[R] (no subject)
Daniel Malter
daniel at umd.edu
Tue Jun 21 09:33:30 CEST 2011
Let us work backward. The pic_onscr() fails because lda_result does not
exist. lda_result does not exist because your lda() fails. Your lda() fails
because "Error in lda.default(x, grouping, ...) :
variables 1 3 5 8 10 15 17 20 27 29 34 appear to be constant within
groups" This indicates that lda_data in lda(lda_data,groups) is constant for
at least some of the groups. This would happen, for example, if certain
groups have only one observation. You will have to remove those groups for
which lda_data is constant or aggregate them to larger groups.
HTH,
Daniel
kaslah wrote:
>
> hello,
> i already include the error in blue color word.
> i hope it can help you to understand my question.
> if not burden you, please give me a guide how to correct the error or
> maybe you
> can correct the coding cause error.
> thank you.
>
>
>
>> # 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
>>
>> #
>> # 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 #####
>>
> [[alternative HTML version deleted]]
>
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