morning, I am currently working with a disabled R user who is a student here at CMU. The student has both sight and mobility issues. The student has asked for an assistant who is well versed in R to enter data for her, which we are having a hard time finding. I would like information from R developers/users about how/how well R interfaces with Excel (an easier skill set to find!) In your opinion, could it be as easy as uploading data from excel into R? Also, do you know of a way to enlarge the R interface or otherwise assist in making the program accessible to a low vision person? My limited understanding leads me to believe that screen magnifiers like zoom text don't work particularly well. If you have information on that, I would very much appreciate it. There was an article not too long ago in the R Journal about this issue; you can read it here: http://journal.r-project.org/archive/2013-1/godfrey.pdf I think the main R thing that has changed since then is the rise in the prominence and maturity of RStudio. At that time the author didn't find it very easy to use, but it might be worth investigating again. The author put together a web page http://r-resources.massey.ac.nz/StatSoftware/ that you might find useful as well. Duncan Murdoch __ 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 guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] help for lay person assisting R user with disability
Almost 20 years ago my son was in the DO-IT program at the University of Washington http://www.washington.edu/doit/. They have been very proactive in reaching out to other institutions. They have been solving problems such as yours and I suspect can suggest several workable solutions. Clint Clint BowmanINTERNET: cl...@ecy.wa.gov Air Quality Modeler INTERNET: cl...@math.utah.edu Department of Ecology VOICE: (360) 407-6815 PO Box 47600FAX:(360) 407-7534 Olympia, WA 98504-7600 USPS: PO Box 47600, Olympia, WA 98504-7600 Parcels:300 Desmond Drive, Lacey, WA 98503-1274 On Thu, 18 Jun 2015, Liz Hare wrote: Hi Courtney and John, The RStudio environment mentioned below will not work with speech output (I tried with Window-Eyes awhile ago). Some of my clients use it but I have no experience with it. Since the student is partially sighted, they might be able to customize the environment with big fonts and contrast, I’m just not sure. Using a screen reader like Window-Eyes, the student could use the R GUI environment, although it’s a little frustrating because it doesn’t speak a lot and you need to use the mouse keys a lot. The other option if you have to stick with Windows is to run R at the command prompt, which makes interaction slightly easier but you’d have to figure out how to log the output. What is being recommended for the rest of the students in the class? Ideally, this student’s experience should be as close as possible to the others’. Liz On Jun 18, 2015, at 12:17 PM, John McKown john.archie.mck...@gmail.com wrote: On Thu, Jun 18, 2015 at 9:32 AM, Courtney Bryant cbry...@andrew.cmu.edu wrote: Good Morning, I am currently working with a disabled R user who is a student here at CMU. The student has both sight and mobility issues. The student has asked for an assistant who is well versed in R to enter data for her, which we are having a hard time finding. I would like information from R developers/users about how/how well R interfaces with Excel (an easier skill set to find!) In your opinion, could it be as easy as uploading data from excel into R? Also, do you know of a way to enlarge the R interface or otherwise assist in making the program accessible to a low vision person? My limited understanding leads me to believe that screen magnifiers like zoom text don't work particularly well. If you have information on that, I would very much appreciate it. Thanks for your help and for bearing with me! Courtney I am a bit confused (a normal condition for me). Is the student writing R code or is the student running a application written in R? Also, since you mentioned Excel, I am assuming that the student is using a PC running Windows as opposed to Linux or a Mac. If the student is writing R code, then I'd suggest that your computer support person install Rstudio. It is cost free and can be downloaded here: http://www.rstudio.com/ . The installer can then customize Rstudio to use a really large font, if that would be helpful. Please forgive my lack of knowledge about accessibility issues. If the student has trouble typing (mobility issue?), this likely won't help. Would a speech to text / text to speech interface help instead of a screen magnifier? I know next to nothing about these tools, other than that they exist. === If the student is running an R application (which is what enter data for her implies to me), then any accessibility issues would need to be addressed in the application itself. But I don't understand why a data entry assistant would need any skills in R itself in order to enter data into it. But without knowing more, that's about all that I can say. One thought: CMU has a college teaching electrical and computer engineering. Depending on what that means, perhaps someone from that college (professor, TA, or grad student) could see what your student is doing and perhaps have some insights on how to help. Or is there a computer club on campus where some geeky student might be found? You might look here: http://www.club.cc.cmu.edu/ If these are true geeks (and the web site sounds promising), then a lure of beer pizza would likely be irresistible grin. === For interfacing R with Excel, you might want to look at RExcel here: http://rcom.univie.ac.at/download.html#RExcel . It has a free student version. But is this more for an Excel user who wants to use R for analysis, not an R user wanting to use Excel for data entry. -- Yoda of Borg, we are. Futile, resistance is, yes. Assimilated, you will be. My sister opened a computer store in Hawaii. She sells C shells down by the seashore. If someone tell you that nothing is impossible: Ask him to dribble a football. He's about as useful as a wax frying pan. 10 to the 12th power microphones = 1 Megaphone Maranatha! John McKown [[alternative HTML version deleted]]
[R] Repeated Measures ANOVA and Missing Values in the data set
I am doing Repeated Measures ANOVA with missing values. When i run my model i get this error message. *aov.out = aov(values ~ time + Error(subject/time), data=mydata2)Warning message:In aov(values ~ time + Error(subject/time), data = mydata2) : Error() model is singular* The missing Values are not a error of my instrument. They mean the element of my analysis is absent and i want to consider this. thanks in advance these are my data: subject - c(1,2,3,4,5,6,7,8,9,10) time1 - c(5040,3637,6384,5309,5420,3549,NA,5140,3890,3910) time2 - c(5067, 3668, NA, 6489, NA, 3922, 3408, 6613, 4063, 3937) time3 - c( 3278, 3814, 8745, 4760, 4911, 5716, 5547, 5844, 4914, 4390) time4 - c( 0, 2971,0, 2776, 2128, 1208, 2935, 2739, 3054, 3363) time5 - c(4161, 3483, 6728, 5008, 5562, 4380, 4006, 7536, 3805, 3923) time6 - c( 3604, 3411, 2523, 3264, 3578, 2941, 2939, NA, 3612, 3604) mydata - data.frame(time1, time2, time3, time4, time5, time6) mydata2 = stack(mydata) subject = factor(rep(subject,6)) mydata2[3] = subject colnames(mydata2) = c(values, time, subject) aov.out = aov(values ~ time + Error(subject/time), data=mydata2) summary(aov.out) model.tables(aov.out,means) [[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 guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Sign of specific elements of a vector
On Jun 18, 2015, at 1:21 PM, Marc Schwartz wrote:
Just to augment Bert’s comment, other options are likely to introduce some
level of overhead that while perhaps looking better, will not be materially
faster. Depending upon the length of your vector, you could do some testing
to see.
Another method which depends upon R recycling of vector arguments:
x - x*c(rep(1,19), -1)
Might be a bit faster:
set.seed(1)
x - rnorm(1e6)
system.time(x - x*c(rep(1,19), -1))
user system elapsed
0.005 0.000 0.005
set.seed(1)
system.time({
+ IND - seq(20,length(x), by=20)
+ x[IND] - -x[IND]})
user system elapsed
0.010 0.001 0.011
--
David.
One thing that might yield a little bit of performance improvement would be
to pre-calculate the indices:
set.seed(1)
x - rnorm(100)
IND - seq(20,100, by=20)
IND
[1] 20 40 60 80 100
x[IND]
[1] 0.5939013 0.7631757 -0.1350546 -0.5895209 -0.4734006
x[IND] - -x[IND]
x[IND]
[1] -0.5939013 -0.7631757 0.1350546 0.5895209 0.4734006
But unless your vector is very large, I suspect the performance gain may be
minimal in real time.
Regards,
Marc Schwartz
On Jun 18, 2015, at 3:07 PM, Bert Gunter bgunter.4...@gmail.com wrote:
Your **is** the coolest and most efficient way to do this. It's
vectorized -- apply() stuff is not.
Cheers,
Bert
Bert Gunter
Data is not information. Information is not knowledge. And knowledge is
certainly not wisdom.
-- Clifford Stoll
On Thu, Jun 18, 2015 at 12:40 PM, Frank S. f_j_...@hotmail.com wrote:
Hi everyone,
I have an x vector and I would want to change the sign every 20
elements. For this puspose,
I wrote the following code:
set.seed(1)
x - rnorm(100)
x
x[seq(20,100, by=20)] - -x[seq(20,100, by=20)]
x
However, I'm afraid it is a rudimentary form to get the desired result.
II wonder wether there is a cool way to do so, that is, for example with
apply or sign function.
Thans in advanced for your help!
Frank S.
__
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 guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
David Winsemius
Alameda, CA, USA
__
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 guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Correlation matrix for pearson correlation (r,p,BH(FDR))
You have multiple options. I will advertise my own solution - install
the package WGCNA, installation instructions at
http://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/Rpackages/WGCNA/#cranInstall
then you can use the function
cp = corAndPvalue(t(genes), t(features)).
You need to transpose both because the function expects variables in
columns and samples in rows.
This will give you a list whose components include 'cor' (matrix of
the correlation values) and 'p' (matrix of the Student p-values). To
get a matrix of the corresponding FDR, use
fdr = apply(cp$p, 2, p.adjust, method = fdr)
Hope this helps,
Peter
On Thu, Jun 18, 2015 at 1:19 AM, Sarah Bazzocco sarah.bazzo...@vhir.org wrote:
This post was called help before, I changed the Subject.
Thanks for the comments.
Here the example: (I have the two lists saved as .csv and I can open them in
R)
Sheet one- Genes (10 genes expression, not binary, meaured in 10 cell lines)
genes
Genes Cell.line1 Cell.line2 Cell.line3 Cell.line4 Cell.line5
1 KCNAB3 12.02005181 11.1400910 15.60381163 13.44151596 25.37161030
2KCNB1 0.02457449 1.3028535 0.81538294 0.59318327 0.15332321
3KCNB2 0.44791862 0.1060137 0.09864136 0. 0.
4 KERA 0.06090217 0.000 0.03352993 0.03634781 0.04190912
5 KGFLP1 0.02450101 0.000 0. 0. 0.
6 KGFLP2 0. 0.000 0. 0. 0.
7KHDC1 0. 0.000 0. 0. 0.
8 KHDC1L 2.31894450 2.8252262 5.29099724 7.44183228 1.94629741
9 KHDC3L 0. 0.000 0. 0. 0.
10 KHDRBS1 0. 0.000 0. 0. 0.
Cell.line6 Cell.line7 Cell.line8 Cell.line9 Cell.line10
1 8.12373424 7.67506261 24.43776341 18.332448189.224225
2 4.18181234 1.65268403 5.98346320 1.514238070.00
3 0.05857207 0.05945414 0.20733924 0.058309820.00
4 0. 0. 0.07752608 0.01585643 16.664245
5 0.02563099 0.03902548 0. 0.0.00
6 0. 0. 0. 0.0.00
7 0. 0. 0. 0.0.00
8 8.56022436 7.50838343 7.17964645 3.286027290.00
9 0. 0. 0. 0.3.598534
10 0. 0.03081180 0. 0.2.600173
Sheet two - features (2 features(Growth rate,drug sensitivity for 10 cell
lines)
features
Cell.line Cell.line1 Cell.line2 Cell.line3 Cell.line4 Cell.line5
1 Growth rate NA NA NA 51.41 NA
2 Drug sensitivity 5.03 6.57 8 1.26 3
Cell.line6 Cell.line7 Cell.line8 Cell.line9 Cell.line10
1 41.33 26.76 24.19 NA NA
2 1.40 1.88 1.33 5.059.12
What I found:
corr.test {psych}
corr.test(x, y = NULL, use =
pairwise,method=pearson,adjust=BH,alpha=.01)
-- I adjusted the original command to what I need (BH insted og holm) and
alpha=.01 insted of 0.05.
I would be very happy, if someone could show me how to use this command, in
particular how to refer as x and y to the two sheets I have (Genes and
Features). I would take it from there.
Thanks a lot in advance.
Sarah
- Original Message -
From: Rainer Schuermann rainer.schuerm...@gmx.net
To: Sarah Bazzocco sarah.bazzo...@vhir.org
Sent: Thursday, 18 June, 2015 8:14:56 AM
Subject: Re: [R] help
Hi Sarah,
Not an answer to our question but a piece of well intended advice:
1. Don't post HTML but plain text. Not only that people will tell you this in
a sometimes not very friendly manner - using HTML actually does make posts
illegible in this mailing list. Code, and R _is_ code, is always plain text.
2. Don't pose an abstract problem - this looks too much like Can you please
do my work for me. Show us what you have tried already, and people will
happily jump in and provide their thoughts and advice.
3. Always make sure that you ave a reproducible example in your mail, and a
set of data of the same type and structure you are using - ideally using
dput().
See further advice here
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
and here:
http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example
For your problem, R has an immense wealth of ideas and solutions.
Rgds,
Rainer
On Wed June 17 2015 16:57:24 Sarah Bazzocco wrote:
Hello,
�
I am a R-beginner and I need some help.�The question is very simple: I need
to do a pearson correlations (r,p-value and FDR with BH) from an Expression
array (with several thousand genes for lets say 20 cell lines)�with some
features of those cell lines.
My problem I
Re: [R] help for lay person assisting R user with disability
Hi Jonathon Godfrey has published some information and guidelines on the accessibility of R (and other stat software), e.g., ... http://r-resources.massey.ac.nz/StatSoftware/ http://journal.r-project.org/archive/2013-1/godfrey.pdf Paul On 06/19/15 02:32, Courtney Bryant wrote: Good Morning, I am currently working with a disabled R user who is a student here at CMU. The student has both sight and mobility issues. The student has asked for an assistant who is well versed in R to enter data for her, which we are having a hard time finding. I would like information from R developers/users about how/how well R interfaces with Excel (an easier skill set to find!) In your opinion, could it be as easy as uploading data from excel into R? Also, do you know of a way to enlarge the R interface or otherwise assist in making the program accessible to a low vision person? My limited understanding leads me to believe that screen magnifiers like zoom text don't work particularly well. If you have information on that, I would very much appreciate it. Thanks for your help and for bearing with me! Courtney Courtney Bryant, EOS Specialist Equal Opportunity Services, Human Resources Carnegie Mellon University 412-268-3930 | cbry...@andrew.cmu.edu __ 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 guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Dr Paul Murrell Department of Statistics The University of Auckland Private Bag 92019 Auckland New Zealand 64 9 3737599 x85392 p...@stat.auckland.ac.nz http://www.stat.auckland.ac.nz/~paul/ __ 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 guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Sign of specific elements of a vector
Hi everyone, I have an x vector and I would want to change the sign every 20 elements. For this puspose, I wrote the following code: set.seed(1) x - rnorm(100) x x[seq(20,100, by=20)] - -x[seq(20,100, by=20)] x However, I'm afraid it is a rudimentary form to get the desired result. II wonder wether there is a cool way to do so, that is, for example with apply or sign function. Thans in advanced for your help! Frank S. [[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 guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] help for lay person assisting R user with disability
Hi Liz, This is a particularly sticky case – the student is attempting to get a PhD but is currently in between programs until her current project (which we’re attempting to hire an assistant for, or better yet some up with a solution she can work on her own) is completed and “accepted” in some way. I believe her main access issue is around mobility, she has little use of her hands. I wasn’t sure if sight was as much of an issue, but from what I’ve learned here it seems that enlarging the text itself is easy enough. I will double check with her about her computer – at the end of the day, if she is game, perhaps I could provide her with a mac. Courtney Bryant, EOS Specialist Equal Opportunity Services, Human Resources Carnegie Mellon University 412-268-3930 | cbry...@andrew.cmu.edumailto:cbry...@andrew.cmu.edu From: Liz Hare [mailto:dogg...@earthlink.net] Sent: Thursday, June 18, 2015 12:42 PM To: John McKown Cc: Courtney Bryant; r-help@R-project.org Subject: Re: [R] help for lay person assisting R user with disability Hi Courtney and John, The RStudio environment mentioned below will not work with speech output (I tried with Window-Eyes awhile ago). Some of my clients use it but I have no experience with it. Since the student is partially sighted, they might be able to customize the environment with big fonts and contrast, I’m just not sure. Using a screen reader like Window-Eyes, the student could use the R GUI environment, although it’s a little frustrating because it doesn’t speak a lot and you need to use the mouse keys a lot. The other option if you have to stick with Windows is to run R at the command prompt, which makes interaction slightly easier but you’d have to figure out how to log the output. What is being recommended for the rest of the students in the class? Ideally, this student’s experience should be as close as possible to the others’. Liz On Jun 18, 2015, at 12:17 PM, John McKown john.archie.mck...@gmail.commailto:john.archie.mck...@gmail.com wrote: On Thu, Jun 18, 2015 at 9:32 AM, Courtney Bryant cbry...@andrew.cmu.edumailto:cbry...@andrew.cmu.edu wrote: Good Morning, I am currently working with a disabled R user who is a student here at CMU. The student has both sight and mobility issues. The student has asked for an assistant who is well versed in R to enter data for her, which we are having a hard time finding. I would like information from R developers/users about how/how well R interfaces with Excel (an easier skill set to find!) In your opinion, could it be as easy as uploading data from excel into R? Also, do you know of a way to enlarge the R interface or otherwise assist in making the program accessible to a low vision person? My limited understanding leads me to believe that screen magnifiers like zoom text don't work particularly well. If you have information on that, I would very much appreciate it. Thanks for your help and for bearing with me! Courtney I am a bit confused (a normal condition for me). Is the student writing R code or is the student running a application written in R? Also, since you mentioned Excel, I am assuming that the student is using a PC running Windows as opposed to Linux or a Mac. If the student is writing R code, then I'd suggest that your computer support person install Rstudio. It is cost free and can be downloaded here: http://www.rstudio.com/ . The installer can then customize Rstudio to use a really large font, if that would be helpful. Please forgive my lack of knowledge about accessibility issues. If the student has trouble typing (mobility issue?), this likely won't help. Would a speech to text / text to speech interface help instead of a screen magnifier? I know next to nothing about these tools, other than that they exist. === If the student is running an R application (which is what enter data for her implies to me), then any accessibility issues would need to be addressed in the application itself. But I don't understand why a data entry assistant would need any skills in R itself in order to enter data into it. But without knowing more, that's about all that I can say. One thought: CMU has a college teaching electrical and computer engineering. Depending on what that means, perhaps someone from that college (professor, TA, or grad student) could see what your student is doing and perhaps have some insights on how to help. Or is there a computer club on campus where some geeky student might be found? You might look here: http://www.club.cc.cmu.edu/ If these are true geeks (and the web site sounds promising), then a lure of beer pizza would likely be irresistible grin. === For interfacing R with Excel, you might want to look at RExcel here: http://rcom.univie.ac.at/download.html#RExcel . It has a free student version. But is this more for an Excel user who wants to use R for analysis, not an R user wanting to use Excel for data entry. -- Yoda of Borg, we are. Futile, resistance is,
[R] R problem
Hi, R users. I am using windows 7 ultimate, as an OS, and the R version 3.2.0. This combination creates some problems when I run R. The problem focuses on the command ‘source’. More precisely, suppose that we have a main function, let call it mainfn, which calls within it another function, call it subfn, with the command source(“C:\\Program Files\\. . .\\subfn.txt”). The files with the R code of the two functions, mainfn and subfn, are .txt files. First I load the mainfn function using File- Source R code… and I get source(“C:\\Program Files\\ . . .\\mainfn.txt”) Then I run the mainfn mainfn () and I get Error in file(filename, r, encoding = encoding) : cannot open the connection Any suggestion what goes wrong? __ 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 guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Sign of specific elements of a vector
Just to augment Bert’s comment, other options are likely to introduce some level of overhead that while perhaps looking better, will not be materially faster. Depending upon the length of your vector, you could do some testing to see. One thing that might yield a little bit of performance improvement would be to pre-calculate the indices: set.seed(1) x - rnorm(100) IND - seq(20,100, by=20) IND [1] 20 40 60 80 100 x[IND] [1] 0.5939013 0.7631757 -0.1350546 -0.5895209 -0.4734006 x[IND] - -x[IND] x[IND] [1] -0.5939013 -0.7631757 0.1350546 0.5895209 0.4734006 But unless your vector is very large, I suspect the performance gain may be minimal in real time. Regards, Marc Schwartz On Jun 18, 2015, at 3:07 PM, Bert Gunter bgunter.4...@gmail.com wrote: Your **is** the coolest and most efficient way to do this. It's vectorized -- apply() stuff is not. Cheers, Bert Bert Gunter Data is not information. Information is not knowledge. And knowledge is certainly not wisdom. -- Clifford Stoll On Thu, Jun 18, 2015 at 12:40 PM, Frank S. f_j_...@hotmail.com wrote: Hi everyone, I have an x vector and I would want to change the sign every 20 elements. For this puspose, I wrote the following code: set.seed(1) x - rnorm(100) x x[seq(20,100, by=20)] - -x[seq(20,100, by=20)] x However, I'm afraid it is a rudimentary form to get the desired result. II wonder wether there is a cool way to do so, that is, for example with apply or sign function. Thans in advanced for your help! Frank S. __ 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 guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Sign of specific elements of a vector
Your **is** the coolest and most efficient way to do this. It's vectorized -- apply() stuff is not. Cheers, Bert Bert Gunter Data is not information. Information is not knowledge. And knowledge is certainly not wisdom. -- Clifford Stoll On Thu, Jun 18, 2015 at 12:40 PM, Frank S. f_j_...@hotmail.com wrote: Hi everyone, I have an x vector and I would want to change the sign every 20 elements. For this puspose, I wrote the following code: set.seed(1) x - rnorm(100) x x[seq(20,100, by=20)] - -x[seq(20,100, by=20)] x However, I'm afraid it is a rudimentary form to get the desired result. II wonder wether there is a cool way to do so, that is, for example with apply or sign function. Thans in advanced for your help! Frank S. [[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 guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[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 guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R problem
Usually, along with that error message, you get a warning that gives a few details about the problem, like the name of the file and the reason it could be opened. E.g., filename - no\\such\\file.blah.blah file(filename, r, encoding=UTF-8) Error in file(filename, r, encoding = UTF-8) : cannot open the connection In addition: Warning message: In file(filename, r, encoding = UTF-8) : cannot open file 'no\such\file.blah.blah': No such file or directory Did you suppress warnings? Bill Dunlap TIBCO Software wdunlap tibco.com On Thu, Jun 18, 2015 at 10:55 AM, Endy pert...@yahoo.gr wrote: Hi, R users. I am using windows 7 ultimate, as an OS, and the R version 3.2.0. This combination creates some problems when I run R. The problem focuses on the command ‘source’. More precisely, suppose that we have a main function, let call it mainfn, which calls within it another function, call it subfn, with the command source(“C:\\Program Files\\. . .\\subfn.txt”). The files with the R code of the two functions, mainfn and subfn, are .txt files. First I load the mainfn function using File- Source R code… and I get source(“C:\\Program Files\\ . . .\\mainfn.txt”) Then I run the mainfn mainfn () and I get Error in file(filename, r, encoding = encoding) : cannot open the connection Any suggestion what goes wrong? __ 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 guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[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 guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Is there a convenient way of extracting the matrix `solve(X %*% t(X) + PENALTY)` from an additive model fit in mgcv?
Yes... ## example fit... library(mgcv) set.seed(2) ## simulate some data... dat - gamSim(1,n=400,dist=normal,scale=2) b - gam(y~s(x0)+s(x1)+s(x2)+s(x3),data=dat) ## extract the thing required in the title b$Vp/b$sig2 best, Simon On 18/06/15 03:23, Andrew Crane-Droesch wrote: The title says it all. An additive model can be fit by `solve(X %*% t(X) + PENALTY)%*%t(X)%*%y` (though of course there are more efficient ways to do it). I want the matrix `solve(X %*% t(X) + PENALTY)` from a fitted gam object. GAM objects can be a bit tricky to navigate -- is there a convenient way of extracting this? Happy to explain why I'm interested in this to anyone who would like to know, off-list. Many thanks! Andrew __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Simon Wood, Mathematical Science, University of Bath BA2 7AY UK +44 (0)1225 386603 http://people.bath.ac.uk/sw283 __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Is there a convenient way of extracting the matrix `solve(X %*% t(X) + PENALTY)` from an additive model fit in mgcv?
...That should have been obvious! I'm a little embarrassed! Thanks, Andrew ** On 06/18/2015 01:14 PM, Simon Wood wrote: Yes... ## example fit... library(mgcv) set.seed(2) ## simulate some data... dat - gamSim(1,n=400,dist=normal,scale=2) b - gam(y~s(x0)+s(x1)+s(x2)+s(x3),data=dat) ## extract the thing required in the title b$Vp/b$sig2 best, Simon On 18/06/15 03:23, Andrew Crane-Droesch wrote: The title says it all. An additive model can be fit by `solve(X %*% t(X) + PENALTY)%*%t(X)%*%y` (though of course there are more efficient ways to do it). I want the matrix `solve(X %*% t(X) + PENALTY)` from a fitted gam object. GAM objects can be a bit tricky to navigate -- is there a convenient way of extracting this? Happy to explain why I'm interested in this to anyone who would like to know, off-list. Many thanks! Andrew __ 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 guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[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 guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Is there a convenient way of extracting the matrix `solve(X %*% t(X) + PENALTY)` from an additive model fit in mgcv?
The title says it all. An additive model can be fit by `solve(X %*% t(X) + PENALTY)%*%t(X)%*%y` (though of course there are more efficient ways to do it). I want the matrix `solve(X %*% t(X) + PENALTY)` from a fitted gam object. GAM objects can be a bit tricky to navigate -- is there a convenient way of extracting this? Happy to explain why I'm interested in this to anyone who would like to know, off-list. Many thanks! Andrew __ 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 guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Grouping in R
Hi We can only guess what you really want. Maybe this. set.seed(111) cust-sample(letters[1:5], 500, replace =T) value-sample(1:1000, 500) month-sample(1:12, 500, replace=T) dat-data.frame(cust, value, month) dat.ag-aggregate(dat$value, list(dat$month, dat$cust), sum) head(dat.ag) Group.1 Group.2x 1 1 a 2444 2 2 a 6234 3 3 a 6082 4 4 a 3691 5 5 a 3044 6 6 a 3534 dput(dat.ag) structure(list(Group.1 = c(1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L), Group.2 = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L), .Label = c(a, b, c, d, e), class = factor), x = c(2444L, 6234L, 6082L, 3691L, 3044L, 3534L, 7444L, 1819L, 2295L, 4774L, 3659L, 1159L, 6592L, 1272L, 8245L, 2324L, 5189L, 3935L, 2945L, 2386L, 2796L, 2869L, 3142L, 4657L, 4411L, 6223L, 3266L, 3842L, 6056L, 7472L, 3879L, 7135L, 4544L, 4498L, 2703L, 3409L, 2748L, 2288L, 2654L, 4995L, 4626L, 5543L, 2162L, 4681L, 5853L, 6229L, 3001L, 5274L, 3852L, 2635L, 5643L, 2809L, 2988L, 3756L, 5180L, 2997L, 4883L, 4208L, 2669L, 3151L)), .Names = c(Group.1, Group.2, x), row.names = c(NA, -60L), class = data.frame) But maybe something different. Who knows? If you wanted grouping by value use ?cut or ?findInterval Cheers Petr -Original Message- From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Shivi82 Sent: Thursday, June 18, 2015 9:22 AM To: r-help@r-project.org Subject: [R] Grouping in R Hi All, I am working on a data where the total row count is 25+ and have approx. 20 variables. One of the var on which i need to summarize the data is Consignor i.e. seller name. Now the issue here is after deleting all the duplicate names i still have 55000 unique customer name and i am not sure on how to summarize the data. Is there a possibility that i could create 8 or 10 groups based on the weight or booking they made from our company and eventually all 55000 customers would fall under these 10 groups. Then it could be easier for me to analyze in which group there is a variance on a month on month level. -- View this message in context: http://r.789695.n4.nabble.com/Grouping- in-R-tp4708800.html Sent from the R help mailing list archive at Nabble.com. __ 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 guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. Tento e-mail a jakékoliv k němu připojené dokumenty jsou důvěrné a jsou určeny pouze jeho adresátům. Jestliže jste obdržel(a) tento e-mail omylem, informujte laskavě neprodleně jeho odesílatele. Obsah tohoto emailu i s přílohami a jeho kopie vymažte ze svého systému. Nejste-li zamýšleným adresátem tohoto emailu, nejste oprávněni tento email jakkoliv užívat, rozšiřovat, kopírovat či zveřejňovat. Odesílatel e-mailu neodpovídá za eventuální škodu způsobenou modifikacemi či zpožděním přenosu e-mailu. V případě, že je tento e-mail součástí obchodního jednání: - vyhrazuje si odesílatel právo ukončit kdykoliv jednání o uzavření smlouvy, a to z jakéhokoliv důvodu i bez uvedení důvodu. - a obsahuje-li nabídku, je adresát oprávněn nabídku bezodkladně přijmout; Odesílatel tohoto e-mailu (nabídky) vylučuje přijetí nabídky ze strany příjemce s dodatkem či odchylkou. - trvá odesílatel na tom, že příslušná smlouva je uzavřena teprve výslovným dosažením shody na všech jejích náležitostech. - odesílatel tohoto emailu informuje, že není oprávněn uzavírat za společnost žádné smlouvy s výjimkou případů, kdy k tomu byl písemně zmocněn nebo písemně pověřen a takové pověření nebo plná moc byly adresátovi tohoto emailu případně osobě, kterou adresát zastupuje, předloženy nebo jejich existence je adresátovi či osobě jím zastoupené známá. This e-mail and any documents attached to it may be confidential and are intended only for its intended recipients. If you received this e-mail by mistake, please immediately inform its sender. Delete the contents of this e-mail with all attachments and its copies from your system. If you are not the intended recipient of this e-mail, you are not authorized to use, disseminate, copy or disclose this e-mail in any manner. The sender of this e-mail shall not be liable for any possible damage caused by modifications of the e-mail or by delay with transfer of the email. In case that this e-mail forms part of business dealings: -
Re: [R] Error bars and CI
Hi Dennis,
I have copied the 'r' group. Could you explain ? Why
can't we compute CI and error bars using this data set ?
The graph generated has equal-sized error bars and a 99% confidence band.
Groups are not needed here. But the error bar and CI calculations could be
incorrect but I am able to draw this.
V1 IDX
1 0.796 1
2 0.542 2
3 0.510 3
4 0.617 4
5 0.482 5
6 0.387 6
7 0.272 7
8 0.536 8
9 0.498 9
10 0.402 10
11 0.328 11
12 0.542 12
13 0.299 13
14 0.647 14
15 0.291 15
16 0.815 16
17 0.680 17
18 0.363 18
19 0.560 19
20 0.334 20
Assume the dataframe is 'jc'.
print(summary(jc$V1))
error - qt(0.995,df=length(jc$V1)-1)*sd(jc$V1)/sqrt(length(jc$V1))
error1 - mean(jc$V1)-error
error2 - mean(jc$V1)+error
print(error1)
print(error2)
q - qplot(geom = line,jc$IDX,jc$V1,
colour='red')+geom_errorbar(aes(x=jc$IDX, ymin=jc$V1-sd(jc$V1),
ymax=jc$V1+sd(jc$V1)), width=0.25)+
geom_ribbon(aes(x=jc$IDX, y=jc$V1, ymin=error1,
ymax=error2),fill=ivory2,alpha = 0.4)+
xlab('Iterations') + ylab(Java Collections)+theme_bw()
Thanks,
Mohan
-Original Message-
From: Dennis Murphy [mailto:djmu...@gmail.com]
Sent: Wednesday, June 17, 2015 8:42 PM
To: Radhakrishnan, Mohan (Cognizant)
Subject: Re: [R] Error bars and CI
Q: How do you expect to get error bars when you plot groups having samples of
size 1? If you are not grouping, then what is the point of trying to
manufacture variation where none exists? I'd suggest you think a little more
deeply about what you can achieve with the available data.
This plot visualizes the data you posted. Every point is accounted for. I named
the input data frame DF.
ggplot(DF, aes(x = IDX, y = V1)) +
geom_line() + geom_point()
If you don't have replicate data at each unique x-value you want to plot, you
cannot legitimately plot error bars, confidence intervals or any other visual
that describes a (summary of) a distribution. If the values of V1 are supposed
to represent averages that come from other data set, then you should have a
corresponding column of standard deviations/standard errors, and *then* you can
plot error bars, CIs, etc. Without a legitimate measure of variation in your
input data frame, I don't see how you can possibly generate a line graph with
accompanying error bars/CIs.
Dennis
On Wed, Jun 17, 2015 at 1:13 AM, mohan.radhakrish...@cognizant.com wrote:
I think it could be something like this. But the mean is for the entire set.
Not groups.
I get a graph with this code but error bars are not there.
p-ggplot(jc,aes(IDX,V1,colour=V1))
p - p + stat_summary(fun.y=mean,geom=point)
p - p + stat_summary(fun.y=mean,geom=line)
p - p + stat_summary(fun.data=mean_cl_normal,conf.int = .99,
geom=errorbar, width=0.2)
Thanks,
Mohan
-Original Message-
From: Radhakrishnan, Mohan (Cognizant)
Sent: Wednesday, June 17, 2015 12:54 PM
To: 'Dennis Murphy'
Cc: r-help@r-project.org
Subject: RE: [R] Error bars and CI
Your sample code is working. But I am missing the logic when my dataset is
involved.
My full dataset is this. It is the V1 column I am interested in. I am not
'grouping' here.
V1 IDX
1 0.796 1
2 0.542 2
3 0.510 3
4 0.617 4
5 0.482 5
6 0.387 6
7 0.272 7
8 0.536 8
9 0.498 9
10 0.402 10
11 0.328 11
12 0.542 12
13 0.299 13
14 0.647 14
15 0.291 15
16 0.815 16
17 0.680 17
18 0.363 18
19 0.560 19
20 0.334 20
Thanks,
Mohan
-Original Message-
From: Dennis Murphy [mailto:djmu...@gmail.com]
Sent: Tuesday, June 16, 2015 1:18 AM
To: Radhakrishnan, Mohan (Cognizant)
Subject: Re: [R] Error bars and CI
Hi:
Firstly, your dplyr code to generate the summary data frame is unnecessary
and distracting, particularly since you didn't provide the input data set;
you are asked to provide a *minimal* reproducible example, which you could
easily have done with a built-in data set.
That said, to get what I perceive you want, I used the InsectSprays data from
the autoloaded datasets package.
# Function to compute standard error of a mean sem - function(x)
sqrt(var(x)/length(x))
## Use insectSprays data for illustration ## Compute mean and SE of
count for each level of spray
library(dplyr)
library(ggplot2)
insectSumm - InsectSprays %%
group_by(spray) %%
summarise(mean = mean(count), se = sem(count))
# Since the x-variable is a factor, need to map group = 1 to # draw lines
between factor levels. geom_pointrange() can be # used to produce the 99% CIs
per factor level, geom_errorbar() # for the mean +/- SE. I ordered the geoms
so that the errorbar # is last, but if you want it (mostly) overwritten, put
the # geom_pointrange() call last.
ggplot(insectSumm, aes(x = spray, y = mean)) +
theme_bw() +
geom_line(aes(group = 1), size = 1, color = darkorange) +
geom_pointrange(aes(ymin = mean -
[R] Grouping in R
Hi All, I am working on a data where the total row count is 25+ and have approx. 20 variables. One of the var on which i need to summarize the data is Consignor i.e. seller name. Now the issue here is after deleting all the duplicate names i still have 55000 unique customer name and i am not sure on how to summarize the data. Is there a possibility that i could create 8 or 10 groups based on the weight or booking they made from our company and eventually all 55000 customers would fall under these 10 groups. Then it could be easier for me to analyze in which group there is a variance on a month on month level. -- View this message in context: http://r.789695.n4.nabble.com/Grouping-in-R-tp4708800.html Sent from the R help mailing list archive at Nabble.com. __ 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 guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Proc Mixed variance of random effects in R
Dear Gram, A few things first: Please don't post in HTML, it mangles your text. R-sig-mixed model is a better list for questions on mixed models. Send further replies only to that list and not to r-help. You are probably not fitting the same model in R as the one in SAS. Please provide the equations of the SAS model and then you can help you translate that into R code. You are assuming that we all speak SAS, but this is an R mailing list. The lingua franca among statistical software is mathematics. Best regards, ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie Kwaliteitszorg / team Biometrics Quality Assurance Kliniekstraat 25 1070 Anderlecht Belgium To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey 2015-06-17 19:52 GMT+02:00 Grams Robins grams_rob...@yahoo.com: Hi, I'm trying to convert the following SAS code in R to get the same result that I get from SAS. Here is the SAS code: DATA plants; INPUT sample $ treatmt $ y ; cards; 1 trt16.426264755 1 trt16.95419631 1 trt16.64385619 1 trt27.348728154 1 trt26.247927513 1 trt26.491853096 2 trt12.807354922 2 trt12.584962501 2 trt13.584962501 2 trt23.906890596 2 trt23 2 trt23.459431619 3 trt12 3 trt14.321928095 3 trt13.459431619 3 trt23.807354922 3 trt23 3 trt22.807354922 4 trt10 4 trt10 4 trt10 4 trt20 4 trt20 4 trt20 ; RUN; PROC MIXED ASYCOV NOBOUND DATA=plants ALPHA=0.05 method=ML; CLASS sample treatmt; MODEL y = treatmt ; RANDOM int treatmt/ subject=sample ; RUN; I get the following covariance estimates from SAS:Intercept sample == 5.5795treatmt sample == -0.08455Residual == 0.3181I tried the following in R, but I get different results. options(contrasts = c(factor = contr.SAS, ordered = contr.poly)) df$sample=as.factor(df$sample) lmer(y~ 1+treatmt+(1+treatmt|sample),REML=FALSE, data = df) Since the results from R are standard deviations, I have to square all results to get the variances.sample== 2.357412^2 = 5.557391 sample*treatmt==0.004977^2 = 2.477053e-05 residual==0.517094^2 = 0.2673862As shown above, the results from SAS and R are different. Do you know how to get the exact values in R?I appreciate any help.Thanks,Gram [[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 guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[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 guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R 3.2.1 liftoff
The build system sent R-3.2.1.tar.gz (codename World-Famous Astronaut) in orbit this morning. The list below details the changes in this release. You can get the source code from http://cran.r-project.org/src/base/R-3/R-3.2.1.tar.gz or wait for it to be mirrored at a CRAN site nearer to you. Binaries for various platforms will appear in due course. For the R Core Team, Peter Dalgaard These are the md5sums for the freshly created files, in case you wish to check that they are uncorrupted: MD5 (AUTHORS) = eb97a5cd38acb1cfc6408988bffef765 MD5 (COPYING) = eb723b61539feef013de476e68b5c50a MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343 MD5 (FAQ) = 181370b39076e34f64b842257076cd5c MD5 (INSTALL) = 3964b9119adeaab9ceb633773fc94aac MD5 (NEWS) = 6342bc1164e9f8e17713f47cff1910b4 MD5 (NEWS.0) = bfcd7c147251b5474d96848c6f57e5a8 MD5 (NEWS.1) = eb78c4d053ec9c32b815cf0c2ebea801 MD5 (NEWS.2) = 8e2f4d1d5228663ae598a09bf1e2bc6b MD5 (R-latest.tar.gz) = c2aac8b40f84e08e7f8c9068de9239a3 MD5 (README) = aece1dfbd18c1760128c3787f5456af6 MD5 (RESOURCES) = a59076c1ac7e9bab0f0a38b3f57a3914 MD5 (THANKS) = ba00f6cc68a823e1741cfa6011f40ccb MD5 (R-3/R-3.2.1.tar.gz) = c2aac8b40f84e08e7f8c9068de9239a3 This is the relevant part of the NEWS file CHANGES IN R 3.2.1: NEW FEATURES: * utf8ToInt() now checks that its input is valid UTF-8 and returns NA if it is not. * install.packages() now allows type = both with repos = NULL if it can infer the type of file. * nchar(x, *) and nzchar(x) gain a new argument keepNA which governs how the result for NAs in x is determined. For the R 3.2.x series, the default remains FALSE which is fully back compatible. From R 3.3.0, the default will change to keepNA = NA and you are advised to consider this for code portability. * news() more flexibly extracts dates from package NEWS.Rd files. * lengths(x) now also works (trivially) for atomic x and hence can be used more generally as an efficient replacement of sapply(x, length) and similar. * The included version of PCRE has been updated to 8.37, a bug-fix release. * diag() no longer duplicates a matrix when extracting its diagonal. * as.character.srcref() gains an argument to allow characters corresponding to a range of source references to be extracted. BUG FIXES: * acf() and ccf() now guarantee values strictly in [-1,1] (instead of sometimes very slightly outside). PR#15832. * as.integer() now gives NA (with a warning) as it does for the corresponding numeric or negative number coercions. Further, as.integer(M + 0.1) now gives M (instead of NA) when M is the maximal representable integer. * On some platforms nchar(x, c) and nchar(x, w) would return values (possibly NA) for inputs which were declared to be UTF-8 but were not, or for invalid strings without a marked encoding in a multi-byte locale, rather than give an error. Additional checks have been added to mitigate this. * apply(a, M, function(u) c(X = ., Y = .)) again has dimnames containing X and Y (as in R 3.2.0). * (Windows only) In some cases, the --clean option to R CMD INSTALL could fail. (PR#16178) * (Windows only) choose.files() would occasionally include characters from the result of an earlier call in the result of a later one. (PR#16270) * A change in RSiteSearch() in R 3.2.0 caused it to submit invalid URLs. (PR#16329) * Rscript and command line R silently ignored incomplete statements at the end of a script; now they are reported as parse errors. (PR#16350) * Parse data for very long strings was not stored. (PR#16354) * plotNode(), the workhorse of the plot method for dendrograms is no longer recursive, thanks to Suharto Anggono, and hence also works for deeply nested dendrograms. (PR#15215) * The parser could overflow internally when given numbers in scientific format with extremely large exponents. (PR#16358) * If the CRAN mirror was not set, install.packages(type = both) and related functions could repeatedly query the user for it. (Part of PR#16362) * The low-level functions .rowSums() etc. did not check the length of their argument, so could segfault. (PR#16367) * The quietly argument of library() is now correctly propagated from .getRequiredPackages2(). * Under some circumstances using the internal PCRE when building R fron source would cause external libs such as -llzma to be omitted from the main link. * The .Primitive default methods of the logic operators, i.e., !, and |, now give correct error messages when appropriate, e.g., for ``(TRUE) or `!`(). (PR#16385) * cummax(x) now correctly propagates NAs also when x is of type integer and begins with an NA. * summaryRprof() could fail
Re: [R] Cross tabulation with top one variable and side as multiple variables
I think my explanation in the post is not giving the full details on the job to be done. Sorry for that. Here is what I am doing.. 1. I have a SPSS data set with more than 2000 variables. However for test purpose I have created a temporary data set with 5 variables which I am reading it to R environment (Attached the test.sav file). 2. There is a variable called “TREND” which has the year data. So all I need to do is cross tabulate the variables with this Trend variable. In SPSS the syntax would be CTABLES /VLABELS VARIABLES =ALL DISPLAY=LABEL /TABLES (AGET +SEXT +EDUCRT +JOBRT ) [COUNT F40.0] by TREND. The final cross tabulation results are placed in the attached excel report with sheet name “Results”. As I am new to R - I tried searching the forums for the cross tabulation with top variable constant and multiple variables as side however I could not find it. Anyhow I tried using the below syntax : Xtabs ( ~ AGET +SEXT +EDUCRT +JOBRT + TREND, data=mydata) summary(~AGET +SEXT +EDUCRT +JOBRT, data= mydata, fun=table) ftable (mydata, row.vars=c(AGET , SEXT , EDUCRT , “JOBRT”), col.vars=TREND) the results are not identical to what I am getting in SPSS Hence I would request to suggest me a R code that helps me in getting the results as shown in the attached excel report with sheet name “Results”. Test.sav http://r.789695.n4.nabble.com/file/n4708799/Test.sav Cross_tabulation.xlsx http://r.789695.n4.nabble.com/file/n4708799/Cross_tabulation.xlsx -- View this message in context: http://r.789695.n4.nabble.com/Cross-tabulation-with-top-one-variable-and-side-as-multiple-variables-tp4708379p4708799.html Sent from the R help mailing list archive at Nabble.com. __ 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 guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Correlation matrix for pearson correlation (r,p,BH(FDR))
This post was called help before, I changed the Subject.
Thanks for the comments.
Here the example: (I have the two lists saved as .csv and I can open them in R)
Sheet one- Genes (10 genes expression, not binary, meaured in 10 cell lines)
genes
Genes Cell.line1 Cell.line2 Cell.line3 Cell.line4 Cell.line5
1 KCNAB3 12.02005181 11.1400910 15.60381163 13.44151596 25.37161030
2KCNB1 0.02457449 1.3028535 0.81538294 0.59318327 0.15332321
3KCNB2 0.44791862 0.1060137 0.09864136 0. 0.
4 KERA 0.06090217 0.000 0.03352993 0.03634781 0.04190912
5 KGFLP1 0.02450101 0.000 0. 0. 0.
6 KGFLP2 0. 0.000 0. 0. 0.
7KHDC1 0. 0.000 0. 0. 0.
8 KHDC1L 2.31894450 2.8252262 5.29099724 7.44183228 1.94629741
9 KHDC3L 0. 0.000 0. 0. 0.
10 KHDRBS1 0. 0.000 0. 0. 0.
Cell.line6 Cell.line7 Cell.line8 Cell.line9 Cell.line10
1 8.12373424 7.67506261 24.43776341 18.332448189.224225
2 4.18181234 1.65268403 5.98346320 1.514238070.00
3 0.05857207 0.05945414 0.20733924 0.058309820.00
4 0. 0. 0.07752608 0.01585643 16.664245
5 0.02563099 0.03902548 0. 0.0.00
6 0. 0. 0. 0.0.00
7 0. 0. 0. 0.0.00
8 8.56022436 7.50838343 7.17964645 3.286027290.00
9 0. 0. 0. 0.3.598534
10 0. 0.03081180 0. 0.2.600173
Sheet two - features (2 features(Growth rate,drug sensitivity for 10 cell lines)
features
Cell.line Cell.line1 Cell.line2 Cell.line3 Cell.line4 Cell.line5
1 Growth rate NA NA NA 51.41 NA
2 Drug sensitivity 5.03 6.57 8 1.26 3
Cell.line6 Cell.line7 Cell.line8 Cell.line9 Cell.line10
1 41.33 26.76 24.19 NA NA
2 1.40 1.88 1.33 5.059.12
What I found:
corr.test {psych}
corr.test(x, y = NULL, use = pairwise,method=pearson,adjust=BH,alpha=.01)
-- I adjusted the original command to what I need (BH insted og holm) and
alpha=.01 insted of 0.05.
I would be very happy, if someone could show me how to use this command, in
particular how to refer as x and y to the two sheets I have (Genes and
Features). I would take it from there.
Thanks a lot in advance.
Sarah
- Original Message -
From: Rainer Schuermann rainer.schuerm...@gmx.net
To: Sarah Bazzocco sarah.bazzo...@vhir.org
Sent: Thursday, 18 June, 2015 8:14:56 AM
Subject: Re: [R] help
Hi Sarah,
Not an answer to our question but a piece of well intended advice:
1. Don't post HTML but plain text. Not only that people will tell you this in a
sometimes not very friendly manner - using HTML actually does make posts
illegible in this mailing list. Code, and R _is_ code, is always plain text.
2. Don't pose an abstract problem - this looks too much like Can you please do
my work for me. Show us what you have tried already, and people will happily
jump in and provide their thoughts and advice.
3. Always make sure that you ave a reproducible example in your mail, and a set
of data of the same type and structure you are using - ideally using dput().
See further advice here
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
and here:
http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example
For your problem, R has an immense wealth of ideas and solutions.
Rgds,
Rainer
On Wed June 17 2015 16:57:24 Sarah Bazzocco wrote:
Hello,
�
I am a R-beginner and I need some help.�The question is very simple: I need
to do a pearson correlations (r,p-value and FDR with BH) from an Expression
array (with several thousand genes for lets say 20 cell lines)�with some
features of those cell lines.
My problem I have is the organization of the excel sheets and how to
introduce the data into R and run the script. I though the easiest and more
organized for me would be two expcel sheets:
1- Only Expression data (in rows the�genes and in colums cell lines)
2- Only the features (In row the features (e.g. a) growth rate, b)
sensitivity to some drugs) and in columns the cell lines).
--That would creat both sheets with 20 colums.
Now I would like to get a correlation of the gene 1: the expression of all
lines with the growth rate.
the same for gene2... and soforth. I sould obtain as many r,p and BH(FDR) as
genes there are.
the same I would need to do for the sensitivity... and so on.
[R] Completing Unordered Categorical missing variables using package mi
Hello all, A perhaps simple question. I am trying to complete unordered categorical missing data using mi package. There are two variables with missing data: Mat and Use. The problem is that the Use has several categories and somehow this means I can't plot the results as I get this error. Any idea how to fix the problem? Any help much appreciated, Best, Ioanna new-read(Sample.csv) new$Use-factor(new$Use) MissingData - missing_data.frame(new) MissingData - change(MissingData, y = DS, what = type, to = ordered-categorical) # STEP 3: look deeper summary(MissingData) summary(MissingData@patterns) show(MissingData) hist(MissingData) # STEP 4: impute ## Not run: IMPsample - mi(MissingData) #STEP5: diagnostics Plot(IMPsample) Error in `rownames-`(`*tmp*`, value = c(Oc11, Oc12, Oc13, Oc14, : length of 'dimnames' [1] not equal to array extent __ 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 guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
