Hi Pradip,
May be this helps:
dat1<-read.table(text="
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
",sep="",header=TRUE,stringsAsFactors=FALSE)
Lines1<-capture.output(printCoefmat(dat1[,-c(1:2)],has.Pvalue=TRUE,eps.Pvalue=0.001))
Lines2<-gsub("\\s+$","",gsub("\\.$","",Lines1[1:15]))
res<-data.frame(dat1[,1:2],read.table(text=Lines2,header=TRUE))
#or
# res<-cbind(dat1[,1:2],read.table(text=Lines2,header=TRUE))
res
# contrast_level1 contrast_level2 mean_level1 mean_level2 rel_diff p_mean
#1 wh 2+hi 18.7 11.91 0.574 0.0000
#2 wh 2+rc 18.7 14.46 0.297 0.0000
#3 wh aian 18.7 13.54 0.384 0.0001
-------------------------------------------------------------
----------------------------------------------------------
# cohens_d
#1 0.1753
#2 0.1101
#3 0.1335
-------------------------------------------------
-------------------------------------------------
str(res)
#'data.frame': 14 obs. of 7 variables:
# $ contrast_level1: chr "wh" "wh" "wh" "wh" ...
# $ contrast_level2: chr "2+hi" "2+rc" "aian" "asan" ...
# $ mean_level1 : num 18.7 18.7 18.7 18.7 18.7 18.7 18.7 18.7 18.7 18.7 ...
# $ mean_level2 : num 11.91 14.46 13.54 6 5.83 ...
# $ rel_diff : num 0.574 0.297 0.384 2.123 2.213 ...
# $ p_mean : num 0e+00 0e+00 1e-04 0e+00 0e+00 0e+00 0e+00 0e+00 0e+00
0e+00 ...
# $ cohens_d : num 0.175 0.11 0.134 0.333 0.349 ...
A.K.
----- Original Message -----
From: "Muhuri, Pradip (SAMHSA/CBHSQ)" <pradip.muh...@samhsa.hhs.gov>
To: 'David Winsemius' <dwinsem...@comcast.net>
Cc: R help <r-help@r-project.org>
Sent: Friday, December 14, 2012 5:18 PM
Subject: Re: [R] format.pval () and printCoefmat ()
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.
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
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______________________________________________
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
