Hi
>
> [R] what is the mistake?? the coding still not function. no result
display
>
> # lda.r
> > #
> > # Author: Amsha Nahid, Jairus Bowne, Gerard Murray
> > # Purpose: Perform Linear Discriminant Analysis (LDA)
> > #
> > # Input: Data matrix as specified in Data-matrix-format.pdf
> > # Output: LDA plot
> > #
> > # Notes: Missing values (if any) are replaced by the half of the
lowest
> > # value in the entire data matrix.
> >
> >
> > #
> > # Load necessary libraries, and install them if they are missing
> > #
> > tryCatch(library(MASS), error=function(err)
> + # if this produces an error:
> + install.packages("MASS",repos="http://cran.ms.unimelb.edu.au/";))
> >
> > #
> > # Prepare the data matrix
> > #
> > # Read in the .csv file
> > data<-read.csv("C:/Users/nadya/Desktop/praktikal
UTM/TASK2/new(40data)S2 100
> >EMS EPI 300-399.csv", sep=",", row.names=1, header=TRUE)
> > # Get groups information
> > groups<-data[,1]
> > # Remove groups for data processing
> > lda_data<-data[,-1]
> > # Replace any missing values (see Notes)
> > lda_data[is.na(lda_data)]<-0.5*(min(lda_data,na.rm=TRUE))
> >
> > #
> > # Perform the LDA
> > #
> > lda_result<-lda(lda_data,groups)
> Error in lda.default(x, grouping, ...) :
> variables 1 3 5 8 10 15 17 20 27 29 34 appear to be constant
within groups
The problem seems to be with your data, which in some groups are constant.
Try
split(lda_data, groups)
or
sapply(split(lda_data, groups), length)
and see your result.
Regards
Petr
> >
> > #
> > # Generate the figures (on screen)
> > #
> > # Image generation - function definition
> > pic_onscr<-function(matrix, title, cex_val=1)
> + {x11()
> + par(mgp=c(5,2,0), # axis margins
> + # (title, labels,
line)
> + mar=c(7,4,4,2), # plot margins
(b,l,t,r)
> + las=1) # horizontal labels
> + plot(matrix, # data to plot
> + cex=cex_val, # font size
> + dimen=2 # dimensions to plot
> + )
> + title(main=title) # title of plot
> + }
> > # Plot LDA scores with sample names
> > pic_onscr(lda_result,"Linear Discriminant Analysis")
> Error in plot(matrix, cex = cex_val, dimen = 2) :
> error in evaluating the argument 'x' in selecting a method for
function
> 'plot': Error: object 'lda_result' not found
> > # For plotting with larger font size, use a different value of cex:
> > # pic_onscr(lda_result, "LDA Plot", dimen=2, cex=3)
> >
> > #
> > # Generate figures as image files
> > #
> > # (Uncomment blocks as necessary)
> >
> > ##### jpeg #####
> > # pic_jpg<-function(filename, matrix, title, cex_val=1)
> > # {# Start jpeg device with basic settings
> > # jpeg(filename,
> > # quality=100, # image quality
(percent)
> > # bg="white", # background colour
> > # res=300, # image resolution
(dpi)
> > # units="in", width=8.3, height=5.8 # image dimensions
(inches)
> > # )
> > # par(mgp=c(5,2,0), # axis margins
> > # # (title, labels,
line)
> > # mar=c(7,4,4,2), # plot margins
(b,l,t,r)
> > # las=1 # horizontal labels
> > # )
> > # # Draw the plot
> > # plot(matrix, # data to plot
> > # cex=cex_val, # font size
> > # dimen=2 # dimensions to plot
> > # )
> > # title(main=title) # title of plot
> > #
> > # dev.off()
> > # }
> > # pic_jpg("LDA.jpg", lda_result, "Linear Discriminant Analysis")
> > ##### end jpeg #####
> >
> > ##### png #####
> > # pic_png<-function(filename, matrix, title, cex_val=1)
> > # {# Start png device with basic settings
> > # png(filename,
> > # bg="white", # background colour
> > # res=300, # image resolution
(dpi)
> > # units="in", width=8.3, height=5.8 # image dimensions
(inches)
> > # )
> > # par(mgp=c(5,2,0), # axis margins
> > # # (title, labels,
line)
> > # mar=c(7,4,4,2), # plot margins
(b,l,t,r)
> > # las=1 # horizontal labels
> > # )
> > # # Draw the plot
> > # plot(matrix, # data to plot
> > # cex=cex_val, # font size
> > # dimen=2 # dimensions to plot
> > # )
> > # title(main=title) # title of plot
> > #
> > # dev.off()
> > # }
> > # pic_png("LDA.png", lda_result, "Linear Discriminant Analysis")
> > ##### end png #####
> >
> > ##### tiff #####
> > # pic_tiff<-function(filename, matrix, title, cex_val=1)
> > # {# Start tiff device with basic settings
> > # tiff(filename,
> > # bg="white", # background colour
> > # res=300, # image resolution
(dpi)
> > # units="in", width=8.3, height=5.8, # image dimensions
(inches)
> > # compression="none" # image compression
> > # # (one of none,
lzw, zip)
> > # )
> > # par(mgp=c(5,2,0), # axis margins
> > # # (title, labels,
line)
> > # mar=c(7,4,4,2), # plot margins
(b,l,t,r)
> > # las=1 # horizontal labels
> > # )
> > # # Draw the plot
> > # plot(matrix, # data to plot
> > # cex=cex_val, # font size
> > # dimen=2 # dimensions to plot
> > # )
> > # title(main=title) # title of plot
> > #
> > # dev.off()
> > # }
> > # pic_tiff("LDA.tif", lda_result, "Linear Discriminant Analysis")
> > ##### end tiff #####
> >
>
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>
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