Re: [R] [R-sig-ME] different results from lme and lmer function
These actually aren't terribly different from each other. I suspect that lmer is slightly closer to the correct answer, because lme reports a log-likelihood (really -1/2 times the REML criterion) of 49.30021, while lmer reports a REML criterion of -98.8 - slightly better fit at -R/2 = 49.4. The residual sds are 0.0447 (lme) vs. 0.0442 (lmer); the intercept sd estimate is 0.016 vs 0.0089, admittedly a bit low, and both month sds are very small. lmer indicates a singular fit (correlation of -1).If you look at the confidence intervals on these estimates (confint(fitted_model) in lme4; intervals(fitted_model) in lme) I think you'll find that the confidence intervals are much wider than these differences (you may even find that lme reports that it can't give you the intervals because the Hessian [curvature] matrix is not positive definite). Both should be comparable to SAS PROC MIXED results, I think, if you get the syntax right ... On Tue, May 26, 2015 at 7:09 PM, li li hannah@gmail.com wrote: Hi all, I am fitting a random slope and random intercept model using R. I used both lme and lmer funciton for the same model. However I got different results as shown below (different variance component estimates and so on). I think that is really confusing. They should produce close results. Anyone has any thoughts or suggestions. Also, which one should be comparable to sas results? Thanks! Hanna ## using lme function mod_lme - lme(ti ~ type*months, random=~ 1+months|lot, na.action=na.omit, + data=one, control = lmeControl(opt = optim)) summary(mod_lme) Linear mixed-effects model fit by REML Data: one AIC BIC logLik -82.60042 -70.15763 49.30021 Random effects: Formula: ~1 + months | lot Structure: General positive-definite, Log-Cholesky parametrization StdDev Corr (Intercept) 8.907584e-03 (Intr) months 6.039781e-05 -0.096 Residual4.471243e-02 Fixed effects: ti ~ type * months Value Std.Error DF t-value p-value (Intercept) 0.25831245 0.016891587 31 15.292373 0. type0.13502089 0.026676101 4 5.061493 0.0072 months 0.00804790 0.001218941 31 6.602368 0. type:months -0.00693679 0.002981859 31 -2.326329 0.0267 Correlation: (Intr) typPPQ months type -0.633 months -0.785 0.497 type:months 0.321 -0.762 -0.409 Standardized Within-Group Residuals: MinQ1 MedQ3 Max -2.162856e+00 -1.962972e-01 -2.771184e-05 3.749035e-01 2.088392e+00 Number of Observations: 39 Number of Groups: 6 ###Using lmer function mod_lmer -lmer(ti ~ type*months+(1+months|lot), na.action=na.omit, data=one) summary(mod_lmer) Linear mixed model fit by REML t-tests use Satterthwaite approximations to degrees of freedom [merModLmerTest] Formula: ti ~ type * months + (1 + months | lot) Data: one REML criterion at convergence: -98.8 Scaled residuals: Min 1Q Median 3Q Max -2.1347 -0.2156 -0.0067 0.3615 2.0840 Random effects: Groups NameVariance Std.Dev. Corr lot (Intercept) 2.870e-04 0.0169424 months 4.135e-07 0.0006431 -1.00 Residual 1.950e-03 0.0441644 Number of obs: 39, groups: lot, 6 Fixed effects: Estimate Std. Errordf t value Pr(|t|) (Intercept) 0.258312 0.018661 4.82 13.842 4.59e-05 *** type 0.135021 0.028880 6.802000 4.675 0.00245 ** months 0.008048 0.001259 11.943000 6.390 3.53e-05 *** type:months -0.006937 0.002991 28.91 -2.319 0.02767 * --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Correlation of Fixed Effects: (Intr) typPPQ months type -0.646 months -0.825 0.533 type:month 0.347 -0.768 -0.421 ___ r-sig-mixed-mod...@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] lme function to obtain pvalue for fixed effect
li li hannah.hlx at gmail.com writes: Hi all, I am using the lme function to run a random coefficient model. Please see output (mod1) as below. Please don't cross-post to different R lists (this is explicitly deprecated by the list policy: http://www.r-project.org/mail.html, cross-posting is considered to be impolite). r-sig-mixed-models seems to be more appropriate for these questions. sincerely Ben Bolker __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] [R-sig-ME] different results from lme and lmer function
Ben, I doubt the very small difference in log likelihood gives much, if any information about which model is a better fit. Even if we overlook the limited precision of the estimate of the REML criterion, the difference is so small as to me of minimal importance. John John David Sorkin M.D., Ph.D. Professor of Medicine Chief, Biostatistics and Informatics University of Maryland School of Medicine Division of Gerontology and Geriatric Medicine 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) On May 26, 2015, at 8:03 PM, Ben Bolker bbol...@gmail.com wrote: These actually aren't terribly different from each other. I suspect that lmer is slightly closer to the correct answer, because lme reports a log-likelihood (really -1/2 times the REML criterion) of 49.30021, while lmer reports a REML criterion of -98.8 - slightly better fit at -R/2 = 49.4. The residual sds are 0.0447 (lme) vs. 0.0442 (lmer); the intercept sd estimate is 0.016 vs 0.0089, admittedly a bit low, and both month sds are very small. lmer indicates a singular fit (correlation of -1).If you look at the confidence intervals on these estimates (confint(fitted_model) in lme4; intervals(fitted_model) in lme) I think you'll find that the confidence intervals are much wider than these differences (you may even find that lme reports that it can't give you the intervals because the Hessian [curvature] matrix is not positive definite). Both should be comparable to SAS PROC MIXED results, I think, if you get the syntax right ... On Tue, May 26, 2015 at 7:09 PM, li li hannah@gmail.com wrote: Hi all, I am fitting a random slope and random intercept model using R. I used both lme and lmer funciton for the same model. However I got different results as shown below (different variance component estimates and so on). I think that is really confusing. They should produce close results. Anyone has any thoughts or suggestions. Also, which one should be comparable to sas results? Thanks! Hanna ## using lme function mod_lme - lme(ti ~ type*months, random=~ 1+months|lot, na.action=na.omit, + data=one, control = lmeControl(opt = optim)) summary(mod_lme) Linear mixed-effects model fit by REML Data: one AIC BIC logLik -82.60042 -70.15763 49.30021 Random effects: Formula: ~1 + months | lot Structure: General positive-definite, Log-Cholesky parametrization StdDev Corr (Intercept) 8.907584e-03 (Intr) months 6.039781e-05 -0.096 Residual4.471243e-02 Fixed effects: ti ~ type * months Value Std.Error DF t-value p-value (Intercept) 0.25831245 0.016891587 31 15.292373 0. type0.13502089 0.026676101 4 5.061493 0.0072 months 0.00804790 0.001218941 31 6.602368 0. type:months -0.00693679 0.002981859 31 -2.326329 0.0267 Correlation: (Intr) typPPQ months type -0.633 months -0.785 0.497 type:months 0.321 -0.762 -0.409 Standardized Within-Group Residuals: MinQ1 MedQ3 Max -2.162856e+00 -1.962972e-01 -2.771184e-05 3.749035e-01 2.088392e+00 Number of Observations: 39 Number of Groups: 6 ###Using lmer function mod_lmer -lmer(ti ~ type*months+(1+months|lot), na.action=na.omit, data=one) summary(mod_lmer) Linear mixed model fit by REML t-tests use Satterthwaite approximations to degrees of freedom [merModLmerTest] Formula: ti ~ type * months + (1 + months | lot) Data: one REML criterion at convergence: -98.8 Scaled residuals: Min 1Q Median 3Q Max -2.1347 -0.2156 -0.0067 0. lot (Intercept) 2.870e-04 0.0169424 months 4.135e-07 0.0006431 -1.00 Residual 1.950e-03 0.0441644 Number of obs: 39, groups: lot, 6 Fixed effects: Estimate Std. Errordf t value Pr(|t|) (Intercept) 0.258312 0.018661 4.82 13.842 4.59e-05 *** type 0.135021 0.028880 6.802000 4.675 0.00245 ** months 0.008048 0.001259 11.943000 6.390 3.53e-05 *** type:months -0.006937 0.002991 28.91 -2.319 0.02767 * --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Correlation of Fixed Effects: (Intr) typPPQ months type -0.646 months -0.825 0.533 type:month 0.347 -0.768 -0.421 ___ r-sig-mixed-mod...@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained,
[R] Find and replace backslashes XXXX
Hi all, I realize that the backslash is an escape character in R, therefore, I am trying to replace it with a forward slash. Can someone please suggest how to get this code to work? lib-gsub(\,/,X:\Classes\TT\Automation) Error: unexpected symbol in lib-gsub(\,/,X Thanks, Dan __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Find and replace backslashes XXXX
Escape the backslash with another backslash, i.e., gsub(\\,/,X:\\Classes\\TT\\Automation, fixed = TRUE) best, Ista On Tue, May 26, 2015 at 9:30 PM, Dan Abner dan.abne...@gmail.com wrote: Hi all, I realize that the backslash is an escape character in R, therefore, I am trying to replace it with a forward slash. Can someone please suggest how to get this code to work? lib-gsub(\,/,X:\Classes\TT\Automation) Error: unexpected symbol in lib-gsub(\,/,X Thanks, Dan __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] nls model singular gradient matrix at initial parameter estimates
Greetings,
I'm trying to use the nls function in my statistics project but I'm really
finding lot of difficulties.
I have a function called apinene_modele_prediction that calculates the
estimations:
library(expm); #exp of a matrixapinene_modele_prediction - function(t,theta) {
x0=c(100,0,0,0,0)
A=matrix(c(-(theta[1]+theta[2]),theta[1],theta[2],0,0,0,0,0,0,0,0,0,-(theta[3]+theta[4]),theta[3],theta[4],0,0,0,0,0,0,0,theta[5],0,-theta[5]),5,5)
X=x0for (i in t[2:length(t)]){ X=c(X,x0%*%expm(A*i))
}return(X)}
My t vector is given by:
t=seq(0,100,by=2)
And the real observations y ara given to us in a txt file called data.txt
that I have joined to this message.
So when I try to fit the theta in my model starting with:
theta=c(0.2,0.2,0.2,0.2,0.2)
And doing:
theta_appr
-nls(y~apinene_modele_prediction(t,theta),start=list(theta=c(0.2,0.2,0.2,0.2,0.2)))
I always got the ERROR : singular gradient matrix at initial parameter estimates
And, when I try:
nls(y~apinene_modele_prediction(t,c(theta,theta,theta,theta,theta)),start=list(theta=0.2))
I got the result: Nonlinear regression model model: y ~
apinene_modele_prediction(t, c(theta, theta, theta, theta, theta)) data:
parent.frame() theta0.04403 residual sum-of-squares: 219002
But I need to have the elements of the theta to be different and not equal.
Thanks in advance for your help. y
99.9232
5.7485
0.6644
-0.4988
0.5019
83.3796
16.0905
3.4184
-0.1619
4.3231
67.6461
17.6714
6.1861
0.4555
3.4022
58.3199
24.0947
7.009
1.3153
7.0712
47.587
35.4656
6.4072
0.715
9.0156
42.3778
34.0976
6.0112
1.0316
14.0637
34.4176
38.188
6.0135
0.8093
14.7598
29.2941
56.7453
5.7462
1.24
15.5634
24.2075
49.4543
4.8968
1.3849
21.834
21.2213
51.3734
5.2268
1.7867
19.4716
18.9238
55.3147
4.5223
2.6202
22.053
13.9119
65.6723
4.4736
2.4025
20.5307
14.0519
64.1892
4.3354
2.6657
23.0909
9.6691
62.9989
4.8074
3.1438
20.2343
8.018
59.7792
3.9934
2.7481
23.0476
7.6965
58.3577
3.6449
3.8192
25.8571
5.7062
54.7404
4.2607
3.1089
25.4888
5.6596
58.5899
3.6794
3.541
25.3896
5.4871
65.4693
3.6679
3.5918
25.7453
2.5278
70.9596
3.933
3.8858
22.8982
5.3682
74.6359
3.7192
4.1048
25.37
3.159
66.7303
3.3373
4.0423
25.6204
-0.3612
72.2608
3.9413
4.9181
22.8085
3.1431
68.0772
3.5597
4.5132
22.3135
0.7453
66.8462
3.9621
4.1373
25.5405
0.8502
63.7415
3.8063
4.9193
24.9146
1.4089
71.1166
3.7259
4.2357
21.76
1.7045
71.7744
3.3515
4.899
23.7245
0.6204
61.9383
3.8477
5.561
22.3485
0.3335
63.1572
3.3009
5.7315
26.3752
1.6638
62.4002
3.1931
5.2699
23.3077
1.7851
66.0386
3.3138
5.79
25.2986
0.3481
61.4702
3.3343
5.6509
22.9967
0.088
59.5469
3.2485
5.9959
21.0902
-0.9691
70.1917
3.3433
5.8771
27.0169
-0.1861
66.933
3.1346
6.0566
20.7277
1.1325
74.0641
3.7472
6.0475
22.177
1.7875
61.0552
3.1733
5.8029
18.2692
-0.6303
69.7692
3.3849
6.6513
22.7722
0.8757
62.7373
2.7142
6.6476
20.6708
-0.5705
61.1083
3.4895
6.077
23.3414
-0.3324
69.8406
3.1186
6.6764
22.7215
0.2536
63.2522
3.2815
7.3864
21.1594
-1.1912
65.0752
3.2217
5.9924
23.3834
0.3408
68.4797
2.7571
6.9196
21.9287
0.6937
75.7468
3.6325
7.5853
21.6415
1.6548
70.4596
2.7858
6.9878
25.7793
-0.2572
73.3611
3.0593
7.6976
21.6229
1.5903
72.4284
2.8289
8.1584
25.5773
-0.5075
63.7588
3.3313
8.1676
23.3128
-0.836
71.0337
3.1666
7.638
20.2517
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[R] Retrieving data from nested lists
Dear R users, I have a question regarding retrieving data from nested lists. To illustrate, here is an example input: d1-data.table(v1=c(3,4),v2=c(2,5)) d2-data.table(v1=c(1,2),v2=c(1,1))l1-list(d1,name=test)l2-list(d2,name=test2)motherlist-list()motherlist$l1-l1motherlist$l2-l2 Let's say we are given motherlist as above. We would like to get the union of the contents of v1 vector from d1 data.table and the v1 vector from d2 data.table. How can we achieve this in a compact one line command using motherlist as input please? Thank you. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Problem merging data frames and duplicates
Hello All, I am attempting to merge two data frames that naturally contain duplicate entries, however when using either merge or dMerge I get even more duplicates. For example: data.frame(state=c(IL, IL, LA,LA, MS,MS, AR, AR), locus=c(1,1,2,2,3,4,5,6))-x data.frame(state=c(IL, IL, AR, AR, TN,TN), locus=c(1,1,2,3,3,4,4))-y These yield: x state locus 1IL 1 2IL 1 3LA 2 4LA 2 5MS 3 6MS 4 7AR 5 8AR 6 y state locus 1IL 1 2IL 1 3AR 2 4AR 3 5TN 3 6TN 4 However, when merged by state: they produce another second set of AR and IL: merge(x,y,by=1,all=T)-z state locus.x locus.y 1 AR 5 2 2 AR 5 3 3 AR 6 2 4 AR 6 3 5 IL 1 1 6 IL 1 1 7 IL 1 1 8 IL 1 1 9 LA 2 NA 10LA 2 NA 11MS 3 NA 12MS 4 NA 13TN NA 3 14TN NA 4 While, the NAs are desired when states are missing, I don't want the extra duplicated states and values but rather: state locus.x locus.y 1 AR 5 2 4 AR 6 3 7 IL 1 1 8 IL 1 1 9 LA 2 NA 10LA 2 NA 11MS 3 NA 12MS 4 NA 13TN NA 3 14TN NA 4 Any help would be much appreciated. Thanks! Frank -- * *Frank T. Burbrink, Ph.D.* *Professor* *Biology Department* *6S-143* *2800 Victory Blvd.* *College of Staten Island/CUNY* *Staten Island, New York 10314* *E-Mail:frank.burbr...@csi.cuny.edu e-mail%3afrank.burbr...@csi.cuny.edu* *Phone:718-982-3961* *Web Page: http://scholar.library.csi.cuny.edu/~fburbrink/ http://scholar.library.csi.cuny.edu/%7Efburbrink/* * *Chair * *Ecology, Evolutionary Biology, and Behavior* *Doctoral Subprogram* *Biology Program* *City University of New York * *Graduate Center* *365 Fifth Avenue* *New York, NY 10016-4309* [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem with comparing multiple data sets
Thank you John. Yes. as you mentioned this is not really what I am looking for. It's interesting because I was really thinking that it should be pretty easy. All I need to do is just compare class1, class2 and class3 for each text and put the most frequent number next to it in each row. Repeat it for all the rows. Apparently it's not that simple. Sorry I didn't notice that I sent it only to you! Thanks for letting me know. I appreciate if anybody can help on this. Thank you. On Tue, May 26, 2015 at 7:27 PM, John Kane jrkrid...@inbox.com wrote: Hi Mohammad, The data came through beautifully despite the fact that you posted in HTML. Please, post in plain text. Oh, just as I was ready to push Send, I noticed you only replied to me. You really should reply to the R-help list since there are a lot more and better people to help there. Besides it's a world-wide list. Others can play with the problem while we sleep :) . I will just reply to you but I really suggest sending all of this to the list. Now I am wondering what to do with the data. As a first swipe I just added up all the values in each class by each text value. Results are below. Not what you want by any means but perhaps a small step. Then I started to think are we really interested in the sum or should we be looking at incidence, that is should we be looking at the frequency rather than the sum? Is class.1 class.2 class #dac 0 2 0 a value of 2 (sum) or a hit of 1 (count or freq) ? Anyway below is what I have tried so far -- it may not be anywhere near what you want but if it makes any sense then I think we just need to pick off the highest values for each combination of terms and class to give you what you want. I suspect our real data-munging gurus can do all this faster and better than I can but hopefully it is a start. Where your data set is dat1 #= # If reshape2 is not installed. install.packages(reshape2) #= library(reshape2) mdat - melt(dat1, id.vars= c(terms), variable.name = class, value.name = value, na.rm = FALSE) mdat1 - aggregate(value ~ terms + class, data = mdat, sum) mdat1[order(mdat1$terms, mdat1$class), ] #= John Kane Kingston ON Canada -Original Message- From: mxalimoha...@ualr.edu Sent: Tue, 26 May 2015 09:50:43 -0500 To: jrkrid...@inbox.com Subject: Re: [R] Problem with comparing multiple data sets Thank you John for being patient with me. My original post was to compare 3 sets of data which had difference in their class value for the same text. However, I thought it might be easier to combine those 3 data sets into one that shows the 3 different classes and then find the most frequent class value for the text. So that's what I did. Now I only want to add the most frequent class value in a new column. I tried to create a dput version of the data set (Only a small part of it) so you can see. I hope it works. Tweet1- read.csv(file=part1_complete.csv,head=TRUE,sep= ,) dput(head(Tweet1, 100)) structure(list(class.1 = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 2L, 1L, 1L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 1L, 2L, 0L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 0L, 2L, 2L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 2L), class.2 = c(2L, 2L, 2L, 2L, 0L, 0L, 2L, 0L, 0L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 2L, 0L, 2L, 2L, 2L, 1L, 1L, 2L, 2L, 0L, 0L, 0L, 0L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 0L, 1L, 1L, 0L, 0L, 1L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 0L, 0L, 1L, 0L, 0L, 1L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), class.3 = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 2L, 1L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 2L, 1L, 2L, 0L, 2L, 2L, 0L, 2L, 1L, 1L, 1L, 1L, 0L, 0L, 0L, 2L, 1L, 0L, 0L, 1L, 0L, 0L, 2L, 2L, 2L, 2L, 2L, 0L, 2L, 2L, 1L, 0L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 2L), terms = structure(c(9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 69L, 69L, 69L, 69L, 69L, 40L, 40L, 40L, 40L, 15L, 15L, 15L, 15L, 15L, 15L, 15L, 15L, 98L, 98L, 98L, 98L, 98L, 98L, 98L, 98L, 98L, 98L, 98L, 98L, 98L, 98L, 23L, 87L, 87L, 87L, 87L, 87L, 87L, 87L, 87L, 87L, 87L, 87L, 87L, 87L, 87L, 87L, 87L, 87L, 87L, 87L, 87L, 87L, 87L, 87L, 87L, 87L, 87L, 87L, 87L, 87L, 87L, 87L), .Label =
[R] X11 font problem
Hi I have this problem and do not know how to solve it, I'm new to R R version 2.15.0 (2012-03-30) Copyright (C) 2012 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: x86_64-unknown-linux-gnu (64-bit) x11 font -adobe-helvetica-%s-%s-*-*-%d-*-*-*-*-*-*-*, face 1 at size 16 could not be loaded [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Path analysis
Hi there, As I'm approaching path analysis I was wondering which packages may suite a path analysis for my data. My data are on interaction of soil biotic and abiotic factor, like microbial biomass carbon, soil carbon, water content, temperature etc. Thanks in advance, Best regards. Alberto Alberto Canarini PhD Student l Faculty of Agriculture and Environment THE UNIVERSITY OF SYDNEY Shared room l CCWF l Camden Campus l NSW 2570 P 02 935 11892 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to pass a variable to a function which use variable name as a parameter
There are functions which use variable names as parameters in some R
packages. However, if the variable name is stored in another variable, how
can I pass this variable to the function. Taking the rms package as an
example:
library(rms)
n - 1000
age - rnorm(n, 50, 10)
sex - factor(sample(c('female','male'), n,TRUE))
y - rnorm(n, 200, 25)
ddist - datadist(age, sex)
options(datadist='ddist')
fit - lrm(y ~ age)
Predict(fit, age, np=4)
options(datadist=NULL)
Here age was a variable name passed to Predict() function, but if age
was stored in variable var, that is, var - age, how can I pass var
to Predict() function? The purpose is that I want to change the parameter
of Predict() in a loop.
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[R] png package in Ubuntu 12.04 with R 3.1.0
Dear All, I am using R to analyse computer simulations of ligand docking in a protein. I am plotting the results as scatterplots and bopxplots, using the code below. This works perfectly fine. I would like now to add a png file to that plot, meaning I want sth like: png(file=analysis.png) par(mfrow=c(1,3), oma=c(0,0,2,0)) plot boxplot PNG figure I read in I am running Ubuntu 12.04 and R 3.1.0. readPNG and the png packge do NOT work for me at this point. when I try to install the png package I get the error below. Any ideas what's wrong or other options to import png files? Thank you in advance for the help. Best regards Gudrun png(file=analysis.png) par(mfrow=c(1,2), oma=c(0,0,2,0)) plot(data, main=all, xlab=simulations run, ylab=steps) boxplot(data, main=steps, horizontal = FALSE, axes = FALSE, staplewex = 1) text(y = boxplot.stats(data)$stats, labels = boxplot.stats(data)$stats, x = 1.35) title(analysis, outer=TRUE) install.packages(png) downloaded 24 Kb * installing *source* package 'png' ... ** package 'png' successfully unpacked and MD5 sums checked ** libs gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG `libpng-config --cflags` -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c read.c -o read.o /bin/bash: libpng-config: command not found read.c:3:17: fatal error: png.h: No such file or directory compilation terminated. make: *** [read.o] Error 1 ERROR: compilation failed for package 'png' * removing '/home/g1/R/x86_64-pc-linux-gnu-library/3.1/png' The downloaded source packages are in '/tmp/Rtmpvo3r8J/downloaded_packages' Warning message: In install.packages(png) : installation of package 'png' had non-zero exit status Gudrun Gygli, MSc PhD candidate Wageningen University Laboratory of Biochemistry Dreijenlaan 3 6703 HA Wageningen The Netherlands Phone 31 317483387 e-mail: gudrun.gy...@wur.nl - - - - - - - - - - - - - - - - - - Project information: http://www.wageningenur.nl/en/show/Bioinformatics-structural-biology-and-molecular-modeling-of-Vanillyl-Alcohol-Oxidases-VAOs.htm __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] (no subject)
Hello guys, I have data set like this Name A B CD Venky 12 157 168 209 Kalai65 8899 889 998 balaji98 877 8787 9888 . . . i want to change Name column as a Charcter and A column as a percentage and B and C column as a thousand seperators [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] apply a function to a list of data frames
Thank you for your help.
Your explanations have been very useful.
Stefano
Da: Rui Barradas [ruipbarra...@sapo.pt]
Inviato: venerdì 22 maggio 2015 20.26
A: Stefano Sofia; r-help@r-project.org
Oggetto: Re: [R] apply a function to a list of data frames
Hello,
You should change your function to accept only one argument, the
data.frames, and then use lapply (not sapply).
Something like the following.
calc - function(dat)
{
bias_dmo_max - round(mean((dat$dmo_12-dat$Eonestep_12), na.rm=TRUE),
digits=2)
rmse_dmo_max - round(sqrt(mean((dat$dmo_12-dat$Eonestep_12)^2,
na.rm=TRUE)), digits=2)
bias_dmo_min - round(mean((dat$dmo_27-dat$Eonestep_27), na.rm=TRUE),
digits=2)
rmse_dmo_min - round(sqrt(mean((dat$dmo_27-dat$Eonestep_27)^2,
na.rm=TRUE)), digits=2)
result - list(bias_dmo_max, rmse_dmo_max, bias_dmo_min, rmse_dmo_min)
result
}
result_lst - lapply(lst, calc)
Hope this helps,
Rui Barradas
Em 22-05-2015 19:02, Stefano Sofia escreveu:
Dear R-users,
given a list of dataframes (like below reported), for each month I need to
apply a function (called calc).
The result should be written in a new list of data frames, one row for each
month.
I have been trying to use sapply, with no success.
Could somebody help me in this?
$df1
day dmo_12 Eonestep_12 tmax dmo_27 Eonestep_27 tmin
2012-12-01 11 13 13 9 8 8
2012-12-02 11 13 13 5 6 8
2012-12-03 6 10 8 6 6 7
2012-12-04 11 13 9 6 6 3
2012-12-05 8 10 12 5 6 7
2012-12-06 8 10 8 4 5 4
2012-12-07 7 9 8 6 6 5
...
calc - function(dmo_12, Eonestep_12, dmo_27, Eonestep_27)
{
bias_dmo_max - round(mean((dmo_12-Eonestep_12), na.rm=TRUE), digits=2)
rmse_dmo_max - round(sqrt(mean((dmo_12-Eonestep_12)^2, na.rm=TRUE)),
digits=2)
bias_dmo_min - round(mean((dmo_27-Eonestep_27), na.rm=TRUE), digits=2)
rmse_dmo_min - round(sqrt(mean((dmo_27-Eonestep_27)^2, na.rm=TRUE)),
digits=2)
result - list(bias_dmo_max, rmse_dmo_max, bias_dmo_min, rmse_dmo_min)
result
}
Thank you for your help
Stefano
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urgenza, la risposta al presente messaggio di posta elettronica può essere
visionata da persone estranee al destinatario.
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confidential and legally privileged. Please do not read, copy, forward, or
store this message unless you are an intended recipient of it. If you have
received this message in error, please forward it to the sender and delete it
completely from your computer system.
Re: [R] png package in Ubuntu 12.04 with R 3.1.0
Have you loaded the png package? library(png) John Kane Kingston ON Canada -Original Message- From: gudrun.gy...@wur.nl Sent: Tue, 26 May 2015 07:10:35 + To: r-help@r-project.org Subject: [R] png package in Ubuntu 12.04 with R 3.1.0 Dear All, I am using R to analyse computer simulations of ligand docking in a protein. I am plotting the results as scatterplots and bopxplots, using the code below. This works perfectly fine. I would like now to add a png file to that plot, meaning I want sth like: png(file=analysis.png) par(mfrow=c(1,3), oma=c(0,0,2,0)) plot boxplot PNG figure I read in I am running Ubuntu 12.04 and R 3.1.0. readPNG and the png packge do NOT work for me at this point. when I try to install the png package I get the error below. Any ideas what's wrong or other options to import png files? Thank you in advance for the help. Best regards Gudrun png(file=analysis.png) par(mfrow=c(1,2), oma=c(0,0,2,0)) plot(data, main=all, xlab=simulations run, ylab=steps) boxplot(data, main=steps, horizontal = FALSE, axes = FALSE, staplewex = 1) text(y = boxplot.stats(data)$stats, labels = boxplot.stats(data)$stats, x = 1.35) title(analysis, outer=TRUE) install.packages(png) downloaded 24 Kb * installing *source* package 'png' ... ** package 'png' successfully unpacked and MD5 sums checked ** libs gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG `libpng-config --cflags` -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c read.c -o read.o /bin/bash: libpng-config: command not found read.c:3:17: fatal error: png.h: No such file or directory compilation terminated. make: *** [read.o] Error 1 ERROR: compilation failed for package 'png' * removing '/home/g1/R/x86_64-pc-linux-gnu-library/3.1/png' The downloaded source packages are in '/tmp/Rtmpvo3r8J/downloaded_packages' Warning message: In install.packages(png) : installation of package 'png' had non-zero exit status Gudrun Gygli, MSc PhD candidate Wageningen University Laboratory of Biochemistry Dreijenlaan 3 6703 HA Wageningen The Netherlands Phone 31 317483387 e-mail: gudrun.gy...@wur.nl - - - - - - - - - - - - - - - - - - Project information: http://www.wageningenur.nl/en/show/Bioinformatics-structural-biology-and-molecular-modeling-of-Vanillyl-Alcohol-Oxidases-VAOs.htm __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. FREE 3D EARTH SCREENSAVER - Watch the Earth right on your desktop! __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Path analysis
Dear Alberto, There are several R packages available on CRAN for structural equation modeling: sem, lavaan, and OpenMx come immediately to mind. If your model is recursive with only observed variables, then you could just use lm(). If your model is nonrecursive with only observed variables, then you could also use the systemfit package. I hope this helps, John John Fox, Professor McMaster University Hamilton, Ontario, Canada http://socserv.mcmaster.ca/jfox/ On Tue, 26 May 2015 05:43:47 + Alberto Canarini alberto.canar...@sydney.edu.au wrote: Hi there, As I'm approaching path analysis I was wondering which packages may suite a path analysis for my data. My data are on interaction of soil biotic and abiotic factor, like microbial biomass carbon, soil carbon, water content, temperature etc. Thanks in advance, Best regards. Alberto Alberto Canarini PhD Student l Faculty of Agriculture and Environment THE UNIVERSITY OF SYDNEY Shared room l CCWF l Camden Campus l NSW 2570 P 02 935 11892 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Path analysis
Given that your problem primarily focuses on a biological context you probably would have better luck with bioconductor (www.bioconductor.org). Regards, Charles On Tue, May 26, 2015 at 12:43 AM, Alberto Canarini alberto.canar...@sydney.edu.au wrote: Hi there, As I'm approaching path analysis I was wondering which packages may suite a path analysis for my data. My data are on interaction of soil biotic and abiotic factor, like microbial biomass carbon, soil carbon, water content, temperature etc. Thanks in advance, Best regards. Alberto Alberto Canarini PhD Student l Faculty of Agriculture and Environment THE UNIVERSITY OF SYDNEY Shared room l CCWF l Camden Campus l NSW 2570 P 02 935 11892 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] (no subject)
Hi venkadesan, Assuming that the Name column is now a factor (and the data set is a data frame named mydata), try: mydata$Name-as.character(mydata$Name) If you mean that you want to display column A with percentage signs: paste(mydata$A,%,sep=) You can use the format function to display the final three columns with thousand separators: format(mydata$B,big.mark=,) Note that the result will be a character variable, not a number. Jim On Tue, May 26, 2015 at 9:41 PM, venkadesan venky venkyno...@gmail.com wrote: Hello guys, I have data set like this Name A B CD Venky 12 157 168 209 Kalai65 8899 889 998 balaji98 877 8787 9888 . . . i want to change Name column as a Charcter and A column as a percentage and B and C column as a thousand seperators [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R CMD methods and ggplot2 advice
This posting should probably go to the new R-package-devel mailing list instead of R-help. If you do re-post there, you should give more information to let people help you. We can see the errors, but we can't see the source to your package, so it's hard to diagnose them. If your source is online somewhere, a link to it would really help. If not, then please include a copy of the DESCRIPTION file (so we can see how you declared dependence on methods), and extracts from the source of CreditEnhancement() where you use Period, etc. Duncan Murdoch On 25/05/2015 8:24 PM, Glenn Schultz wrote: Hello All, I have two packages Bond Lab and the Companion to Investing in MBS. Bond Lab clears the check and I am working on the on.load() to copy a needed directory per Duncan Murdoch's advise to make Bond Lab CRAN-able. The companion passes with two notes. The output is below: I get two notes (highlighted in red) Not sure on this one as I tried to declare methods but I get another note methods declared but not used. The second note is related to ggplot2 they are variable passed to ggplot2 within a function. I am not sure why they appear in the R CMD check. If someone could point in the right direction to resolve these I would appreciate the advice. These are my last remaining two issues to make the packages pass CRAN aside from the on.load() Best Regards, Glenn * checking dependencies in R code ... NOTE package ‘methods’ is used but not declared * checking R code for possible problems ... NOTE CreditEnhancement: no visible binding for global variable ‘Period’ CreditEnhancement: no visible binding for global variable ‘Value’ CreditEnhancement: no visible binding for global variable ‘Variable’ CreditEnhancement: no visible binding for global variable ‘..density..’ PassThrough.OAS: no visible binding for global variable ‘value’ PassThrough.OAS: no visible binding for global variable ‘..density..’ PassThroughCashFlow: no visible binding for global variable ‘Period’ PassThroughCashFlow: no visible binding for global variable ‘value’ PassThroughCashFlow: no visible binding for global variable ‘variable’ PlotMtgKeyRates: no visible binding for global variable ‘Tenor’ PlotMtgKeyRates: no visible binding for global variable ‘Duration’ PlotTermStructure: no visible binding for global variable ‘value’ PlotTermStructure: no visible binding for global variable ‘variable’ REMICOAS: no visible binding for global variable ‘value’ REMICOAS: no visible binding for global variable ‘..density..’ TotalReturn: no visible binding for global variable ‘Scenario’ TotalReturn: no visible binding for global variable ‘value’ TotalReturn: no visible binding for global variable ‘variable’ TwistScenario: no visible binding for global variable ‘Scenario’ TwistScenario: no visible binding for global variable ‘Return’ ValuationFramework: no visible binding for global variable ‘value’ ValuationFramework: no visible binding for global variable ‘variable’ == devtools::check() Updating Companion2IMBS documentation Loading Companion2IMBS '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla CMD build \ '/Users/glennschultz/Companion to Investing in MBS' --no-resave-data \ --no-manual * checking for file ‘/Users/glennschultz/Companion to Investing in MBS/DESCRIPTION’ ... OK * preparing ‘Companion2IMBS’: * checking DESCRIPTION meta-information ... OK * checking for LF line-endings in source and make files * checking for empty or unneeded directories Removed empty directory ‘Companion2IMBS/inst’ Removed empty directory ‘Companion2IMBS/test/testthat’ Removed empty directory ‘Companion2IMBS/test’ * building ‘Companion2IMBS_1.0.tar.gz’ '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla CMD check \ '/var/folders/tv/sq6gmnvs13j8jrhkt87f_zmcgn/T//RtmpOabREs/Companion2IMBS_1.0.tar.gz' \ --timings * using log directory ‘/Users/glennschultz/Companion2IMBS.Rcheck’ * using R version 3.0.3 (2014-03-06) * using platform: x86_64-apple-darwin10.8.0 (64-bit) * using session charset: UTF-8 * checking for file ‘Companion2IMBS/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Companion2IMBS’ version ‘1.0’ * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘Companion2IMBS’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ...
Re: [R] Issues with loading csv file
Hi Pat, Thanks for the suggestion. It worked for me. Actually I had not saved the file in the WD accidentally and with the help of get files syntax I got to know what was the issue. Thanks a ton. Shivi -- View this message in context: http://r.789695.n4.nabble.com/Issues-with-loading-csv-file-tp4707637p4707675.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Help with urnsamples and all possible combination
Thanks for your help. So I have to try it on the long way, because I need exactly all combinations, but thanks for the idea. Best wishes Michelle Galla -- View this message in context: http://r.789695.n4.nabble.com/Help-with-urnsamples-and-all-possible-combination-tp4707560p4707676.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] logistic regression R and Stata – grouping variable
Hello, I mostly use Stata 13 for my regression analysis. I want to conduct a logistic regression on a proportion/number of success. Because I receive errors in Stata I did not expect nor understand (if there are Stata experts who want to know more about the problems I face and can potentially help me solve them, I would be glad to give more details), I want to repeat the analysis in R. In Stata I would use the command: xtlogit DEP_PROP INDEP_A INDEP_B INDEP_C, i(ID). ID is the identifier for each subject. There are eight lines with data for each subject because there are three within factors (INDEP_A, B, C) with two levels each (0 and 1). I can repeat this analysis in R by using the command: glm(DEP_SUC ~ INDEP_A + INDEP_B + INDEP_C, family = �binomial�). DEP_SUC is here a table with the successes and misses per row. Again, there are eight rows for each subject. But while I know how to group these lines in Stata by using the option i(ID ), I do not know what to do in R. I have search for more information about the i() command, but did not find any usefull information. So, to summarize: I want to find out how three variables (binary) influence a proportion and use logistic regression. In Stata I can group multiple lines per subject using the i( ) command in logistic regression. What is the equivalent in R? Thank you in advance! [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Hadoop R integration
Hi,
I need to showcase how R and Hadoop can work together using ORCH. I have found
a sample code from the ORACLE website as follows
dfs - hdfs.attach(ontime_DB)
res - hadoop.run(
dfs,
mapper = function(key, value) {
if (key == 'SFO' !is.na(x$ARRDELAY)) {
keyval(key, value)
}
else {
NULL
}
},
reducer = function(key, values) {
for (x in values) {
sumAD - sumAD + x$ARRDELAY
count - count + 1
}
res - sumAD / count
keyval(key, res)
})
OUTPUT:
hdfs.get(res)
key val1
1 SFO 17.44828
I could not understand in this code where is ORCH acting as a connector. Even
if you can explain how ORCH acts as a connector to Hadoop with another example
it would also be helpful.
Regards,
Lalitha Kristipati
Associate Software Engineer
Disclaimer: This message and the information contained herein is proprietary
and confidential and subject to the Tech Mahindra policy statement, you may
review the policy at http://www.techmahindra.com/Disclaimer.html externally
http://tim.techmahindra.com/tim/disclaimer.html internally within TechMahindra.
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Re: [R] How to pass a variable to a function which use variable name as a parameter
On Tue, May 26, 2015 at 5:14 AM, wong jane jane.wong...@gmail.com wrote:
There are functions which use variable names as parameters in some R
packages. However, if the variable name is stored in another variable, how
can I pass this variable to the function. Taking the rms package as an
example:
library(rms)
n - 1000
age - rnorm(n, 50, 10)
sex - factor(sample(c('female','male'), n,TRUE))
y - rnorm(n, 200, 25)
ddist - datadist(age, sex)
options(datadist='ddist')
fit - lrm(y ~ age)
Predict(fit, age, np=4)
options(datadist=NULL)
Here age was a variable name passed to Predict() function, but if age
was stored in variable var, that is, var - age, how can I pass var
to Predict() function? The purpose is that I want to change the parameter
of Predict() in a loop.
Please turn off HMTL email. The forum software doesn't really like it.
What you want is the get() function.
var-age
library(rms)
n - 1000
age - rnorm(n, 50, 10)
sex - factor(sample(c('female','male'), n,TRUE))
y - rnorm(n, 200, 25)
#
ddist - datadist(age, sex)
ddist - datadist(get(var),sex)
options(datadist='ddist')
fit - lrm(y ~ age)
#
Predict(fit, age, np=4)
Predict(fit,get(var),np=4)
options(datadist=NULL)
--
My sister opened a computer store in Hawaii. She sells C shells down by the
seashore.
If someone tell you that nothing is impossible:
Ask him to dribble a football.
He's about as useful as a wax frying pan.
10 to the 12th power microphones = 1 Megaphone
Maranatha!
John McKown
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[R] lme function to obtain pvalue for fixed effect
Hi all, I am using the lme function to run a random coefficient model. Please see output (mod1) as below. I need to obtain the pvalue for the fixed effect. As you can see, the pvalues given using the summary function is different from the resutls given in anova function. Why should they be different and which one is the correct one to use? Thanks! Hanna summary(mod1) Linear mixed-effects model fit by REML Data: minus20C1 AIC BIC logLik -82.60042 -70.15763 49.30021 Random effects: Formula: ~1 + months | lot Structure: General positive-definite, Log-Cholesky parametrization StdDev Corr (Intercept) 8.907584e-03 (Intr) months 6.039781e-05 -0.096 Residual4.471243e-02 Fixed effects: ti ~ type * months Value Std.Error DF t-value p-value (Intercept) 0.25831245 0.016891587 31 15.292373 0. type 0.13502089 0.026676101 4 5.061493 0.0072 months 0.00804790 0.001218941 31 6.602368 0. type:months -0.00693679 0.002981859 31 -2.326329 0.0267 Correlation: (Intr) typ months type-0.633 months -0.785 0.497 type:months 0.321 -0.762 -0.409 Standardized Within-Group Residuals: MinQ1 MedQ3 Max -2.162856e+00 -1.962972e-01 -2.771184e-05 3.749035e-01 2.088392e+00 Number of Observations: 39 Number of Groups: 6 anova(mod1) numDF denDF F-value p-value (Intercept) 131 2084.0265 .0001 type1 4 10.8957 0.0299 months 131 38.3462 .0001 type:months 1315.4118 0.0267 __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] png package in Ubuntu 12.04 with R 3.1.0
sudo apt-get install libpng12-dev I'm not sure about Ubuntu 12.04. You may need a different libpng??-dev. Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http://yihui.name On Tue, May 26, 2015 at 2:10 AM, Gygli, Gudrun gudrun.gy...@wur.nl wrote: Dear All, I am using R to analyse computer simulations of ligand docking in a protein. I am plotting the results as scatterplots and bopxplots, using the code below. This works perfectly fine. I would like now to add a png file to that plot, meaning I want sth like: png(file=analysis.png) par(mfrow=c(1,3), oma=c(0,0,2,0)) plot boxplot PNG figure I read in I am running Ubuntu 12.04 and R 3.1.0. readPNG and the png packge do NOT work for me at this point. when I try to install the png package I get the error below. Any ideas what's wrong or other options to import png files? Thank you in advance for the help. Best regards Gudrun png(file=analysis.png) par(mfrow=c(1,2), oma=c(0,0,2,0)) plot(data, main=all, xlab=simulations run, ylab=steps) boxplot(data, main=steps, horizontal = FALSE, axes = FALSE, staplewex = 1) text(y = boxplot.stats(data)$stats, labels = boxplot.stats(data)$stats, x = 1.35) title(analysis, outer=TRUE) install.packages(png) downloaded 24 Kb * installing *source* package 'png' ... ** package 'png' successfully unpacked and MD5 sums checked ** libs gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG `libpng-config --cflags` -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c read.c -o read.o /bin/bash: libpng-config: command not found read.c:3:17: fatal error: png.h: No such file or directory compilation terminated. make: *** [read.o] Error 1 ERROR: compilation failed for package 'png' * removing '/home/g1/R/x86_64-pc-linux-gnu-library/3.1/png' The downloaded source packages are in '/tmp/Rtmpvo3r8J/downloaded_packages' Warning message: In install.packages(png) : installation of package 'png' had non-zero exit status Gudrun Gygli, MSc PhD candidate Wageningen University Laboratory of Biochemistry Dreijenlaan 3 6703 HA Wageningen The Netherlands Phone 31 317483387 e-mail: gudrun.gy...@wur.nl - - - - - - - - - - - - - - - - - - Project information: http://www.wageningenur.nl/en/show/Bioinformatics-structural-biology-and-molecular-modeling-of-Vanillyl-Alcohol-Oxidases-VAOs.htm __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to pass a variable to a function which use variable name as a parameter
One way to use variable names in functions like Predict() that
do not evaluate their arguments in the standard way is to use
do.call() along with as.name(). E.g.,
varName-age
do.call(Predict, list(fit, as.name(varName), np=4))})
gives the same result as
Predict(fit, age, np=4)
Bill Dunlap
TIBCO Software
wdunlap tibco.com
On Tue, May 26, 2015 at 3:14 AM, wong jane jane.wong...@gmail.com wrote:
There are functions which use variable names as parameters in some R
packages. However, if the variable name is stored in another variable, how
can I pass this variable to the function. Taking the rms package as an
example:
library(rms)
n - 1000
age - rnorm(n, 50, 10)
sex - factor(sample(c('female','male'), n,TRUE))
y - rnorm(n, 200, 25)
ddist - datadist(age, sex)
options(datadist='ddist')
fit - lrm(y ~ age)
Predict(fit, age, np=4)
options(datadist=NULL)
Here age was a variable name passed to Predict() function, but if age
was stored in variable var, that is, var - age, how can I pass var
to Predict() function? The purpose is that I want to change the parameter
of Predict() in a loop.
[[alternative HTML version deleted]]
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http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] [R-sig-ME] lme function to obtain pvalue for fixed effect
Because they test different hypothesis. ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie Kwaliteitszorg / team Biometrics Quality Assurance Kliniekstraat 25 1070 Anderlecht Belgium To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey 2015-05-26 21:46 GMT+02:00 li li hannah@gmail.com: Thanks so much for replying. Yes LimerTest package could be used to get pvalues when using lmer function. But still the summary and anova function give different pvalues. Hanna 2015-05-26 15:19 GMT-04:00, byron vinueza byronvin...@hotmail.com: You can use the lmerTest package . Enviado desde mi iPhone El 26/5/2015, a las 13:18, li li hannah@gmail.com escribió: Hi all, I am using the lme function to run a random coefficient model. Please see output (mod1) as below. I need to obtain the pvalue for the fixed effect. As you can see, the pvalues given using the summary function is different from the resutls given in anova function. Why should they be different and which one is the correct one to use? Thanks! Hanna summary(mod1) Linear mixed-effects model fit by REML Data: minus20C1 AIC BIC logLik -82.60042 -70.15763 49.30021 Random effects: Formula: ~1 + months | lot Structure: General positive-definite, Log-Cholesky parametrization StdDev Corr (Intercept) 8.907584e-03 (Intr) months 6.039781e-05 -0.096 Residual4.471243e-02 Fixed effects: ti ~ type * months Value Std.Error DF t-value p-value (Intercept) 0.25831245 0.016891587 31 15.292373 0. type 0.13502089 0.026676101 4 5.061493 0.0072 months 0.00804790 0.001218941 31 6.602368 0. type:months -0.00693679 0.002981859 31 -2.326329 0.0267 Correlation: (Intr) typ months type-0.633 months -0.785 0.497 type:months 0.321 -0.762 -0.409 Standardized Within-Group Residuals: MinQ1 MedQ3 Max -2.162856e+00 -1.962972e-01 -2.771184e-05 3.749035e-01 2.088392e+00 Number of Observations: 39 Number of Groups: 6 anova(mod1) numDF denDF F-value p-value (Intercept) 131 2084.0265 .0001 type1 4 10.8957 0.0299 months 131 38.3462 .0001 type:months 1315.4118 0.0267 ___ r-sig-mixed-mod...@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models ___ r-sig-mixed-mod...@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] [R-sig-ME] lme function to obtain pvalue for fixed effect
You can use the lmerTest package . Enviado desde mi iPhone El 26/5/2015, a las 13:18, li li hannah@gmail.com escribió: Hi all, I am using the lme function to run a random coefficient model. Please see output (mod1) as below. I need to obtain the pvalue for the fixed effect. As you can see, the pvalues given using the summary function is different from the resutls given in anova function. Why should they be different and which one is the correct one to use? Thanks! Hanna summary(mod1) Linear mixed-effects model fit by REML Data: minus20C1 AIC BIC logLik -82.60042 -70.15763 49.30021 Random effects: Formula: ~1 + months | lot Structure: General positive-definite, Log-Cholesky parametrization StdDev Corr (Intercept) 8.907584e-03 (Intr) months 6.039781e-05 -0.096 Residual4.471243e-02 Fixed effects: ti ~ type * months Value Std.Error DF t-value p-value (Intercept) 0.25831245 0.016891587 31 15.292373 0. type 0.13502089 0.026676101 4 5.061493 0.0072 months 0.00804790 0.001218941 31 6.602368 0. type:months -0.00693679 0.002981859 31 -2.326329 0.0267 Correlation: (Intr) typ months type-0.633 months -0.785 0.497 type:months 0.321 -0.762 -0.409 Standardized Within-Group Residuals: MinQ1 MedQ3 Max -2.162856e+00 -1.962972e-01 -2.771184e-05 3.749035e-01 2.088392e+00 Number of Observations: 39 Number of Groups: 6 anova(mod1) numDF denDF F-value p-value (Intercept) 131 2084.0265 .0001 type1 4 10.8957 0.0299 months 131 38.3462 .0001 type:months 1315.4118 0.0267 ___ r-sig-mixed-mod...@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] [R-sig-ME] lme function to obtain pvalue for fixed effect
Thanks so much for replying. Yes LimerTest package could be used to get pvalues when using lmer function. But still the summary and anova function give different pvalues. Hanna 2015-05-26 15:19 GMT-04:00, byron vinueza byronvin...@hotmail.com: You can use the lmerTest package . Enviado desde mi iPhone El 26/5/2015, a las 13:18, li li hannah@gmail.com escribió: Hi all, I am using the lme function to run a random coefficient model. Please see output (mod1) as below. I need to obtain the pvalue for the fixed effect. As you can see, the pvalues given using the summary function is different from the resutls given in anova function. Why should they be different and which one is the correct one to use? Thanks! Hanna summary(mod1) Linear mixed-effects model fit by REML Data: minus20C1 AIC BIC logLik -82.60042 -70.15763 49.30021 Random effects: Formula: ~1 + months | lot Structure: General positive-definite, Log-Cholesky parametrization StdDev Corr (Intercept) 8.907584e-03 (Intr) months 6.039781e-05 -0.096 Residual4.471243e-02 Fixed effects: ti ~ type * months Value Std.Error DF t-value p-value (Intercept) 0.25831245 0.016891587 31 15.292373 0. type 0.13502089 0.026676101 4 5.061493 0.0072 months 0.00804790 0.001218941 31 6.602368 0. type:months -0.00693679 0.002981859 31 -2.326329 0.0267 Correlation: (Intr) typ months type-0.633 months -0.785 0.497 type:months 0.321 -0.762 -0.409 Standardized Within-Group Residuals: MinQ1 MedQ3 Max -2.162856e+00 -1.962972e-01 -2.771184e-05 3.749035e-01 2.088392e+00 Number of Observations: 39 Number of Groups: 6 anova(mod1) numDF denDF F-value p-value (Intercept) 131 2084.0265 .0001 type1 4 10.8957 0.0299 months 131 38.3462 .0001 type:months 1315.4118 0.0267 ___ r-sig-mixed-mod...@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Installing Blotterand Rtoolsin R
HI, Im trying to install the blotter package in R however I get the following message: Warning in install.packages : package ‘blotter’ is not available (for R version 3.2.0) I have been told to first install the Rtools package, which gives me the same message. I also believe that there is a way to install Rtools directly from the website: http://cran.r-project.org/bin/windows/Rtools/; However do not know how to do this. Any help would be much aprreciated? Thanks -- View this message in context: http://r.789695.n4.nabble.com/Installing-Blotter-and-Rtools-in-R-tp4707688.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] different results from lme and lmer function
Hi all, I am fitting a random slope and random intercept model using R. I used both lme and lmer funciton for the same model. However I got different results as shown below (different variance component estimates and so on). I think that is really confusing. They should produce close results. Anyone has any thoughts or suggestions. Also, which one should be comparable to sas results? Thanks! Hanna ## using lme function mod_lme - lme(ti ~ type*months, random=~ 1+months|lot, na.action=na.omit, + data=one, control = lmeControl(opt = optim)) summary(mod_lme) Linear mixed-effects model fit by REML Data: one AIC BIC logLik -82.60042 -70.15763 49.30021 Random effects: Formula: ~1 + months | lot Structure: General positive-definite, Log-Cholesky parametrization StdDev Corr (Intercept) 8.907584e-03 (Intr) months 6.039781e-05 -0.096 Residual4.471243e-02 Fixed effects: ti ~ type * months Value Std.Error DF t-value p-value (Intercept) 0.25831245 0.016891587 31 15.292373 0. type0.13502089 0.026676101 4 5.061493 0.0072 months 0.00804790 0.001218941 31 6.602368 0. type:months -0.00693679 0.002981859 31 -2.326329 0.0267 Correlation: (Intr) typPPQ months type -0.633 months -0.785 0.497 type:months 0.321 -0.762 -0.409 Standardized Within-Group Residuals: MinQ1 MedQ3 Max -2.162856e+00 -1.962972e-01 -2.771184e-05 3.749035e-01 2.088392e+00 Number of Observations: 39 Number of Groups: 6 ###Using lmer function mod_lmer -lmer(ti ~ type*months+(1+months|lot), na.action=na.omit, data=one) summary(mod_lmer) Linear mixed model fit by REML t-tests use Satterthwaite approximations to degrees of freedom [merModLmerTest] Formula: ti ~ type * months + (1 + months | lot) Data: one REML criterion at convergence: -98.8 Scaled residuals: Min 1Q Median 3Q Max -2.1347 -0.2156 -0.0067 0.3615 2.0840 Random effects: Groups NameVariance Std.Dev. Corr lot (Intercept) 2.870e-04 0.0169424 months 4.135e-07 0.0006431 -1.00 Residual 1.950e-03 0.0441644 Number of obs: 39, groups: lot, 6 Fixed effects: Estimate Std. Errordf t value Pr(|t|) (Intercept) 0.258312 0.018661 4.82 13.842 4.59e-05 *** type 0.135021 0.028880 6.802000 4.675 0.00245 ** months 0.008048 0.001259 11.943000 6.390 3.53e-05 *** type:months -0.006937 0.002991 28.91 -2.319 0.02767 * --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Correlation of Fixed Effects: (Intr) typPPQ months type -0.646 months -0.825 0.533 type:month 0.347 -0.768 -0.421 __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to pass a variable to a function which use variable name as a parameter
On May 26, 2015, at 8:30 AM, William Dunlap wrote:
One way to use variable names in functions like Predict() that
do not evaluate their arguments in the standard way is to use
do.call() along with as.name(). E.g.,
varName-age
do.call(Predict, list(fit, as.name(varName), np=4))})
gives the same result as
Predict(fit, age, np=4)
Here's another approach, developed after looking at the code and the help page,
where I noticed that the factors argument was given an an alternate route for
specifying the variables for evaluation. The requirements for the 'factors'
argument are that it be provided as a named list and have either specific
values or NA.
var=age
vlist - list(dum=NA)
names(vlist)=var
Predict(fit, factors=vlist, np=4)
#- same result ---
age yhatlowerupper
1 25.04901 6.834836 4.856497 8.813174
2 41.14259 6.882369 4.919433 8.845306
3 57.23618 6.929903 4.967118 8.892688
4 73.32977 6.977437 4.999548 8.955325
Response variable (y): log odds
Limits are 0.95 confidence limits
--
David.
Bill Dunlap
TIBCO Software
wdunlap tibco.com
On Tue, May 26, 2015 at 3:14 AM, wong jane jane.wong...@gmail.com wrote:
There are functions which use variable names as parameters in some R
packages. However, if the variable name is stored in another variable, how
can I pass this variable to the function. Taking the rms package as an
example:
library(rms)
n - 1000
age - rnorm(n, 50, 10)
sex - factor(sample(c('female','male'), n,TRUE))
y - rnorm(n, 200, 25)
ddist - datadist(age, sex)
options(datadist='ddist')
fit - lrm(y ~ age)
Predict(fit, age, np=4)
options(datadist=NULL)
Here age was a variable name passed to Predict() function, but if age
was stored in variable var, that is, var - age, how can I pass var
to Predict() function? The purpose is that I want to change the parameter
of Predict() in a loop.
[[alternative HTML version deleted]]
--
David Winsemius
Alameda, CA, USA
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Re: [R] Installing Blotterand Rtoolsin R
On May 26, 2015, at 6:29 AM, nmrql wrote: HI, Im trying to install the blotter package in R however I get the following message: How? Warning in install.packages : package ‘blotter’ is not available (for R version 3.2.0) I do not see it in the list of packages available from CRAN. I have been told to first install the Rtools package, which gives me the same message. Rtools is a set of Windows utilities. I don't think it's possible to be installed from an R console session. I also believe that there is a way to install Rtools directly from the website: http://cran.r-project.org/bin/windows/Rtools/; However do not know how to do this. http://cran.r-project.org/bin/windows/Rtools/index.html http://cran.r-project.org/bin/windows/Rtools/installer.html Any help would be much aprreciated? Thanks -- View this message in context: http://r.789695.n4.nabble.com/Installing-Blotter-and-Rtools-in-R-tp4707688.html Sent from the R help mailing list archive at Nabble.com. Posting from Nabble is somewhat discouraged. If it is at all feasible you should use a regular mail client and post directly to the list. -- David Winsemius Alameda, CA, USA __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
