Re: [R] Changing sign of columns and values
Hi Hana, I didn't look closely. The simplest rule that I can see is that the letters (nucleotides?) should be swapped if there has been a sign change in the beta value. Therefore: mydf<-read.table(text= "IDnumber OA EA beta 1 C A -0.05 2 GA0.098 3 GT-0.789", header=TRUE,stringsAsFactors=FALSE) # logical vector marking the rows to be swapped swap_letters<-mydf$beta < 0 # save the OA values to be swapped newEA<-mydf$OA[swap_letters] # change the OAs to EAs mydf$OA[swap_letters]<-mydf$EA[swap_letters] # set the relevant EA values to the old OA values mydf$EA[swap_letters]<-newEA # change the beta values mydf$beta<-abs(mydf$beta) mydf Jim On Sun, Jun 12, 2022 at 9:11 AM hanatezera wrote: > > Dear jim thanks for your help! I want to change also the value of OA and EF > simultaneously. > For instance i am looking the data > mydf > IDnumber OA EA beta > 11 A C 0.050 > 22 G A 0.098 > 33 T G 0.789 > > Best, > Hana > > > > Original message > From: Jim Lemon > Date: 6/12/22 1:59 AM (GMT+03:00) > To: hanatezera , r-help mailing list > > Subject: Re: [R] Changing sign of columns and values > > Hi Hana, > I think this is what you want: > > # first read in your example > mydf<-read.table(text= > "IDnumber OA EA beta > 1 C A -0.05 > 2 GA0.098 > 3 GT-0.789", > header=TRUE,stringsAsFactors=FALSE) > # check it > mydf > IDnumber OA EA beta > 11 C A -0.050 > 22 G A 0.098 > 33 G T -0.789 > # change values of mydf$beta to absolute values > mydf$beta<-abs(mydf$beta) > mydf > IDnumber OA EA beta > 11 C A 0.050 > 22 G A 0.098 > 33 G T 0.789 > > Jim > > On Sun, Jun 12, 2022 at 8:27 AM hanatezera wrote: > > > > I have the following data set in data frameIDnumber OA EA beta1 > >C A -0.052 GA > > 0.0983 GT-0.789I want to > > change the sign of negative beta. If the negative value change to postive i > > want to switch its EA and OA.My desire result will beIDnumber OA EA > > beta1 A C 0.052 G > > A0.0983 T G > > 0.789Any one can help me with r codes? kind regards,Hana > > [[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-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 do non-parametric calculations in R
Imagine that it's the year 2022 and you don't know how to look up information about performing a Kruskal-Wallis H test. It would take you longer to join the listserv and then write such a cokamemie email than to open the stats textbook you are supposed to have for the course, much less doing a simple search query. On 2022-06-11 19:19, Ebert,Timothy Aaron wrote: LOL. Thank goodness I successfully rolled my saving throw and resisted, at least for this round. Tim -Original Message- From: R-help On Behalf Of Jeff Newmiller Sent: Saturday, June 11, 2022 5:27 PM To: r-help@r-project.org; J C Nash Subject: Re: [R] How to do non-parametric calculations in R [External Email] Really? But it is such a random list that I thought it was a test of our ability to resist providing impromptu lectures on off-list-topics, since we all like to expound on "stuff" even when R isn't needed to understand them. Or perhaps "A R Lover" just didn't read the Posting Guide warnings about HTML email, homework, and statistics, and will soon have done do and be sharing some R code that is giving them an error. On June 11, 2022 1:53:37 PM PDT, J C Nash wrote: Homework! On 2022-06-11 10:24, Shantanu Shimpi wrote: Dear R community, Please help me in knowing how to do following non-parametric tests: 1. kruskal-Wallis test 2. Wilcoxson rank sum test 3. Lee Cronbac Alpha test 4. Spearman's Rank correlation test 5. Henry Garrett method formula calculations 6. Factor Analysis 7. Chi square test Kindly guide me on the above queries in the easiest way. A R lover, Col Shantanu. India. attitudeshantanu1...@gmail.com 7722030088 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mai lman_listinfo_r-2Dhelp=DwICAg=sJ6xIWYx-zLMB3EPkvcnVg=9PEhQh2kVe AsRzsn7AkP-g=4tM4fJqtbe_uTsyPRnMDpR560AlVh83t9wmvJuUPvfsciEQhPSY5Yb F8c2Lixwy8=zhlVVKEML3MeOEdjlR2Z1gqYLVcrE0gpEiFPdo0MxNg= PLEASE do read the posting guide https://urldefense.proofpoint.com/v2/url?u=http-3A__www.R-2Dproject.o rg_posting-2Dguide.html=DwICAg=sJ6xIWYx-zLMB3EPkvcnVg=9PEhQh2kV eAsRzsn7AkP-g=4tM4fJqtbe_uTsyPRnMDpR560AlVh83t9wmvJuUPvfsciEQhPSY5Y bF8c2Lixwy8=IRGFPuDAXZu6xEr36GrRy5jeXkI0D62fDLt-FxbIqBs= and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailm an_listinfo_r-2Dhelp=DwICAg=sJ6xIWYx-zLMB3EPkvcnVg=9PEhQh2kVeAsRz sn7AkP-g=4tM4fJqtbe_uTsyPRnMDpR560AlVh83t9wmvJuUPvfsciEQhPSY5YbF8c2Li xwy8=zhlVVKEML3MeOEdjlR2Z1gqYLVcrE0gpEiFPdo0MxNg= PLEASE do read the posting guide https://urldefense.proofpoint.com/v2/url?u=http-3A__www.R-2Dproject.org _posting-2Dguide.html=DwICAg=sJ6xIWYx-zLMB3EPkvcnVg=9PEhQh2kVeAsR zsn7AkP-g=4tM4fJqtbe_uTsyPRnMDpR560AlVh83t9wmvJuUPvfsciEQhPSY5YbF8c2L ixwy8=IRGFPuDAXZu6xEr36GrRy5jeXkI0D62fDLt-FxbIqBs= and provide commented, minimal, self-contained, reproducible code. -- Sent from my phone. Please excuse my brevity. __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Dhelp=DwICAg=sJ6xIWYx-zLMB3EPkvcnVg=9PEhQh2kVeAsRzsn7AkP-g=4tM4fJqtbe_uTsyPRnMDpR560AlVh83t9wmvJuUPvfsciEQhPSY5YbF8c2Lixwy8=zhlVVKEML3MeOEdjlR2Z1gqYLVcrE0gpEiFPdo0MxNg= PLEASE do read the posting guide https://urldefense.proofpoint.com/v2/url?u=http-3A__www.R-2Dproject.org_posting-2Dguide.html=DwICAg=sJ6xIWYx-zLMB3EPkvcnVg=9PEhQh2kVeAsRzsn7AkP-g=4tM4fJqtbe_uTsyPRnMDpR560AlVh83t9wmvJuUPvfsciEQhPSY5YbF8c2Lixwy8=IRGFPuDAXZu6xEr36GrRy5jeXkI0D62fDLt-FxbIqBs= 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. __ 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] Changing sign of columns and values
Dear jim thanks for your help! I want to change also the value of OA and EF simultaneously.For instance i am looking the datamydf IDnumber OA EA beta1 1 A C 0.0502 2 G A 0.0983 3 T G 0.789Best, Hana Original message From: Jim Lemon Date: 6/12/22 1:59 AM (GMT+03:00) To: hanatezera , r-help mailing list Subject: Re: [R] Changing sign of columns and values Hi Hana,I think this is what you want:# first read in your examplemydf<-read.table(text="IDnumber OA EA beta1 C A -0.052 G A 0.0983 G T -0.789",header=TRUE,stringsAsFactors=FALSE)# check itmydf IDnumber OA EA beta1 1 C A -0.0502 2 G A 0.0983 3 G T -0.789# change values of mydf$beta to absolute valuesmydf$beta<-abs(mydf$beta)mydf IDnumber OA EA beta1 1 C A 0.0502 2 G A 0.0983 3 G T 0.789JimOn Sun, Jun 12, 2022 at 8:27 AM hanatezera wrote:>> I have the following data set in data frameIDnumber OA EA beta1 C A -0.052 G A 0.0983 G T -0.789I want to change the sign of negative beta. If the negative value change to postive i want to switch its EA and OA.My desire result will beIDnumber OA EA beta1 A C 0.052 G A 0.0983 T G 0.789Any one can help me with r codes? kind regards,Hana> [[alternative HTML version deleted]]>> __> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see> https://stat.ethz.ch/mailman/listinfo/r-help> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html> and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Changing sign of columns and values
Hi Hana, I think this is what you want: # first read in your example mydf<-read.table(text= "IDnumber OA EA beta 1 C A -0.05 2 GA0.098 3 GT-0.789", header=TRUE,stringsAsFactors=FALSE) # check it mydf IDnumber OA EA beta 11 C A -0.050 22 G A 0.098 33 G T -0.789 # change values of mydf$beta to absolute values mydf$beta<-abs(mydf$beta) mydf IDnumber OA EA beta 11 C A 0.050 22 G A 0.098 33 G T 0.789 Jim On Sun, Jun 12, 2022 at 8:27 AM hanatezera wrote: > > I have the following data set in data frameIDnumber OA EA beta1 > C A -0.052 GA > 0.0983 GT-0.789I want to change > the sign of negative beta. If the negative value change to postive i want to > switch its EA and OA.My desire result will beIDnumber OA EA beta1 >A C 0.052 GA > 0.0983 T G0.789Any one can help > me with r codes? kind regards,Hana > [[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-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] Changing sign of columns and values
This is a plain text list. Your html post got mangled (see below). You are more likely to get a useful response if you follow the posting guide (linked below) and post in plain text. Bert Gunter "The trouble with having an open mind is that people keep coming along and sticking things into it." -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) On Sat, Jun 11, 2022 at 3:27 PM hanatezera wrote: > > I have the following data set in data frameIDnumber OA EA beta1 > C A -0.052 GA > 0.0983 GT-0.789I want to change > the sign of negative beta. If the negative value change to postive i want to > switch its EA and OA.My desire result will beIDnumber OA EA beta1 >A C 0.052 GA > 0.0983 T G0.789Any one can help > me with r codes? kind regards,Hana > [[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-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] Changing sign of columns and values
I have the following data set in data frameIDnumber OA EA beta1 C A -0.052 G A 0.0983 G T -0.789I want to change the sign of negative beta. If the negative value change to postive i want to switch its EA and OA.My desire result will beIDnumber OA EA beta1 A C 0.052 G A 0.0983 T G 0.789Any one can help me with r codes? kind regards,Hana [[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] How to do non-parametric calculations in R
Homework! On 2022-06-11 10:24, Shantanu Shimpi wrote: Dear R community, Please help me in knowing how to do following non-parametric tests: 1. kruskal-Wallis test 2. Wilcoxson rank sum test 3. Lee Cronbac Alpha test 4. Spearman's Rank correlation test 5. Henry Garrett method formula calculations 6. Factor Analysis 7. Chi square test Kindly guide me on the above queries in the easiest way. A R lover, Col Shantanu. India. attitudeshantanu1...@gmail.com 7722030088 [[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-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] Interpreting the result of a model with random effects
Looks like the center effect improves overall accuracy while being independent of the other terms. A few things to try Compare coef(model.fix) to fixef(model.rand). Add center as a fixed effect to model .fix Try a conditional logit (clogit from survival) See how consistent the coefficients are On Sat, Jun 11, 2022 at 11:14 AM Frank S. wrote: > Dear R users, > > I'm analyzing a particular score "y" among several individuals, each of > which belongs to a center, a factor with three > different levels (3 possible centers). I have treated the "center" as a > fixed effect, and as a random term (package lme4): > > 1) model.fix <- glm(y ~ var.1 + var.2 + var.3 + var.4 + var.5 + center, > family = "binomial", data = dat) > 2) model.rand <- glmer(y ~ var.1 + var.2 + var.3 + var.4 + var.5 + (1 | > center), family = "binomial", data = dat) > > The issue is that both models provide exactly the same coefficients and > p-values for the 5 baseline variables, so I assumed > that it was due to the small number of levels (in fact, too few ). > However, when computing anova(model.rand, model.fix), > the output indicates a p-value < 0.001 in favour of the "model.rand". > What's happening? Should I take the random terms? > > Thanks for any 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. > -- Sent from Gmail Mobile [[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] Interpreting the result of a model with random effects
Dear R users, I'm analyzing a particular score "y" among several individuals, each of which belongs to a center, a factor with three different levels (3 possible centers). I have treated the "center" as a fixed effect, and as a random term (package lme4): 1) model.fix <- glm(y ~ var.1 + var.2 + var.3 + var.4 + var.5 + center, family = "binomial", data = dat) 2) model.rand <- glmer(y ~ var.1 + var.2 + var.3 + var.4 + var.5 + (1 | center), family = "binomial", data = dat) The issue is that both models provide exactly the same coefficients and p-values for the 5 baseline variables, so I assumed that it was due to the small number of levels (in fact, too few ). However, when computing anova(model.rand, model.fix), the output indicates a p-value < 0.001 in favour of the "model.rand". What's happening? Should I take the random terms? Thanks for any 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] igraph: layout help
Hello,
The code below is a hack.
First I create a layout ll, then see that vertex K coordinates are in
the layout matrix 2nd row.
Now, to multiply K's coordinates by a number d>1 will move the point
away from A. Add that value to the K group and plot.
ll <- layout_with_kk(my.graph)
d <- ll[2, ]*5
ll[c(2, 9:11), ] <- t(t(ll[c(2, 9:11), ]) + d)
plot(my.graph, layout = ll)
Hope this helps,
Rui Barradas
Às 19:20 de 10/06/2022, Brian Smith escreveu:
Hi,
I was trying to make a network plot of this data:
library(igraph)
library(network)
df1 <- data.frame(from="A",to=c("B","C","D","E","F","G"),value=1)
df2 <- data.frame(from="K",to=c("L","M","N"),value=1)
df3 <- data.frame(from="A",to="K",value=3)
my.df <- rbind(df1,df2,df3)
my.graph <- graph_from_data_frame(my.df,directed = F)
plot(my.graph)
What I wanted was for nodes A to G to be very close together (touching each
other). Similarly, nodes K to N should be very close together. The
connecting edge (A to K) between these sets of points/vertices should be
the only edge visible. How should I go about doing this?
Also, how can I change the parameters (node label, node color, etc.) of the
graph?
Any help or link to documentation would be helpful. Or would
thanks!
[[alternative HTML version deleted]]
__
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and provide commented, minimal, self-contained, reproducible code.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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[R] A humble request regarding QAMG method in R
Hi, Dear Respected Professors! I hope that you are doing well. Now all files are in .txt files. Now kindly help me with the following: I have the R-codes for the "Quantile Augmented Mean Group" method. The relevant codes and data are attached herewith. Note: The link to the reference paper is: https://www.econ.cam.ac.uk/people-files/emeritus/mhp1/fp20/qmg40-rev21.pdf My Issue: When I run the given codes to estimate the results for my own data. I have to face several errors. I humbly request the experts to help me to estimate the results for my data. Thank you so much for your precious time. Regards Muhammad Zubair Chishti Ph.D. Student School of Business, Zhengzhou University, Henan, China. My Google scholar link: https://scholar.google.com/citationshl=en=YPqNJMwJ My ResearchGate link: https://www.researchgate.net/profile/Muhammad-Chishti __ 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] igraph: layout help
Hi,
I was trying to make a network plot of this data:
library(igraph)
library(network)
df1 <- data.frame(from="A",to=c("B","C","D","E","F","G"),value=1)
df2 <- data.frame(from="K",to=c("L","M","N"),value=1)
df3 <- data.frame(from="A",to="K",value=3)
my.df <- rbind(df1,df2,df3)
my.graph <- graph_from_data_frame(my.df,directed = F)
plot(my.graph)
What I wanted was for nodes A to G to be very close together (touching each
other). Similarly, nodes K to N should be very close together. The
connecting edge (A to K) between these sets of points/vertices should be
the only edge visible. How should I go about doing this?
Also, how can I change the parameters (node label, node color, etc.) of the
graph?
Any help or link to documentation would be helpful. Or would
thanks!
[[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.
