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 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)

#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)

####################### 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
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@samhsa.hhs.gov<mailto:Pradip.Muhuri@samhsa.hhs.gov>

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