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Today's Topics:
1. line wrap in R console under windows (William Simpson)
2. lme for between-within anova (William Simpson)
3. Re: joined R-today (Liviu Andronic)
4. Package or packages for randomization in a clinical trial
(John Sorkin)
5. Re: joined R-today (Bala subramanian)
6. Sampling in R (Seyit Ali Kayis)
7. search through a matrix (onyourmark)
8. Re: bug when subtracting decimals? (Duncan Murdoch)
9. Re: search through a matrix (Uwe Ligges)
10. Re: Sampling in R (Uwe Ligges)
11. Odp: Sampling in R (Petr PIKAL)
12. Re: search through a matrix (Dimitris Rizopoulos)
13. Re: line wrap in R console under windows (Duncan Murdoch)
14. Re: Sampling in R (Mike Lawrence)
15. Re: Sampling in R: Please read my email from attached text.
(David Winsemius)
16. Re: Question on binomial data (David Winsemius)
17. Fix/Edit Error (Bronagh Grimes)
18. Re: joined R-today (Dimitri Liakhovitski)
19. Re: Random Forests: Question about R^2 (Liaw, Andy)
20. Re: Random Forests: Predictor importance for Regression Trees
(Liaw, Andy)
21. Re: joined R-today (Bala subramanian)
22. Re: Sampling in R (Jorge Ivan Velez)
23. Re: joined R-today (Bala subramanian)
24. rmysql fetch issues (Albert Vilella)
25. Re: search through a matrix (onyourmark)
26. Help with R 2.9.0 and XML (Luis Orlindo Tedeschi)
27. Re: search through a matrix (David Winsemius)
28. Re: search through a matrix (Kushantha Perera)
29. Re: search through a matrix (onyourmark)
30. Re: bug when subtracting decimals? (Marc Schwartz)
31. Re: automatic exploration of all possible loglinear models?
(Frank E Harrell Jr)
32. Re: Matrix package,solve() errors and crashes (Martin Maechler)
33. OT: Strange bootstrap approach to significance testing
(Mike Lawrence)
34. Re: search through a matrix (Dimitri Liakhovitski)
35. Re: Package or packages for randomization in a clinical trial
(Marc Schwartz)
36. Re: search through a matrix (David Winsemius)
37. Re: bug when subtracting decimals? (ivan valencia)
38. ncdf,RNetCDF (Bala subramanian)
39. Re: what is R best for? Evidence please. (John C Nash)
40. Re: Cross-Correlation function (CCF) issues (manta)
41. Re: ncdf,RNetCDF (Andris Jankevics)
42. Re: automatic exploration of all possible loglinear models?
(Ben Bolker)
43. Re: bug when subtracting decimals? (John C Nash)
44. broken example: lme() + multcomp() Tukey on repeated measures
design (William Simpson)
45. Re: joined R-today (Peter Dalgaard)
46. Re: broken example: lme() + multcomp() Tukey on repeated
measures design (Dieter Menne)
47. Re: broken example: lme() + multcomp() Tukey on repeated
measures design (David Winsemius)
48. Re: ncdf,RNetCDF (Bala subramanian)
49. Re: Cross-Correlation function (CCF) issues (David Winsemius)
50. ggplot2 - boxplot of variables / columns (Andreas Christoffersen)
51. Re: joined R-today (Marc Schwartz)
52. Re: joined R-today (Bala subramanian)
53. Re: Cross-Correlation function (CCF) issues (manta)
54. plotting with R (Bala subramanian)
55. Re: joined R-today (Marc Schwartz)
56. Re: ggplot2 - boxplot of variables / columns (ONKELINX, Thierry)
57. Re: Fitting linear models (Vemuri, Aparna)
58. Re: ggplot2 - boxplot of variables / columns (David Winsemius)
59. Re: Cross-Correlation function (CCF) issues (David Winsemius)
60. Re: plotting with R (David Winsemius)
61. Re: Fitting linear models (Dimitri Liakhovitski)
62. Re: plotting with R (Stephen J. Barr)
63. Re: Fitting linear models (Vemuri, Aparna)
64. Re: Fitting linear models (Dimitri Liakhovitski)
65. Re: Fitting linear models (Vemuri, Aparna)
66. Re: Fitting linear models (Dimitri Liakhovitski)
67. Re: Fitting linear models (David Winsemius)
68. Re: ggplot2 - boxplot of variables / columns
(Andreas Christoffersen)
69. Re: Fitting linear models (Vemuri, Aparna)
70. My surprising experience in trying out REvolution's R (Jason Liao)
71. Blanchard Quah/Impulse Response Functions (Laura Carvalho)
72. fitting assimptotic decaing with - and + on X (milton ruser)
73. Polyspline Integration (Denney, William S.)
74. DNAcopy package in R (Selena Niu)
75. Re: Fitting linear models (Dimitri Liakhovitski)
76. Re: Fitting linear models (Marc Schwartz)
77. Re: Fitting linear models (Vemuri, Aparna)
78. Re: bug when subtracting decimals? (hadley wickham)
79. Re: Fitting linear models (Dimitri Liakhovitski)
80. Re: Fitting linear models (Vemuri, Aparna)
81. Re: DNAcopy package in R (David Winsemius)
82. Re: Fitting linear models (David Winsemius)
83. Re: bug when subtracting decimals? (Sarah Goslee)
84. how to inspect content of save file (Benno P?tz)
85. Re: joined R-today [SELinux] (William Dunlap)
86. Re: how to inspect content of save file (Dimitri Liakhovitski)
87. Re: My surprising experience in trying out REvolution's R
(Bert Gunter)
88. Changing the binning of collected data (Lorenzo Isella)
89. Re: automatic exploration of all possible loglinear models?
(Christopher W. Ryan)
90. Re: My surprising experience in trying out REvolution's R
(David M Smith)
91. Re: Changing the binning of collected data (Luc Villandre)
92. Signed-Binary transform test (Fisher.test??) (Jorge Cornejo)
93. multiple plots in same graph window (BARRES-DE-ALMEIDA U.)
94. Re: Polyspline Integration (Denney, William S.)
95. Re: automatic exploration of all possible loglinear models?
(Dimitris Rizopoulos)
96. Re: multiple plots in same graph window (David Winsemius)
97. Quality control and possible QC in R book? (Erin Hodgess)
98. Re: Cross-Correlation function (CCF) issues (manta)
99. Re: create objects in a loop and adding sqlQuery content to
them (Katharina May)
100. plot with 2 y axes (Christophe Dutang)
101. Re: multiple plots in same graph window (William Dunlap)
102. Deleting rows or cols that do not meet cut off (Crosby, Jacy R)
103. Re: Cross-Correlation function (CCF) issues (David Winsemius)
104. Re: Deleting rows or cols that do not meet cut off
(Stephan Kolassa)
105. Re: Deleting rows or cols that do not meet cut off (Rolf Turner)
106. Re: plot with 2 y axes (Ben Bolker)
107. Re: Cross-Correlation function (CCF) issues (manta)
108. Re: Question on binomial data (ehud cohen)
109. Re: Cross-Correlation function (CCF) issues (David Winsemius)
110. Re: Deleting rows or cols that do not meet cut off
(Wacek Kusnierczyk)
111. Re: Cross-Correlation function (CCF) issues (manta)
112. Re: Deleting rows or cols that do not meet cut off
(Wacek Kusnierczyk)
113. Re: Deleting rows or cols that do not meet cut off
(Stephan Kolassa)
114. Re: Cross-Correlation function (CCF) issues (David Winsemius)
115. sas.get() exit (Nirav Mehta)
116. Re: Question on binomial data (David Winsemius)
117. Re: sas.get() exit (Nordlund, Dan (DSHS/RDA))
118. Re: sas.get() exit (Nirav Mehta)
119. Re: sas.get() exit (Nordlund, Dan (DSHS/RDA))
120. Re: sas.get() exit (Nirav Mehta)
121. anova table with lmer (Julien Beguin)
122. How to extract integer in a data frame (Gundala Viswanath)
123. error when using vcovHC() (oliviax)
124. Re: How to extract integer in a data frame (Marc Schwartz)
125. Re: How to extract integer in a data frame (Duncan Murdoch)
126. Re: How to compare parameters of non linear fitting curves
(spencerg)
127. using Rmath in c-functions of R packages (Volodymyr Melnykov)
128. Re: using Rmath in c-functions of R packages (Duncan Murdoch)
129. Re: Quality control and possible QC in R book? (C.H.)
130. Re: plotting with R (Erik Iverson)
131. memory.limit (Derek Stephen Elmerick)
132. Finding and moving files (Daniel Bradley)
133. Re: using Rmath in c-functions of R packages (Volodymyr Melnykov)
134. Re: Finding and moving files (Bill.Venables at csiro.au)
135. Color coded 3D plot (mauede at alice.it)
136. Re: Question on binomial data (ehud cohen)
137. Subsetting a vector of numerics such that standard deviation
is less than 0.5 ? (Daren Tan)
138. Re: search through a matrix (onyourmark)
139. Re: Color coded 3D plot (Kingsford Jones)
140. Re: Finding and moving files (Stephen J. Barr)
141. Re: My surprising experience in trying out REvolution's R
(Dieter Menne)
142. integrate lgamma from 0 to Inf (Andreas Wittmann)
143. Merging data frames, or one column/vector with a data frame
filling out empty rows with NA's (joe1985)
144. Copula package (Roslina Zakaria)
145. Re: automatic exploration of all possible loglinear models?
(bartjoosen)
146. Re: Copula package (Pfaff, Bernhard Dr.)
147. Re: Generate bivariate binomial data (ONKELINX, Thierry)
148. Intervention Time Series Analyis Tutorial/Package
(Dominik Hattrup)
149. Re: DNAcopy package in R (Ramon Diaz-Uriarte)
150. R: Color coded 3D plot (mauede at alice.it)
151. Better 'documenting' R? (Was: Re: bug when subtracting
decimals?) (Gavin Simpson)
152. converting histogram to barchart (Thomas Fr?jd)
153. Gee with nested desgin (ONKELINX, Thierry)
154. Re: how to inspect content of save file (Benno P?tz)
155. Re: broken example: lme() + multcomp() Tukey on repeated
measures design (William Simpson)
156. Re: plotting with R (baptiste auguie)
157. Re: Gee with nested desgin (Dimitris Rizopoulos)
158. Re: bug when subtracting decimals? (Martin Maechler)
159. Re: graph with 15 combinations (Jim Lemon)
160. Re: using Rmath in c-functions of R packages (Martin Maechler)
161. Re: SEM package (Jim Lemon)
----------------------------------------------------------------------
Message: 1
Date: Tue, 21 Apr 2009 11:03:52 +0100
From: William Simpson <william.a.simpson at gmail.com>
Subject: [R] line wrap in R console under windows
To: r-help at r-project.org
Message-ID:
<21ce39b20904210303h34a95282q122dc554cb7ca0de at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
I would like the R console to wrap lines at 80 cols.
It does not do so, even though I have used the Rgui Configuration
Editor to set the Console cols at 80 and the Pager cols at 80.
Please tell me how to set it up so I have word wrap.
Just to be clear: in older/other R versions, console input is wrapped
at 80 cols and so you have something that looks like
blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah
blah blah blah blah blah blah blah blah blah blah blah blah blah blah
blah blah blah blah
Instead of what I see, which is
blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah blah$
and I need to scroll sideways to see the rest of the stuff past $
I checked the archives and saw no postings on this.
Thanks very much for any help.
Bill
------------------------------
Message: 2
Date: Tue, 21 Apr 2009 11:10:10 +0100
From: William Simpson <william.a.simpson at gmail.com>
Subject: [R] lme for between-within anova
To: r-help at r-project.org
Message-ID:
<21ce39b20904210310i139a53berd38642cddd13038a at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
I have the following between-within anova:
aovn1 <- aov(amplitude ~ stereo*site*stimulus +
Error(subject/(site*stimulus)), stereon1)
This works fine. BUT I need to do Tukey HSD multiple comparisons, and
the aov() approach won't work. So I am trying the method posted on
r-help:
lmen1 <- lme(amplitude ~ stereo*site*stimulus, random =
~1|subject/(site*stimulus), stereon1)
This doesn't work:
lmen1 <- lme(amplitude ~ stereo*site*stimulus, random = ~1|subject/(site*stimulus), stereon1)
Error in getGroups.data.frame(dataMix, groups) :
Invalid formula for groups
Please tell me what to do to get the lme() fit to work.
After I get lmen1, I will do:
anova(lmen1)
summary(lmen1)
summary(glht(lmen1, linfct=mcp(V="Tukey")))
Please tell me if that sounds right.
Thanks very much for any help!
Bill
============= This is the example I am following (with modifications
for my expt design)
You want to use lme() in package nlme, then glht() in the multcomp
package. This will give you multiplicity adjusted p-values and
confidence intervals.
## Example
require(MASS) ## for oats data set
require(nlme) ## for lme()
require(multcomp) ## for multiple comparison stuff
Aov.mod <- aov(Y ~ N + V + Error(B/V), data = oats)
Lme.mod <- lme(Y ~ N + V, random = ~1 | B/V, data = oats)
summary(Aov.mod)
anova(Lme.mod)
summary(Lme.mod)
summary(glht(Lme.mod, linfct=mcp(V="Tukey")))
------------------------------
Message: 3
Date: Tue, 21 Apr 2009 12:12:34 +0200
From: Liviu Andronic <landronimirc at gmail.com>
Subject: Re: [R] joined R-today
To: Bala subramanian <bala.biophysics at gmail.com>
Cc: r-help at r-project.org
Message-ID:
<68b1e2610904210312g651337b6v3c4d0d29d0bd41df at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
On Tue, Apr 21, 2009 at 11:57 AM, Bala subramanian
<bala.biophysics at gmail.com> wrote:
Dear Simon,
I installed the ncdf package in the way you suggested but still i got the
same error i got before. I haves pasted below the installation log and
errors.
Does ncdf depend on netcdf [1]? If so, perhaps it is missing, or is
not up-to-date. Also, it's a good habit to install.packages('ncdf',
dep=TRUE).
Regards,
Liviu
[1] http://www.unidata.ucar.edu/software/netcdf/
------------------------------
Message: 4
Date: Tue, 21 Apr 2009 06:12:32 -0400
From: "John Sorkin" <jsorkin at grecc.umaryland.edu>
Subject: [R] Package or packages for randomization in a clinical trial
To: <r-help at r-project.org>
Message-ID: <49ED63CE.91DF.00CB.0 at grecc.umaryland.edu>
Content-Type: text/plain; charset=US-ASCII
Can anyone recommend a package that can be used to randomize subjects? I am looking for a generalized package, or several packages that can accomplish
unrestricted randomization (i.e. simple random assignment)
restricted randomization including stratified randomization, blocked randomization, and adaptive randomization.
Thanks,
John
John David Sorkin M.D., Ph.D.
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing)
Confidentiality Statement:
This email message, including any attachments, is for th...{{dropped:6}}
------------------------------
Message: 5
Date: Tue, 21 Apr 2009 12:21:09 +0200
From: Bala subramanian <bala.biophysics at gmail.com>
Subject: Re: [R] joined R-today
To: Liviu Andronic <landronimirc at gmail.com>
Cc: r-help at r-project.org
Message-ID:
<288df32a0904210321l64d25470yea9aef47c5859221 at mail.gmail.com>
Content-Type: text/plain
Hi,
Yes ncdf needs netcdf, netcdf is already installed in my fedora10. I
reinstalled ncdf with the following option
install.packages('ncdf',dep=TRUE)
library(ncdf)> library(ncdf)
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared library '/usr/lib/R/library/ncdf/libs/ncdf.so':
/usr/lib/R/library/ncdf/libs/ncdf.so: cannot restore segment prot after
reloc: Permission denied
Error in library(ncdf) : .First.lib failed for 'ncdf'
Again the same error,
Bala
On Tue, Apr 21, 2009 at 12:12 PM, Liviu Andronic <landronimirc at gmail.com>wrote:
On Tue, Apr 21, 2009 at 11:57 AM, Bala subramanian
<bala.biophysics at gmail.com> wrote:
Dear Simon,
I installed the ncdf package in the way you suggested but still i got the
same error i got before. I haves pasted below the installation log and
errors.
Does ncdf depend on netcdf [1]? If so, perhaps it is missing, or is
not up-to-date. Also, it's a good habit to install.packages('ncdf',
dep=TRUE).
Regards,
Liviu
[1] http://www.unidata.ucar.edu/software/netcdf/
[[alternative HTML version deleted]]
------------------------------
Message: 6
Date: Tue, 21 Apr 2009 22:25:01 +1200
From: Seyit Ali Kayis <s_a_kayis at hotmail.com>
Subject: [R] Sampling in R
To: <r-help at r-project.org>
Message-ID: <BAY105-W34886F283B2E531D6C5844B4770 at phx.gbl>
Content-Type: text/plain
Dear R users,
I need to do sampling without replacement (bootstraps). I have two variables (Xvar, Yvar).
I have a correlation from original data set cor(Xvar, Yvar)=0.6174221. I am doing 50000 sampling,
and in each sampling calculating correlations, saving, sorting and getting 95% cutt off point (0.1351877).
I am getting maximum value as 0.3507219 (much smaller than correlation of my original data).
I repeated the sampling a couple of time and none of them produced a correlation
coefficient higher than my original data set. However, if I sort out my Xvar and Yvar and
obtain correlation it is 0.9657125 which is much higher than correlation for my original data.
I am doing sampling in another program and getting at least 1% higher correlation than mine.
Now I am getting confused with sampling(random data) in R. My data and codes for the scenario above are below
Xvar<-c(0.1818182,0.5384615,0.5535714,0.4680851,0.4545455,0.4385965,0.5185185,0.4035088,0.4901961,0.3650794,0.462963,0.4,0.56,0.3965517,0.4909091,
0.4716981,0.4310345,0.2,0.1509434,0.2647059,0.173913,0.1914894,0.1914894,0.1489362,0.1363636,0.2244898,0.2325581,0.1333333,0.1818182,0.1702128,
0.2173913,0.2380952,0.1632653,0.5614035,0.3396226,0.4909091,0.3770492,0.5,0.5185185,0.5,0.4666667,0.4464286,0.362069,0.4285714,0.4561404,
0.4736842,0.4545455,0.4166667,0.4181818,0.4590164,0.5166667,0.5423729,0.4833333,0.5454545,0.4393939,0.5172414,0.4098361,0.4745763,0.4754098,
0.5166667,0.5,0.4603175,0.42,0.4038462,0.4897959,0.3148148,0.3673469,0.4,0.4583333,0.3877551,0.4375,0.4117647,0.4313725,0.5333333,0.3962264,
0.3548387,0.5272727,0.4137931,0.3928571,0.4666667,0.4210526,0.4363636,0.4545455,0.4310345,0.4237288,0.4814815,0.4912281,0.4333333,0.4,0.4285714,
0.4516129,0.5090909,0.4464286,0.4642857,0.4166667,0.4098361,0.4909091,0.3809524,0.5272727,0.4814815,0.5254237,0.627451,0.5,0.5471698,0.5454545,
0.5925926,0.5769231,0.5818182,0.4444444,0.4915254,0.4727273,0.4107143,0.4285714,0.4310345,0.4237288,0.4285714,0.440678,0.4237288,0.4807692,
0.4150943,0.4615385,0.4107143,0.4814815,0.4074074,0.4210526,0.5263158,0.440678,0.4576271,0.5344828,0.5,0.5636364,0.4677419,0.5,0.5192308,
0.4642857,0.5090909,0.58,0.4482759,0.5098039,0.4035088,0.4210526,0.5098039,0.4385965,0.5283019,0.5471698,0.625,0.4310345,0.4912281,0.5283019,
0.4576271,0.5471698,0.4745763,0.4821429)
Yvar<-c(0.2553191,0.4107143,0.5660377,0.3888889,0.3606557,0.2898551,0.3818182,0.4,0.4,0.3278689,0.2903226,0.4074074,0.4181818,0.3,0.2238806,0.3728814,
0.3709677,0.2307692,0.2830189,0.2244898,0.2142857,0.2131148,0.22,0.2258065,0.2321429,0.2,0.2264151,0.22,0.2115385,0.2459016,0.1166667,0.1785714,
0.2068966,0.6,0.4285714,0.3134328,0.4461538,0.3965517,0.4769231,0.6181818,0.4827586,0.3709677,0.3965517,0.4821429,0.4545455,0.359375,0.4576271,
0.4516129,0.5272727,0.4603175,0.4,0.4912281,0.5384615,0.5,0.4516129,0.4126984,0.4655172,0.5263158,0.4925373,0.358209,0.4285714,0.4920635,
0.4482759,0.3235294,0.4,0.4375,0.440678,0.3898305,0.35,0.4528302,0.58,0.4153846,0.3174603,0.5185185,0.3870968,0.2894737,0.3709677,0.369863,
0.3676471,0.3636364,0.3088235,0.328125,0.4032258,0.4084507,0.3188406,0.3636364,0.3823529,0.2816901,0.4722222,0.5,0.3521127,0.4393939,0.3787879,
0.453125,0.4324324,0.4057971,0.4545455,0.4492754,0.5,0.4098361,0.4067797,0.3666667,0.3928571,0.4285714,0.5,0.2923077,0.4561404,0.45,0.5538462,
0.4626866,0.4057971,0.3676471,0.5322581,0.5428571,0.375,0.4411765,0.4571429,0.4,0.3846154,0.3870968,0.4915254,0.530303,0.4375,0.4918033,0.4179104,
0.4032258,0.3606557,0.5178571,0.4848485,0.390625,0.375,0.4375,0.3666667,0.4,0.4477612,0.2571429,0.4032258,0.3382353,0.4814815,0.4090909,0.3548387,
0.4821429,0.5,0.557377,0.4333333,0.5454545,0.4590164,0.3943662,0.5076923,0.5,0.3283582,0.3676471,0.559322)
my.cor<-cor(Xvar, Yvar)
print(my.cor)
nperm<-49999
Perm.Cor<-NULL
for (iperm in 1:nperm) {
XvarNew<-sample(Xvar, size=length(Xvar), replace=FALSE)
YvarNew<-sample(Yvar, size=length(Yvar), replace=FALSE)
perm.cor<-cor(XvarNew, YvarNew)
Perm.Cor<-c(Perm.Cor, perm.cor)
}
print(max(Perm.Cor))
XvarSorted<-sort(Xvar, decreasing=TRUE)
YvarSorted<-sort(Yvar, decreasing=TRUE)
max.cor<-cor(XvarSorted, YvarSorted)
print(max.cor)
if(mat.cor>0) Perm.Cor.Sorted<-sort(Perm.Cor, decreasing=TRUE)
if(mat.cor<0) Perm.Cor.Sorted<-sort(Perm.Cor, decreasing=FALSE)
T95<-Perm.Cor.Sorted[(nperm+1)*0.05] # 95% treshold value
T99<-Perm.Cor.Sorted[(nperm+1)*0.01] # 99% treshold value
I want to understand where I am making a mistake. Any comment is deeply appreciated.
Kind Regards
Seyit Ali
------------------------------------------------------------------------------------------------------------------
Dr. Seyit Ali KAYIS
Selcuk University
Faculty of Agriculture
Kampus, Konya, TURKEY
s_a_kayis at yahoo.com, s_a_kayis at hotmail.com
Tell: +90 332 223 2830 Mobile: +90 535 587 1139 Fax: +90 332 241 0108
Greetings from Konya, TURKEY
http://www.ziraat.selcuk.edu.tr/skayis/
----------------------------------------------------------------------------------------------------------------------
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Message: 7
Date: Tue, 21 Apr 2009 03:52:57 -0700 (PDT)
From: onyourmark <william108 at gmail.com>
Subject: [R] search through a matrix
To: r-help at r-project.org
Message-ID: <23153538.post at talk.nabble.com>
Content-Type: text/plain; charset=us-ascii
Hi. I have a 925 by 925 correlation matrix corM. I want to identify all
variables that have correlation greater than 0.9. Can anyone suggest an "R
way" of doing this?
Thank you.