Re: [R] QQ plotting of various distributions...
#same shape some_data - rgamma(500,shape=6,scale=2) test_data - rgamma(500,shape=6,scale=2) plot(sort(some_data),sort(test_data)) # You can also use qqplot(some_data,test_data) abline(0,1) # different shape some_data - rgamma(500,shape=6,scale=2) test_data - rgamma(500,shape=4,scale=2) plot(sort(some_data),sort(test_data)) abline(0,1) It is helpful to assess the sampling variability, by creating repeated sets of test_data, and plotting all of these along with your observations to create a confidence envelope. The SuppDists provides Inverse Gauss. On Thu, Sep 17, 2009 at 11:46 AM, Petar Milin pmi...@ff.uns.ac.rs wrote: Hello! I am trying with this question again: I would like to test few distributional assumptions for some behavioral response data. There are few theories about true distribution of those data, like: normal, lognormal, gamma, ex-Gaussian (exponential-Gaussian), Wald (inverse Gaussian) etc. The best way would be via qq-plot, to show to students differences. First two are trivial: qqnorm(dat$X) qqnorm(log(dat$X)) Then, things are getting more hairy. I am not sure how to make plots for the rest. I tried gamma with: qqmath(~ X, data=dat, distribution=function(X) qgamma(X, shape, scale)) Which should be the same as: plot(qgamma(ppoints(dat$X), shape, scale), sort(dat$X)) Shape and scale parameters I got via mhsmm package that has gammafit() for shape and scale parameters estimation. Am I on right track? Does anyone know how to plot the rest: ex-Gaussian (exponential-Gaussian), Wald (inverse Gaussian)? Thanks, PM __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://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 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] plotting least-squares regression against x-axis
x - seq(50) y - 10 + x * 2 + rnorm(50,0,10) plot(y~x) mylm = lm(y~x) # Use str(mylm) to see how to get the residuals plot(x,mylm$residuals) On Sat, Sep 19, 2009 at 8:35 PM, Jason Priem pr...@email.unc.edu wrote: Hi, I want to plot the residuals of a least-squares regression. plot(lm(y~x), which=1) does this, but it plots the y-axis of my data on the x-axis of the residuals plot. That is, it plots the residual for each y-value in the data. Can I instead use the x-axis of my data as the x-axis of the residuals plot, showing the residual for a given x? Thanks! Jason Priem University of North Carolina at Chapel Hill School of Information and Library Science __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://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 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] What does model.matrix() return?
This describes the way in which categorical variables are coded in
the model. In this case, we see treatment coding,
although this can go by different names in textbooks (for example, reference
cell coding).
attr(,assign)
[1] 0 1 2 2
means that the first column of the model matrix corresponds to the
intercept,
the second column corresponds to the first variable A,
and the third and fourth columns correspond to the second variable B.
A has 2 levels so it can be represented by 1 column.
Similarly, B has 3 levels so it is represented by 2 columns.
For variable A, the regression coefficient represents an estimated contrast
(difference)
between the two levels when B is held constant.
On Thu, Sep 17, 2009 at 11:13 AM, Peng Yu pengyu...@gmail.com wrote:
Hi,
I don't understand what the meaning of the following lines returned by
model.matrix(). Can somebody help me understand it? What can they be
used for?
attr(,assign)
[1] 0 1 2 2
attr(,contrasts)
attr(,contrasts)$A
[1] contr.treatment
attr(,contrasts)$B
[1] contr.treatment
Regards,
Peng
a=2
b=3
n=4
A = rep(sapply(1:a,function(x){rep(x,n)}),b)
B = as.vector(sapply(sapply(1:b, function(x){rep(x,n)}),
function(x){rep(x,a)}))
Y = A + B + rnorm(a*b*n)
fr = data.frame(Y=Y,A=as.factor(A),B=as.factor(B))
afit=aov(Y ~ A + B,fr)
model.matrix(afit)
(Intercept) A2 B2 B3
11 0 0 0
21 0 0 0
31 0 0 0
41 0 0 0
51 1 0 0
61 1 0 0
71 1 0 0
81 1 0 0
91 0 1 0
10 1 0 1 0
11 1 0 1 0
12 1 0 1 0
13 1 1 1 0
14 1 1 1 0
15 1 1 1 0
16 1 1 1 0
17 1 0 0 1
18 1 0 0 1
19 1 0 0 1
20 1 0 0 1
21 1 1 0 1
22 1 1 0 1
23 1 1 0 1
24 1 1 0 1
attr(,assign)
[1] 0 1 2 2
attr(,contrasts)
attr(,contrasts)$A
[1] contr.treatment
attr(,contrasts)$B
[1] contr.treatment
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Re: [R] lean text label below barplot table
#Example data df - data.frame(trt = factor(c(A long label, Another long \n label)), outcome = c(1,4)) #Install ggplot2 if needed library(ggplot2) p - ggplot(df, aes(y=outcome, x=trt)) p - p + geom_bar(position=dodge, stat=identity) p - p + opts(axis.text.x = theme_text(angle = 45, hjust=1)) p On Mon, Sep 7, 2009 at 5:03 PM, Xiaogang Yang gavinxy...@gmail.com wrote: Hi, everyone: I am plotting an graph with bar plot, but the label after every bar is too long, I wanna if I can draw the label lean to an angle thanks -- Xiaogang Yang Sensorweb Research Laboratory http://sensorweb.vancouver.wsu.edu/ Washington State University Vancouver [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://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 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] standard error associated with correlation coefficient
Here are some options for confidence intervals. #by hand sample_r - .5 n_sample - 100 df - n_sample-1 fisher_z - 0.5*(log(1+sample_r)-log(1-sample_r)) se_z - 1/sqrt(n_sample-3) t_crit - qt(.975,df ,lower.tail=TRUE) z_lci - fisher_z - (t_crit * se_z) z_uci - fisher_z + (t_crit * se_z) (r_lci - tanh(z_lci)) (r_uci - tanh(z_uci)) # Compare to the CIr function in psychometric library #that uses standard normal instead of t library(psychometric) CIr(sample_r,n_sample) And see http://www.stat.umn.edu/geyer/5601/examp/bse.html for bootstrap options. On Thu, Aug 27, 2009 at 3:03 PM, Donald Braman dbra...@law.gwu.edu wrote: I want the standard error associated with a correlation. I can calculate using cor var, but am wondering if there are libraries that already provide this function. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://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 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] Select values at random by id value
#Highlight the text below (without the header) # read the data in from clipboard df - do.call(data.frame, scan(clipboard, what=list(id=0, date=,loctype=0 ,haptype=0))) # split the data by date, sample 1 observation from each split, and rbind sampled_df - do.call(rbind, lapply(split(df, df$date),function(x)x[sample(1:nrow(x), 1),])) On Mon, Jun 29, 2009 at 9:11 AM, James Martin just.strut...@gmail.comwrote: All, I have data that looks like below. For each id there may be more than one value per day. I want to select a random value for that day for that id. The end result would hopefully be a matrix with the id as rows, date as columns and populated by the random hab value. Thanks to someone on here (Jim) I know how to do the matrix, but now realize I need to randomly select some of my values. All help is appreciated. jm id, date, loctype, habtype 50022 1/25/2006 0 6 50022 1/31/2006 0 6 50022 2/8/2006 0 6 50022 2/13/2006 0 6 50022 2/15/2006 0 6 50022 2/24/2006 0 6 50022 3/2/2006 0 6 50022 3/9/2006 0 6 50022 3/16/2006 0 6 50022 3/24/2006 0 6 50022 4/9/2006 0 3 50022 4/18/2006 0 6 50022 4/27/2006 0 3 50022 5/23/2006 1 3 50022 5/23/2006 1 6 50022 5/24/2006 1 3 50022 5/24/2006 1 3 50022 5/24/2006 1 3 50022 5/24/2006 1 3 50022 5/25/2006 1 3 50022 5/25/2006 1 3 50022 5/25/2006 1 3 50022 5/26/2006 1 5 50022 5/26/2006 1 3 50022 5/27/2006 1 5 50022 5/27/2006 1 3 50022 5/28/2006 1 3 50022 5/29/2006 1 3 50022 5/30/2006 1 5 50022 5/30/2006 1 3 50022 5/31/2006 1 3 50022 5/31/2006 1 3 50022 6/1/2006 1 3 50022 6/2/2006 1 3 50022 6/3/2006 1 3 50022 6/4/2006 1 3 50022 6/5/2006 1 3 50022 6/6/2006 1 5 50022 6/6/2006 1 5 50022 6/6/2006 1 5 50022 6/6/2006 1 3 50022 6/6/2006 1 3 50022 6/7/2006 1 5 50022 6/7/2006 1 3 50022 6/7/2006 1 3 50022 6/7/2006 1 3 50022 6/7/2006 1 3 50022 6/8/2006 1 3 50022 6/8/2006 1 3 50022 6/8/2006 1 3 50022 6/9/2006 1 5 50022 6/10/2006 1 3 50022 6/11/2006 1 5 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://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 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] text() to label points in ggplot
# Here are two options: p - ggplot(mtcars, aes(wt, mpg)) + geom_point() + geom_text(aes(x = 5, y = 30, label = A Label)) #or response - c(2,4) xvar - c(1,2) label - response; myData - data.frame(response,xvar,label) p - ggplot(myData, aes(y=response, x=xvar)) p + geom_bar(position=dodge, stat=identity) + geom_text(aes(y=response+1,label=label)) On Thu, May 14, 2009 at 1:22 PM, stephenb sten...@go.com wrote: is there a way to label points in a graph using text(locator(1),text) after ggplot() or qplot() ? qplot(date, psavert, data = economics, geom = line,main=jhdjd)-p p+opts(text(locator(1),),new=T) does not work. -- View this message in context: http://www.nabble.com/text%28%29-to-label-points-in-ggplot-tp23545135p23545135.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://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 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 control lattice plot parameters
We can see the plotting options using trellis.par.get(). For example, one
listed parameter is $superpose.line for which we can set col, lty, and lwd.
Load the mlmRev package to obtain the Gcsemv data (used in Lattice book).
One way to set the parameters is
data(Gcsemv, package = mlmRev)
my.fonts - list(font = 2,cex = 2)
my.theme - list(
superpose.symbol = list(col=c(1,3)),
superpose.line=list(col=c(1,3),lwd=c(1,2)),
par.xlab.text = my.fonts,
par.ylab.text = my.fonts
)
xyplot(written ~ course , data = Gcsemv, groups = gender, type = c(p,r),
par.settings = my.theme,
auto.key = list(lines = TRUE, points = FALSE))
On Wed, Apr 15, 2009 at 5:40 AM, Paulo E. Cardoso pecard...@netcabo.ptwrote:
I'm not being able to control all parameters of a xyplot.
dataset example:
tabp[1:10,]
time n X id name
1 1 95 0.00 1 Coral reef
2 1 93 0.00 2 Coral reef
3 1 92 0.00 3 Coral reef
4 1 90 0.00 4 Coral reef
5 1 87 8.994321 5 Coral reef
6 1 86 12.580143 6 Coral reef
7 1 84 17.004030 7 Coral reef
8 1 83 18.469500 8 Coral reef
9 1 82 37.919033 9 Coral reef
101 81 39.059352 10 Coral reef
...
plot code:
xyplot(
X~n,groups=name,data=tabp[tabp$time %in% c(1,4,8),],
ylab=% of target,
xlab=PU selection Frequency,
lty=c(1,3,5), #! not responding
xlim=c(-10,110),
scales=list(cex=0.7,at=seq(0,360,by=20),labels=seq(0,360,by=20)), #!
not responding
panel=function(x,y,groups,subscripts)
{
panel.xyplot(x,y,
subscripts=subscripts,
groups=groups,
type=l)
panel.abline(h=30,lty=2,col=grey50)
},
key=list(
space=top,
columns=1,
text=list(levels(tabp$name)[c(2,5,11)]),
lines=list(col=c(grey,blue,green))
)
)
A few controls are not responding and I don't know how to:
1) control cex for xlab and ylab
2) control position of legend
3) control lty for each group level
4) control plot groups colors
5) match legend colors with graph colors
Any help will be very appreciated.
Paulo E. Cardoso
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Re: [R] loglm fitting
If we check the data, we see a mistake in the entry. tbl.8.3 mara cig alc count 1 Yes Yes Yes 911 2 No No No 538 3 Yes Yes Yes44 4 No No No 456 5 Yes Yes Yes 3 6 No No No43 7 Yes Yes Yes 2 8 No No No 279 Try: table8.3 - read.table(textConnection(alc cig mar count Yes Yes Yes 911 Yes Yes No 538 Yes No Yes 44 Yes No No 456 No Yes Yes 3 No Yes No 43 No No Yes 2 No No No 279),header=TRUE) closeAllConnections() myglm - glm(count ~ mar+cig+alc, family=poisson, data=table8.3) myglm$fitted.values myglm$fitted.values 1 2 3 4 5 6 7 8 539.98258 740.22612 282.09123 386.70007 90.59739 124.19392 47.32880 64.87990 This reproduces the fitted values for your example (Agresti, pg 323) On Wed, Jan 14, 2009 at 7:23 AM, Gerard M. Keogh gmke...@justice.ie wrote: Dear all, sorry to bother you all with this but I've been trying to use the loglm in MASS package (v2.8.0) and cannot get any sensible output. I'm wondering am I doing something very foolish or missing something obvious. For example, I tried the documentation help(loglm) example - here's the code # Case 1: frequencies specified as an array. sapply(minn38, function(x) length(levels(x))) ## hs phs fol sex f ## 3 4 7 2 0 minn38a - array(0, c(3,4,7,2), lapply(minn38[, -5], levels)) minn38a[data.matrix(minn38[,-5])] - minn38$fol fm - loglm(~1 + 2 + 3 + 4, minn38a) # numerals as names. deviance(fm) [1] 0 The deviance is zero. I tried other examples as well (Laura Thompson) and get pretty much nonsense. E.g. library(MASS) options(contrasts=c(contr.treatment, contr.poly)) tbl.8.3 = data.frame(mara =factor(c(Yes,No),levels=c(Yes,No)), cig =factor(c(Yes,No),levels=c(No,Yes)), alc =factor(c(Yes,No),levels=c(Yes,No)), count=c(911,538,44,456,3,43,2,279) ) fit.acm = loglm( count ~ alc*cig*mara,data=tbl.8.3, param=T, fit=T) Any advice greatly appreciated. Gerard ** The information transmitted is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please contact the sender and delete the material from any computer. It is the policy of the Department of Justice, Equality and Law Reform and the Agencies and Offices using its IT services to disallow the sending of offensive material. Should you consider that the material contained in this message is offensive you should contact the sender immediately and also mailminder[at] justice.ie. Is le haghaidh an duine nó an eintitis ar a bhfuil sí dírithe, agus le haghaidh an duine nó an eintitis sin amháin, a bheartaítear an fhaisnéis a tarchuireadh agus féadfaidh sé go bhfuil ábhar faoi rún agus/nó faoi phribhléid inti. Toirmisctear aon athbhreithniú, atarchur nó leathadh a dhéanamh ar an bhfaisnéis seo, aon úsáid eile a bhaint aisti nó aon ghníomh a dhéanamh ar a hiontaoibh, ag daoine nó ag eintitis seachas an faighteoir beartaithe. Má fuair tú é seo trí dhearmad, téigh i dteagmháil leis an seoltóir, le do thoil, agus scrios an t-ábhar as aon ríomhaire. Is é beartas na Roinne Dlí agus Cirt, Comhionannais agus Athchóirithe Dlí, agus na nOifígí agus na nGníomhaireachtaí a úsáideann seirbhísí TF na Roinne, seoladh ábhair cholúil a dhícheadú. Más rud é go measann tú gur ábhar colúil atá san ábhar atá sa teachtaireacht seo is ceart duit dul i dteagmháil leis an seoltóir láithreach agus le mailminder[ag]justice.ie chomh maith. *** __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://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 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.
