Re: [R] loop for comparing two or more groups using bootstrapping
Thank you Jim, it worked. I am very grateful for your help.
Thanks
KG
On Tue, Sep 11, 2018 at 3:51 PM Jim Lemon wrote:
> Hi Kristi,
> My fault, I only worked out how to assign the values to the names and pick
> out the columns of daT for the calculations. I think this does what you
> want, but I can't guarantee the result.
>
> daT<-structure(list(year1=c(0.417,0.538,0.69,0.688,0.688,0.606,
> 0.667,0.7,0.545,0.462,0.711,0.642,0.744,0.604,0.612,
> 0.667,0.533,0.556,0.444,0.526,0.323,0.308,0.195,0.333,
> 0.323,0.256,0.345,0.205,0.286,0.706,0.7,0.6,0.571,0.364,
> 0.429,0.326,0.571,0.424,0.341,0.387,0.341,0.324,0.696,
> 0.696,0.583,0.556,0.645,0.435,0.471,0.556),year2=c(0.385,
> 0.552,0.645,0.516,0.629,0.595,0.72,0.638,0.557,0.588,
> 0.63,0.744,0.773,0.571,0.723,0.769,0.667,0.667,0.526,
> 0.476,0.294,0.323,0.222,0.556,0.263,0.37,0.357,0.25,
> 0.323,0.778,0.667,0.636,0.583,0.432,0.412,0.333,0.571,
> 0.39,0.4,0.452,0.326,0.471,0.7,0.75,0.615,0.462,0.556,
> 0.4,0.696,0.465),year3=c(0.435,0.759,0.759,0.759,0.714,
> 0.593,0.651,0.683,0.513,0.643,0.652,0.757,0.791,0.649,
> 0.78,0.5,0.5,0.5,0.533,0.429,0.333,0.286,0.231,0.533,
> 0.303,0.417,0.333,0.333,0.357,0.909,1,0.952,0.8,0.556,
> 0.529,0.562,0.762,0.513,0.733,0.611,0.733,0.647,0.909,
> 0.857,0.8,0.556,0.588,0.562,0.857,0.513),year4=c(0.333,
> 0.533,0.6,0.483,0.743,0.5,0.691,0.619,0.583,0.385,0.653,
> 0.762,0.844,0.64,0.667,0.571,0.571,0.615,0.421,0.5,0.205,
> 0.308,0.25,0.6,0.242,0.308,0.276,0.235,0.211,0.9,0.632,
> 0.72,0.727,0.356,0.5,0.368,0.5,0.41,0.562,0.514,0.4,
> 0.409,0.632,0.72,0.727,0.4,0.5,0.421,0.5,0.462)),.Names=c("year1",
> "year2","year3","year4"),row.names=c(NA,-50L),class="data.frame")
> colname.mat<-combn(paste0("year",1:4),2)
> samplenames<-apply(colname.mat,2,paste,collapse="")
> k<-1
> meandiff<-function(x) return(mean(x[[1]])-mean(x[[2]]))
> for(column in 1:ncol(colname.mat)) {
> assign(samplenames[column],
> replicate(k,data.frame(sample(daT[,colname.mat[1,column]],3,TRUE),
>sample(daT[,colname.mat[2,column]],3,TRUE
> meandiffs<-unlist(apply(get(samplenames[column]),2,meandiff))
> cat(samplenames[column],"\n")
> cat("mean diff =",mean(meandiffs),"95% CI =",
> quantile(meandiffs,c(0.025,0.975)),"\n")
> png(paste0(samplenames[column],".png")
> hist(meandiffs)
> dev.off()
> }
>
> You should get a printout of the means and CIs and bunch of PNG files with
> the histograms.
>
> Jim
>
>
> On Tue, Sep 11, 2018 at 11:55 PM Kristi Glover
> wrote:
>
> > Dear Jim,
> >
> > Thank you very much for the code. I run it but it gave me row names
> > like "year224", "year142".
> >
> > are these the difference between columns? If we want to get bootstrapping
> > means of difference between years (year2-year1; year3-year1), its CI and
> > exact p value, how can we get it?
> >
> > thanks
> >
> > KG
> >
> >
> >
> > head(daT)
> >
> > colname.mat<-combn(paste0("year",1:4),2)
> >
> > samplenames<-apply(colname.mat,2,paste,collapse="")
> >
> > k<-10
> >
> > for(column in 1:ncol(colname.mat)) {
> >
> > assign(samplenames[column],replicate(k,sample(unlist(daT[,colname.mat[,
> > column]]),3,TRUE)))
> >
> > }
> >
> > > get(samplenames[1])
> > [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
> > year224 0.556 0.667 0.571 0.526 0.629 0.696 0.323 0.526 0.256 0.667
> > year142 0.324 0.324 0.706 0.638 0.600 0.294 0.612 0.688 0.432 0.387
> > year237 0.571 0.696 0.629 0.471 0.462 0.471 0.452 0.595 0.333 0.435
> >
> >
> >
> >
> > --
> > *From:* Jim Lemon
> > *Sent:* September 11, 2018 1:44 AM
> > *To:* Kristi Glover
> > *Cc:* r-help mailing list
> > *Subject:* Re: [R] loop for comparing two or more groups using
> > bootstrapping
> >
> > Hi Kristy,
> > Try this:
> >
> > colname.mat<-combn(paste0("year",1:4),2)
> > samplenames<-apply(colname.mat,2,paste,collapse="")
> > k<-1
> > for(column in 1:ncol(colname.mat)) {
> >
> >
> assign(samplenames[column],replicate(k,sample(unlist(daT[,colname.mat[,column]]),3,TRUE)))
> > }
> >
> > Then use get(samplenames[1]) and so on to access the values.
> >
> > Jim
> > On Tue, Sep 11, 2018 at 4:52 PM Kristi Glover >
> > wrote:
> > >
> > > Hi R users,
> > >
> > > I was trying to test a null hypothesis of difference between two groups
> > was 0. I have many years data, such as year1, year2,, year3, year4 and I
> > was trying to compare between year1 and year2, year1 and year3, year2 and
> > year3 and so on and have used following code with an example data.
> > >
> > >
> > > I tried to make a loop but did not work to compare between many years,
> > and also want to obtain the exact p value. Would you mind to help me to
> > make a loop?
> > >
> > > Thanks for your help.
> > >
> > >
> > > KG
> > >
> > >
> > > daT<-structure(list(year1 = c(0.417, 0.538, 0.69, 0.688, 0.688, 0.606,
> > > 0.667, 0.7, 0.545, 0.462, 0.711, 0.642, 0.744, 0.604, 0.612,
> > > 0.667, 0.533, 0.556, 0.444, 0.526, 0.323, 0.308, 0.195, 0.333,
> > > 0.323, 0.256, 0.345, 0.205, 0.286, 0.706, 0.7,
[R] Correcting dates in research / medical record using R
Hi,
I'm not that well versed with R - I'm trying to correct the dates of
service in a de-identified research medical record of several subjects.
The correct dates come from a csv file, in the VisitDate column, that
looks like this in Excel. The empty cells have other data in them that
I don't need and the file name is DateR.csv:
Id1 Id2
VisitDate
12345 12345
4/3/2018
The research medical record is a text file and the "DATE OF SERVICE" in
the top matter is in error in all of the subjects and needs to be
replaced with the "VisitDate" in the csv file. The file name for the
medical records is test3.NEW. Here is a screen grab of the top matter
of the research medical record; below this data excerpt is other
gathered data for that subject:
PATIENT NAME: CONFIDENTIAL,#12345
PATIENT ID #: 12345
DATE OF SERVICE: 04/10/2018
ACCESSION NUMBER: RR1234567
TEST PROCEDURE HIGH/LOW TEST RESULTS UNITS NORMAL VALUES
As described above, I need to update the text file DATE OF SERVICE:
date with the VisitDate in the csv file.
I made several attempts at this to failure and so now I turn to you.
Here is the code that exhibits my attempts:
clinicVdate <- read.csv("DateR.csv")
rownames(clinicVdate) <- as.character(clinicVdate[,'Id2'])
Id2 <- NA
input_data <- readLines("D:/test/test3.NEW")
output_data <- c()
for(input_line in input_data){
output_line = input_line
if(length(grep('PATIENT ID #:', input_line))>0) {
Id2 = as.character(strsplit(input_line, ':')[[1]][2])
}
if (length(grep( 'DATE OF SERVICE: ', input_line))){
output_line = paste('DATE OF SERVICE', clinicVdate[Id2,
'VisitDate'], sep=':')
}
output_data = paste(output_data, output_line, sep='\n')
}
cat(output_data)
The results of the above remove the erroneous date and replace it with
NA. Here is an example of the results:
PATIENT NAME: CONFIDENTIAL,#12345
PATIENT ID #: 12345
DATE OF SERVICE: NA
ACCESSION NUMBER: RR1234567
TEST PROCEDURE HIGH/LOW TEST RESULTS UNITS NORMAL VALUES
Where am I going wrong? If I didn't pose my question appropriately,
please let me know too!! Any help with this would be greatly appreciated!!
Kind regards,
Nic Cecchino
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Re: [R] Undesired tick marks on top, right axes [RESOLVED]
On Tue, 11 Sep 2018, Bert Gunter wrote: You do that. Your error is obvious. Bert, Yep. Forgot to remove the 'p' from the type attribute. Mea culpa! Rich __ 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] Undesired tick marks on top, right axes
You do that. Your error is obvious. -- Bert On Tue, Sep 11, 2018 at 5:39 PM Rich Shepard wrote: > > On Tue, 11 Sep 2018, Bert Gunter wrote: > > > As I thought, you did not do what I told you to. > > Look *carefully* at the two to see your error. > > Bert, > >You're correct, of course. After moving the tck parameter in front of the > x list the right-side ticks are gone. Unfortunately, so are the data: the > panel is empty. > >Corrected command: > > rain.all.sum <- xyplot(Sum ~ Month, data=agg.all, col = 'black', type = 'p, > h', > main = 'Monthly Total Precipitation\n2005-2018', > xlab = 'Year and Month', ylab = 'Precipitation (in)', > scales = list(tck = c(1,0), x = list(at = > seq(1,162,by=6), >cex = 0.7, rot = 90))) > >Tomorrow I'll work on why the panel display disappeared along with the > right axes tick marks. Parentheses all match according to emacs. > > Thanks, > > Rich > > __ > 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] Undesired tick marks on top, right axes
On Tue, 11 Sep 2018, Bert Gunter wrote: As I thought, you did not do what I told you to. Look *carefully* at the two to see your error. Bert, You're correct, of course. After moving the tck parameter in front of the x list the right-side ticks are gone. Unfortunately, so are the data: the panel is empty. Corrected command: rain.all.sum <- xyplot(Sum ~ Month, data=agg.all, col = 'black', type = 'p, h', main = 'Monthly Total Precipitation\n2005-2018', xlab = 'Year and Month', ylab = 'Precipitation (in)', scales = list(tck = c(1,0), x = list(at = seq(1,162,by=6), cex = 0.7, rot = 90))) Tomorrow I'll work on why the panel display disappeared along with the right axes tick marks. Parentheses all match according to emacs. Thanks, Rich __ 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] Undesired tick marks on top, right axes
As I thought, you did not do what I told you to. Look *carefully* at the two to see your error. -- Bert On Tue, Sep 11, 2018 at 5:01 PM Rich Shepard wrote: > > On Tue, 11 Sep 2018, Bert Gunter wrote: > > > Not when I run your code with the tck specification added. Show us > > your xyplot invocation. It should be > > scales = list(tck = c(1,0), x= etc.) > > Bert, > >Command: > > rain.all.sum <- xyplot(Sum ~ Month, data=agg.all, col = 'black', type = 'h', > main = 'Monthly Total Precipitation\n2005-2018', > xlab = 'Year and Month', ylab = 'Precipitation (in)', > scales = list(x = list(tck = c(1, 0), at = > seq(1,162,by=6), >cex = 0.7, rot = 90))) > > rain.all.sum.pdf attached. > > Regards, > > Rich > __ > 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] Undesired tick marks on top, right axes
On Tue, 11 Sep 2018, Bert Gunter wrote: Not when I run your code with the tck specification added. Show us your xyplot invocation. It should be scales = list(tck = c(1,0), x= etc.) Bert, Command: rain.all.sum <- xyplot(Sum ~ Month, data=agg.all, col = 'black', type = 'h', main = 'Monthly Total Precipitation\n2005-2018', xlab = 'Year and Month', ylab = 'Precipitation (in)', scales = list(x = list(tck = c(1, 0), at = seq(1,162,by=6), cex = 0.7, rot = 90))) rain.all.sum.pdf attached. Regards, Rich rain.all.sum.pdf Description: Adobe PDF document __ 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] Hierarchical Cluster Analysis
agnes (cluster) Jim On Wed, Sep 12, 2018 at 8:10 AM Bryan Mac wrote: > > > Bryan Mac > Data Scientist > Research Analytics > Ipsos Insight LLC > > > > > > [[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] Undesired tick marks on top, right axes
?? Not when I run your code with the tck specification added. Show us your xyplot invocation. It should be scales = list(tck = c(1,0), x= etc.) Bert On Tue, Sep 11, 2018 at 3:51 PM Rich Shepard wrote: > > On Tue, 11 Sep 2018, Bert Gunter wrote: > > > Adding > > tck = c(1, 0) > > to the "scales =" list will probably solve your problem. > > Bert, > >How interesting. This removed the tick marks on top but left them on the > right axes. Will think more about this. > > Regards, > > Rich > > __ > 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] Remove plot axis values in dotplot graph
Hi Abou,
Surprisingly you can't omit the x axis in dotchart. This hack will work:
sink("dotchar_noax.R")
sink()
Edit the resulting file by joining the first two lines with the
assignment symbol (<-), delete the two lines at the bottom and comment
out the line "axis(1)".
source("dotchart.noax.R")
dotchart.noax(scores,cex=1.5, pch = 18, col=c(1:3), xaxt = "n", main="Dot Plot
child’s cough data", xlab="cough Scores")
library(plotrix)
staxlab(1,0:16)
I used "staxlab" so that you could have all of the labels 0:16.
Jim
On Wed, Sep 12, 2018 at 5:57 AM AbouEl-Makarim Aboueissa
wrote:
>
> Dear All:
>
> One more thing. I want to Remove the plot x-axis values in dotplot graph. I
> am trying to use xaxt = "n", but it seems NOT working. Also after removing
> the x-axis values, I want to use the command axis(1, at=0:16, cex.axis=1)
> to add x-axis values from 0 to 16, but it seems not working as expect.
>
>
>
> Honey.Dosage<-c(12,11,15,11,10,13,10,4,15,16,9,14,10,6,10,8,11,12,12,8,12,9,11,15,10,15,9,13,8,12,10,8,9,5,12)
>
> DM.Dosage<-c(4,6,9,4,7,7,7,9,12,10,11,6,3,4,9,12,7,6,8,12,12,4,12,13,7,10,13,9,4,4,10,15,9)
>
> No.Dosage<-c(5,8,6,1,0,8,12,8,7,7,1,6,7,7,12,7,9,7,9,5,11,9,5,6,8,8,6,7,10,9,4,8,7,3,1,4,3)
>
> scores<-c(Honey.Dosage,DM.Dosage,No.Dosage)
>
> min(scores)
> max(scores)
>
> dotchart(scores,cex=1.5, pch = 18, col=c(1:3), xaxt = "n", main="Dot Plot
> child’s cough data", xlab="cough Scores")
>
> axis(1, at=0:16, cex.axis=1.5)
>
>
>
>
> with many thanks
> abou
> __
>
>
> *AbouEl-Makarim Aboueissa, PhD*
>
> *Professor of Statistics*
> *Graduate Coordinator*
>
> *Department of Mathematics and Statistics*
> *University of Southern Maine*
>
> [[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
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Increasing size of label in Taylor plot of Plotrix package
Hi Sonam, You're right. Although the cex.axis argument is present, it doesn't seem to be used. I will have to debug this, which may take a day or two. Jim On Tue, Sep 11, 2018 at 6:37 PM Sonam Sandeep Dash wrote: > > Respected Sir, > I have created a Taylor plot using the plotrix package. However, I am unable > to increase the size of labels of axis. I have tried so many ways but all are > in vein. There is no change to size of label of either axis. Kindly tell me > the procedure to do the same. > Thank you, > > Regards: > Sonam Sandeep Dash > Research scholar > School of Water Resources > Indian Institute of Technology, Kharagpur > West Bengal-721302 __ 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] loop for comparing two or more groups using bootstrapping
Hi Kristi,
My fault, I only worked out how to assign the values to the names and pick
out the columns of daT for the calculations. I think this does what you
want, but I can't guarantee the result.
daT<-structure(list(year1=c(0.417,0.538,0.69,0.688,0.688,0.606,
0.667,0.7,0.545,0.462,0.711,0.642,0.744,0.604,0.612,
0.667,0.533,0.556,0.444,0.526,0.323,0.308,0.195,0.333,
0.323,0.256,0.345,0.205,0.286,0.706,0.7,0.6,0.571,0.364,
0.429,0.326,0.571,0.424,0.341,0.387,0.341,0.324,0.696,
0.696,0.583,0.556,0.645,0.435,0.471,0.556),year2=c(0.385,
0.552,0.645,0.516,0.629,0.595,0.72,0.638,0.557,0.588,
0.63,0.744,0.773,0.571,0.723,0.769,0.667,0.667,0.526,
0.476,0.294,0.323,0.222,0.556,0.263,0.37,0.357,0.25,
0.323,0.778,0.667,0.636,0.583,0.432,0.412,0.333,0.571,
0.39,0.4,0.452,0.326,0.471,0.7,0.75,0.615,0.462,0.556,
0.4,0.696,0.465),year3=c(0.435,0.759,0.759,0.759,0.714,
0.593,0.651,0.683,0.513,0.643,0.652,0.757,0.791,0.649,
0.78,0.5,0.5,0.5,0.533,0.429,0.333,0.286,0.231,0.533,
0.303,0.417,0.333,0.333,0.357,0.909,1,0.952,0.8,0.556,
0.529,0.562,0.762,0.513,0.733,0.611,0.733,0.647,0.909,
0.857,0.8,0.556,0.588,0.562,0.857,0.513),year4=c(0.333,
0.533,0.6,0.483,0.743,0.5,0.691,0.619,0.583,0.385,0.653,
0.762,0.844,0.64,0.667,0.571,0.571,0.615,0.421,0.5,0.205,
0.308,0.25,0.6,0.242,0.308,0.276,0.235,0.211,0.9,0.632,
0.72,0.727,0.356,0.5,0.368,0.5,0.41,0.562,0.514,0.4,
0.409,0.632,0.72,0.727,0.4,0.5,0.421,0.5,0.462)),.Names=c("year1",
"year2","year3","year4"),row.names=c(NA,-50L),class="data.frame")
colname.mat<-combn(paste0("year",1:4),2)
samplenames<-apply(colname.mat,2,paste,collapse="")
k<-1
meandiff<-function(x) return(mean(x[[1]])-mean(x[[2]]))
for(column in 1:ncol(colname.mat)) {
assign(samplenames[column],
replicate(k,data.frame(sample(daT[,colname.mat[1,column]],3,TRUE),
sample(daT[,colname.mat[2,column]],3,TRUE
meandiffs<-unlist(apply(get(samplenames[column]),2,meandiff))
cat(samplenames[column],"\n")
cat("mean diff =",mean(meandiffs),"95% CI =",
quantile(meandiffs,c(0.025,0.975)),"\n")
png(paste0(samplenames[column],".png")
hist(meandiffs)
dev.off()
}
You should get a printout of the means and CIs and bunch of PNG files with
the histograms.
Jim
On Tue, Sep 11, 2018 at 11:55 PM Kristi Glover
wrote:
> Dear Jim,
>
> Thank you very much for the code. I run it but it gave me row names
> like "year224", "year142".
>
> are these the difference between columns? If we want to get bootstrapping
> means of difference between years (year2-year1; year3-year1), its CI and
> exact p value, how can we get it?
>
> thanks
>
> KG
>
>
>
> head(daT)
>
> colname.mat<-combn(paste0("year",1:4),2)
>
> samplenames<-apply(colname.mat,2,paste,collapse="")
>
> k<-10
>
> for(column in 1:ncol(colname.mat)) {
>
> assign(samplenames[column],replicate(k,sample(unlist(daT[,colname.mat[,
> column]]),3,TRUE)))
>
> }
>
> > get(samplenames[1])
> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
> year224 0.556 0.667 0.571 0.526 0.629 0.696 0.323 0.526 0.256 0.667
> year142 0.324 0.324 0.706 0.638 0.600 0.294 0.612 0.688 0.432 0.387
> year237 0.571 0.696 0.629 0.471 0.462 0.471 0.452 0.595 0.333 0.435
>
>
>
>
> --
> *From:* Jim Lemon
> *Sent:* September 11, 2018 1:44 AM
> *To:* Kristi Glover
> *Cc:* r-help mailing list
> *Subject:* Re: [R] loop for comparing two or more groups using
> bootstrapping
>
> Hi Kristy,
> Try this:
>
> colname.mat<-combn(paste0("year",1:4),2)
> samplenames<-apply(colname.mat,2,paste,collapse="")
> k<-1
> for(column in 1:ncol(colname.mat)) {
>
>
> assign(samplenames[column],replicate(k,sample(unlist(daT[,colname.mat[,column]]),3,TRUE)))
> }
>
> Then use get(samplenames[1]) and so on to access the values.
>
> Jim
> On Tue, Sep 11, 2018 at 4:52 PM Kristi Glover
> wrote:
> >
> > Hi R users,
> >
> > I was trying to test a null hypothesis of difference between two groups
> was 0. I have many years data, such as year1, year2,, year3, year4 and I
> was trying to compare between year1 and year2, year1 and year3, year2 and
> year3 and so on and have used following code with an example data.
> >
> >
> > I tried to make a loop but did not work to compare between many years,
> and also want to obtain the exact p value. Would you mind to help me to
> make a loop?
> >
> > Thanks for your help.
> >
> >
> > KG
> >
> >
> > daT<-structure(list(year1 = c(0.417, 0.538, 0.69, 0.688, 0.688, 0.606,
> > 0.667, 0.7, 0.545, 0.462, 0.711, 0.642, 0.744, 0.604, 0.612,
> > 0.667, 0.533, 0.556, 0.444, 0.526, 0.323, 0.308, 0.195, 0.333,
> > 0.323, 0.256, 0.345, 0.205, 0.286, 0.706, 0.7, 0.6, 0.571, 0.364,
> > 0.429, 0.326, 0.571, 0.424, 0.341, 0.387, 0.341, 0.324, 0.696,
> > 0.696, 0.583, 0.556, 0.645, 0.435, 0.471, 0.556), year2 = c(0.385,
> > 0.552, 0.645, 0.516, 0.629, 0.595, 0.72, 0.638, 0.557, 0.588,
> > 0.63, 0.744, 0.773, 0.571, 0.723, 0.769, 0.667, 0.667, 0.526,
> > 0.476, 0.294, 0.323, 0.222, 0.556, 0.263, 0.37, 0.357, 0.25,
> > 0.323, 0.778, 0.667, 0.636, 0.583,
Re: [R] Undesired tick marks on top, right axes
On Tue, 11 Sep 2018, Bert Gunter wrote: Adding tck = c(1, 0) to the "scales =" list will probably solve your problem. Bert, How interesting. This removed the tick marks on top but left them on the right axes. Will think more about this. Regards, Rich __ 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] getting 21 very different colours
Have a look at the Polychrome package by Kevin Coombes and Guy Brock: https://CRAN.R-project.org/package=Polychrome This employs the LUV space (with HCL = polar LUV) to get many distinct distinguishable colors. For a few first steps, see: https://CRAN.R-project.org/web/packages/Polychrome/vignettes/polychrome.html On Wed, 12 Sep 2018, Zach Simpson wrote: Hi Federico For a possible alternative, the scico package provides a nice collection of color palettes that are designed to be both color-blind friendly and differentiable: https://www.data-imaginist.com/2018/scico-and-the-colour-conundrum/ You could generate a vector of 21 colors (spaced as far apart as possible on the palette) to pass to your plot arguments with something like: library(scico) scico(21, palette = 'oleron') Not sure if this works for your case though. But maybe another feature (shape?) could help differentiate the 21 points. Hope this helps, Zach Simpson Message: 11 Date: Tue, 11 Sep 2018 07:34:51 + From: Federico Calboli To: "r-help@r-project.org" Subject: [R] getting 21 very different colours Message-ID: <08a6397b-4d67-4195-a53a-1fd394f72...@kuleuven.be> Content-Type: text/plain; charset="utf-8" Hi All, I am plotting a scatterplot of 21 populations, and I am using rainbow(21)[pops.col] to generate 21 colours for the plot (which works). Maybe it is because I can really process few colours at a time, but the differences between the colours are not as strong as I’d like. I can specify start and end for rainbow(), but if anything that looks worse if I do not just stick to 0 and 1. Is there a way of getting a set of 21 colours that maximises the differences between them? I could pick them by hand, but that is about 15 colours more than I know (I have a detailed colourchart, but the visual differences between ’skyblue’ and ’slategrey’ elude me when plotted as dots on a plot). Cheers F -- Federico Calboli LBEG - Laboratory of Biodiversity and Evolutionary Genomics Charles Deberiotstraat 32 box 2439 3000 Leuven +32 16 32 87 67 __ 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] Undesired tick marks on top, right axes
On Tue, 11 Sep 2018, Bert Gunter wrote: Well, you might try ?xyplot -- in particular the "scales" list section and in particular there the "tck" parameter. Adding tck = c(1, 0) to the "scales =" list will probably solve your problem. Bert, I missed the end of the tck description in the book (the same text as the help file but with more information) where it mentions that tck can be a vector of length 2 where the first element affects the left/bottom axes and the second element affects the right/top axes. I also did not grok turning the first element on and the second element off. Now I wonder why this wasn't an issue before now in the xyplots I created. Thanks much, Rich __ 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] getting 21 very different colours
Hi Federico For a possible alternative, the scico package provides a nice collection of color palettes that are designed to be both color-blind friendly and differentiable: https://www.data-imaginist.com/2018/scico-and-the-colour-conundrum/ You could generate a vector of 21 colors (spaced as far apart as possible on the palette) to pass to your plot arguments with something like: library(scico) scico(21, palette = 'oleron') Not sure if this works for your case though. But maybe another feature (shape?) could help differentiate the 21 points. Hope this helps, Zach Simpson > Message: 11 > Date: Tue, 11 Sep 2018 07:34:51 + > From: Federico Calboli > To: "r-help@r-project.org" > Subject: [R] getting 21 very different colours > Message-ID: <08a6397b-4d67-4195-a53a-1fd394f72...@kuleuven.be> > Content-Type: text/plain; charset="utf-8" > > Hi All, > > I am plotting a scatterplot of 21 populations, and I am using > rainbow(21)[pops.col] to generate 21 colours for the plot (which works). > Maybe it is because I can really process few colours at a time, but the > differences between the colours are not as strong as I’d like. I can specify > start and end for rainbow(), but if anything that looks worse if I do not > just stick to 0 and 1. > > Is there a way of getting a set of 21 colours that maximises the differences > between them? > > I could pick them by hand, but that is about 15 colours more than I know (I > have a detailed colourchart, but the visual differences between ’skyblue’ and > ’slategrey’ elude me when plotted as dots on a plot). > > Cheers > > F > -- > Federico Calboli > LBEG - Laboratory of Biodiversity and Evolutionary Genomics > Charles Deberiotstraat 32 box 2439 > 3000 Leuven > +32 16 32 87 67 __ 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] Undesired tick marks on top, right axes
Well, you might try ?xyplot -- in particular the "scales" list section
and in particular there the "tck" parameter. Adding
tck = c(1, 0)
to the "scales =" list will probably solve your problem.
-- Bert
On Tue, Sep 11, 2018 at 2:46 PM Rich Shepard wrote:
>
>Every lattice xyplot() I've created before this one has tick marks on only
> the left and bottom axes. The current plot has sprouted tick marks on the
> top and right side, too, and I want to remove them. I've not found an answer
> to this issue in Deepayan's book or on the web. I would appreciate also
> learning why the extra tick marks appeared. The dput() data are included.
>
>The plotting command;
>
> rain.all.sum <- xyplot(Sum ~ Month, data=agg.all, col = 'black', type = 'h',
> main = 'Monthly Total Precipitation\n2005-2018',
> xlab = 'Year and Month', ylab = 'Precipitation (in)',
> scales = list(x = list(at = seq(1,162,by=6), cex =
> 0.7, rot = 90)))
>
> plot(rain.all.sum)
>
>The data:
>
> structure(list(Month = structure(1:162, .Label = c("2005-01",
> "2005-02", "2005-03", "2005-04", "2005-05", "2005-06", "2005-07",
> "2005-08", "2005-09", "2005-10", "2005-11", "2005-12", "2006-01",
> "2006-02", "2006-03", "2006-04", "2006-05", "2006-06", "2006-07",
> "2006-08", "2006-09", "2006-10", "2006-11", "2006-12", "2007-01",
> "2007-02", "2007-03", "2007-04", "2007-05", "2007-06", "2007-07",
> "2007-08", "2007-09", "2007-10", "2007-11", "2007-12", "2008-01",
> "2008-02", "2008-03", "2008-04", "2008-05", "2008-06", "2008-07",
> "2008-08", "2008-09", "2008-10", "2008-11", "2008-12", "2009-01",
> "2009-02", "2009-03", "2009-04", "2009-05", "2009-06", "2009-07",
> "2009-08", "2009-09", "2009-10", "2009-11", "2009-12", "2010-01",
> "2010-02", "2010-03", "2010-04", "2010-05", "2010-06", "2010-07",
> "2010-08", "2010-09", "2010-10", "2010-11", "2010-12", "2011-01",
> "2011-02", "2011-03", "2011-04", "2011-05", "2011-06", "2011-07",
> "2011-08", "2011-09", "2011-10", "2011-11", "2011-12", "2012-01",
> "2012-02", "2012-03", "2012-04", "2012-05", "2012-06", "2012-07",
> "2012-08", "2012-09", "2012-10", "2012-11", "2012-12", "2013-01",
> "2013-02", "2013-03", "2013-04", "2013-05", "2013-06", "2013-07",
> "2013-08", "2013-09", "2013-10", "2013-11", "2013-12", "2014-01",
> "2014-02", "2014-03", "2014-04", "2014-05", "2014-06", "2014-07",
> "2014-08", "2014-09", "2014-10", "2014-11", "2014-12", "2015-01",
> "2015-02", "2015-03", "2015-04", "2015-05", "2015-06", "2015-07",
> "2015-08", "2015-09", "2015-10", "2015-11", "2015-12", "2016-01",
> "2016-02", "2016-03", "2016-04", "2016-05", "2016-06", "2016-07",
> "2016-08", "2016-09", "2016-10", "2016-11", "2016-12", "2017-01",
> "2017-02", "2017-03", "2017-04", "2017-05", "2017-06", "2017-07",
> "2017-08", "2017-09", "2017-10", "2017-11", "2017-12", "2018-01",
> "2018-02", "2018-03", "2018-04", "2018-05", "2018-06"), class = "factor"),
> Sum = c(53.51, 24.2, 88.54, 72.85, 77.3, 49.19, 8.77, 5.75,
> 27.83, 79.75, 123.89, 168.29, 229.69, 70.91, 74.15, 62.3,
> 43.56, 35.08, 3.6, 2.76, 26.83, 47.72, 293.23, 139.84, 103.48,
> 120.91, 85.96, 55.91, 26.56, 29.44, 9.9, 15.38, 33.47, 93.6,
> 105.61, 277.41, 279.38, 144.26, 220.88, 149.75, 82.28, 55.87,
> 5.29, 52.27, 21.1, 64.76, 182.31, 207.13, 196.29, 89.27,
> 187.72, 111.67, 111.72, 38.19, 6.07, 15.25, 52.46, 127.75,
> 208.43, 146.62, 169.34, 94.54, 154.21, 131.39, 151.27, 135.46,
> 9.98, 8.72, 86.67, 142.04, 225.61, 274.93, 196.68, 153.24,
> 263.54, 231.49, 122.23, 58.26, 34.65, 2.96, 28.21, 103.92,
> 217.52, 166.16, 305.27, 168.73, 333.28, 145.68, 101.2, 127.77,
> 15.41, 1.85, 3.49, 245.99, 272.35, 297.05, 177.17, 105.71,
> 118.44, 136.34, 161.01, 53.31, 1.15, 23.43, 200.97, 69.12,
> 158.51, 131.67, 156.95, 266.38, 291.7, 147.15, 101.49, 78.89,
> 26.99, 24.35, 35.76, 210.2, 225.55, 282.85, 153.91, 148.13,
> 187.03, 133.99, 62.28, 17.58, 13.41, 35.58, 47.04, 154.92,
> 317.77, 604.04, 288.91, 210.86, 266.04, 121.62, 78.17, 85.96,
> 29.84, 7.02, 72.13, 404.33, 247.71, 255.5, 138.22, 339.5,
> 368.99, 209.41, 110.08, 63.9, 0.62, 6.97, 133.75, 227.1,
> 312.99, 178.58, 255.8, 155.05, 135.27, 225.55, 15.23, 1.58
> ), Median = c(0.01, 0, 0, 0.1, 0.1, 0, 0, 0, 0, 0.02, 0.1,
> 0.04, 0.5, 0, 0.1, 0.07, 0, 0, 0, 0, 0, 0, 0.57, 0.03, 0,
> 0.2, 0.055, 0, 0, 0, 0, 0, 0, 0, 0, 0.21, 0.21, 0.02, 0.2,
> 0.11, 0.02, 0, 0, 0, 0, 0, 0.1, 0.165, 0.01, 0.01, 0.15,
> 0.01, 0, 0, 0, 0, 0, 0.02, 0.125, 0, 0.1, 0.08, 0.055, 0.1,
> 0.13, 0.01, 0, 0, 0, 0, 0.2, 0.17, 0.02, 0.07, 0.23, 0.15,
> 0.06, 0, 0, 0, 0, 0.03, 0.1, 0, 0.1, 0.1, 0.2, 0.07, 0, 0.02,
> 0, 0, 0, 0.04, 0.115, 0.24, 0.02, 0.03, 0.01, 0.01, 0.02,
> 0, 0, 0, 0, 0, 0.02, 0, 0, 0.2, 0.18, 0.05, 0, 0, 0, 0, 0,
> 0.08, 0.07, 0.1, 0, 0.01, 0, 0.02, 0, 0, 0, 0, 0, 0, 0.09,
> 0.4, 0.18, 0.1, 0.2, 0, 0, 0, 0,
[R] Hierarchical Cluster Analysis
Bryan Mac Data Scientist Research Analytics Ipsos Insight LLC [[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] Undesired tick marks on top, right axes
Every lattice xyplot() I've created before this one has tick marks on only
the left and bottom axes. The current plot has sprouted tick marks on the
top and right side, too, and I want to remove them. I've not found an answer
to this issue in Deepayan's book or on the web. I would appreciate also
learning why the extra tick marks appeared. The dput() data are included.
The plotting command;
rain.all.sum <- xyplot(Sum ~ Month, data=agg.all, col = 'black', type = 'h',
main = 'Monthly Total Precipitation\n2005-2018',
xlab = 'Year and Month', ylab = 'Precipitation (in)',
scales = list(x = list(at = seq(1,162,by=6), cex = 0.7,
rot = 90)))
plot(rain.all.sum)
The data:
structure(list(Month = structure(1:162, .Label = c("2005-01",
"2005-02", "2005-03", "2005-04", "2005-05", "2005-06", "2005-07",
"2005-08", "2005-09", "2005-10", "2005-11", "2005-12", "2006-01",
"2006-02", "2006-03", "2006-04", "2006-05", "2006-06", "2006-07",
"2006-08", "2006-09", "2006-10", "2006-11", "2006-12", "2007-01",
"2007-02", "2007-03", "2007-04", "2007-05", "2007-06", "2007-07",
"2007-08", "2007-09", "2007-10", "2007-11", "2007-12", "2008-01",
"2008-02", "2008-03", "2008-04", "2008-05", "2008-06", "2008-07",
"2008-08", "2008-09", "2008-10", "2008-11", "2008-12", "2009-01",
"2009-02", "2009-03", "2009-04", "2009-05", "2009-06", "2009-07",
"2009-08", "2009-09", "2009-10", "2009-11", "2009-12", "2010-01",
"2010-02", "2010-03", "2010-04", "2010-05", "2010-06", "2010-07",
"2010-08", "2010-09", "2010-10", "2010-11", "2010-12", "2011-01",
"2011-02", "2011-03", "2011-04", "2011-05", "2011-06", "2011-07",
"2011-08", "2011-09", "2011-10", "2011-11", "2011-12", "2012-01",
"2012-02", "2012-03", "2012-04", "2012-05", "2012-06", "2012-07",
"2012-08", "2012-09", "2012-10", "2012-11", "2012-12", "2013-01",
"2013-02", "2013-03", "2013-04", "2013-05", "2013-06", "2013-07",
"2013-08", "2013-09", "2013-10", "2013-11", "2013-12", "2014-01",
"2014-02", "2014-03", "2014-04", "2014-05", "2014-06", "2014-07",
"2014-08", "2014-09", "2014-10", "2014-11", "2014-12", "2015-01",
"2015-02", "2015-03", "2015-04", "2015-05", "2015-06", "2015-07",
"2015-08", "2015-09", "2015-10", "2015-11", "2015-12", "2016-01",
"2016-02", "2016-03", "2016-04", "2016-05", "2016-06", "2016-07",
"2016-08", "2016-09", "2016-10", "2016-11", "2016-12", "2017-01",
"2017-02", "2017-03", "2017-04", "2017-05", "2017-06", "2017-07",
"2017-08", "2017-09", "2017-10", "2017-11", "2017-12", "2018-01",
"2018-02", "2018-03", "2018-04", "2018-05", "2018-06"), class = "factor"),
Sum = c(53.51, 24.2, 88.54, 72.85, 77.3, 49.19, 8.77, 5.75,
27.83, 79.75, 123.89, 168.29, 229.69, 70.91, 74.15, 62.3,
43.56, 35.08, 3.6, 2.76, 26.83, 47.72, 293.23, 139.84, 103.48,
120.91, 85.96, 55.91, 26.56, 29.44, 9.9, 15.38, 33.47, 93.6,
105.61, 277.41, 279.38, 144.26, 220.88, 149.75, 82.28, 55.87,
5.29, 52.27, 21.1, 64.76, 182.31, 207.13, 196.29, 89.27,
187.72, 111.67, 111.72, 38.19, 6.07, 15.25, 52.46, 127.75,
208.43, 146.62, 169.34, 94.54, 154.21, 131.39, 151.27, 135.46,
9.98, 8.72, 86.67, 142.04, 225.61, 274.93, 196.68, 153.24,
263.54, 231.49, 122.23, 58.26, 34.65, 2.96, 28.21, 103.92,
217.52, 166.16, 305.27, 168.73, 333.28, 145.68, 101.2, 127.77,
15.41, 1.85, 3.49, 245.99, 272.35, 297.05, 177.17, 105.71,
118.44, 136.34, 161.01, 53.31, 1.15, 23.43, 200.97, 69.12,
158.51, 131.67, 156.95, 266.38, 291.7, 147.15, 101.49, 78.89,
26.99, 24.35, 35.76, 210.2, 225.55, 282.85, 153.91, 148.13,
187.03, 133.99, 62.28, 17.58, 13.41, 35.58, 47.04, 154.92,
317.77, 604.04, 288.91, 210.86, 266.04, 121.62, 78.17, 85.96,
29.84, 7.02, 72.13, 404.33, 247.71, 255.5, 138.22, 339.5,
368.99, 209.41, 110.08, 63.9, 0.62, 6.97, 133.75, 227.1,
312.99, 178.58, 255.8, 155.05, 135.27, 225.55, 15.23, 1.58
), Median = c(0.01, 0, 0, 0.1, 0.1, 0, 0, 0, 0, 0.02, 0.1,
0.04, 0.5, 0, 0.1, 0.07, 0, 0, 0, 0, 0, 0, 0.57, 0.03, 0,
0.2, 0.055, 0, 0, 0, 0, 0, 0, 0, 0, 0.21, 0.21, 0.02, 0.2,
0.11, 0.02, 0, 0, 0, 0, 0, 0.1, 0.165, 0.01, 0.01, 0.15,
0.01, 0, 0, 0, 0, 0, 0.02, 0.125, 0, 0.1, 0.08, 0.055, 0.1,
0.13, 0.01, 0, 0, 0, 0, 0.2, 0.17, 0.02, 0.07, 0.23, 0.15,
0.06, 0, 0, 0, 0, 0.03, 0.1, 0, 0.1, 0.1, 0.2, 0.07, 0, 0.02,
0, 0, 0, 0.04, 0.115, 0.24, 0.02, 0.03, 0.01, 0.01, 0.02,
0, 0, 0, 0, 0, 0.02, 0, 0, 0.2, 0.18, 0.05, 0, 0, 0, 0, 0,
0.08, 0.07, 0.1, 0, 0.01, 0, 0.02, 0, 0, 0, 0, 0, 0, 0.09,
0.4, 0.18, 0.1, 0.2, 0, 0, 0, 0, 0, 0, 0.29, 0.09, 0.09,
0, 0.26, 0.3, 0.16, 0, 0, 0, 0, 0, 0, 0.25, 0, 0.16, 0.03,
0.02, 0.08, 0, 0), Max = c(3, 1.1, 3.2, 1.2, 1.6, 1.48, 0.8,
0.6, 3.2, 4.9, 3.1, 3.63, 3.4, 2.6, 2, 3.25, 1.6, 2.1, 0.4,
0.5, 1.1, 2, 6.6, 3.2, 3.6, 5.8, 2.3, 1.7, 1.3, 1.2, 1, 2.1,
2, 3, 3, 5.9, 3.3, 2.9, 5.2, 1.8, 1.4, 2.2, 0.6, 2.5, 1.02,
2, 4.4, 3.6, 5.3, 2.2, 2.7, 2.5, 1.5, 1.4, 0.8, 1.4, 1.4,
2.11,
[R] Remove plot axis values in dotplot graph
Dear All: One more thing. I want to Remove the plot x-axis values in dotplot graph. I am trying to use xaxt = "n", but it seems NOT working. Also after removing the x-axis values, I want to use the command axis(1, at=0:16, cex.axis=1) to add x-axis values from 0 to 16, but it seems not working as expect. Honey.Dosage<-c(12,11,15,11,10,13,10,4,15,16,9,14,10,6,10,8,11,12,12,8,12,9,11,15,10,15,9,13,8,12,10,8,9,5,12) DM.Dosage<-c(4,6,9,4,7,7,7,9,12,10,11,6,3,4,9,12,7,6,8,12,12,4,12,13,7,10,13,9,4,4,10,15,9) No.Dosage<-c(5,8,6,1,0,8,12,8,7,7,1,6,7,7,12,7,9,7,9,5,11,9,5,6,8,8,6,7,10,9,4,8,7,3,1,4,3) scores<-c(Honey.Dosage,DM.Dosage,No.Dosage) min(scores) max(scores) dotchart(scores,cex=1.5, pch = 18, col=c(1:3), xaxt = "n", main="Dot Plot child’s cough data", xlab="cough Scores") axis(1, at=0:16, cex.axis=1.5) with many thanks abou __ *AbouEl-Makarim Aboueissa, PhD* *Professor of Statistics* *Graduate Coordinator* *Department of Mathematics and Statistics* *University of Southern Maine* [[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] Bar Graph
Dear Rui:
thank you very much
abou
__
*AbouEl-Makarim Aboueissa, PhD*
*Professor of Statistics*
*Graduate Coordinator*
*Department of Mathematics and Statistics*
*University of Southern Maine*
On Tue, Sep 11, 2018 at 2:24 PM Rui Barradas wrote:
> Hello,
>
> Use function text() with the return of barplot() as x value and
> Number.of.Death as y.
> Note that the limits of the y axis are not the automatic ones.
>
>
>
> bp <- barplot(Number.of.Death, names.arg=Cause.of.Death, main="Bar Graph
> for
> Death Data", ylab="Number of Death", xlab="Cause of Death", ylim = c(0,
> 500))
>
> text(x = bp, y = Number.of.Death, labels = Number.of.Death, pos = 3)
>
>
> Hope this helps,
>
> Rui Barradas
>
> On 11-09-2018 19:02, AbouEl-Makarim Aboueissa wrote:
> > Dear All:
> >
> >
> > I do need your help on how to add frequency to bar plot on the top of
> each
> > bar.
> >
> >
> > here is the R code.
> >
> >
> > *Number.of.Death <- c(432, 217,93, 34, 224)# Number of Death*
> >
> > *Cause.of.Death <- c("Heart disease", "Cancer", "Stroke", "Accidents",
> > "Other") *
> >
> > *barplot(Number.of.Death, names.arg=Cause.of.Death, main="Bar Grapg for
> > Death Data", ylab="Number of Death", xlab="Cause of Death") *
> >
> >
> >
> > Thank you very much for your help in advance.
> >
> >
> > with many thanks
> > abou
> > __
> >
> >
> > *AbouEl-Makarim Aboueissa, PhD*
> >
> > *Professor of Statistics*
> > *Graduate Coordinator*
> >
> > *Department of Mathematics and Statistics*
> > *University of Southern Maine*
> >
> > [[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]]
__
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Re: [R] Bar Graph
Dear Bert:
thank you very much
abou
__
*AbouEl-Makarim Aboueissa, PhD*
*Professor of Statistics*
*Graduate Coordinator*
*Department of Mathematics and Statistics*
*University of Southern Maine*
On Tue, Sep 11, 2018 at 2:47 PM Bert Gunter wrote:
> Not quite -- he wanted the frequencies not the counts. So something
> like this (using the adj argument to center the frequencies above each
> bar:
>
> bp <-barplot(Number.of.Death, names.arg=Cause.of.Death, main="Bar
> Graph for Death Data", ylab="Number of Deaths", xlab="Cause of Death",
> ylim = c(0,500) )
>
> text(bp, y = Number.of.Death + 30, adj = .5,
> lab = round(Number.of.Death/sum(Number.of.Death),2))
>
> Cheers,
> Bert
>
> "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 Tue, Sep 11, 2018 at 11:02 AM AbouEl-Makarim Aboueissa
> wrote:
> >
> > Dear All:
> >
> >
> > I do need your help on how to add frequency to bar plot on the top of
> each
> > bar.
> >
> >
> > here is the R code.
> >
> >
> > *Number.of.Death <- c(432, 217,93, 34, 224)# Number of Death*
> >
> > *Cause.of.Death <- c("Heart disease", "Cancer", "Stroke", "Accidents",
> > "Other") *
> >
> > *barplot(Number.of.Death, names.arg=Cause.of.Death, main="Bar Grapg for
> > Death Data", ylab="Number of Death", xlab="Cause of Death") *
> >
> >
> >
> > Thank you very much for your help in advance.
> >
> >
> > with many thanks
> > abou
> > __
> >
> >
> > *AbouEl-Makarim Aboueissa, PhD*
> >
> > *Professor of Statistics*
> > *Graduate Coordinator*
> >
> > *Department of Mathematics and Statistics*
> > *University of Southern Maine*
> >
> > [[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]]
__
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] [FORGED] Re: getting 21 very different colours
You could also take a look at the 'Polychrome' package Paul On 12/09/18 03:36, Barry Rowlingson wrote: On Tue, Sep 11, 2018 at 11:43 AM, Duncan Murdoch wrote: On 11/09/2018 3:34 AM, Federico Calboli wrote: Hi All, I am plotting a scatterplot of 21 populations, and I am using rainbow(21)[pops.col] to generate 21 colours for the plot (which works). Maybe it is because I can really process few colours at a time, but the differences between the colours are not as strong as I’d like. I can specify start and end for rainbow(), but if anything that looks worse if I do not just stick to 0 and 1. Is there a way of getting a set of 21 colours that maximises the differences between them? The LAB and LUV color spaces (in the colorspace package) attempt to map perceptual differences to equal distances. You could try using a grid of points in one of those spaces, but not all triples are valid. However, 21 colours is probably too many for your purpose. If you really want to distinguish 21 groups, you're likely going to have to use other characteristics as well, such as the symbol. You could plot 21 different letters in 5 different colours and it might work, but it's not going to be easy for viewers. The `alphabet` and `alphabet2` palettes from the `pals` package claim 26 "distinguishable" colours: Details: The ‘alphabet’ palette has 26 distinguishable colors that have logical names starting with the English alphabet letters A, B, ... Z. This palette is based on the work by Green-Armytage (2010), but uses the names 'orange' instead of 'orpiment', and 'magenta' instead of 'mallow'. There are some other palettes in that help page (?alphabet) that might also work. But 21 colours is pushing it. Barry Duncan Murdoch I could pick them by hand, but that is about 15 colours more than I know (I have a detailed colourchart, but the visual differences between ’skyblue’ and ’slategrey’ elude me when plotted as dots on a plot). Cheers F -- Federico Calboli LBEG - Laboratory of Biodiversity and Evolutionary Genomics Charles Deberiotstraat 32 box 2439 3000 Leuven +32 16 32 87 67 __ 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. [[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. -- 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.
Re: [R] Bar Graph
Not quite -- he wanted the frequencies not the counts. So something
like this (using the adj argument to center the frequencies above each
bar:
bp <-barplot(Number.of.Death, names.arg=Cause.of.Death, main="Bar
Graph for Death Data", ylab="Number of Deaths", xlab="Cause of Death",
ylim = c(0,500) )
text(bp, y = Number.of.Death + 30, adj = .5,
lab = round(Number.of.Death/sum(Number.of.Death),2))
Cheers,
Bert
"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 Tue, Sep 11, 2018 at 11:02 AM AbouEl-Makarim Aboueissa
wrote:
>
> Dear All:
>
>
> I do need your help on how to add frequency to bar plot on the top of each
> bar.
>
>
> here is the R code.
>
>
> *Number.of.Death <- c(432, 217,93, 34, 224)# Number of Death*
>
> *Cause.of.Death <- c("Heart disease", "Cancer", "Stroke", "Accidents",
> "Other") *
>
> *barplot(Number.of.Death, names.arg=Cause.of.Death, main="Bar Grapg for
> Death Data", ylab="Number of Death", xlab="Cause of Death") *
>
>
>
> Thank you very much for your help in advance.
>
>
> with many thanks
> abou
> __
>
>
> *AbouEl-Makarim Aboueissa, PhD*
>
> *Professor of Statistics*
> *Graduate Coordinator*
>
> *Department of Mathematics and Statistics*
> *University of Southern Maine*
>
> [[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
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Bar Graph
Hello,
Use function text() with the return of barplot() as x value and
Number.of.Death as y.
Note that the limits of the y axis are not the automatic ones.
bp <- barplot(Number.of.Death, names.arg=Cause.of.Death, main="Bar Graph for
Death Data", ylab="Number of Death", xlab="Cause of Death", ylim = c(0,
500))
text(x = bp, y = Number.of.Death, labels = Number.of.Death, pos = 3)
Hope this helps,
Rui Barradas
On 11-09-2018 19:02, AbouEl-Makarim Aboueissa wrote:
Dear All:
I do need your help on how to add frequency to bar plot on the top of each
bar.
here is the R code.
*Number.of.Death <- c(432, 217,93, 34, 224)# Number of Death*
*Cause.of.Death <- c("Heart disease", "Cancer", "Stroke", "Accidents",
"Other") *
*barplot(Number.of.Death, names.arg=Cause.of.Death, main="Bar Grapg for
Death Data", ylab="Number of Death", xlab="Cause of Death") *
Thank you very much for your help in advance.
with many thanks
abou
__
*AbouEl-Makarim Aboueissa, PhD*
*Professor of Statistics*
*Graduate Coordinator*
*Department of Mathematics and Statistics*
*University of Southern Maine*
[[alternative HTML version deleted]]
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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
and provide commented, minimal, self-contained, reproducible code.
[R] Bar Graph
Dear All:
I do need your help on how to add frequency to bar plot on the top of each
bar.
here is the R code.
*Number.of.Death <- c(432, 217,93, 34, 224)# Number of Death*
*Cause.of.Death <- c("Heart disease", "Cancer", "Stroke", "Accidents",
"Other") *
*barplot(Number.of.Death, names.arg=Cause.of.Death, main="Bar Grapg for
Death Data", ylab="Number of Death", xlab="Cause of Death") *
Thank you very much for your help in advance.
with many thanks
abou
__
*AbouEl-Makarim Aboueissa, PhD*
*Professor of Statistics*
*Graduate Coordinator*
*Department of Mathematics and Statistics*
*University of Southern Maine*
[[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] getting 21 very different colours
On Tue, Sep 11, 2018 at 11:43 AM, Duncan Murdoch wrote: > On 11/09/2018 3:34 AM, Federico Calboli wrote: > > Hi All, > > > > I am plotting a scatterplot of 21 populations, and I am using > rainbow(21)[pops.col] to generate 21 colours for the plot (which works). > Maybe it is because I can really process few colours at a time, but the > differences between the colours are not as strong as I’d like. I can > specify start and end for rainbow(), but if anything that looks worse if I > do not just stick to 0 and 1. > > > > Is there a way of getting a set of 21 colours that maximises the > differences between them? > > The LAB and LUV color spaces (in the colorspace package) attempt to map > perceptual differences to equal distances. You could try using a grid > of points in one of those spaces, but not all triples are valid. > > However, 21 colours is probably too many for your purpose. If you > really want to distinguish 21 groups, you're likely going to have to use > other characteristics as well, such as the symbol. You could plot 21 > different letters in 5 different colours and it might work, but it's not > going to be easy for viewers. > > The `alphabet` and `alphabet2` palettes from the `pals` package claim 26 "distinguishable" colours: Details: The ‘alphabet’ palette has 26 distinguishable colors that have logical names starting with the English alphabet letters A, B, ... Z. This palette is based on the work by Green-Armytage (2010), but uses the names 'orange' instead of 'orpiment', and 'magenta' instead of 'mallow'. There are some other palettes in that help page (?alphabet) that might also work. But 21 colours is pushing it. Barry > Duncan Murdoch > > > > > I could pick them by hand, but that is about 15 colours more than I know > (I have a detailed colourchart, but the visual differences between > ’skyblue’ and ’slategrey’ elude me when plotted as dots on a plot). > > > > Cheers > > > > F > > -- > > Federico Calboli > > LBEG - Laboratory of Biodiversity and Evolutionary Genomics > > Charles Deberiotstraat 32 box 2439 > > 3000 Leuven > > +32 16 32 87 67 > > > > > > > > > > > > __ > > 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. > [[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] For loop with multiple iteration indexes
Just for fun, there are ways to do this in R without an explicit loop:
> set.seed(42)
> dat <- matrix(rnorm(10*5), 10, 5)
> x <- sample(1:5)
> y <- sample(1:5)
> diag(cor(dat[, x], dat[, y]))
[1] -0.69156568 -0.06002371 -0.37492894 0.46477742 -0.37972866
You can use as.list() to convert the vector to a list.
> i <- seq_len(length(x))
> sapply(i, function(j) cor(dat[, x[j]], dat[, y[j]]))
[1] -0.69156568 -0.06002371 -0.37492894 0.46477742 -0.37972866
> xy <- cbind(x, y)
> sapply(i, function(j) cor(dat[, xy[j, ]])[1, 2])
[1] -0.69156568 -0.06002371 -0.37492894 0.46477742 -0.37972866
Change sapply() to lapply() to get list output.
David L Carlson
Department of Anthropology
Texas A University
College Station, TX 77843-4352
-Original Message-
From: R-help On Behalf Of David Disabato
Sent: Monday, September 10, 2018 8:33 PM
To: r-help@r-project.org
Subject: Re: [R] For loop with multiple iteration indexes
Thank you everyone. After thinking about each response, I realized a fairly
simple solution is available (obviously, other suggested approaches work as
well):
stopifnot(length(x) == length(y); stopifnot(length(x) > 0) r <- list() for (i
in 1:length(x) ) {
r[[i]] <- cor(x = dat[, x[i] ], y = dat[, y[i] ]) }
print(r)
On Mon, Sep 10, 2018 at 11:30 AM Berry, Charles wrote:
> I have a sense of deja vu:
>
> https://www.mail-archive.com/r-help@r-project.org/msg250494.html
>
> There is some good advice there.
>
> > On Sep 9, 2018, at 3:49 PM, David Disabato wrote:
> >
> > Hi R-help,
> >
> > I am trying to create a for loop with multiple iteration indexes. I
> > don't want to use two different for loops nested together because I
> > don't need the full matrix of the two indexes, just the diagonal
> > elements (e.g.,
> i[1]
> > & j[1] and i[2] & j[2], but not i[1] & j[2]). Is there a way to
> > specify both i and j in a single for loop? Here is a simplified
> > example of pseudo-code where x and y are equally sized character
> > vectors with column names and dat is their dataframe (obviously this
> > code doesn't run in R,
> but
> > hopefully you perceive my goal):
> >
> > r <- list()
> > n <- 0
> > for (i in x; j in y) {
> > n <- n + 1
> > r[[n]] <- cor(x = dat[, i], y = dat[, j]) }
> > print(r)
> >
> > I realize there are other solutions to this particular correlation
> example,
> > but my actual problem is much more complicated, so I am hoping for a
> > solution that generalizes across any code within the for loop.
>
> A more aRtful way (than a for loop) to approach this is with mapply:
>
>
> i <- head(colnames(mtcars))
> j <- tail(colnames(mtcars))
>
> r <- mapply(function(i, j, dat) cor( x = dat[, i], y = dat[, j]),
>i=i , j=j , MoreArgs = list( dat = mtcars),
>SIMPLIFY = FALSE, USE.NAMES = FALSE)
>
>
> and if you want, maybe USE.NAMES = paste(i, j, sep="_")
>
> Chuck
>
>
--
David J. Disabato, M.A.
Clinical Psychology Doctoral Student
George Mason University
ddisa...@gmu.edu
Email is not a secure form of communication as information and confidentiality
cannot be guaranteed. Information provided in an email is not intended to be a
professional service. In the case of a crisis or emergency situation, call 911.
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
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Re: [R] loop for comparing two or more groups using bootstrapping
Dear Jim,
Thank you very much for the code. I run it but it gave me row names like
"year224", "year142".
are these the difference between columns? If we want to get bootstrapping means
of difference between years (year2-year1; year3-year1), its CI and exact p
value, how can we get it?
thanks
KG
head(daT)
colname.mat<-combn(paste0("year",1:4),2)
samplenames<-apply(colname.mat,2,paste,collapse="")
k<-10
for(column in 1:ncol(colname.mat)) {
assign(samplenames[column],replicate(k,sample(unlist(daT[,colname.mat[,column]]),3,TRUE)))
}
> get(samplenames[1])
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
year224 0.556 0.667 0.571 0.526 0.629 0.696 0.323 0.526 0.256 0.667
year142 0.324 0.324 0.706 0.638 0.600 0.294 0.612 0.688 0.432 0.387
year237 0.571 0.696 0.629 0.471 0.462 0.471 0.452 0.595 0.333 0.435
From: Jim Lemon
Sent: September 11, 2018 1:44 AM
To: Kristi Glover
Cc: r-help mailing list
Subject: Re: [R] loop for comparing two or more groups using bootstrapping
Hi Kristy,
Try this:
colname.mat<-combn(paste0("year",1:4),2)
samplenames<-apply(colname.mat,2,paste,collapse="")
k<-1
for(column in 1:ncol(colname.mat)) {
assign(samplenames[column],replicate(k,sample(unlist(daT[,colname.mat[,column]]),3,TRUE)))
}
Then use get(samplenames[1]) and so on to access the values.
Jim
On Tue, Sep 11, 2018 at 4:52 PM Kristi Glover wrote:
>
> Hi R users,
>
> I was trying to test a null hypothesis of difference between two groups was
> 0. I have many years data, such as year1, year2,, year3, year4 and I was
> trying to compare between year1 and year2, year1 and year3, year2 and year3
> and so on and have used following code with an example data.
>
>
> I tried to make a loop but did not work to compare between many years, and
> also want to obtain the exact p value. Would you mind to help me to make a
> loop?
>
> Thanks for your help.
>
>
> KG
>
>
> daT<-structure(list(year1 = c(0.417, 0.538, 0.69, 0.688, 0.688, 0.606,
> 0.667, 0.7, 0.545, 0.462, 0.711, 0.642, 0.744, 0.604, 0.612,
> 0.667, 0.533, 0.556, 0.444, 0.526, 0.323, 0.308, 0.195, 0.333,
> 0.323, 0.256, 0.345, 0.205, 0.286, 0.706, 0.7, 0.6, 0.571, 0.364,
> 0.429, 0.326, 0.571, 0.424, 0.341, 0.387, 0.341, 0.324, 0.696,
> 0.696, 0.583, 0.556, 0.645, 0.435, 0.471, 0.556), year2 = c(0.385,
> 0.552, 0.645, 0.516, 0.629, 0.595, 0.72, 0.638, 0.557, 0.588,
> 0.63, 0.744, 0.773, 0.571, 0.723, 0.769, 0.667, 0.667, 0.526,
> 0.476, 0.294, 0.323, 0.222, 0.556, 0.263, 0.37, 0.357, 0.25,
> 0.323, 0.778, 0.667, 0.636, 0.583, 0.432, 0.412, 0.333, 0.571,
> 0.39, 0.4, 0.452, 0.326, 0.471, 0.7, 0.75, 0.615, 0.462, 0.556,
> 0.4, 0.696, 0.465), year3 = c(0.435, 0.759, 0.759, 0.759, 0.714,
> 0.593, 0.651, 0.683, 0.513, 0.643, 0.652, 0.757, 0.791, 0.649,
> 0.78, 0.5, 0.5, 0.5, 0.533, 0.429, 0.333, 0.286, 0.231, 0.533,
> 0.303, 0.417, 0.333, 0.333, 0.357, 0.909, 1, 0.952, 0.8, 0.556,
> 0.529, 0.562, 0.762, 0.513, 0.733, 0.611, 0.733, 0.647, 0.909,
> 0.857, 0.8, 0.556, 0.588, 0.562, 0.857, 0.513), year4 = c(0.333,
> 0.533, 0.6, 0.483, 0.743, 0.5, 0.691, 0.619, 0.583, 0.385, 0.653,
> 0.762, 0.844, 0.64, 0.667, 0.571, 0.571, 0.615, 0.421, 0.5, 0.205,
> 0.308, 0.25, 0.6, 0.242, 0.308, 0.276, 0.235, 0.211, 0.9, 0.632,
> 0.72, 0.727, 0.356, 0.5, 0.368, 0.5, 0.41, 0.562, 0.514, 0.4,
> 0.409, 0.632, 0.72, 0.727, 0.4, 0.5, 0.421, 0.5, 0.462)), .Names = c("year1",
> "year2", "year3", "year4"), row.names = c(NA, -50L), class = "data.frame")
>
> head(daT)
>
> # null hypothesis; difference is equal to zero
>
> dif1.2<-daT$year2-daT$year1
>
> k=1
>
> mysamples1.2=replicate(k, sample(dif1.2, replace=T))
>
> mymeans1.2=apply(mysamples1.2, 2, mean)
>
> quantile(mymeans1.2, c(0.025, 0.975))
>
> hist(mysamples1.2)
>
> mean(mymeans1.2)
>
> #what is p value?
>
>
> #similarly Now I want to compare between year 1 and year3,
>
> dif1.3<-daT$year3-daT$year1
>
> mysamples1.3=replicate(k, sample(dif1.3, replace=T))
>
> mymeans1.3=apply(mysamples1.3, 2, mean)
>
> quantile(mymeans1.3, c(0.025, 0.975))
>
>
> [[alternative HTML version deleted]]
>
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[R] Problem with lm.resid() when weights are provided
Dear R Help Team. I get some weird results when I use the lm function with weight. The issue can be reproduced by the example below: The input data is (weights are intentionally designed to reflect some structures in the data) > df y x weight 1.51156139 0.55209240 2.117337e-34 -0.63653132 -0.12599316 2.117337e-34 0.37782776 0.42095384 4.934135e-31 3.03792318 1.40315446 2.679495e-24 1.53646523 0.46076858 2.679495e-24 -2.37727874 -0.73963576 6.244160e-21 0.37183065 0.20407468 1.455107e-17 -1.53917553 -0.95519361 1.455107e-17 1.10926675 0.03897129 3.390908e-14 -0.37786333 -0.17523593 3.390908e-14 2.43973603 0.97970095 7.902000e-11 -0.35432394 -0.03742559 7.902000e-11 2.19296613 1.00355263 4.289362e-04 0.49845532 0.34816207 4.289362e-04 1.25005260 0.76306225 5.00e-01 0.84360691 0.45152356 5.00e-01 0.29565993 0.53880068 5.00e-01 -0.54081334 -0.28104525 5.00e-01 0.83612836 -0.12885659 9.995711e-01 -1.42526769 -0.87107631 9.98e-01 0.10204789 -0.11649899 1.00e+00 1.14292898 0.37249631 1.00e+00 -3.02942081 -1.28966997 1.00e+00 -1.37549764 -0.74676145 1.00e+00 -2.00118016 -0.55182759 1.00e+00 -4.24441674 -1.94603608 1.00e+00 1.17168144 1.00868008 1.00e+00 2.64007761 1.26333069 1.00e+00 1.98550114 1.18509599 1.00e+00 -0.58941683 -0.61972416 9.98e-01 -4.57559611 -2.30914920 9.995711e-01 -0.82610544 -0.39347576 9.995711e-01 -0.02768220 0.20076910 9.995711e-01 0.78186399 0.25690215 9.995711e-01 -0.88314153 -0.20200148 5.00e-01 -4.17076452 -2.03547588 5.00e-01 0.93373070 0.54190626 4.289362e-04 -0.08517734 0.17692491 4.289362e-04 -4.47546619 -2.14876688 4.289362e-04 -1.65509103 -0.76898087 4.289362e-04 -0.39403030 -0.12689705 4.289362e-04 0.01203300 -0.18689898 1.841442e-07 -4.82762639 -2.31391121 1.841442e-07 -0.72658380 -0.39751171 3.397282e-14 -2.35886866 -1.01082109 0.00e+00 -2.03762707 -0.96439902 0.00e+00 0.90115123 0.60172286 0.00e+00 1.55999194 0.83433953 0.00e+00 3.07994058 1.30942776 0.00e+00 1.78871462 1.10605530 0.00e+00 Running simple linear model returns: > lm(y~x,data=df) Call: lm(formula = y ~ x, data = df) Coefficients: (Intercept)x -0.04173 2.03790 and > max(resid(lm(y~x,data=df))) [1] 1.14046 *HOWEVER if I use the weighted model then:* lm(formula = y ~ x, data = df, weights = df$weights) Coefficients: (Intercept)x -0.05786 1.96087 and > max(resid(lm(y~x,data=df,weights=df$weights))) [1] 60.91888 as you see, the estimation of the coefficients are nearly the same but the resid() function returns a giant residual (I have some cases where the value is much much higher). Further, if I calculate the residuals by simply predict(lm(y~x,data=df,weights=df$weights))-df$y then I get the true value for the residuals. Thanks. Please do not hesitate to contact me for more details. Regards, Hamed. [[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] getting 21 very different colours
On 11/09/2018 3:34 AM, Federico Calboli wrote: Hi All, I am plotting a scatterplot of 21 populations, and I am using rainbow(21)[pops.col] to generate 21 colours for the plot (which works). Maybe it is because I can really process few colours at a time, but the differences between the colours are not as strong as I’d like. I can specify start and end for rainbow(), but if anything that looks worse if I do not just stick to 0 and 1. Is there a way of getting a set of 21 colours that maximises the differences between them? The LAB and LUV color spaces (in the colorspace package) attempt to map perceptual differences to equal distances. You could try using a grid of points in one of those spaces, but not all triples are valid. However, 21 colours is probably too many for your purpose. If you really want to distinguish 21 groups, you're likely going to have to use other characteristics as well, such as the symbol. You could plot 21 different letters in 5 different colours and it might work, but it's not going to be easy for viewers. Duncan Murdoch I could pick them by hand, but that is about 15 colours more than I know (I have a detailed colourchart, but the visual differences between ’skyblue’ and ’slategrey’ elude me when plotted as dots on a plot). Cheers F -- Federico Calboli LBEG - Laboratory of Biodiversity and Evolutionary Genomics Charles Deberiotstraat 32 box 2439 3000 Leuven +32 16 32 87 67 __ 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] getting 21 very different colours
On Tue, 11 Sep 2018 07:34:51 +
Federico Calboli wrote:
> Is there a way of getting a set of 21 colours that maximises the
> differences between them?
In my limited experience, getting even 10 colours to look different
enough is a serious undertaking. Take a look at RColorBrewer:
display.brewer.all(n, "qual") stops offering palettes for n>12.
When I needed a 10-colour categorical/qualitative palette, I opted for
brute force approach of maximising the minimal distance between points
in HCL colourspace, although later my colleague told me that I just
needed an existing algorithm to place the points uniformly. It has to
be HCL and not RGB because HCL signifies the way people perceive
different colours while RGB is only a good representation hardware-wise.
Here is my code; the usual disclaimers about stuff written between 1 and
3 AM apply:
# -8<---
require(nloptr)
h <- c(0,360)
c <- c(0,137) # see the warning about fixup in `?hcl`: not all HCL points are
representable in RGB
# NOTE: depending on your plot background, you may have to change at least
luminance range
l <- c(30,90)
npoints <- 24 # I had only 10 here
pts <- matrix(ncol=3, nrow=npoints, dimnames=list(NULL, c("h","c","l")))
pts[,"h"] <- runif(npoints, min=h[1], max=h[2])
pts[,"c"] <- runif(npoints, min=c[1], max=c[2])
pts[,"l"] <- runif(npoints, min=l[1], max=l[2])
lb <- cbind(h=rep(h[1],npoints), c=rep(c[1],npoints), l=rep(l[1],npoints))
ub <- cbind(h=rep(h[2],npoints), c=rep(c[2],npoints), l=rep(l[2],npoints))
obj <- function(x) {
pts[,c("h","c","l")] <- x
# somehow the best results were achieved by calculating Euclidean
distance from cylindrical coordinates
pts <- cbind(pts[,"c"]*sin(pts[,'h']/360*2*pi),
pts[,'c']*cos(pts[,'h']/360*2*pi), pts[,'l'])
d <- as.matrix(dist(pts))
diag(d) <- NA
# maximise minimal distance <=> minimize negative of minimal distance
-min(d, na.rm=T)
}
# the stopping criterion is a bit lame, but the objective function here is very
hard to minimize
# 1e6 iterations take a few minutes on a relatively modern desktop
sol <- nloptr(as.vector(pts), obj, lb=as.vector(lb), ub=as.vector(ub),
opts=list(algorithm="NLOPT_GN_CRS2_LM", maxeval=1e6))
pts[,c("h","c",'l')] <- sol$solution
plot(pts[,"c"] * sin(pts[,"h"]/360*2*pi), pts[,"c"] * cos(pts[,"h"]/360*2*pi),
col=hcl(pts[,"h"], pts[,"c"], l), pch=19, cex=2)
# -8<---
I couldn't get my code to produce 24 acceptably different colours, but
maybe you will succeed with a similar approach.
--
Best regards,
Ivan
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Re: [R] getting 21 very different colours
You could look at combning a number of palettes from the RColorBrewer package to get the palette length you want. S Ellison > -Original Message- > From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Federico > Calboli > Sent: 11 September 2018 08:35 > To: r-help@r-project.org > Subject: [R] getting 21 very different colours > > Hi All, > > I am plotting a scatterplot of 21 populations, and I am using > rainbow(21)[pops.col] to generate 21 colours for the plot (which works). > Maybe it is because I can really process few colours at a time, but the > differences between the colours are not as strong as I’d like. I can specify > start and end for rainbow(), but if anything that looks worse if I do not just > stick to 0 and 1. > > Is there a way of getting a set of 21 colours that maximises the differences > between them? > > I could pick them by hand, but that is about 15 colours more than I know (I > have a detailed colourchart, but the visual differences between ’skyblue’ and > ’slategrey’ elude me when plotted as dots on a plot). > > Cheers > > F > -- > Federico Calboli > LBEG - Laboratory of Biodiversity and Evolutionary Genomics > Charles Deberiotstraat 32 box 2439 > 3000 Leuven > +32 16 32 87 67 > > > > > > __ > 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. *** This email and any attachments are confidential. Any use, copying or disclosure other than by the intended recipient is unauthorised. If you have received this message in error, please notify the sender immediately via +44(0)20 8943 7000 or notify postmas...@lgcgroup.com and delete this message and any copies from your computer and network. LGC Limited. Registered in England 2991879. Registered office: Queens Road, Teddington, Middlesex, TW11 0LY, UK __ 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] getting 21 very different colours
Hi All, I am plotting a scatterplot of 21 populations, and I am using rainbow(21)[pops.col] to generate 21 colours for the plot (which works). Maybe it is because I can really process few colours at a time, but the differences between the colours are not as strong as I’d like. I can specify start and end for rainbow(), but if anything that looks worse if I do not just stick to 0 and 1. Is there a way of getting a set of 21 colours that maximises the differences between them? I could pick them by hand, but that is about 15 colours more than I know (I have a detailed colourchart, but the visual differences between ’skyblue’ and ’slategrey’ elude me when plotted as dots on a plot). Cheers F -- Federico Calboli LBEG - Laboratory of Biodiversity and Evolutionary Genomics Charles Deberiotstraat 32 box 2439 3000 Leuven +32 16 32 87 67 __ 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] loop for comparing two or more groups using bootstrapping
Hi Kristy,
Try this:
colname.mat<-combn(paste0("year",1:4),2)
samplenames<-apply(colname.mat,2,paste,collapse="")
k<-1
for(column in 1:ncol(colname.mat)) {
assign(samplenames[column],replicate(k,sample(unlist(daT[,colname.mat[,column]]),3,TRUE)))
}
Then use get(samplenames[1]) and so on to access the values.
Jim
On Tue, Sep 11, 2018 at 4:52 PM Kristi Glover wrote:
>
> Hi R users,
>
> I was trying to test a null hypothesis of difference between two groups was
> 0. I have many years data, such as year1, year2,, year3, year4 and I was
> trying to compare between year1 and year2, year1 and year3, year2 and year3
> and so on and have used following code with an example data.
>
>
> I tried to make a loop but did not work to compare between many years, and
> also want to obtain the exact p value. Would you mind to help me to make a
> loop?
>
> Thanks for your help.
>
>
> KG
>
>
> daT<-structure(list(year1 = c(0.417, 0.538, 0.69, 0.688, 0.688, 0.606,
>
> 0.667, 0.7, 0.545, 0.462, 0.711, 0.642, 0.744, 0.604, 0.612,
>
> 0.667, 0.533, 0.556, 0.444, 0.526, 0.323, 0.308, 0.195, 0.333,
>
> 0.323, 0.256, 0.345, 0.205, 0.286, 0.706, 0.7, 0.6, 0.571, 0.364,
>
> 0.429, 0.326, 0.571, 0.424, 0.341, 0.387, 0.341, 0.324, 0.696,
>
> 0.696, 0.583, 0.556, 0.645, 0.435, 0.471, 0.556), year2 = c(0.385,
>
> 0.552, 0.645, 0.516, 0.629, 0.595, 0.72, 0.638, 0.557, 0.588,
>
> 0.63, 0.744, 0.773, 0.571, 0.723, 0.769, 0.667, 0.667, 0.526,
>
> 0.476, 0.294, 0.323, 0.222, 0.556, 0.263, 0.37, 0.357, 0.25,
>
> 0.323, 0.778, 0.667, 0.636, 0.583, 0.432, 0.412, 0.333, 0.571,
>
> 0.39, 0.4, 0.452, 0.326, 0.471, 0.7, 0.75, 0.615, 0.462, 0.556,
>
> 0.4, 0.696, 0.465), year3 = c(0.435, 0.759, 0.759, 0.759, 0.714,
>
> 0.593, 0.651, 0.683, 0.513, 0.643, 0.652, 0.757, 0.791, 0.649,
>
> 0.78, 0.5, 0.5, 0.5, 0.533, 0.429, 0.333, 0.286, 0.231, 0.533,
>
> 0.303, 0.417, 0.333, 0.333, 0.357, 0.909, 1, 0.952, 0.8, 0.556,
>
> 0.529, 0.562, 0.762, 0.513, 0.733, 0.611, 0.733, 0.647, 0.909,
>
> 0.857, 0.8, 0.556, 0.588, 0.562, 0.857, 0.513), year4 = c(0.333,
>
> 0.533, 0.6, 0.483, 0.743, 0.5, 0.691, 0.619, 0.583, 0.385, 0.653,
>
> 0.762, 0.844, 0.64, 0.667, 0.571, 0.571, 0.615, 0.421, 0.5, 0.205,
>
> 0.308, 0.25, 0.6, 0.242, 0.308, 0.276, 0.235, 0.211, 0.9, 0.632,
>
> 0.72, 0.727, 0.356, 0.5, 0.368, 0.5, 0.41, 0.562, 0.514, 0.4,
>
> 0.409, 0.632, 0.72, 0.727, 0.4, 0.5, 0.421, 0.5, 0.462)), .Names = c("year1",
>
> "year2", "year3", "year4"), row.names = c(NA, -50L), class = "data.frame")
>
> head(daT)
>
> # null hypothesis; difference is equal to zero
>
> dif1.2<-daT$year2-daT$year1
>
> k=1
>
> mysamples1.2=replicate(k, sample(dif1.2, replace=T))
>
> mymeans1.2=apply(mysamples1.2, 2, mean)
>
> quantile(mymeans1.2, c(0.025, 0.975))
>
> hist(mysamples1.2)
>
> mean(mymeans1.2)
>
> #what is p value?
>
>
> #similarly Now I want to compare between year 1 and year3,
>
> dif1.3<-daT$year3-daT$year1
>
> mysamples1.3=replicate(k, sample(dif1.3, replace=T))
>
> mymeans1.3=apply(mysamples1.3, 2, mean)
>
> quantile(mymeans1.3, c(0.025, 0.975))
>
>
> [[alternative HTML version deleted]]
>
> __
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> 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.
__
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