[R] help! complete the reviewer's suggest: carry out GA+GP (gaussian process)!

Hello, all experts, My major is computer-aied drug design ( main QSAR). Now, my paper need be reviesed, and one reviewer ask me do genetic algorithm coupled with gaussian process method (GA+GP). my data: training set: 191*106 test set: 73*106 here, I need use GA+GP to do variable

Re: [R] how to replace my double for loop which is little efficient!

Thank Berend, It seems like that it is better to attach a PDF file for avoiding messy code. Yes, I want to obtain is Tanimoto coefficient and your web site wikipedia is about this coefficient. I also search R site about tanimoto coefficient and learn it more. About your code, I has saved and

[R] how to replace my double for loop which is little efficient!

Dear all, My double for loop as follows, but it is little efficient, I hope all friends can give me a vectorized program to replace my code. thanks x: is a matrix 202*263, that is 202 samples, and 263 independent variables num.compd-nrow(x); # number of compounds diss.all-0 for( i in

Re: [R] how to replace my double for loop which is little efficient!

thanks for your help, it is great. In addition, In the beginning, the format of x is dataframe, and i run my code, it is so slow, after your help, I change x for matirx, it is so quick. I am very grateful your kind help, and your code is so good! kevin -- View this message in context:

Re: [R] how to replace my double for loop which is little efficient!

thanks for your help. I am sorry I do not full understand your code, so i can not correct using your code to my data. here is the attachment of my data, and what I want to compute is the equation in the word document of the attachment: the code form Berend can get the answer i want to get.

[R] how to get the plot like the attachment?

http://r.789695.n4.nabble.com/file/n3060425/fig_1.png fig. 1 http://r.789695.n4.nabble.com/file/n3060425/fig_2.png fig. 2 I want to the picture like the above one, the origin crossover together, while the following picture can be obtained by default and the origin is detached, but throgut

Re: [R] how to get the plot like the attachment?

thanks, I succeed. kevin -- View this message in context: http://r.789695.n4.nabble.com/how-to-get-the-plot-like-the-attachment-tp3060425p3061217.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list

Re: [R] help! kennard-stone algorithm in soil.spec packages does not work for my dataset!!!

http://r.789695.n4.nabble.com/file/n3032045/rsv1.txt rsv1.txt I am very grateful to David's suggestion, here , I upload my dataset rsv1.txt, also the question, ks-ken.sto(rsv1,per=TRUE,per.n=0.3,va=FALSE,sav=FALSE) it does not work, all results are NULL, i do not known why it is ? hope,

[R] help! kennard-stone algorithm in soil.spec packages does not work for my dataset!!!

http://r.789695.n4.nabble.com/file/n3031344/RSV.Rdata RSV.Rdata I want to split my dataset to training set and test set using kennard-stone(KS) algorithm, it is lucky there is R packages soil.spec to implement it. but when I used it to my dataset, it does not work, who can help me, how reasons

Re: [R] update R 2.11.0，there is error when usi ng plot(), how can I do?

now. it is ok. I uninstall R2.11.0, then delete an packages in the library, and install again R2.11.0. ok, it does works. thank you! -- View this message in context: http://r.789695.n4.nabble.com/update-R-2-11-0-there-is-error-when-using-plot-how-can-I-do-tp2164517p2165235.html Sent from

[R] How to estimate whether overfitting?

1. is there some criterion to estimate overfitting? e.g. R2 and Q2 in the training set, as well as R2 in the test set, when means overfitting. for example, in my data, I have R2=0.94 for the training set and for the test set R2=0.70, is overfitting? 2. in this scatter, can one say this

[R] update R 2.11.0，there is error when usi ng plot(), how can I do?

a-1:5 b-2:6 plot(a,b) Error in function (width, height, pointsize, record, rescale, xpinch, : Graphics API version mismatch before, R 2.10 , plot() is ok. Now, R 2.11.0 does not work -- View this message in context:

Re: [R] How to estimate whether overfitting?

thanks for your suggestion. many I need to learn indeed. I will buy that good book. kevin -- View this message in context: http://r.789695.n4.nabble.com/How-to-estimate-whether-overfitting-tp2164417p2164847.html Sent from the R help mailing list archive at Nabble.com.

Re: [R] How to estimate whether overfitting?

thank you, I have downloaded it. studying -- View this message in context: http://r.789695.n4.nabble.com/How-to-estimate-whether-overfitting-tp2164417p2164932.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org

Re: [R] How to estimate whether overfitting?

many thanks . I can try to use test set with 100 samples. anther question is that how can I rationally split my data to training set and test set? (training set with 108 samples, and test set with 100 samples) as I know, the test set should the same distribute to the training set. and what

Re: [R] how can I plot the histogram like this using R?

thanks, it is ok! -- View this message in context: http://n4.nabble.com/how-can-I-plot-the-histogram-like-this-using-R-tp1839303p2013782.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list

Re: [R] how can I plot the histogram like this using R?

Thanks for your reply, I just want to get the figure like y1.jpg using the data from y1.txt. Through the figure I want to obtain the split point like y1.jpg, and consider 2.5 as the plit point. This figure is drawn by other people, I just want to draw it using R, but I can not, so I hope,

Re: [R] how can I plot the histogram like this using R?

thanks for your help. I can have a try. -- View this message in context: http://n4.nabble.com/how-can-I-plot-the-histogram-like-this-using-R-tp1839303p1839534.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org

Re: [R] how can I plot the histogram like this using R?

thank you, I will try this function barplot. -- View this message in context: http://n4.nabble.com/how-can-I-plot-the-histogram-like-this-using-R-tp1839303p1839541.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org

[R] how can I plot the histogram like this using R?

I want to get the plot like this, http://n4.nabble.com/file/n1839303/%25E9%25A2%2591%25E7%258E%2587%25E5%2588%2586%25E5%25B8%2583%25E5%259B%25BE%25E6%25A0%2587%25E5%2587%2586.jpg %E9%A2%91%E7%8E%87%E5%88%86%E5%B8%83%E5%9B%BE%E6%A0%87%E5%87%86.jpg not this,

[R] caret package, how can I deal with RFE+SVM wrong message?

Hello, I am learning caret package, and I want to use the RFE to reduce the feature. I want to use RFE coupled Random Forest (RFE+FR) to complete this task. As we know, there are a number of pre-defined sets of functions, like random Forest(rfFuncs), however,I want to tune the parameters

[R] How can I understand this sentence,and express it by means of Mathematical approach？

This topic refer to independent variables reduction, as we know ,a lot of method can do with it,however, for pre-processing independent varibles, a method like the sentence below can reduce many variable, How can I understand it? what is significant correlation at 5% level, what is the

[R] Help, How can I boxplot mse and mtry using 20 5-fold cross-validation?

Hello, I am learning randomForest, now I want to boxplot mse and mtry using 20 5-fold cross-validation(using median value), but I have no a good method to do it, except a not good method. randomforest package itself did not contain cross-validating method, and caret package contain cross

Re: [R] Help, How can I boxplot mse and mtry using 20 5-fold cross-validation?

at 9:47 AM, bbslover [hidden email] wrote: Hello, I am learning randomForest, now I want to boxplot mse and mtry using 20 5-fold cross-validation(using median value), but I have no a good method to do it, except a not good method. randomforest package itself did not contain cross

Re: [R] Help me! using random Forest package, how to calculate Error Rates in the training set ?

...@yeah.net 主题:Re: [R] Help me! using random Forest package, how to calculate Error Rates in the training set ? From: bbslover now I am learining random forest and using random forest package, I can get the OOB error rates, and test set rate, now I want to get the training set error

[R] Help me! using random Forest package, how to calculate Error Rates in the training set ?

now I am learining random forest and using random forest package, I can get the OOB error rates, and test set rate, now I want to get the training set error rate, how can I do? pgp.rf-randomForest(x.tr,y.tr,x.ts,y.ts,ntree=1e3,keep.forest=FALSE,do.trace=1e2) using the code can get oob and

[R] help, how self-oganizing map show 2D picture and put all samples into the picture?

http://n4.nabble.com/file/n998182/pca.jpg pca.jpg http://n4.nabble.com/file/n998182/som.jpg som.jpg http://n4.nabble.com/file/n998182/all%2Bindepents.xls all+indepents.xls As we know, som is a good tool to cluster hign demension to 2D and show as a 2D picture, just like in the attachment

Re: [R] Please help me!!!! Error in `[.data.frame`(x, , retained, drop = FALSE) : undefined columns selected

create a modified version of lmFuncs that suits your needs or remove variables prior to modeling (or try some other method that doesn't require more samples than predictors, such as the lasso or elasticnet). Max On Fri, Jan 1, 2010 at 10:14 PM, bbslover [hidden email] wrote: I am

Re: [R] Please help me!!!! Error in `[.data.frame`(x, , retained, drop = FALSE) : undefined columns selected

. Either create a modified version of lmFuncs that suits your needs or remove variables prior to modeling (or try some other method that doesn't require more samples than predictors, such as the lasso or elasticnet). Max On Fri, Jan 1, 2010 at 10:14 PM, bbslover dlu...@yeah.net wrote: I

[R] Please help me!!!! Error in `[.data.frame`(x, , retained, drop = FALSE) : undefined columns selected

I am learning the package caret, after I do the rfe function, I get the error ,as follows: Error in `[.data.frame`(x, , retained, drop = FALSE) : undefined columns selected In addition: Warning message: In predict.lm(object, x) : prediction from a rank-deficient fit may be misleading I

[R] Help，Suggest me some methods to identify t raining set and test set!!!

I want to split my whole dateset to training set and test set, building model in training set, and validate model using test set. Now, How can I split my dataset to them reasonally. Please give me a hand, It is better to give me some R code. and I see some ways like using SOM to project whole

Re: [R] Help，Suggest me some methods to identify tr aining set and test set!!!

Thank you for all help. It is helpful for me. Max Kuhn wrote: I noticed Max already pointed you to the caret package. Load the library and look at the help for the createFolds function, eg: library(caret) ?createFolds I think that the createDataPartition function in caret might work

Re: [R] Hello all, How can I get corss-validation MSE of SVM in e1071?

://www.jstatsoft.org/v28/i05/paper about the package. Max On Fri, Dec 18, 2009 at 12:26 PM, bbslover [hidden email] wrote: as known, svm need tune some parameters like cost,gamma and epsilon to get better performance,but one question appear, how can i monitor the performance . generally

[R] what is criterion of removing independence?

Hello, all I have a lot of independents and one dependent, finally, I want to build one model using them, and predict the new samples value, that is regression. before it, I must remove some independents according to some criterion: 1. constant values independent. 2. variant near zero.

Re: [R] Hello all, How can I get corss-validation MSE of SVM in e1071?

/v28/i05/paper about the package. Max On Fri, Dec 18, 2009 at 12:26 PM, bbslover dlu...@yeah.net wrote: as known, svm need tune some parameters like  cost,gamma and epsilon to get better performance,but one question appear, how can i monitor the performance . generally speaking ,we

[R] Hello all, How can I get corss-validation MSE of SVM in e1071?

as known, svm need tune some parameters like cost,gamma and epsilon to get better performance,but one question appear, how can i monitor the performance . generally speaking ,we chose the cross-validation MSE in the training set, but It seems svm can not return the cross-validation MSE value, we

[R] p.value OR F.value?

Hi，all friends, Please help me understand this sentence below: “From this set, 858 columns not significantly correlated with the response variable TBG at the 5% level were removed, leaving a set of 390 columns.” and “ the F-test's value for the one-parameter correlation with the descriptor

[R] How can I remove one of variables which both variables have correlation coefficient more than 0.95 randomly?

http://old.nabble.com/file/p26443595/Edragonr.txt Edragonr.txt HI all, I have a 72*495 matrix, and the first column is the response, and the remaining are independences. Final I want to select some independence to fit y, but there are so many independences, the fit result is not meaning, so

[R] help, GA for varialbe selection. ?!

Dear all, I am learning the subselect package in R, now I want to use GA to select some potent variable, but some questions are puzzled. what i want to resolve is that I have one column dependent y and 219 columns independent x. A total 72 observations is contained in the dataset. I want

Re: [R] after PCA, the pc values are so large, wrong?

ok,I understand your means, maybe PLS is better for my aim. but I have done that, also bad. the most questions for me is how to select less variables from the independent to fit dependent. GA maybe is good way, but I do not learn it well. Ben Bolker wrote: bbslover dluthm at yeah.net writes

[R] how to remove one of any two indices with a correlation greater than 0.90 in a matrix (or data.frame)

my code is not right below: rm(list=ls()) #define data.frame a=c(1,2,3,5,6); b=c(1,2,3,4,7); c=c(1,2,3,4,8); d=c(1,2,3,5,1); e=c(1,2,3,5,7) data.f=data.frame(a,b,c,d,e) #backup data.f origin.data-data.f #get correlation matrix cor.matrix-cor(origin.data) #backup

Re: [R] another question: how to delete one of columes in two ones with high correlation(0.95)

use modulus instead of integer divison. (which(cor.matrix =0.95) %% dim(cor.matrix)[1]) There are probably better ways than this. Nikhil but probably a better way to do this would be On 6 Nov 2009, at 3:16AM, bbslover wrote: for(i in 1:(cor.matrix[1]-1)) { for(j in (i+1

[R] after PCA, the pc values are so large, wrong?

rm(list=ls()) yx.df-read.csv(c:/MK-2-72.csv,sep=',',header=T,dec='.') dim(yx.df) #get X matrix y-yx.df[,1] x-yx.df[,2:643] #conver to matrix mat-as.matrix(x) #get row number rownum-nrow(mat) #remove the constant parameters mat1-mat[,apply(mat,2,function(.col)!(all(.col[1]==.col[2:rownum])))]

[R] how can I delete those columes with the same element in every row?

e.g. a= a b c d e 1 1 1 3 1 1 2 1 2 3 4 5 3 1 3 3 8 3 4 1 4 3 3 5 5 1 1 3 1 1I want to delete colume a and colume c, because they have the same values in every row, then ,I want to get this data.frame . b= b d e 1 1 1 1 2 2 4 5 3 3 8 3 4 4 3 5 5 1 1 1the following

[R] another question: how to delete one of columes in two ones with high correlation(0.95)

my programe is below: a=c(1,2,1,1,1); b=c(1,2,3,4,1); c=c(3,4,3,3,3); d=c(1,2,3,5,1); e=c(1,5,3,5,1) data.f=data.frame(a,b,c,d,e) origin.data-data.f cor.matrix-cor(origin.data) origin.cor-cor.matrix m-0 for(i in 1:(cor.matrix[1]-1)) { for(j in (i+1):(cor.matrix[2])) { if

Re: [R] variable selectin---reduce the numbers of initial variable

is the dimension of your problem? HTH, Rick -- From: Frank E Harrell Jr f.harr...@vanderbilt.edu Sent: Thursday, November 05, 2009 4:12 PM To: Ricardo Gonçalves Silva ricard...@terra.com.br Cc: bbslover dlu...@yeah.net; r-help@r-project.org

[R] variable selectin---reduce the numbers of initial variable

hello, my problem is like this: now after processing the varibles, the remaining 160 varibles(independent) and a dependent y. when I used PLS method, with 10 components, the good r2 can be obtained. but I donot know how can I express my equation with the less varibles and the y. It is better to

Re: [R] variable selectin---reduce the numbers of initial variable

-- From: bbslover dlu...@yeah.net Sent: Wednesday, November 04, 2009 10:23 AM To: r-help@r-project.org Subject: [R] variable selectin---reduce the numbers of initial variable hello, my problem is like this: now after processing the varibles

Re: [R] how can I convert .csv format to matrix???

thank you for your help,it is a good way. Steven Kang wrote: can try matrix.x - as.matrix(x) On Mon, Nov 2, 2009 at 8:38 PM, bbslover dlu...@yeah.net wrote: In my disk C:/ have a a.csv file, I want to read it to R, importantly, when I use x=read.csv(C:/a.csv) ,the x format

[R] how can I convert .csv format to matrix???

In my disk C:/ have a a.csv file, I want to read it to R, importantly, when I use x=read.csv(C:/a.csv) ,the x format is data.frame, I want to it to become matrix format, how can I do it ? thank you! -- View this message in context:

Re: [R] data frame is killing me! help

how to put my data into R. James W. MacDonald wrote: bbslover wrote: Steve Lianoglou-6 wrote: Hi, On Oct 22, 2009, at 2:35 PM, bbslover wrote: Usage data(gasoline) Format A data frame with 60 observations on the following 2 variables. octane a numeric

Re: [R] data frame is killing me! help

I have try it, past can add to wanted letter, but can not past the colume names. May be I should learn it hard. Don MacQueen wrote: At 4:57 AM -0700 10/23/09, bbslover wrote: Steve Lianoglou-6 wrote: Hi, On Oct 22, 2009, at 2:35 PM, bbslover wrote: Usage data(gasoline) Format

Re: [R] data frame is killing me! help

thank you Don MacQueen , I will try it. Don MacQueen wrote: At 4:57 AM -0700 10/23/09, bbslover wrote: Steve Lianoglou-6 wrote: Hi, On Oct 22, 2009, at 2:35 PM, bbslover wrote: Usage data(gasoline) Format A data frame with 60 observations on the following 2 variables. octane

[R] how can I kown which package is added, or updated?

there are many R packages, yesterday, 2031 but today 2033 packages. how can I kown which package is added, or updated? -- View this message in context: http://www.nabble.com/how-can-I-kown-which-package-is-added%2C-or-updated--tp26037150p26037150.html Sent from the R help mailing list archive

Re: [R] how can I kown which package is added, or updated?

It is so dramatical. Thank Gabor Grothendieck . I got it. Gabor Grothendieck wrote: Google for CRANberries aggregates and check first hit. On Sat, Oct 24, 2009 at 4:44 AM, bbslover dlu...@yeah.net wrote: there are many R packages, yesterday, 2031 but today 2033 packages. how can I

Re: [R] data frame is killing me! help

Steve Lianoglou-6 wrote: Hi, On Oct 22, 2009, at 2:35 PM, bbslover wrote: Usage data(gasoline) Format A data frame with 60 observations on the following 2 variables. octane a numeric vector. The octane number. NIR a matrix with 401 columns. The NIR spectrum and I see

Re: [R] data frame is killing me! help

I have read that one ,I want to this method to be used to my data.but I donot know how to put my data into R. James W. MacDonald wrote: bbslover wrote: Steve Lianoglou-6 wrote: Hi, On Oct 22, 2009, at 2:35 PM, bbslover wrote: Usage data(gasoline) Format A data frame with 60

[R] data frame is killing me! help

Usage data(gasoline) Format A data frame with 60 observations on the following 2 variables. octane a numeric vector. The octane number. NIR a matrix with 401 columns. The NIR spectrum and I see the gasoline data to see below NIR.1686 nm NIR.1688 nm NIR.1690 nm NIR.1692 nm NIR.1694 nm