Re: [R] simple save question
Well, that took a bit of detective work! Thanks. I am still not doing something right here in my efforts to implement the easy way. Can you point out my error? library(survival) library(ISwR) dat.s - Surv(melanom$days,melanom$status==1) fit - survfit(dat.s~1) print(fit, print.rmean=TRUE) Call: survfit(formula = dat.s ~ 1) records n.maxn.start events *rmean *se(rmean) median 205205205 57 4125161 NA 0.95LCL0.95UCL NA NA * restricted mean with upper limit = 5565 sfit - summary(fit) sfit$table[ ,5] Error in sfit$table[, 5] : incorrect number of dimensions -- View this message in context: http://r.789695.n4.nabble.com/simple-save-question-tp3429148p3664808.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.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] simple save question
No cigar. This is what I get and my session info. Any suggestions? library(survival) library(ISwR) dat.s - Surv(melanom$days,melanom$status==1) fit - survfit(dat.s~1) print(fit, print.rmean=TRUE) Call: survfit(formula = dat.s ~ 1) records n.maxn.start events *rmean *se(rmean) median 205205205 57 4125161 NA 0.95LCL0.95UCL NA NA * restricted mean with upper limit = 5565 sfit - summary(fit) sfit$table[5] median NA sessionInfo() R version 2.13.1 (2011-07-08) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] splines stats graphics grDevices utils datasets methods [8] base other attached packages: [1] ISwR_2.0-5 survival_2.36-9 rj_0.5.5-4 loaded via a namespace (and not attached): [1] tools_2.13.1 -- View this message in context: http://r.789695.n4.nabble.com/simple-save-question-tp3429148p3665289.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] simple save question
I want to assign the value of rmean from a survfit object to a variable so
that it can be used in subsequent calculations, which is also what I
interpreted the original poster to want. I did not understand Dr. Therneau's
answer to the original poster, so I figured I would provide a simple example
and see if someone could spoon feed me on how to do this. Dr. Winsemius
seemed to have gotten an answer, but I have not been able to reproduce it.
It appears to me that summary(fit) and summary.survfit(fit), where fit is an
object created by survfit, are the same thing (the example on the
summary.survfit help page reinforces this idea). I have played with the
rmean=getOption('survfit.rmean') option in summary but I can't seem to get
anywhere.
Tom
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Re: [R] simple save question
Here is a worked example. Can you point out to me where in temp rmean is stored? Thanks. Tom library(survival) library(ISwR) dat.s - Surv(melanom$days,melanom$status==1) fit - survfit(dat.s~1) plot(fit) summary(fit) Call: survfit(formula = dat.s ~ 1) time n.risk n.event survival std.err lower 95% CI upper 95% CI 185201 10.995 0.004960.9851.000 204200 10.990 0.007000.9761.000 210199 10.985 0.008550.9681.000 232198 10.980 0.009850.9611.000 279196 10.975 0.011000.9540.997 295195 10.970 0.012020.9470.994 386193 10.965 0.012970.9400.991 426192 10.960 0.013840.9330.988 469191 10.955 0.014650.9270.984 529189 10.950 0.015420.9200.981 621188 10.945 0.016150.9140.977 629187 10.940 0.016830.9070.973 659186 10.935 0.017480.9010.970 667185 10.930 0.018110.8950.966 718184 10.925 0.018700.8890.962 752183 10.920 0.019270.8830.958 779182 10.915 0.019810.8770.954 793181 10.910 0.020340.8710.950 817180 10.904 0.020840.8650.946 833178 10.899 0.021340.8590.942 858177 10.894 0.021810.8530.938 869176 10.889 0.022270.8470.934 872175 10.884 0.022720.8410.930 967174 10.879 0.023150.8350.926 977173 10.874 0.023570.8290.921 982172 10.869 0.023970.8230.917 1041171 10.864 0.024360.8170.913 1055170 10.859 0.024740.8120.909 1062169 10.854 0.025110.8060.904 1075168 10.849 0.025470.8000.900 1156167 10.844 0.025820.7940.896 1228166 10.838 0.026160.7890.891 1252165 10.833 0.026490.7830.887 1271164 10.828 0.026810.7770.883 1312163 10.823 0.027130.7720.878 1435161 10.818 0.027440.7660.874 1506159 10.813 0.027740.7600.869 1516155 10.808 0.028050.7550.865 1548152 10.802 0.028370.7490.860 1560150 10.797 0.028680.7430.855 1584148 10.792 0.028990.7370.851 1621146 10.786 0.029290.7310.846 1667137 10.780 0.029630.7250.841 1690134 10.775 0.029980.7180.836 1726131 10.769 0.030330.7120.831 1933110 10.762 0.030850.7040.825 2061 95 10.754 0.031550.6940.818 2062 94 10.746 0.032210.6850.812 2103 90 10.737 0.032900.6760.805 2108 88 10.729 0.033580.6660.798 2256 80 10.720 0.034380.6560.791 2388 75 10.710 0.035230.6450.783 2467 69 10.700 0.036190.6330.775 2565 63 10.689 0.037290.6200.766 2782 57 10.677 0.038540.6050.757 3042 52 10.664 0.039940.5900.747 3338 35 10.645 0.043070.5660.735 print(fit, print.rmean=TRUE) Call: survfit(formula = dat.s ~ 1) records n.maxn.start events *rmean *se(rmean) median 205205205 57 4125161 NA 0.95LCL0.95UCL NA NA * restricted mean with upper limit = 5565 temp - summary(fit) str(temp) List of 12 $ surv: num [1:57] 0.995 0.99 0.985 0.98 0.975 ... $ time: num [1:57] 185 204 210 232 279 295 386 426 469 529 ... $ n.risk : num [1:57] 201 200 199 198 196 195 193 192 191 189 ... $ n.event : num [1:57] 1 1 1 1 1 1 1 1 1 1 ... $ conf.int: num 0.95 $ type: chr right $ table : Named num [1:7] 205 205 205 57 NA NA NA ..- attr(*, names)= chr [1:7] records n.max n.start events ... $ n.censor: num [1:57] 0 0 0 1 0 0 0 0 0 0 ... $ std.err : num [1:57] 0.00496 0.007 0.00855 0.00985 0.011 ... $ lower : num [1:57] 0.985 0.976 0.968 0.961 0.954 ... $ upper : num [1:57] 1 1 1 1 0.997 ... $ call: language survfit(formula =
Re: [R] simple save question
Thank you for the reply Dr. Winsemius. Can you take your answer a step further and, in the context of the simple, reproducible example, illustrate how it is done? I would appreciate it. Tom -- View this message in context: http://r.789695.n4.nabble.com/simple-save-question-tp3429148p3663645.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.html and provide commented, minimal, self-contained, reproducible code.
[R] How to Extract Information from SIMEX Output
Below is a SIMEX object that was generated with the simex function from the
simex package applied to a logistic regression fit. From this mountain of
information I would like to extract all of the values summarized in this
line:
.. ..$ variance.jackknife: num [1:5, 1:4] 1.684 1.144 0.85 0.624 0.519 ...
Can someone suggest how to go about doing this? I can extract the upper
level results like fit.simex$coefficients but I have had no success getting
at the lower levels.
Tom
str(fit.simex)
List of 24
$ coefficients : Named num [1:2] -17.1 3
..- attr(*, names)= chr [1:2] (Intercept) x
$ SIMEX.estimates : num [1:6, 1:3] -1 0 0.5 1 1.5 ...
..- attr(*, dimnames)=List of 2
.. ..$ : NULL
.. ..$ : chr [1:3] lambda (Intercept) x
$ lambda : num [1:5] 0 0.5 1 1.5 2
$ model:List of 31
..$ coefficients : Named num [1:2] -13.27 2.32
.. ..- attr(*, names)= chr [1:2] (Intercept) x
..$ residuals: Named num [1:1615] -1.12 -1.42 -1.23 -1.07 -1.44
...
.. ..- attr(*, names)= chr [1:1615] 1 2 3 4 ...
..$ fitted.values: Named num [1:1615] 0.1032 0.2952 0.1847 0.0656
0.3062 ...
.. ..- attr(*, names)= chr [1:1615] 1 2 3 4 ...
..$ effects : Named num [1:1615] 19.552 -9.275 -0.473 -0.283
-0.641 ...
.. ..- attr(*, names)= chr [1:1615] (Intercept) x ...
..$ R: num [1:2, 1:2] -15.6 0 -81 -4
.. ..- attr(*, dimnames)=List of 2
.. .. ..$ : chr [1:2] (Intercept) x
.. .. ..$ : chr [1:2] (Intercept) x
..$ rank : int 2
..$ qr :List of 5
.. ..$ qr : num [1:1615, 1:2] -15.6232 0.0292 0.0248 0.0159 0.0295 ...
.. .. ..- attr(*, dimnames)=List of 2
.. .. .. ..$ : chr [1:1615] 1 2 3 4 ...
.. .. .. ..$ : chr [1:2] (Intercept) x
.. ..$ rank : int 2
.. ..$ qraux: num [1:2] 1.02 1.02
.. ..$ pivot: int [1:2] 1 2
.. ..$ tol : num 1e-11
.. ..- attr(*, class)= chr qr
..$ family :List of 12
.. ..$ family: chr binomial
.. ..$ link : chr logit
.. ..$ linkfun :function (mu)
.. ..$ linkinv :function (eta)
.. ..$ variance :function (mu)
.. ..$ dev.resids:function (y, mu, wt)
.. ..$ aic :function (y, n, mu, wt, dev)
.. ..$ mu.eta:function (eta)
.. ..$ initialize: expression({ if (NCOL(y) == 1) { if
(is.factor(y)) y - y != levels(y)[1L] n - rep.int(1,
nobs) y[weights == 0] - 0 if (any(y 0 | y 1))
stop(y values must be 0 = y = 1) mustart - (weights * y +
0.5)/(weights + 1) m - weights * y if (any(abs(m -
round(m)) 0.001)) warning(non-integer #successes in a
binomial glm!) } else if (NCOL(y) == 2) { if (any(abs(y -
round(y)) 0.001)) warning(non-integer counts in a binomial
glm!) n - y[, 1] + y[, 2] y - ifelse(n == 0, 0, y[, 1]/n)
weights - weights * n mustart - (n * y + 0.5)/(n + 1) }
else stop(for the binomial family, y must be a vector of 0 and 1's\n,
or a 2 column matrix where col 1 is no. successes and col 2 is no.
failures) })
.. ..$ validmu :function (mu)
.. ..$ valideta :function (eta)
.. ..$ simulate :function (object, nsim)
.. ..- attr(*, class)= chr family
..$ linear.predictors: Named num [1:1615] -2.162 -0.87 -1.485 -2.656
-0.818 ...
.. ..- attr(*, names)= chr [1:1615] 1 2 3 4 ...
..$ deviance : num 1521
..$ aic : num 1525
..$ null.deviance: num 1622
..$ iter : int 4
..$ weights : Named num [1:1615] 0.0926 0.208 0.1506 0.0613
0.2125 ...
.. ..- attr(*, names)= chr [1:1615] 1 2 3 4 ...
..$ prior.weights: Named num [1:1615] 1 1 1 1 1 1 1 1 1 1 ...
.. ..- attr(*, names)= chr [1:1615] 1 2 3 4 ...
..$ df.residual : int 1613
..$ df.null : int 1614
..$ y: Named num [1:1615] 0 0 0 0 0 0 0 0 0 0 ...
.. ..- attr(*, names)= chr [1:1615] 1 2 3 4 ...
..$ converged: logi TRUE
..$ boundary : logi FALSE
..$ model:'data.frame': 1615 obs. of 2 variables:
.. ..$ y: Factor w/ 2 levels 0,1: 1 1 1 1 1 1 1 1 1 1 ...
.. ..$ x: num [1:1615] 4.79 5.35 5.09 4.58 5.37 ...
.. ..- attr(*, terms)=Classes 'terms', 'formula' length 3 y ~ x
.. .. .. ..- attr(*, variables)= language list(y, x)
.. .. .. ..- attr(*, factors)= int [1:2, 1] 0 1
.. .. .. .. ..- attr(*, dimnames)=List of 2
.. .. .. .. .. ..$ : chr [1:2] y x
.. .. .. .. .. ..$ : chr x
.. .. .. ..- attr(*, term.labels)= chr x
.. .. .. ..- attr(*, order)= int 1
.. .. .. ..- attr(*, intercept)= int 1
.. .. .. ..- attr(*, response)= int 1
.. .. .. ..- attr(*, .Environment)=environment: R_GlobalEnv
.. .. .. ..- attr(*, predvars)= language list(y, x)
.. .. .. ..- attr(*, dataClasses)= Named chr [1:2] factor numeric
.. .. .. .. ..- attr(*, names)= chr [1:2] y x
..$ x: num [1:1615, 1:2] 1 1 1
Re: [R] Failing to install {rggobi} on win-7 R 2.12.0
I recall that my problem on Windows was related to having a number of stray versions of GTK+ installed. I went back and deleted all versions and reinstalled the latest GTK+ and that seemed to fix things. However, when I went to do any work of substance ggobi locked up and became unresponsive. Never did get it working right on Windows. Had much more luck with R/ggobi on Ubuntu 10.10. Tom -- View this message in context: http://r.789695.n4.nabble.com/Failing-to-install-rggobi-on-win-7-R-2-12-0-tp3236602p3237166.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.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Tutorial Tinn-R
Seems to be a relevant and reasonable question to me. -- View this message in context: http://r.789695.n4.nabble.com/Tutorial-Tinn-R-tp2300451p2300648.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.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Sampling with replacement
How about library(TeachingSampling) SupportWR(20,4) Tom -- View this message in context: http://r.789695.n4.nabble.com/Sampling-with-replacement-tp2257450p2257644.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.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Ellipse that Contains 95% of the Observed Data
Concisely, here is what I am trying to do:
#I take a random sample of 300 measurements. After I have the measurements
#I post stratify them to 80 type A measurements and 220 type B measurements.
#These measurements tend to be lognormally distributed so I fit them to
#determine the geometric mean and geometric standard deviation of each
stratum.
#The question is: are the geometric mean and geometric standard deviation of
#the type A measurements the same as the geometric mean and geometric
#standard deviation of the type B measurements?
library(MASS)
library(car)
setwd(C:/Documents and Settings/Tom/workspace/Work)
source(bagplot.r)
#http://addictedtor.free.fr/graphiques/RGraphGallery.php?graph=112
#Here are the data. Unknown to me, they are indeed drawn from the same
#lognormal distribution
X - cbind(1:300,rlnorm(300,log(30),log(3)))
X.A - X[1:80,2]
X.B - X[81:300,2]
#These are the data I see. Fit the type A and type B measurements
fit.XA - fitdistr(X.A,lognormal)
fit.XB - fitdistr(X.B,lognormal)
#Fit 2000 random samples of size 80 and 220 and calculate the difference in
#the GM and GSD for each
x - numeric(2000)
y - numeric(2000)
for (i in 1:2000) {
k - sample(X[,1],80,replace=FALSE)
x.a - X[k,2]
x.b - X[setdiff(1:300,k),2]
fit.xa - fitdistr(x.a,lognormal)
fit.xb - fitdistr(x.b,lognormal)
x[i] - coef(fit.xa)[1] - coef(fit.xb)[1]
y[i] - coef(fit.xa)[2] - coef(fit.xb)[2]
}
#Create the bagplot and superimpose the 95% joint normal confidence ellipse.
#Does the difference in GM and GSD actually observed for the type A and type
B
#measurements look like the result of the random draw?
bagplot(x,y,show.whiskers=FALSE,approx.limit=1000)
data.ellipse(x,y,plot.points=FALSE,levels=c(0.95),col=black,center.cex=0)
box()
points(coef(fit.XA)[1]-coef(fit.XB)[1],coef(fit.XA)[2]-coef(fit.XB)[2],
cex=1.5,col=black,pch=19)
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Re: [R] Ellipse that Contains 95% of the Observed Data
I know what get a bigger sample means. I have no clue what ask a more statistically meaningful question means. Can you elaborate a bit? Tom -- View this message in context: http://n4.nabble.com/Ellipse-that-Contains-95-of-the-Observed-Data-tp1694538p1695357.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.html and provide commented, minimal, self-contained, reproducible code.
[R] Design of a survey using the survey package
I have looked through the new Complex Surveys book and the documentation for the survey package and it appears to me that there are no functions in survey that help one to design a sampling scheme. For example, in the book section 2.8 discusses the design of stratified samples, but there is no mention of any functions in the survey package that implement the discussed strategies. So, am I missing something obvious here or is the survey package meant only for analyzing survey data once you have it in hand? Tom -- View this message in context: http://n4.nabble.com/Design-of-a-survey-using-the-survey-package-tp1694075p1694075.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.html and provide commented, minimal, self-contained, reproducible code.
[R] Ellipse that Contains 95% of the Observed Data
I can take the results of a simulation with one random variable and generate an empirical interval that contains 95% of the observations, e.g., x - rnorm(1) quantile(x,probs=c(0.025,0.975)) Is there an R function that can take the results from two random variables and generate an empirical ellipse that contains 95% of the observations, e.g., x - rnorm(1) y - rnorm(1) ? I am specifically looking for an ellipse that does not assume normality. Tom -- View this message in context: http://n4.nabble.com/Ellipse-that-Contains-95-of-the-Observed-Data-tp1694538p1694538.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.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Ubunut + Eclipse + StatET: Console terminates upon error
I don't want to hijack the thread here, but since you mentioned hover pop-up help can you suggest a way to turn it OFF, totally and completely? Tom LaBone -- View this message in context: http://n4.nabble.com/Ubunut-Eclipse-StatET-Console-terminates-upon-error-tp1589479p1589800.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.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Rounding a Measurement to be Consistent with its Uncertainty
Uwe Ligges-3 wrote: Tom La Bone wrote: I have a measurement of 8165.666 and an uncertainty of 338.9741 (the units of both are unimportant). I can easily round the uncertainty to two significant digits with signif(338.9741,2), which gives 340. Is there a function in R that will take 8165.666 and round it to be consistent with its uncertainty, i.e., 8170? That's not consistent, you have 3 significant digits here, but 2 for the uncertainty (whatever that is) ... Uwe Ligges Tom In metrology, what I did is indeed consistent (provided that I have correctly interpreted the guidance given in the ISO Guide to the Expression of Uncertainty in Measurement). The uncertainty is basically a way of specifying in which digits I begin to doubt my result. So, I while I will usually have two digits in my uncertainty, I can have 10 significant digits in my result. Some folks have given me some ideas off-line on how to write a function that will round a number in this fashion, but I always prefer to use an existing R function if it already exists rather than write my own. And, with the tens of thousands of R functions in existence, it is always a good idea to ask the forum if they know of one. Tom __ 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. -- View this message in context: http://n4.nabble.com/Rounding-a-Measurement-to-be-Consistent-with-its-Uncertainty-tp948151p949395.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.html and provide commented, minimal, self-contained, reproducible code.
[R] Rounding a Measurement to be Consistent with its Uncertainty
I have a measurement of 8165.666 and an uncertainty of 338.9741 (the units of both are unimportant). I can easily round the uncertainty to two significant digits with signif(338.9741,2), which gives 340. Is there a function in R that will take 8165.666 and round it to be consistent with its uncertainty, i.e., 8170? Tom -- View this message in context: http://n4.nabble.com/Rounding-a-Measurement-to-be-Consistent-with-its-Uncertainty-tp948151p948151.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.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Comparison of Output from dwtest and durbin.watson
Allow me to reword this question. I have performed two fits to the same set of data below: a weighted fit and an unweighted fit. I performed the Durbin-Watson tests on each fit using dwtest and durbin.watson. For a given fit (weighted or unweighted), should both dwtest and durbin.watson be giving me the same DW statistic and p-value? Should I get the same DW statistic and p-value for the weighted and unweighted fits as I do using dwtest? library(lmtest) Loading required package: zoo Attaching package: 'zoo' The following object(s) are masked from package:base : as.Date.numeric library(car) X - c(4.8509E-1,8.2667E-2,6.4010E-2,5.1188E-2,3.4492E-2,2.1660E-2, + 3.2242E-3,1.8285E-3) Y - c(2720,1150,1010,790,482,358,78,35) W - 1/Y^2 fit - lm(Y ~ X - 1) dwtest(fit,alternative=two.sided) Durbin-Watson test data: fit DW = 0.7599, p-value = 0.05935 alternative hypothesis: true autocorelation is not 0 durbin.watson(fit,alternative=two.sided) lag Autocorrelation D-W Statistic p-value 1 0.5897666 0.7599161 0.368 Alternative hypothesis: rho != 0 fit - lm(Y ~ X - 1,weights=W) dwtest(fit,alternative=two.sided) Durbin-Watson test data: fit DW = 0.7599, p-value = 0.05935 alternative hypothesis: true autocorelation is not 0 durbin.watson(fit,alternative=two.sided) lag Autocorrelation D-W Statistic p-value 1 -0.07663672 1.2090760.77 Alternative hypothesis: rho != 0 -- View this message in context: http://www.nabble.com/Comparison-of-Output-from-%22dwtest%22-and-%22durbin.watson%22-tp24783494p24808540.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.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Comparison of Output from dwtest and durbin.watson
My concern is that the two tests give different DW statistics for the weighted fit and very different p-values for the same DW statistic for the unweighted fit. Is there a right answer here? -- View this message in context: http://www.nabble.com/Comparison-of-Output-from-%22dwtest%22-and-%22durbin.watson%22-tp24783494p24809734.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.html and provide commented, minimal, self-contained, reproducible code.
[R] Character from Symbol Font on rgl Plot
I want to print characters from the symbol font (or perhaps even Wingdings) in an rgl 3d plot, but I am having no luck. So, what do I have to do in order to get this snippet to print out a character from the symbol font? library(rgl) open3d() text3d(1,1,1,a,adj=c(0.5,0.5),cex=10,family=symbol,font=1) I am on Windows XP with R 2.9.1. Tom -- View this message in context: http://www.nabble.com/Character-from-Symbol-Font-on-rgl-Plot-tp24781990p24781990.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.html and provide commented, minimal, self-contained, reproducible code.
[R] Comparison of Output from dwtest and durbin.watson
Should dwtest and durbin.watson be giving me the same DW statistic and p-value for these two fits? library(lmtest) library(car) X - c(4.8509E-1,8.2667E-2,6.4010E-2,5.1188E-2,3.4492E-2,2.1660E-2, 3.2242E-3,1.8285E-3) Y - c(2720,1150,1010,790,482,358,78,35) W - 1/Y^2 fit - lm(Y ~ X - 1) dwtest(fit,alternative=two.sided) durbin.watson(fit,alternative=two.sided) fit - lm(Y ~ X - 1,weights=W) dwtest(fit,alternative=two.sided) durbin.watson(fit,alternative=two.sided) Tom -- View this message in context: http://www.nabble.com/Comparison-of-Output-from-%22dwtest%22-and-%22durbin.watson%22-tp24783494p24783494.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.html and provide commented, minimal, self-contained, reproducible code.
[R] Selecting Bootstrap Method for Quantile Regression
The help page and vignette for summary.rq(quantreg) mention that there are three different bootstrap methods available for the se=bootstrap argument, but I can't figure out how to select a particular method. For example, if I want to use the xy-pair bootstrap how do I indicate this in summary.rq? Tom -- View this message in context: http://www.nabble.com/Selecting-Bootstrap-Method-for-Quantile-Regression-tp24737299p24737299.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.html and provide commented, minimal, self-contained, reproducible code.
[R] Re placing a + in a string
I know this is easy, but I am stumped: gsub(0,K,8.00+00) [1] 8.KK+KK gsub(+,K,8.00+00) Error in gsub(+, K, 8.00+00) : invalid regular expression '+' In addition: Warning message: In gsub(+, K, 8.00+00) : regcomp error: 'Invalid preceding regular expression' I don't understand the error message. How do I go about replacing the + in the string 8.00+00 with another character? Tom -- View this message in context: http://www.nabble.com/Replacing-a-%22%2B%22-in-a-string-tp23655515p23655515.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.html and provide commented, minimal, self-contained, reproducible code.
[R] R 64-bit for Ubuntu 9.04 64-bit
I just installed Ubuntu 9.04 but there does not seem to be repository for binaries for this version. Are there going to be such repositories set up in the near future? Tom -- View this message in context: http://www.nabble.com/R-64-bit-for-Ubuntu-9.04-64-bit-tp23246229p23246229.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.html and provide commented, minimal, self-contained, reproducible code.
[R] R 2.9.0 MASS package
I can't seem to find MASS for the latest version of R. Is it coming or has the name of the package changed? Tom -- View this message in context: http://www.nabble.com/R-2.9.0-MASS-package-tp23144198p23144198.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.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R 2.9.0 MASS package
In Windows Xp Pro: R2.8.1 USA(CA1) repository markerSearchPower MASS(VR) MasterBayes R2.9.0 USA(CA1) repository markerSearchPower MasterBayes MASS is not where it used to be. I checked a couple of other repositories in the US and got similar results. Tom Peter Dalgaard wrote: Tom La Bone wrote: I can't seem to find MASS for the latest version of R. Is it coming or has the name of the package changed? Tom Where did you look? It is in the sources (as part of VR), and also in my (SUSE) test builds. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - (p.dalga...@biostat.ku.dk) FAX: (+45) 35327907 __ 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. -- View this message in context: http://www.nabble.com/R-2.9.0-MASS-package-tp23144198p23144721.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.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] what is R best for; what should one learn in addition to R
What do folks think about the c/gsl/Apophenia combination as one of the other stat packages? http://modelingwithdata.org/ http://apophenia.sourceforge.net/ Tom Greg Snow-2 wrote: I also recommend that people doing statistics know at least the basics of 3 different stats packages (S-Plus and R don't count as 2 separate packages) -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -- View this message in context: http://www.nabble.com/what-is-R-best-for--what-should-one-learn-in-addition-to-R-tp23139415p23145728.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.html and provide commented, minimal, self-contained, reproducible code.
[R] Physical Units in Calculations
Back in 2005 I had been doing most of my work in Mathcad for over 10 years. For a number of reasons I decided to switch over to R. After much effort and help from you folks I am finally thinking in R rather than thinking in Mathcad and trying to translating to R. Anyway, the only task I still use Mathcad for is calculations that involve physical quantities and units. For example, in Mathcad I can add 1 kilometer to 1 mile and get the right answer in the units of length I choose. Likewise, if I try to add 1 kilometer to 1 kilogram I get properly chastised. Is there a way in R to assign quantities and units to numbers and have R keep track of them like Mathcad does? Tom -- View this message in context: http://www.nabble.com/Physical-Units-in-Calculations-tp23016092p23016092.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.html and provide commented, minimal, self-contained, reproducible code.
[R] Inverse of data.ellipse function
The following code generates 85% and 95% bivariate normal confidence ellipses using the data.ellipse routine in the car package. Can anyone suggest a routine in R that will tell me the confidence ellipse that would intersect the green point, or more generally, any specified point on the plot? Tom library(car) x - c( 2.495507,2.800855,1.956886,2.093559,2.317661,2.134128,2.445757,2.449865, 2.157123,2.656724,2.514258,2.049239,2.302236,2.187003,2.064303,2.307158, 2.639794,2.095725,2.055517,2.095392,2.499140,1.997258,2.099004,2.485946, 2.390299,2.380655,1.986580,2.452259,2.016017,2.115884,2.448890,2.039421, 2.086519,1.905574,2.507067,2.222586,2.232333,2.286176,2.065320,2.136335, 1.956130,2.211561,2.196912,2.527431,1.935607,2.482722,2.234416,1.892957, 2.261484,2.172877,2.429097,2.132760,1.915024,2.474201,2.108019,2.098176, 2.464809,2.242213,2.604528,2.221102,2.226034,2.285435,1.981518,2.026446, 2.190195,2.108399,2.554589,1.866505,2.569580,2.263412,2.037287,1.723514, 2.068335,1.960022,2.233751,2.357066,2.164031,2.001292,2.356718,1.974896, 2.263872,2.483966,2.517231,2.346250,2.072050,2.110444,2.230884,2.501742, 2.239098,1.858333,2.104560,2.195149,2.501683,2.079934,2.397314,2.152187, 2.359440,2.111259,2.160616,1.976223) y - c( -5.600474,-5.661683,-5.007292,-4.874088,-5.339055,-5.858137,-5.594482, -5.826471,-5.959325,-6.031502,-5.381492,-5.232014,-5.497670,-5.151676, -5.520301,-5.589677,-6.037540,-4.999751,-6.166536,-4.722158,-5.876276, -5.420056,-5.773584,-5.428882,-5.669146,-5.546504,-4.973831,-6.201381, -5.217770,-4.969737,-5.905475,-5.390086,-5.003606,-4.937802,-5.324172, -4.991389,-5.500224,-5.836389,-5.136990,-5.067671,-5.189699,-5.273695, -5.761629,-5.400335,-4.672323,-5.390257,-5.176363,-4.747799,-5.246505, -5.357218,-5.819997,-5.307132,-4.660002,-5.103505,-5.060687,-5.242942, -5.357381,-4.881723,-5.952129,-5.361586,-5.202132,-5.522287,-5.638168, -5.589786,-4.997126,-5.116822,-5.786722,-5.205465,-5.836223,-5.730740, -5.345793,-5.081353,-4.932470,-5.917560,-5.001224,-5.050188,-5.246825, -5.303896,-5.945083,-5.001067,-5.296180,-6.290440,-5.682263,-5.526831, -6.298252,-5.361611,-5.422722,-5.356166,-5.618755,-5.141482,-5.472014, -4.973340,-5.608222,-4.600451,-5.638057,-5.093730,-5.221353,-5.497442, -4.817821,-5.767386) means - c(mean(x),mean(y)) sigma2 - var(cbind(x,y)) sx - sqrt(sigma2[1,1]) sy - sqrt(sigma2[2,2]) a - c(means[1]+qnorm(0.975)*sx,means[2]+qnorm(0.975)*sy) a plot(x,y) data.ellipse(x,y,levels=c(0.85,0.95)) points(a[1],a[2],col=green,pch=19) abline(h=a[2]) abline(v=a[1]) -- View this message in context: http://www.nabble.com/Inverse-of-data.ellipse-function-tp21843738p21843738.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.html and provide commented, minimal, self-contained, reproducible code.
[R] Extracting Coefficients and Such from mle2 Output
The mle2 function (bbmle library) gives an example something like the following in its help page. How do I access the coefficients, standard errors, etc in the summary of a? x - 0:10 y - c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8) LL - function(ymax=15, xhalf=6) + -sum(stats::dpois(y, lambda=ymax/(1+x/xhalf), log=TRUE)) a - mle2(LL, fixed=list(xhalf=6)) summary(a) Maximum likelihood estimation Call: mle2(minuslogl = LL, fixed = list(xhalf = 6)) Coefficients: Estimate Std. Error z value Pr(z) ymax 19.2881 1.7115 11.269 2.2e-16 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 -2 log L: 60.39244 Tom -- View this message in context: http://www.nabble.com/Extracting-Coefficients-and-Such-from-mle2-Output-tp21770860p21770860.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.html and provide commented, minimal, self-contained, reproducible code.
[R] Dates in Common
I have two collections of dates and I want to figure out what dates they have in common. This is not giving me what I want (I don't know what it is giving me). What is the best way to do this? Tom data1 [1] 1948-02-24 EST 1949-04-12 EST 1950-05-29 EDT 1951-05-21 EDT [5] 1951-12-20 EST 1953-01-22 EST 1955-02-28 EST 1956-03-08 EST [9] 1957-03-22 EST 1958-02-07 EST data2 [1] 1948-02-24 EST 1949-04-12 EST 1950-05-29 EDT 1951-05-21 EDT [5] 1951-12-20 EST 1953-01-22 EST 1955-02-28 EST 1956-03-08 EST [9] 1957-03-22 EST 1958-02-07 EST intersect(data1,data2) [1] -689626800 -653943600 -618350400 -587505600 -569098800 -534625200 [7] -468356400 -436042800 -403297200 -375476400 -- View this message in context: http://www.nabble.com/Dates-in-Common-tp21624909p21624909.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.html and provide commented, minimal, self-contained, reproducible code.
[R] text rather than html help in Windows
I would like to use Rterm in Windows XP and have the help files appear in text format in the terminal rather than in the html popup window. For example, I would like to enter help(lm) and get the text to appear in the terminal window. Can anyone suggest a way to do this? Thanks and Happy Hew Year. Tom -- View this message in context: http://www.nabble.com/text-rather-than-html-help-in-Windows-tp21251223p21251223.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.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] text rather than html help in Windows
Duncan Murdoch-2 wrote: Whoops, sorry, Uwe's advice is right. Text help is only the default when run outside a console; I use Cygwin, which doesn't look like a console to R. I am using eclipse with StatET to run R under Ubuntu 8.04 and Windows XP Pro. I would like both implementations to act the same, and your suggestion to use options(chmhelp=FALSE) in Windows did what I wanted. Uwe's suggestion to put the option in Rprofile completed the task. Thanks. Tom -- View this message in context: http://www.nabble.com/text-rather-than-html-help-in-Windows-tp21251223p21251607.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.html and provide commented, minimal, self-contained, reproducible code.
[R] Using transform to add a date column to a dataframe
I would like to add a column to the airquality dataset that contains the date 1950-01-01 in each row. This method does not appear to work: attach(airquality) data1 - transform(airquality,Date=as.Date(1950-01-01)) Error in data.frame(list(Ozone = c(41L, 36L, 12L, 18L, NA, 28L, 23L, 19L, : arguments imply differing number of rows: 153, 1 I can't decipher what the error message is trying to tell me. Any suggestions on how to do this? -- View this message in context: http://www.nabble.com/Using-transform-to-add-a-date-column-to-a-dataframe-tp21144414p21144414.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.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Using transform to add a date column to a dataframe
Gavin Simpson wrote: It says that the two arguments have different numbers of observations. The reason for which should now be pretty obvious as you provided a single Date whereas airquality has 153 observations. Thanks. I did look at ?transform but I was a bit confused because this worked data1 - transform(airquality,LTMDA=T) whereas this did not data1 - transform(airquality,Date=as.Date(1950-01-01)) Why does the first one work with one argument but the second one does not? -- View this message in context: http://www.nabble.com/Using-transform-to-add-a-date-column-to-a-dataframe-tp21144414p21146167.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.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Left-truncated regression
Look at the sand package, which is available at http://www.csm.ornl.gov/esh/statoed/ and the NADA package, which is available from CRAN. One or both may have items of interest. Tom Zita wrote: Hi. I am looking for a function for left-truncated data. I have one data set with 2 variables (Hours~Yrs_Ed). I already left-censored the data at 200 and left-truncated it at the same spot, so that I am able to make 2 estimations (one for censoring and one for truncation). I know how to make the linear regression for the left-censored variable (hours) and how to plot the regression line into the (x,y) plot (packages AER, Zeileis, Survival, ...): tfit-survreg(Surv(Hours,Hours0, type='left')~Yrs_Ed,data=DataWomen,dist='gaussian') z-predict(tfit,type=response) plot(Yrs_Ed,Hours) abline(tfit) My aim is to compare the effects of truncation and censoring graphically by plotting the two regression lines into one plot with both datasets (censored and truncated). I just can't figure out how to write the function for left-truncated data and what package to use for this. I only need left-truncation, not left-truncation and right-censoring. I hope somebody can help me with that matter. Zita -- View this message in context: http://www.nabble.com/Left-truncated-regression-tp20789446p20798448.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.html and provide commented, minimal, self-contained, reproducible code.
[R] Kolmogorov–Smirnov Test for Left Censored Data
Can someone recommend a package in R that will perform a two-sample Kolmogorov–Smirnov test on left censored data? The package surv2sample appears to offer such a test for right censored data and I guess that I can use this package if I flip my data, but I figured I would first ask if there was a package specific to left-censored data. Tom -- View this message in context: http://www.nabble.com/Kolmogorov%E2%80%93Smirnov-Test-for-Left-Censored-Data-tp20602916p20602916.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.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Accessing Results from cenmle function in NADA package
This is very nice also. I am going to use this approach in the future when I use lm. However, I can't seem to get to work the way I want with cenmle. I will continue to experiment. Thanks folks for the suggestions. Tom David Winsemius wrote: On Nov 12, 2008, at 8:48 AM, Tom La Bone wrote: I figured it out. In case anyone else ever has this question -- given the following output from cenmle: fit.cen - cenmle(obs, censored, groups) fit.cen Value Std. Errorz p (Intercept) 1.19473 0.0772 15.4695 5.58e-54 groups1 0.00208 0.0789 0.0263 9.79e-01 Log(scale) -0.40221 0.0168 -23.9034 2.82e-126 Scale= 0.669 Log Normal distribution Loglik(model)= -3908.9 Loglik(intercept only)= -3908.9 Loglik-r: 0.0006265534 Chisq= 0 on 1 degrees of freedom, p= 0.98 Number of Newton-Raphson Iterations: 1 n = 1766 The p-value is (for example): p.value - summary(fit.cen)[[9]][[11]] An approach that may yield somewhat more self-documenting code would be to examine either the fit object or the summary object with str and then to access results by extracting named elements. Since I don't have the package in question, let me use the lm object on its help page as an example: ctl - c(4.17,5.58,5.18,6.11,4.50,4.61,5.17,4.53,5.33,5.14) trt - c(4.81,4.17,4.41,3.59,5.87,3.83,6.03,4.89,4.32,4.69) group - gl(2,10,20, labels=c(Ctl,Trt)) weight - c(ctl, trt) lm.D9 - lm(weight ~ group) str(lm.D9) str(summary(lm.D9)) summary(lm.D9)$coefficients summary(lm.D9)$coefficients[groupTrt, Pr(|t|)] # to get the p-value summary(lm.D9)$coefficients[groupTrt,Pr(|t|)] [1] 0.2490232 You had originally asked for a method to extract coefficients and for that purpose you may want to look at: ?coefficients slope - coefficients(lm.D9)[groupTrt] slope groupTrt -0.371 -- David Winsemius Heritage Labs Tom Tom La Bone wrote: The cenmle function is used to fit two sets of censored data and test if they are significantly different. I can print out the results of the analysis on the screen but can't seem to figure out how to access these results in R and assign them to new variables, e.g., assign the slope calculated with cenmle to the variable m. Any suggestions? Tom -- View this message in context: http://www.nabble.com/Accessing-Results-from-cenmle-function-in-NADA-package-tp20437420p20460676.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.html and provide commented, minimal, self-contained, reproducible code. __ 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. -- View this message in context: http://www.nabble.com/Accessing-Results-from-cenmle-function-in-NADA-package-tp20437420p20464040.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.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Accessing Results from cenmle function in NADA package
I figured it out. In case anyone else ever has this question -- given the following output from cenmle: fit.cen - cenmle(obs, censored, groups) fit.cen Value Std. Errorz p (Intercept) 1.19473 0.0772 15.4695 5.58e-54 groups1 0.00208 0.0789 0.0263 9.79e-01 Log(scale) -0.40221 0.0168 -23.9034 2.82e-126 Scale= 0.669 Log Normal distribution Loglik(model)= -3908.9 Loglik(intercept only)= -3908.9 Loglik-r: 0.0006265534 Chisq= 0 on 1 degrees of freedom, p= 0.98 Number of Newton-Raphson Iterations: 1 n = 1766 The p-value is (for example): p.value - summary(fit.cen)[[9]][[11]] Tom Tom La Bone wrote: The cenmle function is used to fit two sets of censored data and test if they are significantly different. I can print out the results of the analysis on the screen but can't seem to figure out how to access these results in R and assign them to new variables, e.g., assign the slope calculated with cenmle to the variable m. Any suggestions? Tom -- View this message in context: http://www.nabble.com/Accessing-Results-from-cenmle-function-in-NADA-package-tp20437420p20460676.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.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Accessing Results from cenmle function in NADA package
Oh, I like your answer better than mine! Thanks.
Tom
Richard Cotton wrote:
I figured it out. In case anyone else ever has this question -- given
the
following output from cenmle:
fit.cen - cenmle(obs, censored, groups)
fit.cen
Value Std. Errorz p
(Intercept) 1.19473 0.0772 15.4695 5.58e-54
groups1 0.00208 0.0789 0.0263 9.79e-01
Log(scale) -0.40221 0.0168 -23.9034 2.82e-126
Scale= 0.669
Log Normal distribution
Loglik(model)= -3908.9 Loglik(intercept only)= -3908.9
Loglik-r: 0.0006265534
Chisq= 0 on 1 degrees of freedom, p= 0.98
Number of Newton-Raphson Iterations: 1
n = 1766
The p-value is (for example):
p.value - summary(fit.cen)[[9]][[11]]
Or slightly more transparently
summary(fit.cen)$table[,'p']
Regards,
Richie.
Mathematical Sciences Unit
HSL
ATTENTION:
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Regards,
Richie.
Mathematical Sciences Unit
HSL
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[R] Accessing Results from cenmle function in NADA package
The cenmle function is used to fit two sets of censored data and test if they are significantly different. I can print out the results of the analysis on the screen but can't seem to figure out how to access these results in R and assign them to new variables, e.g., assign the slope calculated with cenmle to the variable m. Any suggestions? Tom -- View this message in context: http://www.nabble.com/Accessing-Results-from-cenmle-function-in-NADA-package-tp20437420p20437420.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.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Doing a Task Without Using a For Loop
I want to thank everyone for the help. I ended up having to use a loop to
assign values from the table to NinYear. However, as I have played with the
full datasets I have noticed that R is MUCH faster if I use vectors in the
loop rather than columns of a dataframe. In the specific case of 43,000
lines of data, assigning values from the table to the 43,000 elements of a
vector took 6 seconds whereas assigning values from the table to 43,000
elements of a dataframe took 21 minutes. Why is there such a huge
difference?
Tom
Tom La Bone wrote:
Assume that I have the dataframe data1, which is listed at the end of
this message. I want count the number of lines that each person has for
each year. For example, the person with ID=213 has 15 entries (NinYear)
for 1953. The following bit of code calculates NinYear:
for (i in 1:length(data1$ID)) {
data1$NinYear[i] - length(data1[data1$Year==data1$Year[i]
data1$ID==data1$ID[i],1]) }
This seems to work but is horribly slow (some files I am working with have
over 500,000 lines). Can anyone suggest a faster way of doing this,
perhaps a way that does not use a for loop? Thanks.
Tom
IDYearNinYear
209 19710
209 19710
213 19510
213 19510
213 19530
213 19530
213 19530
213 19530
213 19530
213 19530
213 19530
213 19530
213 19530
213 19530
213 19530
213 19530
213 19530
213 19530
213 19530
213 19540
213 19540
213 19540
213 19540
213 19540
213 19540
213 19540
213 19540
213 19540
213 19540
213 19540
213 19550
213 19550
234 19530
234 19530
234 19530
234 19530
234 19530
234 19580
234 19580
234 19650
234 19650
234 19650
249 19520
249 19520
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[R] Doing a Task Without Using a For Loop
Assume that I have the dataframe data1, which is listed at the end of this
message. I want count the number of lines that each person has for each
year. For example, the person with ID=213 has 15 entries (NinYear) for 1953.
The following bit of code calculates NinYear:
for (i in 1:length(data1$ID)) {
data1$NinYear[i] - length(data1[data1$Year==data1$Year[i]
data1$ID==data1$ID[i],1]) }
This seems to work but is horribly slow (some files I am working with have
over 500,000 lines). Can anyone suggest a faster way of doing this, perhaps
a way that does not use a for loop? Thanks.
Tom
ID YearNinYear
209 19710
209 19710
213 19510
213 19510
213 19530
213 19530
213 19530
213 19530
213 19530
213 19530
213 19530
213 19530
213 19530
213 19530
213 19530
213 19530
213 19530
213 19530
213 19530
213 19540
213 19540
213 19540
213 19540
213 19540
213 19540
213 19540
213 19540
213 19540
213 19540
213 19540
213 19550
213 19550
234 19530
234 19530
234 19530
234 19530
234 19530
234 19580
234 19580
234 19650
234 19650
234 19650
249 19520
249 19520
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Re: [R] Doing a Task Without Using a For Loop
The table function, which I was unaware of, works great. However, I still
don't see how to assign the values calculated with table to data1$NinYear
without using a loop.
Tom
Henrique Dallazuanna wrote:
Try this:
with(data1, table(ID, Year))
On Tue, Oct 14, 2008 at 10:58 AM, Tom La Bone
[EMAIL PROTECTED]wrote:
Assume that I have the dataframe data1, which is listed at the end of
this
message. I want count the number of lines that each person has for each
year. For example, the person with ID=213 has 15 entries (NinYear) for
1953.
The following bit of code calculates NinYear:
for (i in 1:length(data1$ID)) {
data1$NinYear[i] - length(data1[data1$Year==data1$Year[i]
data1$ID==data1$ID[i],1]) }
This seems to work but is horribly slow (some files I am working with
have
over 500,000 lines). Can anyone suggest a faster way of doing this,
perhaps
a way that does not use a for loop? Thanks.
Tom
ID YearNinYear
209 19710
209 19710
213 19510
213 19510
213 19530
213 19530
213 19530
213 19530
213 19530
213 19530
213 19530
213 19530
213 19530
213 19530
213 19530
213 19530
213 19530
213 19530
213 19530
213 19540
213 19540
213 19540
213 19540
213 19540
213 19540
213 19540
213 19540
213 19540
213 19540
213 19540
213 19550
213 19550
234 19530
234 19530
234 19530
234 19530
234 19530
234 19580
234 19580
234 19650
234 19650
234 19650
249 19520
249 19520
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--
Henrique Dallazuanna
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25° 25' 40 S 49° 16' 22 O
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[R] How do I Convert 1 to the number 1?
Is there an elegant way in R to change a number reported as a less-than number in text format, 1 for example, to the numeric equivalent 1? I have been trying to use as.numeric, but have not come up with anything clever yet. Tom -- View this message in context: http://www.nabble.com/How-do-I-Convert-%22%3C1%22-to-the-number-1--tp19651018p19651018.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.html and provide commented, minimal, self-contained, reproducible code.
[R] Upgrade to R 2.7.2 from Debian Repository
I am running R 2.7.1 on an eeepc with the standard Xandros Linux. I install/upgrade R binaries using synaptic from the http://cran.r-project.org/bin/linux/debian/etch-cran/ repository. R 2.7.2 does not appear to be available from this repository. Will it be available soon or is there another repository I should be using? Tom -- View this message in context: http://www.nabble.com/Upgrade-to-R-2.7.2-from-Debian-Repository-tp19328325p19328325.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.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Error: can not allocate vector of 117.3 Mb
To see some useful discussions of this problem in various settings search R-Help for the phrase cannot allocate vector of size. Tom ram basnet wrote: Hi R users, I am doing multiscale bootstrapping for clustering through pvclust package. I have large data set (observations 182 and variables 5546). When i tried to make bootstrapping, then i got message as Bootstrap (r = 0.5)Error: cannot allocate vector of size 117.3 Mb. I am new R user and could not understand what is the problem and also don't know the easiet solution. If someone knows, pls help me. Thanks in advance. Ram Kumar Basnet Graduate student. [[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. -- View this message in context: http://www.nabble.com/Error%3A-can-not-allocate-vector-of-117.3-Mb-tp19330258p19331629.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.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How Can I Tell if the R Running is 64 bit or 32 bit?
Well, I am indeed running 64-bit Ubuntu and 64-bit R. Thanks! Tom Peter Dalgaard wrote: Marc Schwartz wrote: Try: 8*4 [1] 32 As per the help page for .Machine: sizeof.pointer the number of *bytes* in a C SEXP type. So: 8 bits per byte * 4 bytes = 32 bits Also (outside of R) type uname -a. This should give something like Linux viggo 2.6.18.8-0.10-default #1 SMP Wed Jun 4 15:46:34 UTC 2008 x86_64 x86_64 x86_64 GNU/Linux on a 64-bit system (SUSE in this case) but Linux turmalin 2.6.22.18-0.2-default #1 SMP 2008-06-09 13:53:20 +0200 i686 i686 i386 GNU/Linux on 32-bitters :-) HTH, Marc Schwartz on 08/08/2008 03:58 PM milton ruser wrote: Dear Prof. B.Ripley, If : .Machine$sizeof.pointer [1] 4 2*2*2*2 [1] 16 So I am running with 16 bits? How can I know the number of bits supported on my machine? Kindly, miltinho astronauta brazil On 8/8/08, Prof Brian Ripley [EMAIL PROTECTED] wrote: Look at .Machine$sizeof.pointer (in bytes). On Fri, 8 Aug 2008, Tom La Bone wrote: I think I installed 64-bit Ubuntu 8.04 and 64-bit R on my computer. I can't seem to find anything that says this is 64-bit Ubuntu or this is 64-bit R. How do I tell what version of R I am running? Tom __ 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. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ 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. -- View this message in context: http://www.nabble.com/How-Can-I-Tell-if-the-R-Running-is-64-bit-or-32-bit--tp18898653p1889.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.html and provide commented, minimal, self-contained, reproducible code.
[R] Will This Computer Run 64 bit Ubuntu/R?
After doing some reading about 64-bit systems and software I am still somewhat uncertain about some things. I have a Dell Dimension XPS 400 with a dual core Intel Pentium D 940 (3.2 GHz) and 4 Gb of memory. I currently dual boot the system with XP Professional and Ubuntu 8.04 (32 bit). If I simply install Ubuntu 8.04 (64 bit) on this system will it run the 64 bit linux version of R? I would appreciate any advice you might be willing to offer on this. Tom -- View this message in context: http://www.nabble.com/Will-This-Computer-Run-64-bit-Ubuntu-R--tp18799376p18799376.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.html and provide commented, minimal, self-contained, reproducible code.
[R] Memory Problems with a Simple Bootstrap - Part II
I have distilled my bootstrap problem down to this bit of code, which
calculates an estimate of the 95th percentile of 7500 random numbers drawn
from a standard normal distribution:
library(boot)
per95 - function( annual.data, b.index) {
sample.data - annual.data[b.index]
return(quantile(sample.data,probs=c(0.95))) }
m - 1
x - rnorm(7500,0,1)
B - boot(data=x,statistic=per95,R=m)
Error: cannot allocate vector of size 286.1 Mb
This was result was observed with R 2.7.1 and 2.7.1patched when run on a
Windows XP computer with 4Gb of memory.
This does not seem to be an excessively large and complicated calculation,
so is this an intentional limitation of the boot function, a result of bad
choices on my part, or a bug?
Tom
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[R] Memory Problems with a Simple Bootstrap
I have a data file called inputdata.csv that looks something like this
ID YearResult Month Date
1 71741954 103 540301
2 7174195443 540322
3 20924 1967 4 2 670223
4 20924 1967 -75 670518
5 20924 1967 -37 670706
...
67209 ...
i.e., it goes on for 67209 rows (~2 Mb file). When I run the following
bootstrap session I get the indicated error:
library(boot)
setwd(C:/Documents and Settings/Tom/Desktop)
data.in - read.csv(inputdata.csv,header=T,as.is=T)
per95 - function( annual.data, b.index) {
+ sample.data - annual.data[b.index,]
+ return(quantile(sample.data$Result,probs=c(0.95))) }
m - 1
for (i in 1:39) {
+ annual.data - data.in[data.in$Year == (i+1949),]
+ B - boot(data=annual.data,statistic=per95,R=m)
+ print(i)
+ print(memory.size())
+ }
[1] 1
[1] 20.26163
[1] 2
[1] 61.6352
[1] 3
[1] 134.4187
[1] 4
[1] 149.4704
[1] 5
[1] 290.3090
[1] 6
[1] 376.7017
[1] 7
[1] 435.7683
[1] 8
[1] 463.7404
[1] 9
[1] 497.7946
Error: cannot allocate vector of size 568.8 Mb
I am running this on a Windows XP Pro machine with 4 Gb of memory. The same
problem occurs when the code is executed on the same box running Ubuntu
8.04. Does anyone see any obvious reason why this should run out of memory?
I would be happy to email the data file to anyone who cares to try it on
their computer.
Tom
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Re: [R] Memory Problems with a Simple Bootstrap
Same problem. The Windows Task Manager indicated that Rgui.exe was using
1,249,722 K of memory when the error occurred. This is R 2.7.1 by the way.
library(boot)
setwd(C:/Documents and Settings/Tom/Desktop)
data.in - read.csv(inputdata.csv,header=T,as.is=T)
per95 - function( annual.data, b.index) {
+ sample.data - annual.data[b.index,]
+ return(quantile(sample.data$Result,probs=c(0.95))) }
m - 1
for (i in 1:39) {
+ annual.data - data.in[data.in$Year == (i+1949),]
+ B - boot(data=annual.data,statistic=per95,R=m)
+ gc()
+ print(i)
+ print(object.size(B))
+ print(memory.size())
+ }
[1] 1
[1] 90352
[1] 12.35335
[1] 2
[1] 111032
[1] 12.39024
[1] 3
[1] 155544
[1] 12.48451
[1] 4
[1] 159064
[1] 11.10526
[1] 5
[1] 243456
[1] 11.23505
[1] 6
[1] 280592
[1] 12.74642
[1] 7
[1] 302416
[1] 11.33087
[1] 8
[1] 319752
[1] 12.84377
[1] 9
[1] 351448
[1] 11.42264
Error: cannot allocate vector of size 284.4 Mb
jholtman wrote:
Use gc() in the loop to possibly free up any fragmented memory. You
might also print out the size of B (object.size(B)) since that appears
to be the only variable in your loop that might be growing.
On Fri, Aug 1, 2008 at 12:09 PM, Tom La Bone [EMAIL PROTECTED]
wrote:
I have a data file called inputdata.csv that looks something like this
ID YearResult Month Date
1 71741954 103 540301
2 7174195443 540322
3 20924 1967 4 2 670223
4 20924 1967 -75 670518
5 20924 1967 -37 670706
...
67209 ...
i.e., it goes on for 67209 rows (~2 Mb file). When I run the following
bootstrap session I get the indicated error:
library(boot)
setwd(C:/Documents and Settings/Tom/Desktop)
data.in - read.csv(inputdata.csv,header=T,as.is=T)
per95 - function( annual.data, b.index) {
+ sample.data - annual.data[b.index,]
+ return(quantile(sample.data$Result,probs=c(0.95))) }
m - 1
for (i in 1:39) {
+ annual.data - data.in[data.in$Year == (i+1949),]
+ B - boot(data=annual.data,statistic=per95,R=m)
+ print(i)
+ print(memory.size())
+ }
[1] 1
[1] 20.26163
[1] 2
[1] 61.6352
[1] 3
[1] 134.4187
[1] 4
[1] 149.4704
[1] 5
[1] 290.3090
[1] 6
[1] 376.7017
[1] 7
[1] 435.7683
[1] 8
[1] 463.7404
[1] 9
[1] 497.7946
Error: cannot allocate vector of size 568.8 Mb
I am running this on a Windows XP Pro machine with 4 Gb of memory. The
same
problem occurs when the code is executed on the same box running Ubuntu
8.04. Does anyone see any obvious reason why this should run out of
memory?
I would be happy to email the data file to anyone who cares to try it on
their computer.
Tom
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Cincinnati, OH
+1 513 646 9390
What is the problem that you are trying to solve?
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Re: [R] Memory Problems with a Simple Bootstrap
Here it is with the gc() in a print statement.
Tom
library(boot)
setwd(C:/Documents and Settings/Tom/Desktop)
data.in - read.csv(inputdata.csv,header=T,as.is=T)
per95 - function( annual.data, b.index) {
+ sample.data - annual.data[b.index,]
+ return(quantile(sample.data$Result,probs=c(0.95))) }
m - 1
for (i in 1:39) {
+ annual.data - data.in[data.in$Year == (i+1949),]
+ B - boot(data=annual.data,statistic=per95,R=m)
+ print(i)
+ print(gc())
+ print(object.size(B))
+ print(memory.size())
+ }
[1] 1
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 145517 3.9 35 9.4 35 9.4
Vcells 304805 2.42602013 19.9 2841664 21.7
[1] 90352
[1] 12.35812
[1] 2
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 145540 3.9 35 9.4 35 9.4
Vcells 309041 2.4 12977679 99.1 15259760 116.5
[1] 111032
[1] 12.39814
[1] 3
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 145540 3.9 35 9.4 35 9.4
Vcells 318147 2.5 35277418 269.2 41833896 319.2
[1] 155544
[1] 12.49432
[1] 4
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 145540 3.9 35 9.4 35 9.4
Vcells 318867 2.5 37046714 282.7 43935337 335.3
[1] 159064
[1] 11.10362
[1] 5
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 145540 3.9 35 9.4 35 9.4
Vcells 336129 2.6 79348305 605.4 94192718 718.7
[1] 243456
[1] 11.2296
[1] 6
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 145540 3.9 35 9.435 9.4
Vcells 343725 2.7 97971904 747.5 116530118 889.1
[1] 280592
[1] 12.75431
[1] 7
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 145540 3.9 35 9.435 9.4
Vcells 348189 2.7 108915204 831.0 129493067 988.0
[1] 302416
[1] 11.32924
[1] 8
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 145540 3.9 35 9.4359.4
Vcells 351735 2.7 117607222 897.3 139706454 1065.9
[1] 319752
[1] 12.85929
[1] 9
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 145540 3.9 359.4359.4
Vcells 358217 2.8 133510676 1018.7 158462984 1209.0
[1] 351448
[1] 11.40765
Error: cannot allocate vector of size 284.4 Mb
jholtman wrote:
It seems like the objects are reasonable size and the memory size also
seems reasonable. That is what I usually go by to see if there are
large objects in my memory. If it was showing that R had 1.2GB of
memory allocated to it, I wonder if there might be a memory leak
somewhere.
On Fri, Aug 1, 2008 at 1:36 PM, Tom La Bone [EMAIL PROTECTED]
wrote:
Same problem. The Windows Task Manager indicated that Rgui.exe was using
1,249,722 K of memory when the error occurred. This is R 2.7.1 by the
way.
library(boot)
setwd(C:/Documents and Settings/Tom/Desktop)
data.in - read.csv(inputdata.csv,header=T,as.is=T)
per95 - function( annual.data, b.index) {
+ sample.data - annual.data[b.index,]
+ return(quantile(sample.data$Result,probs=c(0.95))) }
m - 1
for (i in 1:39) {
+ annual.data - data.in[data.in$Year == (i+1949),]
+ B - boot(data=annual.data,statistic=per95,R=m)
+ gc()
+ print(i)
+ print(object.size(B))
+ print(memory.size())
+ }
[1] 1
[1] 90352
[1] 12.35335
[1] 2
[1] 111032
[1] 12.39024
[1] 3
[1] 155544
[1] 12.48451
[1] 4
[1] 159064
[1] 11.10526
[1] 5
[1] 243456
[1] 11.23505
[1] 6
[1] 280592
[1] 12.74642
[1] 7
[1] 302416
[1] 11.33087
[1] 8
[1] 319752
[1] 12.84377
[1] 9
[1] 351448
[1] 11.42264
Error: cannot allocate vector of size 284.4 Mb
jholtman wrote:
Use gc() in the loop to possibly free up any fragmented memory. You
might also print out the size of B (object.size(B)) since that appears
to be the only variable in your loop that might be growing.
On Fri, Aug 1, 2008 at 12:09 PM, Tom La Bone [EMAIL PROTECTED]
wrote:
I have a data file called inputdata.csv that looks something like this
ID YearResult Month Date
1 71741954 103 540301
2 7174195443 540322
3 20924 1967 4 2 670223
4 20924 1967 -75 670518
5 20924 1967 -37 670706
...
67209 ...
i.e., it goes on for 67209 rows (~2 Mb file). When I run the following
bootstrap session I get the indicated error:
library(boot)
setwd(C:/Documents and Settings/Tom/Desktop)
data.in - read.csv(inputdata.csv,header=T,as.is=T)
per95 - function( annual.data, b.index) {
+ sample.data - annual.data[b.index,]
+ return(quantile(sample.data$Result,probs=c(0.95))) }
m - 1
for (i in 1:39) {
+ annual.data - data.in[data.in$Year == (i+1949),]
+ B - boot(data=annual.data,statistic=per95,R=m)
+ print(i)
+ print(memory.size())
+ }
[1] 1
[1] 20.26163
[1] 2
[1] 61.6352
[1] 3
[1] 134.4187
[1] 4
[1] 149.4704
[1] 5
[1] 290.3090
[1] 6
[1
Re: [R] re sponse surface analysis
There appears to be a very promising response surface package being discussed at useR-2008, but I have been unable to find the package on CRAN or contact the authors. www.statistik.uni-dortmund.de/useR-2008/abstracts/Sztendur+Diamond.pdf Tom Jinsong Zhao wrote: Hi, Is there a package that could do response surface analysis equivalent to SAS RSREG procedure? Thanks! Regards, Jinsong __ 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. -- View this message in context: http://www.nabble.com/response-surface-analysis-tp18666106p18675308.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.html and provide commented, minimal, self-contained, reproducible code.
[R] Tutorial on rgl Graphics
Can anyone point me towards a tutorial on using the rgl graphics package? Something with lots of examples would be nice. Thanks. Tom -- View this message in context: http://www.nabble.com/Tutorial-on-rgl-Graphics-tp18649114p18649114.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.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Tutorial on rgl Graphics
After looking around a bit more I found the example I was looking for --
plotlm3d, which I found on the R wiki
http://wiki.r-project.org/rwiki/doku.php?id=graph_gallery:new-graphics
The original author was John Fox, and it was modified by Jose Claudio Faria
and Duncan Murdoch. Below is a simplified version of the function and two
examples. One example was presented as a test of the function and it works
fine. The second example is the plot I want to make and I can't seem to get
the scale on the x and y axes correct. Being unfamiliar with rgl, can
someone provide a hint on how to get the scales right? Thanks for the help.
Tom
plotlm3d - function (x, y, z,
surface= T,
model = 'z ~ x + y',
simple.axes= T,
box= F,
xlab = deparse(substitute(x)),
ylab = deparse(substitute(y)),
zlab = deparse(substitute(z)),
surface.col= c('blue', 'orange', 'red', 'green',
'magenta', 'cyan', 'yellow',
'gray', 'brown'),
point.col = 'yellow',
grid.col = material3d(color),
grid = T,
grid.lines = 26,
sphere.factor = 1,
threshold = 0.01)
{
require(rgl)
require(mgcv)
xlab; ylab; zlab
size - max(c(x,y,z))/100 * sphere.factor
if (size threshold)
spheres3d(x, y, z, color = point.col, radius = size)
else
points3d(x, y, z, color = point.col)
aspect3d(c(1, 1, 1))
if (surface) {
xvals - seq(min(x), max(x), length = grid.lines)
yvals - seq(min(y), max(y), length = grid.lines)
dat - expand.grid(x = xvals, y = yvals)
for (i in 1:length(model)) {
mod - lm(formula(model[i]))
zhat - matrix(predict(mod, newdata = dat), grid.lines, grid.lines)
surface3d(xvals, yvals, zhat, color = surface.col[i], alpha = 0.5, lit
= F)
if (grid)
surface3d(xvals, yvals, zhat, color = grid.col, alpha = 0.5,
lit = F, front = 'lines', back = 'lines') }}
if(simple.axes) {
axes3d(c('x', 'y', 'z'))
title3d(xlab = xlab, ylab = ylab, zlab = zlab)
}
else
decorate3d(xlab = xlab, ylab = ylab, zlab = zlab, box = box)
}
#This is an example of a 3D scatterplot that works fine
x - c( 274, 180, 375, 205, 86, 265, 98, 330, 195, 53,
430, 372, 236, 157, 370)
y - c(2450, 3254, 3802, 2838, 2347, 3782, 3008, 2450, 2137, 2560,
4020, 4427, 2660, 2088, 2605)
z - c( 162, 120, 223, 131, 67, 169, 81, 192, 116, 55,
252, 232, 144, 103, 212)
open3d()
plotlm3d(x, y, z,
surface = T,
model = 'z ~ x + y',
xlab= 'x',
ylab= 'y',
zlab= 'z')
#This is the plot I am trying to make - scales on x and y axes are wrong
x - c(0.3405,0.1220,0.1028,0.08451,0.05668,0.0345,0.003788,0.002121)
y - c(0.3460,0.1227,0.1097,0.09666,0.07677,0.06278,0.02168,0.01303)
z - c(2720,1150,1010,790,482,358,78,35)
open3d()
plotlm3d(x, y, z,
surface = T,
model = 'z ~ x + y - 1',
xlab= 'x',
ylab= 'y',
zlab= 'z')
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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] Problem with scatterplot3d example
I tried to run the following example from section 4.1.4 of the Scatterplot3d - an R package for Visualizing Multivariate Data vignette and got an error on the part that plots the regression plane: library(scatterplot3d) data(trees) s3d - scatterplot3d(trees, type = h, color = blue, + angle = 55, scale.y = 0.7, pch = 16, main = Adding elements) my.lm - lm(trees$Volume ~ trees$Girth + trees$Height) s3d$plain3d(my.lm) Error: attempt to apply non-function s3d$points3d(seq(10, 20, 2), seq(85, 60, -5), seq(60, 10, -10), + col = red, type = h, pch = 8) Any ideas on what I need to change in order to get the plane to plot? Tom -- View this message in context: http://www.nabble.com/Problem-with-scatterplot3d-example-tp18630468p18630468.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.html and provide commented, minimal, self-contained, reproducible code.
[R] Backgrounds in Multiple Plots made with fig
The following code was adapted from an example Vincent Zoonekynd gave on his web site http://zoonek2.free.fr/UNIX/48_R/03.html: n - 1000 x - rnorm(n) qqnorm(x) qqline(x, col=red) op - par(fig=c(.02,.5,.5,.98), new=TRUE) hist(x, probability=T, col=light blue, xlab=, ylab=, main=, axes=F) lines(density(x), col=red, lwd=2) box() par(op) How can I make the background in the small box in the upper left-hand corner be a different color than the background in the main plot and erase any of the main plot that happens to be behind the box? Tom -- View this message in context: http://www.nabble.com/Backgrounds-in-Multiple-Plots-made-with-%22fig%22-tp18302602p18302602.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.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Deming Regression
I believe that Deming regression also goes by the name of orthogonal regression, which can be performed in R using pca methods. If you do a search of the list for orthogonal regression you can see the previous discussions of this topic. Tom Dexter Riley wrote: Hi all. Has anyone ever done a Deming Regression in R? I'm wondering if there's a simple way to do it. Thanks for all your help! -Ed -- View this message in context: http://www.nabble.com/Deming-Regression-tp17949318p17981875.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.html and provide commented, minimal, self-contained, reproducible code.
[R] Simultaneous Confidence/Prediction Bands
Is there a built-in function in R that will generate simultaneous confidence and prediction bands for linear regression? Tom -- View this message in context: http://www.nabble.com/Simultaneous-Confidence-Prediction-Bands-tp17941537p17941537.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.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R on an ASUS eee PC, continued - installing packages
I am running R in the konsole of the Kate editor on an eeePC 900 (standard
Xandros OS). When a plot is generated it is initially too large to fit in
the screen, but if I click on the plot it automatically resizes to fit
properly. I have no idea if this is a default behavior.
Tom
Millo Giovanni wrote:
Dear all,
I just went through the process of installing R on an eeePC 900 running
Linux. As a Windows useR utterly ignorant about Linux, I'd never have
done it without reading your posts and the R Wiki, so first of all:
thank you!
Next, taking up your thread from some weeks ago, I thought this could be
useful for somebody else too, so here's what I did:
1) I followed wolfgang's step-by-step guide at
http://finzi.psych.upenn.edu/R/Rhelp02a/archive/128565.html,
plus
2) I installed the build dependencies as shown in R Wiki:
## quoting from
http://wiki.r-project.org/rwiki/doku.php?id=getting-started:installation
:debian#build_r ##
How much supporting software you need to install depends on how much
compilation you want to be able to do with R. If you just want to be
able to run R, you can get r-base-core and all the recommended packages
by doing:
sudo apt-get install r-base
If you want to be able to build and install R packages (including those
from CRAN), you can get all the common header files, as well as
r-base-core by doing:
sudo apt-get install r-base-dev
If you want to be able to build R from its source code, you can get
build dependencies for R (e.g., compilers, header files) by doing:
sudo apt-get build-dep r-base
## end quote ##
This way I got all the necessary compilers, headers etc. automagically
installed as well, so that install.packages() works fine now: I
installed the whole Econometrics task view without problems. I still
haven't tried to install Rmetrics in order to save space on the little
machine, because I do not currently need it, but it should go the same
way: maybe this can solve John's problem?
I am aware that probably removing the original OS and installing Debian
as suggested by Dirk Eddelbuettel here
http://finzi.psych.upenn.edu/R/Rhelp02a/archive/128605.html would be a
better solution, but I am a complete Linux newbie, never ever tried it
before, so it's good both for me and for family use to retain the
original easy mode GUI while having R running on the same machine.
Full desktop mode (=standard KDE) is also easily enabled by adding
kicker and ksmserver (see http://wiki.eeeuser.com/howto:getkde, I did it
the manual way and it worked; just take heed that kicker and ksmserver
were not found in the '900's repository and I had to take them from the
'701's).
The only thing I wish I were able to do now is to have the graphics
windows defaults changed to a size fitting the small 9'' screen, as now
I have to reduce it and move it to the right by hand every time to
reproduce the results of 'windowstile in Windows. If anybody can
help...
HTH,
Giovanni
Giovanni Millo
Research Dept.,
Assicurazioni Generali SpA
Via Machiavelli 4,
34131 Trieste (Italy)
tel. +39 040 671184
fax +39 040 671160
# original message:
From: John C Frain frainj
Date: Mon, 28 Apr 2008 15:33:31 +0100
Thanks for the step by step guide. It installs a base R and some
libraries very well. I tries to load some of the Rmetrics libraries,
using install.packages() nu ran into problems. I used apt-get install
to install make and gcc from the Xandros repository. gcc also included
binutils, gcc-4.1 and libsspo. Is there an easy answer to the
question what I need to install to get the install process working.
The R Installation and Administration guide says that I just need the
compilers and tools. Installing robustbase gives the following
messages. (If it is as simple as R not being able to find the header
files how do I tell R where to find them?).
Best Regards
John
output in original message suppressed
--
John C Frain
Trinity College Dublin
Dublin 2
Ireland
www.tcd.ie/Economics/staff/frainj/home.html
mailto:frainj at tcd.ie
mailto:frainj at gmail.com
Ai sensi del D.Lgs. 196/2003 si precisa che le informazi...{{dropped:13}}
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[R] Units of Difference Between Two Dates
I would like all three of these calculations to give an answer in days (or at least the same units): as.POSIXct(1971-08-01 00:00:00) - as.POSIXct(1971-08-01 00:00:00) Time difference of 0 secs as.POSIXct(1971-08-01 12:00:00) - as.POSIXct(1971-08-01 00:00:00) Time difference of 12 hours as.POSIXct(1971-09-01 00:00:00) - as.POSIXct(1971-08-01 00:00:00) Time difference of 31 days What is the best way to do this? Tom -- View this message in context: http://www.nabble.com/Units-of-Difference-Between-Two-Dates-tp17251994p17251994.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.html and provide commented, minimal, self-contained, reproducible code.
[R] Statistical Methods and Software for the Analysis of Occupational Exposure Data With Non-Detectable Values
FYI This is a nice package that is not on CRAN for some reason. You can get it at http://www.csm.ornl.gov/esh/statoed/ Tom -- View this message in context: http://www.nabble.com/Statistical-Methods-and-Software-for-the-Analysis-of-Occupational-Exposure-Data-With-Non-Detectable-Values-tp16966228p16966228.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.html and provide commented, minimal, self-contained, reproducible code.
[R] ARAR Time Series Analysis in R
Does R have a function for doing an ARAR analysis of a time series? Tom -- View this message in context: http://www.nabble.com/ARAR-Time-Series-Analysis-in-R-tp16722577p16722577.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.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Specifying relative position of text in a plot
Thanks for all of the suggestions. The key key here seems to be using the par function to change the coordinate system like so plot(rnorm(100), rnorm(100)) op - par(usr) par(usr = c(0, 1, 0, 1)) text(0.5,0.5,TEST) par(usr = op) Prof Ripley commented that this approach will also work on log plots, but I don't think I completely understand what is going on because this does not work for me plot(rlnorm(100), rlnorm(100),log=xy) op - par(usr) par(usr = c(0, 1, 0, 1)) text(0.5,0.5,TEST) par(usr = op) Any hints on what I am doing wrong with the log plots? Thanks again for the help. Tom -- View this message in context: http://www.nabble.com/Specifying-relative-position-of-text-in-a-plot-tp16002549p16024549.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.html and provide commented, minimal, self-contained, reproducible code.
[R] Specifying relative position of text in a plot
What is the simplest way to specify the location of text in a scatter plot (created using the plot function) in relative terms rather than specific x-y coordinates? For example, rather than putting text at (300,49) on a plot, how do I put it 1/10 of the way over from the y axis and 1/2 of the way up from the x axis? Thanks. Tom -- View this message in context: http://www.nabble.com/Specifying-relative-position-of-text-in-a-plot-tp16002549p16002549.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.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] I need to buy a book in R
This is a nice list: http://www.amazon.com/Use-R/lm/RNFBA3UHW2M73/ref=cm_lmt_srch_f_1_rsrsrs0 Tom kayj wrote: Hi All, I am a new user in R and I would like to buy a book that teaches me how to use R. In addition, I may nees to do some advanced statistical analysis. Does anyone recommend some books or websites where I can learn R. Thanks -- View this message in context: http://www.nabble.com/I-need-to-buy-a-book-in-R-tp15811699p15818270.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.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] best text editor for Linux?
I am in a similar situation and found that Kate combined with Konsole operates very much like Tinn-R. I actually use Kate for all interpreters like Python, R, and Octave under linux. Tom Wade Wall wrote: Hi all, I know this question has been asked in the past, but I am wondering if anyone running R on Linux has any guidance as to a text editor that works well with R. At the present time I am running R on Windows and using TINN-R. For a number of reasons I want to switch to Linux, but can't find much in the way of a text editor in sync with R. Any experiences, recommendations would be appreciated. Wade Wall [[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. -- View this message in context: http://www.nabble.com/best-text-editor-for-Linux--tp15239201p15242799.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.html and provide commented, minimal, self-contained, reproducible code.
[R] Meaning of Error Message from decompose
Greetings, For the following quarterly data I did a classical decomposition by hand in a spreadsheet and got reasonably similar results using Minitab 15. x 1 36 2 44 3 45 4 106 5 38 6 46 7 47 8 112 9 42 10 49 11 48 12 118 13 42 14 50 15 51 16 118 Trying my luck with R, I tried to use the decompose function but it gives me the following: Error in decompose(data.t) : time series has no or less than 3 periods data.t is indeed a time series (is.ts returns true) and when I plot data.t it looks like a times series. Any suggestions on how to use decompose here (if it is the right function)? Thanks. Tom [[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] Problems with EMACS-ESS on Ubuntu
Yes indeed. As usual, I found the answer to my question shortly after I posted it to the forum. John Fox clearly describes this behavior in his paper An Introduction to ESS + XEmacs for Windows Users of R. I guess I was confused because the version of Emacs/ESS I installed on Windows (courtesy of Vincent Goulet) did not require me to confirm that I wanted to use R. Thanks everyone for the assistance. Tom Ben Bolker wrote: Tom La Bone booboo at gforcecable.com writes: I installed EMACS-ESS on Windows XP-Pro and it worked with R perfectly right out of the box. I was impressed with how easy it is to use (I normally use Tinn-R). I then switched over to Ubuntu 7.10 and installed EMACS-ESS. Everything worked the same as in Windows (which is my main reason for using EMACS) until I tried to send a line of code from the EMACS buffer to R -- R is running but the code just will not go to it. All I get is a line at the bottom of the editor window that says Process to load into: R. I am new to EMACS and did not see any fixes that looked promising in the ESS manual. Can anyone offer some suggestions on things to check? Thanks. Emacs just wants you to confirm which buffer the code is getting sent to (and the buffer called R is its default). The focus should automatically have gotten set to the mini-buffer at the bottom of the window, so if you just hit ENTER in response to this query everything should work fine! Ben Bolker __ 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. -- View this message in context: http://www.nabble.com/Problems-with-EMACS-ESS-on-Ubuntu-tp14492497p14497587.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.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] The R Book - great resource for R beginners
IMHO The R Book is far better than indicated in that review and should be near the top of the list for beginners looking for a manual for R. Tom Katharine Mullen wrote: It was reviewed in the most recent R News (http://www.r-project.org/doc/Rnews/Rnews_2007-2.pdf). On Thu, 29 Nov 2007, Robert Harris wrote: Hi all, I've recently discovered The R Book by Micheal J. Crawley. I am new to R and I am finding it incredibly useful. With my background in math and programming, I expected that I would be able to pick it up quickly, but even after reading several other intro books, I found it was still hard to figure out how to get data into R and how dataframes relate to vectors and actually doing statistics with R. But, The R Book is well written and gives plenty of examples and explains many of the often used tools within R. It's both a tutorial and a relatively advanced reference book for R, very accessible to a beginner like me. Just curious: What have been the experiences of others who have used The R Book? Thanks, Bob Harris - [[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. __ 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. -- View this message in context: http://www.nabble.com/Recommended-textbooks-for-R--tf4895638.html#a14039487 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.html and provide commented, minimal, self-contained, reproducible code.
[R] Linear Regression with lm Forcing the Slope to Equal 1
Is there a way to do a linear regression with lm (having one predictor variable) and constrain the slope of the line to equal 1? Tom -- View this message in context: http://www.nabble.com/Linear-Regression-with-lm-Forcing-the-Slope-to-Equal-1-tf4828804.html#a13815432 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.html and provide commented, minimal, self-contained, reproducible code.
[R] Bootstrap CI of Slope in a Weighted Simple Linear Regression
Greetings,
I would like to use the boot function to generate a bootstrap confidence
interval for the slope in a SLR that has a zero intercept. My attempt to do
this is shown below. Is this the correct implementation of the boot function
to solve this problem? In particular, should I be doing anything with the
residuals in the bs function (e.g., using weighted residuals)? Thanks for
the help.
X - c(0.875691867,0.871198003,0.814833892,0.788439976,0.738949275,
0.662589259,0.625487458,0.596570413,0.573693499,0.541569432,0.490628528,
0.440835275,0.397729163,0.358838088,0.323749892,0.24980067,0.213632079,
0.159989195,0.127709133,0.109218152,0.104276109,0.086467125,0.075718558,
0.059271067,0.05441905,0.049097803,0.044388138,0.014282204,0.004744354)
Y -
c(1.710091172,1.719901584,1.677683515,1.586374357,1.492977191,1.327498848,
1.301327304,1.25174086,1.149220115,1.130543366,0.974774745,0.912550499,0.752369319,
0.745150543,0.639280298,0.478799628,0.433639966,0.346051447,0.280818024,0.230285038,
0.201046915,0.179974417,0.163766453,0.102048289,0.75621,0.100711353,0.072401066,
0.023761328,0.013927331)
W - 1/X
fit - lm(Y ~ X - 1,weights=W)
Y.hat - predict(fit)
r - resid(fit)
data.df - as.data.frame(cbind(X,Y,W))
bs - function(data, indices) {
Y.b - Y.hat + r[indices]
fit.b - lm(Y.b ~ X - 1,weights=W)
return(coef(fit.b))}
results - boot(data=data.df, statistic=bs,R=1000)
boot.ci(results, type=perc, index=1)
--
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[R] lm.boot function gives error
When I run this calculation library(ISwR) library(simple.boot) data(thuesen) fit - lm(thuesen$short.velocity~thuesen$blood.glucose) summary(fit) fit.sb - lm.boot(fit,R=1000,rows=F) summary(fit.sb) I get the following error from the lm.boot routine: newdata' had 100 rows but variable(s) found have 24 rows I don't know what this error means. Also, this example is not vastly different than the one given in the simple.boot documentation and yet I can't get it to run. Any suggestions? Thanks. Tom -- View this message in context: http://www.nabble.com/lm.boot-function-gives-error-tf4714183.html#a13475530 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.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] In a SLR, Why Does the Hat Matrix Depend on the Weights?
Because it does. I should have looked ahead a few chapters in the book before I asked the question. However, I can't seem to reproduce the values of the hat matrix given by R for the weighted fit example I gave. Any suggestions (other than looking ahead a few more chapters)? Tom [[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.
[R] Documentation for Pearson Residuals
Greetings, I have been using lm to perform weighted linear regressions and resid to extract the residuals. I happened upon some class notes on the internet that described how one can specify type=pearson in resid to extract the weighted residuals. Where is this option documented? And if you know that, what is the best way to find such documentation if you don't know that the option exists? Thanks for the advice. Tom [[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.
