format.pval () and printCoefmat ()
On Dec 14, 2012, at 2:18 PM, Muhuri, Pradip (SAMHSA/CBHSQ) wrote:
Hi David, Thank you so much for helping me with the code. Your suggested code gives me the following results. Please see below. I don't understand why I am getting two blocks of prints (5 columns, and then 7 columns), with some columns repeated.
I am not sure why you think we will be able to answer this question. Your data is on your drive and you have not provided it in a form that would allow one to assist any further than the apparently inaccurate guesses already offered. You should consult this function: ?dput # use this with: y0410_1825_mf_alc
David. > > Regards, > > Pradip > ############################# > >> cbind( y0410_1825_mf_alc[ 1:2], > + printCoefmat(y0410_1825_mf_alc[ -(1:2) ], has.Pvalue=TRUE, eps.Pvalue=0.0001) > + ) > mean_level1 mean_level2 rel_diff p_mean cohens_d > 1 18.744 11.911 0.574 0.00 0.175 > 2 18.744 14.455 0.297 0.00 0.110 > 3 18.744 13.540 0.384 0.00 0.133 > 4 18.744 6.002 2.123 0.00 0.333 > 5 18.744 5.834 2.213 0.00 0.349 > 6 18.744 7.933 1.363 0.00 0.279 > 7 18.744 10.849 0.728 0.00 0.203 > 8 18.744 7.130 1.629 0.00 0.298 > 9 18.744 9.720 0.928 0.00 0.242 > 10 18.744 9.600 0.952 0.00 0.242 > 11 18.744 16.135 0.162 0.17 0.067 . > 12 18.744 NA NA NA NA > 13 18.744 10.465 0.791 0.00 0.213 > 14 18.744 15.149 0.237 0.02 0.092 . > --- > Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 > contrast_level1 contrast_level2 mean_level1 mean_level2 rel_diff p_mean cohens_d > 1 wh 2+hi 18.7 11.91 0.574 1.64e-05 0.1753 > 2 wh 2+rc 18.7 14.46 0.297 9.24e-06 0.1101 > 3 wh aian 18.7 13.54 0.384 9.01e-05 0.1335 > 4 wh asan 18.7 6.00 2.123 2.20e-119 0.3326 > 5 wh blck 18.7 5.83 2.213 0.00e+00 0.3490 > 6 wh csam 18.7 7.93 1.363 1.27e-47 0.2793 > 7 wh cub 18.7 10.85 0.728 6.12e-08 0.2025 > 8 wh dmcn 18.7 7.13 1.629 1.59e-15 0.2981 > 9 wh hisp 18.7 9.72 0.928 3.27e-125 0.2420 > 10 wh mex 18.7 9.60 0.952 8.81e-103 0.2420 > 11 wh nhpi 18.7 16.14 0.162 1.74e-01 0.0669 > 12 wh othh 18.7 NA NA NA NA > 13 wh pr 18.7 10.47 0.791 3.64e-23 0.2131 > 14 wh spn 18.7 15.15 0.237 1.58e-02 0.0922 > > Pradip K. Muhuri, PhD > Statistician > Substance Abuse & Mental Health Services Administration > The Center for Behavioral Health Statistics and Quality > Division of Population Surveys > 1 Choke Cherry Road, Room 2-1071 > Rockville, MD 20857 > > Tel: 240-276-1070 > Fax: 240-276-1260 > e-mail: Pradip.Muhuri at samhsa.hhs.gov > > The Center for Behavioral Health Statistics and Quality your feedback. Please click on the following link to complete a brief customer survey: http://cbhsqsurvey.samhsa.gov > > -----Original Message----- > From: David Winsemius [mailto:dwinsemius at comcast.net] > Sent: Friday, December 14, 2012 3:22 PM > To: Muhuri, Pradip (SAMHSA/CBHSQ) > Cc: R help > Subject: Re: [R] format.pval () and printCoefmat () > > > On Dec 14, 2012, at 11:48 AM, Muhuri, Pradip (SAMHSA/CBHSQ) wrote: > >> Hi List, >> >> My goal is to force R not to print in scientific notation in the sixth column (rel_diff - for the p-value) of my data frame (not a matrix). >> >> I have used the format.pval () and printCoefmat () functions on the data frame. The R script is appended below. >> >> This issue is that use of the format.pval () and printCoefmat () functions on the data frame gives me the desired results, but coerces the character string into NAs for the two character variables, because my object is a data frame, not a matrix. Please see the first output below: contrast_level1 contrast_level2). >> >> Is there a way I could have avoid printing the NAs in the character fields > > They are probably factor columns. > >> when using the format.pval () and printCoefmat () on the data frame? >> >> I would appreciate receiving your help. >> >> Thanks, >> >> Pradip >> setwd ("F:/PR1/R_PR1") >> >> load (file = "sigtests_overall_withid.rdata") >> >> #format.pval(tt$p.value, eps=0.0001) >> >> # keep only selected columns from the above data frame >> keep_cols1 <- c("contrast_level1", "contrast_level2","mean_level1", >> "mean_level2", "rel_diff", >> "p_mean", "cohens_d") >> >> #subset the data frame >> y0410_1825_mf_alc <- subset (sigtests_overall_withid, >> years=="0410" & age_group=="1825" >> & gender_group=="all" & drug=="alc" >> & contrast_level1=="wh", >> select=keep_cols1) >> #change the row.names >> row.names (y0410_1825_mf_alc)= 1:dim(y0410_1825_mf_alc)[1] >> >> #force >> format.pval(y0410_1825_mf_alc$p_mean, eps=0.0001) > > Presumably that call will produce desired results since it is on only one column. (I'm not sure why you think format.pval contributed to your NA output.) > >> >> #print the observations from the sub-data frame >> options (width=120,digits=3 ) >> #y0410_1825_mf_alc >> >> printCoefmat(y0410_1825_mf_alc, has.Pvalue=TRUE, eps.Pvalue=0.0001) > > Why not use `cbind.data.frame` rather than trying to get `printCoefmat` to do something it (apparently) wasn't designed to do? > > cbind( y0410_1825_mf_alc[ 1:2], > printCoefmat(y0410_1825_mf_alc[ -(1:2) ], has.Pvalue=TRUE, eps.Pvalue=0.0001) > ) > > -- > David. > >> >> ####################### When format.pval () and printCoefmat () used >> >> >> contrast_level1 contrast_level2 mean_level1 mean_level2 rel_diff p_mean cohens_d >> >> 1 NA NA 18.744 11.911 0.574 0.00 0.175 >> 2 NA NA 18.744 14.455 0.297 0.00 0.110 >> 3 NA NA 18.744 13.540 0.384 0.00 0.133 >> 4 NA NA 18.744 6.002 2.123 0.00 0.333 >> 5 NA NA 18.744 5.834 2.213 0.00 0.349 >> 6 NA NA 18.744 7.933 1.363 0.00 0.279 >> 7 NA NA 18.744 10.849 0.728 0.00 0.203 >> 8 NA NA 18.744 7.130 1.629 0.00 0.298 >> 9 NA NA 18.744 9.720 0.928 0.00 0.242 >> 10 NA NA 18.744 9.600 0.952 0.00 0.242 >> 11 NA NA 18.744 16.135 0.162 0.17 0.067 . >> 12 NA NA 18.744 NA NA NA NA >> 13 NA NA 18.744 10.465 0.791 0.00 0.213 >> 14 NA NA 18.744 15.149 0.237 0.02 0.092 . >> --- >> Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 >> Warning messages: >> 1: In data.matrix(x) : NAs introduced by coercion >> 2: In data.matrix(x) : NAs introduced by coercion >> >> ####################### When format.pval () and printCoefmat () not used >> >> contrast_level1 contrast_level2 mean_level1 mean_level2 rel_diff p_mean cohens_d >> 1 wh 2+hi 18.7 11.91 0.574 1.64e-05 0.1753 >> 2 wh 2+rc 18.7 14.46 0.297 9.24e-06 0.1101 >> 3 wh aian 18.7 13.54 0.384 9.01e-05 0.1335 >> 4 wh asan 18.7 6.00 2.123 2.20e-119 0.3326 >> 5 wh blck 18.7 5.83 2.213 0.00e+00 0.3490 >> 6 wh csam 18.7 7.93 1.363 1.27e-47 0.2793 >> 7 wh cub 18.7 10.85 0.728 6.12e-08 0.2025 >> 8 wh dmcn 18.7 7.13 1.629 1.59e-15 0.2981 >> 9 wh hisp 18.7 9.72 0.928 3.27e-125 0.2420 >> 10 wh mex 18.7 9.60 0.952 8.81e-103 0.2420 >> 11 wh nhpi 18.7 16.14 0.162 1.74e-01 0.0669 >> 12 wh othh 18.7 NA NA NA NA >> 13 wh pr 18.7 10.47 0.791 3.64e-23 0.2131 >> 14 wh spn 18.7 15.15 0.237 1.58e-02 0.0922 >> >> >> >> Pradip K. Muhuri, PhD >> > > > David Winsemius > Alameda, CA, USA > David Winsemius Alameda, CA, USA