From anh25 at cam.ac.uk Mon Oct 2 00:13:15 2017 From: anh25 at cam.ac.uk (AndrewHolding) Date: Sun, 1 Oct 2017 15:13:15 -0700 (MST) Subject: [datatable-help] Trouble understanding CRAN package errors Message-ID: <1506895995970-0.post@n4.nabble.com> Forgive me for possibly being naive. I have run the current version of my package, Brundle, through the test systems on win-builder, and the development and stable tests both pass. The package builds on my desktop (MacOS) still runs fine. Yet for the last two days I the package has caused warnings from CRAN. https://cran.r-project.org/web/checks/check_results_Brundle.html >From the logs it appears to me that several of the errors are due missing BioConductor package. e.g. Packages required but not available: ?DiffBind? ?Rsamtools? ?DESeq2? Am I missing something obvious? I understood that the test environment included these packages. -- Sent from: http://r.789695.n4.nabble.com/datatable-help-f2315188.html From Davide.cortellino at gmail.com Tue Oct 3 20:57:28 2017 From: Davide.cortellino at gmail.com (Davidecortellino) Date: Tue, 3 Oct 2017 11:57:28 -0700 (MST) Subject: [datatable-help] Multiple proportion test with glm Message-ID: <1507057048470-0.post@n4.nabble.com> I'm currently facing the following situation. We have run a marketing campaign providing to some members one of two type of coupones. In addition to this, some of these members were already contacted in the previous one by another campaign. So I have the following dataset, where: -mixpre3M= is a flag variable telling us if the customer had already purchased somethign in the past bono recibido: is the kind of coupon recived by the customer. The type "3euros" is the coupon identifying the customers already touched in the past by a campaign. the type "benchmark" identify the customer who haven't received any coupon (control group) tran_during: is the N of redeemers or purchasers enviados: is the number of people included in each group mixpre3M bono_recibido TRAN_DURING_CAMP_FLG enviados 0 benchmark 5948 33336 1 benchmark 557 2102 0 BONO3EUROS 96 1233 1 BONO3EUROS 17 83 0 BONO6EUROS 4823 25434 1 BONO6EUROS 626 1793 What I want achive is if there is a redemption or purchasing rate significatively different between each group, and see between which group there is difference Now, I have the following doubts: a. I understand I should run a multiple comparison test, like maybe a GLM with binominal distribution, but I'm not sure it is a correct procedure, considering that some of the groups (for instance the fourth one, with n=83) are quite smaller than the main other groups. Is the model I choose the correct one for this kind of analysis, and I should exclude the smaller groups? b. I understand this is a kinda similar to a multiple A/B test. Does anyone know any tutorial or material which could help with the topic? Never managed this kind of test before Many thanks for the help Bests -- Sent from: http://r.789695.n4.nabble.com/datatable-help-f2315188.html From mate.geczi.lfgeb at gmail.com Sun Oct 8 21:26:05 2017 From: mate.geczi.lfgeb at gmail.com (gmateb) Date: Sun, 8 Oct 2017 12:26:05 -0700 (MST) Subject: [datatable-help] Split not Working! Not splitting with right proportion Message-ID: <1507490765621-0.post@n4.nabble.com> I would llike to split my dataset into training (70%) and testing (30%) sets, but R does not split it with the right proportion. my code: after execution: -- Sent from: http://r.789695.n4.nabble.com/datatable-help-f2315188.html From 01chrikelly at gmail.com Mon Oct 9 21:20:48 2017 From: 01chrikelly at gmail.com (christinelly) Date: Mon, 9 Oct 2017 12:20:48 -0700 (MST) Subject: [datatable-help] My filter is not working Message-ID: <1507576848439-0.post@n4.nabble.com> Hello, I am new to R, can someone please what is wrong with my code? I want to filter my result to only show people who have answered "no" but my result generates 0 rows. Does it have anything to do with the fact that my data is stored as factors and not characters? I also tried another code but gave me three rows, what am I doing wrong? Thanks in advance, Christine 'data.frame': 491775 obs. of 1 variable: $ hivtst6: Factor w/ 2 levels "Yes","No": 2 1 1 2 2 1 2 2 2 2 ... brfss2013 %>% filter(as.character(hivtst6) == "yes") %>% group_by(hivtst6) %>% summarise(count = n()) brfss2013 %>% filter (hivtst6 != "yes") %>% group_by(hivtst6) %>% summarise(count = n()) -- Sent from: http://r.789695.n4.nabble.com/datatable-help-f2315188.html From by.hook.or at gmail.com Mon Oct 9 21:24:37 2017 From: by.hook.or at gmail.com (Frank Erickson) Date: Mon, 9 Oct 2017 15:24:37 -0400 Subject: [datatable-help] My filter is not working In-Reply-To: <1507576848439-0.post@n4.nabble.com> References: <1507576848439-0.post@n4.nabble.com> Message-ID: This mailing list is about questions related to the data.table package. You might want to try https://community.rstudio.com/ instead. I'm not sure why your code doesn't work, but another approach would be something like DF %>% group_by(g) %>% summarise(count = sum(x != "yes")) If this works, it's because TRUE/FALSE is treated as 1/0 when summed. You might also want to look at the dplyr functions ?tally and ?count. On Mon, Oct 9, 2017 at 3:20 PM, christinelly <01chrikelly at gmail.com> wrote: > Hello, > > I am new to R, can someone please what is wrong with my code? I want to > filter my result to only show people who have answered "no" but my result > generates 0 rows. Does it have anything to do with the fact that my data is > stored as factors and not characters? > > I also tried another code but gave me three rows, what am I doing wrong? > Thanks in advance, > Christine > > 'data.frame': 491775 obs. of 1 variable: > $ hivtst6: Factor w/ 2 levels "Yes","No": 2 1 1 2 2 1 2 2 2 2 ... > > brfss2013 %>% > filter(as.character(hivtst6) == "yes") %>% > group_by(hivtst6) %>% > summarise(count = n()) > > brfss2013 %>% > filter (hivtst6 != "yes") %>% > group_by(hivtst6) %>% > summarise(count = n()) > > 2017-10-09_at_21.png> > > > > -- > Sent from: http://r.789695.n4.nabble.com/datatable-help-f2315188.html > _______________________________________________ > datatable-help mailing list > datatable-help at lists.r-forge.r-project.org > https://lists.r-forge.r-project.org/cgi-bin/mailman/ > listinfo/datatable-help > -------------- next part -------------- An HTML attachment was scrubbed... URL: From bhavnavb.94 at gmail.com Wed Oct 11 10:15:47 2017 From: bhavnavb.94 at gmail.com (Bhavna Vb) Date: Wed, 11 Oct 2017 13:45:47 +0530 Subject: [datatable-help] Remove from mailing list Message-ID: Hi, Request you to kindly remove me from the mailing list Thanks, Bhavna -------------- next part -------------- An HTML attachment was scrubbed... URL: From memonsalim2008 at yahoo.co.in Mon Oct 16 10:34:10 2017 From: memonsalim2008 at yahoo.co.in (memonsalim2008) Date: Mon, 16 Oct 2017 01:34:10 -0700 (MST) Subject: [datatable-help] how to grouping of data in R Message-ID: <1508142850217-0.post@n4.nabble.com> Hi All, is it possible in R groping of data ?Please check blow example. student_id Fee 5555 1200 5555 1200 1111 1200 6666 1500 6666 1500 6666 1000 7777 1000 8888 1000 8888 1000 8888 1000 8888 1000 output of will be student_id count 5555 2 1111 1 6666 3 7777 1 8888 4 -- Sent from: http://r.789695.n4.nabble.com/datatable-help-f2315188.html From serdar.akin76 at gmail.com Mon Oct 16 18:41:40 2017 From: serdar.akin76 at gmail.com (Serdar Akin) Date: Mon, 16 Oct 2017 16:41:40 +0000 Subject: [datatable-help] datatable-help Digest, Vol 92, Issue 6 In-Reply-To: References: Message-ID: How about DT[, .N , by = .(student_fee)] m?n 16 okt. 2017 kl. 12:00 skrev < datatable-help-request at lists.r-forge.r-project.org>: > Send datatable-help mailing list submissions to > datatable-help at lists.r-forge.r-project.org > > To subscribe or unsubscribe via the World Wide Web, visit > > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/datatable-help > > or, via email, send a message with subject or body 'help' to > datatable-help-request at lists.r-forge.r-project.org > > You can reach the person managing the list at > datatable-help-owner at lists.r-forge.r-project.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of datatable-help digest..." > > > Today's Topics: > > 1. how to grouping of data in R (memonsalim2008) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 16 Oct 2017 01:34:10 -0700 (MST) > From: memonsalim2008 > To: datatable-help at lists.r-forge.r-project.org > Subject: [datatable-help] how to grouping of data in R > Message-ID: <1508142850217-0.post at n4.nabble.com> > Content-Type: text/plain; charset=us-ascii > > Hi All, > > is it possible in R groping of data ?Please check blow example. > > > student_id Fee > 5555 1200 > 5555 1200 > 1111 1200 > 6666 1500 > 6666 1500 > 6666 1000 > 7777 1000 > 8888 1000 > 8888 1000 > 8888 1000 > 8888 1000 > > output of will be > > student_id count > 5555 2 > 1111 1 > 6666 3 > 7777 1 > 8888 4 > > > > > > -- > Sent from: http://r.789695.n4.nabble.com/datatable-help-f2315188.html > > > ------------------------------ > > _______________________________________________ > datatable-help mailing list > datatable-help at lists.r-forge.r-project.org > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/datatable-help > > End of datatable-help Digest, Vol 92, Issue 6 > ********************************************* > -------------- next part -------------- An HTML attachment was scrubbed... URL: From khelifi.rach at free.fr Mon Oct 16 21:52:05 2017 From: khelifi.rach at free.fr (rach) Date: Mon, 16 Oct 2017 12:52:05 -0700 (MST) Subject: [datatable-help] =?utf-8?q?need_urgently_some_help_to_understand_?= =?utf-8?q?summary_and_anova_functions_in_linear_on_Oct_16=2C_2017=3B_?= =?utf-8?q?=E2=80=93_mixed_analysis=2E?= Message-ID: <1508183525148-0.post@n4.nabble.com> I'm newby in linear mixed model, so my first question is very basic. I'm doing a linear mixed analysis with one fixed factor (frequency) and two random factors (subject and item) I run an expriment where participant were required to read a text with high and low fr?quent. First duration fixation (FF) on high and low frequency word (HF vs BF) were recorded I want to know if frequency have an effect on first fixation. I have two model : > m0=lmer(FF~(1|subject)+(1|item),data=donfreq) > m1=lmer(FFms~frequency+(1|subject)+(1|item),data=donfreq) 1)I use anova fonction (anova(m0,m1)) which gives me the following result : 2)I use the summary function ((summary(m1) which gives the following results I would like to know which of those to analysis give the correct statistical result (anova fonction with p =0.004156 or summary fonction with p =0.00754). Thank you in advance for any help rach -- Sent from: http://r.789695.n4.nabble.com/datatable-help-f2315188.html From fjbuch at gmail.com Fri Oct 20 20:14:11 2017 From: fjbuch at gmail.com (Farrel Buchinsky) Date: Fri, 20 Oct 2017 18:14:11 +0000 Subject: [datatable-help] Generating data.tables from a j function Message-ID: I am relatively certain that data.table can handle a function in the J position that generates a data.frame or a data.table. However, how does one handle the output? Can you please point me to a url that discusses the capability? For instance, I sometimes use the package dtables to generate descriptive statistics. It generates a table for So one could go library(dtables) dtable(dt) But what if one wanted to get descriptive statistics by a trichotomous variable dt[ , dtable(.SD), by=trichotomous.variable] *I am looking for a general article or blogpost about how to handle outputs that are not single numbers or two numbers. *There are functions that yield data.tables or lists or specialized objects such a models. Any suggestions? I know one can simply print the output to the console dt[ , print(dtable(.SD)_, by=trichotomous.variable] But that does not let me do anything intelligent afterwards. -- Farrel Buchinsky (412) 567-7870 (gets me everywhere) -------------- next part -------------- An HTML attachment was scrubbed... URL: From MEC at stowers.org Fri Oct 20 20:28:41 2017 From: MEC at stowers.org (Cook, Malcolm) Date: Fri, 20 Oct 2017 18:28:41 +0000 Subject: [datatable-help] Generating data.tables from a j function In-Reply-To: References: Message-ID: Result.dt<-dt[ , list(sd.dtable=dtable(.SD)), by=trichotomous.variable] # untested will return a Result.dt with 2 columns: trichotomous.variable and sd.dtable The value of Result.dt[1,sd.dtable][[1]] will give the 1st groups dtable results ~malcolm_cook at stowers.org From: datatable-help-bounces at lists.r-forge.r-project.org [mailto:datatable-help-bounces at lists.r-forge.r-project.org] On Behalf Of Farrel Buchinsky Sent: Friday, October 20, 2017 1:14 PM To: datatable-help at lists.r-forge.r-project.org Subject: [datatable-help] Generating data.tables from a j function I am relatively certain that data.table can handle a function in the J position that generates a data.frame or a data.table. However, how does one handle the output? Can you please point me to a url that discusses the capability? For instance, I sometimes use the package dtables to generate descriptive statistics. It generates a table for So one could go library(dtables) dtable(dt) But what if one wanted to get descriptive statistics by a trichotomous variable dt[ , dtable(.SD), by=trichotomous.variable] I am looking for a general article or blogpost about how to handle outputs that are not single numbers or two numbers. There are functions that yield data.tables or lists or specialized objects such a models. Any suggestions? I know one can simply print the output to the console dt[ , print(dtable(.SD)_, by=trichotomous.variable] But that does not let me do anything intelligent afterwards. -- Farrel Buchinsky (412) 567-7870 (gets me everywhere) -------------- next part -------------- An HTML attachment was scrubbed... URL: From fjbuch at gmail.com Fri Oct 20 22:31:13 2017 From: fjbuch at gmail.com (Farrel Buchinsky) Date: Fri, 20 Oct 2017 20:31:13 +0000 Subject: [datatable-help] Generating data.tables from a j function In-Reply-To: References: Message-ID: Thank you. That did it. I would still like to read more. What does one call this? What are the correct buzzwords to search for. Do you know of any blog posts / articles? On Fri, Oct 20, 2017 at 2:28 PM Cook, Malcolm wrote: > > > Result.dt<-dt[ , list(sd.dtable=dtable(.SD)), by=trichotomous.variable] # > untested > > > > will return a Result.dt with 2 columns: trichotomous.variable and sd.dtable > > > > The value of Result.dt[1,sd.dtable][[1]] will give the 1st groups dtable > results > > > > ~malcolm_cook at stowers.org > > > > *From:* datatable-help-bounces at lists.r-forge.r-project.org [mailto: > datatable-help-bounces at lists.r-forge.r-project.org] *On Behalf Of *Farrel > Buchinsky > *Sent:* Friday, October 20, 2017 1:14 PM > *To:* datatable-help at lists.r-forge.r-project.org > *Subject:* [datatable-help] Generating data.tables from a j function > > > > I am relatively certain that data.table can handle a function in the J > position that generates a data.frame or a data.table. However, how does one > handle the output? Can you please point me to a url that discusses the > capability? > > > > For instance, I sometimes use the package dtables to generate descriptive > statistics. It generates a table for > > > > So one could go > > > > library(dtables) > > dtable(dt) > > > > But what if one wanted to get descriptive statistics by a trichotomous > variable > > > > dt[ , dtable(.SD), by=trichotomous.variable] > > > > *I am looking for a general article or blogpost about how to handle > outputs that are not single numbers or two numbers. *There are functions > that yield data.tables or lists or specialized objects such a models. Any > suggestions? > > > > I know one can simply print the output to the console > > > > dt[ , print(dtable(.SD)_, by=trichotomous.variable] > > > > But that does not let me do anything intelligent afterwards. > > -- > > Farrel Buchinsky > > (412) 567-7870 (gets me everywhere) > -- Farrel Buchinsky (412) 567-7870 (gets me everywhere) -------------- next part -------------- An HTML attachment was scrubbed... URL: From MEC at stowers.org Fri Oct 20 23:47:25 2017 From: MEC at stowers.org (Cook, Malcolm) Date: Fri, 20 Oct 2017 21:47:25 +0000 Subject: [datatable-help] Generating data.tables from a j function In-Reply-To: References: Message-ID: Hmm. Good question. Not sure where I learned this. I use data.table allot for many years now. Search https://cran.r-project.org/web/packages/data.table/vignettes/datatable-intro.html for ?do in j? Read https://rawgit.com/wiki/Rdatatable/data.table/vignettes/datatable-faq.html#im-using-c-in-j-and-getting-strange-results. Then search the same document for ? j ? and selectively read what seems pertinent. That should get you most of the way there. ~malcolm_cook at stowers.org From: Farrel Buchinsky [mailto:fjbuch at gmail.com] Sent: Friday, October 20, 2017 3:31 PM To: Cook, Malcolm ; datatable-help at lists.r-forge.r-project.org Subject: Re: [datatable-help] Generating data.tables from a j function Thank you. That did it. I would still like to read more. What does one call this? What are the correct buzzwords to search for. Do you know of any blog posts / articles? On Fri, Oct 20, 2017 at 2:28 PM Cook, Malcolm > wrote: Result.dt<-dt[ , list(sd.dtable=dtable(.SD)), by=trichotomous.variable] # untested will return a Result.dt with 2 columns: trichotomous.variable and sd.dtable The value of Result.dt[1,sd.dtable][[1]] will give the 1st groups dtable results ~malcolm_cook at stowers.org From: datatable-help-bounces at lists.r-forge.r-project.org [mailto:datatable-help-bounces at lists.r-forge.r-project.org] On Behalf Of Farrel Buchinsky Sent: Friday, October 20, 2017 1:14 PM To: datatable-help at lists.r-forge.r-project.org Subject: [datatable-help] Generating data.tables from a j function I am relatively certain that data.table can handle a function in the J position that generates a data.frame or a data.table. However, how does one handle the output? Can you please point me to a url that discusses the capability? For instance, I sometimes use the package dtables to generate descriptive statistics. It generates a table for So one could go library(dtables) dtable(dt) But what if one wanted to get descriptive statistics by a trichotomous variable dt[ , dtable(.SD), by=trichotomous.variable] I am looking for a general article or blogpost about how to handle outputs that are not single numbers or two numbers. There are functions that yield data.tables or lists or specialized objects such a models. Any suggestions? I know one can simply print the output to the console dt[ , print(dtable(.SD)_, by=trichotomous.variable] But that does not let me do anything intelligent afterwards. -- Farrel Buchinsky (412) 567-7870 (gets me everywhere) -- Farrel Buchinsky (412) 567-7870 (gets me everywhere) -------------- next part -------------- An HTML attachment was scrubbed... URL: From memonsalim2008 at yahoo.co.in Tue Oct 24 12:54:47 2017 From: memonsalim2008 at yahoo.co.in (memonsalim2008) Date: Tue, 24 Oct 2017 03:54:47 -0700 (MST) Subject: [datatable-help] is it possible Time series with multiple subjects and multiple variables in R? Message-ID: <1508842487657-0.post@n4.nabble.com> is it possible Time series with multiple subjects and multiple variables in R? -- Sent from: http://r.789695.n4.nabble.com/datatable-help-f2315188.html From juknu10 at student.sdu.dk Tue Oct 31 09:55:59 2017 From: juknu10 at student.sdu.dk (r-dreamer) Date: Tue, 31 Oct 2017 01:55:59 -0700 (MST) Subject: [datatable-help] visualize dataframes and working with quantitative values Message-ID: <1509440159335-0.post@n4.nabble.com> I am new at doing r programming and I have a couple of questions. I want to visualize a data frame containing transcripts of 2000 genes from 3 mice of the knockout group and 3 mice of the control group. How would I start? And what should I remember? Also, I established a standard protocol for my experiments. The bioinformatics part provides quantitative values for 200 features over a course of 10 time points. How can I use r to work with these data? -- Sent from: http://r.789695.n4.nabble.com/datatable-help-f2315188.html From fairytales-for-ever at hotmail.com Tue Oct 31 09:58:23 2017 From: fairytales-for-ever at hotmail.com (mystixangel) Date: Tue, 31 Oct 2017 01:58:23 -0700 (MST) Subject: [datatable-help] group of differentially regulated genes Message-ID: <1509440303847-0.post@n4.nabble.com> I hope someone can help. I want to find a group of differentially regulated genes in data consisting of 4 different conditions with 5 replicates per condition. How should I proceed? I am not that familiar with R yet. -- Sent from: http://r.789695.n4.nabble.com/datatable-help-f2315188.html From galaxie2485 at yahoo.co.in Tue Oct 31 09:58:56 2017 From: galaxie2485 at yahoo.co.in (Priya Arasu) Date: Tue, 31 Oct 2017 08:58:56 +0000 (UTC) Subject: [datatable-help] R files in server In-Reply-To: <1542575009.7844456.1509380492603@mail.yahoo.com> References: <1542575009.7844456.1509380492603.ref@mail.yahoo.com> <1542575009.7844456.1509380492603@mail.yahoo.com> Message-ID: <93692759.8368412.1509440336452@mail.yahoo.com> Hi, ?I was running some analysis in RStudio. The analysis was running in the the server through? terminal in my system, now the terminal is closed accidentally. But the analysis is still running in the server. Confirmed that the analysis is running by checking the system monitor. Is there any way to access the files after the analysis is over in RStudio or access the temporary files? . Please help me with this issue.?Thank you Priya -------------- next part -------------- An HTML attachment was scrubbed... URL: From fairytales-for-ever at hotmail.com Tue Oct 31 10:08:17 2017 From: fairytales-for-ever at hotmail.com (mystixangel) Date: Tue, 31 Oct 2017 02:08:17 -0700 (MST) Subject: [datatable-help] thousands of proteins Message-ID: <1509440897651-0.post@n4.nabble.com> I have several samples containing quantitative information about thousands of proteins. How do I check whether they can be compared, using r? -- Sent from: http://r.789695.n4.nabble.com/datatable-help-f2315188.html From juknu10 at student.sdu.dk Tue Oct 31 10:10:29 2017 From: juknu10 at student.sdu.dk (r-dreamer) Date: Tue, 31 Oct 2017 02:10:29 -0700 (MST) Subject: [datatable-help] non linear Message-ID: <1509441029385-0.post@n4.nabble.com> How can I compare curves and function if I want to use a non-linear function in R? -- Sent from: http://r.789695.n4.nabble.com/datatable-help-f2315188.html