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.muh...@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:dwinsem...@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 ______________________________________________ R-help@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.
