[R] brlr function

[Min-Han Tan]

Hi,

I'm trying the brlr function in a penalized logistic regression function. 

However, I am not sure why I am encountering errors. I hope to seek
your advice here. (output below)

Thank you! Your help is truly appreciated.

Min-Han


#No error here, the glm seems to work fine
> genes.cox1.glm1<-glm(as.formula(paste(paste('as.integer(sim.cv.cox.yhat1)~'),paste('sim.dat.tst[',genes.cox1.rows,',]',sep="",collapse='+'))))

#Something happened here ... I only substituted brlr for glm
 > genes.cox1.glm1<-brlr(as.formula(paste(paste('as.integer(sim.cv.cox.yhat1)~'),paste('sim.dat.tst[',genes.cox1.rows,',]',sep="",collapse='+'))))
Error in eval(expr, envir, enclos) : y values must be 0 <= y <= 1

#using the test data in brlr gives the same error if the dependent is
reduced to one column, is it a problem with my dependent? It works
fine as per the original vignette with
brlr(cbind(grahami,opalinus)~height ...)
> brlr(grahami~height+diameter,data=lizards)
Error in eval(expr, envir, enclos) : y values must be 0 <= y <= 1
 
#This is how the objects look
> as.integer(sim.cv.cox.yhat1)
 [1] 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 2 2 2 1 1 2 2 1 1 1 2 1 2 2 2
1 2 1 1 2 1 1 2 1 1 1 2 2 2 2

> as.formula(paste(paste('as.integer(sim.cv.cox.yhat1)~'),paste('sim.dat.tst[',genes.cox1.rows,',]',sep="",collapse='+')))
as.integer(sim.cv.cox.yhat1) ~ sim.dat.tst[27, ] + sim.dat.tst[35, 
    ] + sim.dat.tst[17, ] + sim.dat.tst[41, ] + sim.dat.tst[38, 
    ] + sim.dat.tst[31, ] + sim.dat.tst[3, ] + sim.dat.tst[32, 
    ] + sim.dat.tst[16, ] + sim.dat.tst[48, ] + sim.dat.tst[13, 
    ] + sim.dat.tst[28, ]
 
> sim.dat.tst[27,]
Sample 1  Sample 2  Sample 3  Sample 4  Sample 5  Sample 6  Sample 7 
Sample 8  Sample 9 Sample 10 Sample 11 Sample 12 Sample 13 Sample 14
Sample 15
     5.79      6.72      6.11      5.58      6.32      6.50      6.45 
    5.77      7.46      6.32      5.64      5.77      5.44      5.83  
   5.57
Sample 16 Sample 17 Sample 18 Sample 19 Sample 20 Sample 21 Sample 22
Sample 23 Sample 24 Sample 25 Sample 26 Sample 27 Sample 28 Sample 29
Sample 30
     5.70      5.67      5.72      5.50      6.34      5.98      6.10 
    6.25      6.13      7.40      7.28      8.37      5.73      6.83  
   5.72
Sample 31 Sample 32 Sample 33 Sample 34 Sample 35 Sample 36 Sample 37
Sample 38 Sample 39 Sample 40 Sample 41 Sample 42 Sample 43 Sample 44
Sample 45
     6.12      6.74      6.64      6.13      7.74      6.70      7.37 
    6.54      6.49      5.75      6.18      6.41      7.68      5.36  
   6.34
Sample 46 Sample 47 Sample 48 
     5.86      6.64      6.69