Hello everyone, I am totally new to the R program. I have had a look at some pdf documents that I downloaded and that explain how to do many things in R; however, I still cannot figure out how to do what I want to do, which is to perform Discriminant Correspondence Analysis on a rectangular matrix of data that I have in an Excel file. I know R users frown upon Excel and recommend converting Excel files to .csv format, which I have done, no problem. That is not an issue. There are several parts to my problem. 1) When I try the read.table command, even if I include the directory name in the filename, R still cannot read the file, even if it is in .csv format 2) I was able to copy my file and then read the clipboard contents into R but then I do not know to assign a name to the data frame in order to conduct any operations on it 3) I need the ADE4 program in order to perform Discriminant Correspondence Analysis, so I used the "install.packages" command to install it. It installed no problem but I do not know how to access the ADE4 program in R. I am unable to open it directly, either. 4) I thought that using the ADE4 GUI (called "ade4TkGUI") would be easier because I do not know many of the R commands; but, again, I downloaded it but cannot open or access it. The following is the suggested coding that I found through the R website, but when I try to use this code, I don't know how to assign a name for the df, or what to put for "fac", and what is worse, I get an error message saying that the program cannot find the "discrimin.coa" command. Usage discrimin.coa(df, fac, scannf = TRUE, nf = 2) Arguments df a data frame containing positive or null values fac a factor defining the classes of discriminant analysis scannf a logical value indicating whether the eigenvalues bar plot should be displayed nf if scannf FALSE, an integer indicating the number of kept axes Examples data(perthi02) plot(discrimin.coa(perthi02$tab, perthi02$cla, scan = FALSE)) For clarification, my data consists of measurements of morphological characters of an assemblage of biological specimens. I have already performed Principal Co-ordinates Analysis, Principal Compionents Analysis and Cluster Analysis in another program (PAST) in order to see if the data fall into distinct groupings that might represent different morphological species. I now want to test the groupings that I found on my test data set using Discriminant Correspondence Analysis.There are both continuous and categorical characters, which is the reason why I need to perform Discriminant Correspondence Analysis, instead of Linear Discriminant Analysis, which is only valid for continuous measurements. R seems to be the only program in which I can perform Discriminant Correspondence Analysis. Thanks for any help offered on any of these points. Wayne [[alternative HTML version deleted]]
Read files, if you're on windows remember to include the path like this: "C:\\Documents and Settings\\USER\\My Documents\\MyFile.csv" -----Original Message----- From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On Behalf Of Wayne Sawtell Sent: Tuesday, December 14, 2010 12:36 PM To: r-help at r-project.org Subject: [R] Discriminant Correspondence Analysis Hello everyone, I am totally new to the R program. I have had a look at some pdf documents that I downloaded and that explain how to do many things in R; however, I still cannot figure out how to do what I want to do, which is to perform Discriminant Correspondence Analysis on a rectangular matrix of data that I have in an Excel file. I know R users frown upon Excel and recommend converting Excel files to .csv format, which I have done, no problem. That is not an issue. There are several parts to my problem. 1) When I try the read.table command, even if I include the directory name in the filename, R still cannot read the file, even if it is in .csv format 2) I was able to copy my file and then read the clipboard contents into R but then I do not know to assign a name to the data frame in order to conduct any operations on it 3) I need the ADE4 program in order to perform Discriminant Correspondence Analysis, so I used the "install.packages" command to install it. It installed no problem but I do not know how to access the ADE4 program in R. I am unable to open it directly, either. 4) I thought that using the ADE4 GUI (called "ade4TkGUI") would be easier because I do not know many of the R commands; but, again, I downloaded it but cannot open or access it. The following is the suggested coding that I found through the R website, but when I try to use this code, I don't know how to assign a name for the df, or what to put for "fac", and what is worse, I get an error message saying that the program cannot find the "discrimin.coa" command. Usage discrimin.coa(df, fac, scannf = TRUE, nf = 2) Arguments df a data frame containing positive or null values fac a factor defining the classes of discriminant analysis scannf a logical value indicating whether the eigenvalues bar plot should be displayed nf if scannf FALSE, an integer indicating the number of kept axes Examples data(perthi02) plot(discrimin.coa(perthi02$tab, perthi02$cla, scan = FALSE)) For clarification, my data consists of measurements of morphological characters of an assemblage of biological specimens. I have already performed Principal Co-ordinates Analysis, Principal Compionents Analysis and Cluster Analysis in another program (PAST) in order to see if the data fall into distinct groupings that might represent different morphological species. I now want to test the groupings that I found on my test data set using Discriminant Correspondence Analysis.There are both continuous and categorical characters, which is the reason why I need to perform Discriminant Correspondence Analysis, instead of Linear Discriminant Analysis, which is only valid for continuous measurements. R seems to be the only program in which I can perform Discriminant Correspondence Analysis. Thanks for any help offered on any of these points. Wayne [[alternative HTML version deleted]] ______________________________________________ R-help at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Wayne,>> I don't know how to assign a name for the df, or what to put for "fac", >> and what is worse, >> I get an error message saying that the program cannot find the >> "discrimin.coa" command.Before you can use a package you have downloaded you need to "activate" it. There are different ways of doing this. Simplest is to type library(ade4). ## library(ade4) ?discrimin.coa Follow Bastiaan and read in your file as follows (single forward slashes also work): ## See ?read.csv as you may need to change some switches MyFile <- read.csv("C:\\Documents and Settings\\USER\\My Documents\\MyFile.csv") str(MyFile) Without data it is difficult to help you further, but your general call to discrimin.coa is ## This may or may not work; depends what's in MyFile T.discrimin <- discrimin.coa(MyFile, fac = someFacInMyFile, scann=F, nf=4) T.discrimin plot(T.discrimin) Regards, Mark. -- View this message in context: http://r.789695.n4.nabble.com/Discriminant-Correspondence-Analysis-tp3087929p3088091.html Sent from the R help mailing list archive at Nabble.com.
Wayne, So far, no one has said the obvious: Please do work your way through (or at least skim) "An Introduction to R" which you'll find right there on your computer under Help/Manuals. Your questions indicate that you have not yet done so. Do it, it really will pay off. Peter Ehlers On 2010-12-14 12:36, Wayne Sawtell wrote:> Hello everyone, > > I am totally new to the R program. I have had a look at some pdf documents > that I downloaded and that explain how to do many things in R; however, I > still cannot figure out how to do what I want to do, which is to perform > Discriminant Correspondence Analysis on a rectangular matrix of data that I > have in an Excel file. I know R users frown upon Excel and recommend > converting Excel files to .csv format, which I have done, no problem. That > is not an issue. > There are several parts to my problem. > 1) When I try the read.table command, even if I include the directory name > in the filename, R still cannot read the file, even if it is in .csv format > 2) I was able to copy my file and then read the clipboard contents into R > but then I do not know to assign a name to the data frame in order to > conduct any operations on it > 3) I need the ADE4 program in order to perform Discriminant Correspondence > Analysis, so I used the "install.packages" command to install it. It > installed no problem but I do not know how to access the ADE4 program in R. > I am unable to open it directly, either. > 4) I thought that using the ADE4 GUI (called "ade4TkGUI") would be easier > because I do not know many of the R commands; but, again, I downloaded it > but cannot open or access it. > > The following is the suggested coding that I found through the R website, > but when I try to use this code, I don't know how to assign a name for the > df, or what to put for "fac", and what is worse, I get an error message > saying that the program cannot find the "discrimin.coa" command. > > > Usage > > discrimin.coa(df, fac, scannf = TRUE, nf = 2) > > Arguments > > df a data frame containing positive or null values > > fac a factor defining the classes of discriminant analysis > > scannf a logical value indicating whether the eigenvalues bar plot should be > displayed > > nf if scannf FALSE, an integer indicating the number of kept axes > > Examples > > data(perthi02) > > plot(discrimin.coa(perthi02$tab, perthi02$cla, scan = FALSE)) > For clarification, my data consists of measurements of morphological > characters of an assemblage of biological specimens. I have already > performed Principal Co-ordinates Analysis, Principal Compionents Analysis > and Cluster Analysis in another program (PAST) in order to see if the data > fall into distinct groupings that might represent different morphological > species. I now want to test the groupings that I found on my test data set > using Discriminant Correspondence Analysis.There are both continuous and > categorical characters, which is the reason why I need to perform > Discriminant Correspondence Analysis, instead of Linear Discriminant > Analysis, which is only valid for continuous measurements. R seems to be the > only program in which I can perform Discriminant Correspondence Analysis. > > Thanks for any help offered on any of these points. > Wayne > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.
On 15/12/2010 9:36 a.m., Wayne Sawtell wrote:> Hello everyone, > > I am totally new to the R program. I have had a look at some pdf documents > that I downloaded and that explain how to do many things in R; however, I > still cannot figure out how to do what I want to do, which is to perform > Discriminant Correspondence Analysis on a rectangular matrix of data that I > have in an Excel file. I know R users frown upon Excel and recommend > converting Excel files to .csv format, which I have done, no problem. That > is not an issue.Actually one of the things we don't like about Excel is how it writes .csv files, so many R users find it much more reliable to read data directly from Excel files. In my case, the two major tools I use on Windows with great satisfaction are xlsReadWrite and RODBC. There are other suitable options if you are working on linux. For more comprehensive information see: http://rwiki.sciviews.org/doku.php?id=tips:data-io:ms_windows David Scott> There are several parts to my problem. > 1) When I try the read.table command, even if I include the directory name > in the filename, R still cannot read the file, even if it is in .csv format > 2) I was able to copy my file and then read the clipboard contents into R > but then I do not know to assign a name to the data frame in order to > conduct any operations on it > 3) I need the ADE4 program in order to perform Discriminant Correspondence > Analysis, so I used the "install.packages" command to install it. It > installed no problem but I do not know how to access the ADE4 program in R. > I am unable to open it directly, either. > 4) I thought that using the ADE4 GUI (called "ade4TkGUI") would be easier > because I do not know many of the R commands; but, again, I downloaded it > but cannot open or access it. > > The following is the suggested coding that I found through the R website, > but when I try to use this code, I don't know how to assign a name for the > df, or what to put for "fac", and what is worse, I get an error message > saying that the program cannot find the "discrimin.coa" command. > > > Usage > > discrimin.coa(df, fac, scannf = TRUE, nf = 2) > > Arguments > > df a data frame containing positive or null values > > fac a factor defining the classes of discriminant analysis > > scannf a logical value indicating whether the eigenvalues bar plot should be > displayed > > nf if scannf FALSE, an integer indicating the number of kept axes > > Examples > > data(perthi02) > > plot(discrimin.coa(perthi02$tab, perthi02$cla, scan = FALSE)) > For clarification, my data consists of measurements of morphological > characters of an assemblage of biological specimens. I have already > performed Principal Co-ordinates Analysis, Principal Compionents Analysis > and Cluster Analysis in another program (PAST) in order to see if the data > fall into distinct groupings that might represent different morphological > species. I now want to test the groupings that I found on my test data set > using Discriminant Correspondence Analysis.There are both continuous and > categorical characters, which is the reason why I need to perform > Discriminant Correspondence Analysis, instead of Linear Discriminant > Analysis, which is only valid for continuous measurements. R seems to be the > only program in which I can perform Discriminant Correspondence Analysis. > > Thanks for any help offered on any of these points. > Wayne > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.-- _________________________________________________________________ David Scott Department of Statistics The University of Auckland, PB 92019 Auckland 1142, NEW ZEALAND Phone: +64 9 923 5055, or +64 9 373 7599 ext 85055 Email: d.scott at auckland.ac.nz, Fax: +64 9 373 7018 Director of Consulting, Department of Statistics