## Settings for RMarkdown http://yihui.name/knitr/options#chunk_options
opts_chunk$set(comment = "", warning = FALSE, message = FALSE, tidy = FALSE,
echo = T, fig.width = 10, fig.height = 10)
options(width = 116, scipen = 5, digits = 5)
setwd("~/statistics/Rmedstats/")
SAScii's author, Anthony Damico gave me additional information!
awesome that you're using the sascii package :)
for nhanes, try my fully-commented scripts in https://github.com/ajdamico/usgsd
i will post a full blog on nhanes in two weeks at http://usgsd.blogspot.com/
The National Health and Nutrition Examination Survey (NHANES) is a series of national survey conducted in the US, and is a rich source of variety of information. NHANES I and II data files are in .dat format with .sas script for import.
NHANES I: http://www.cdc.gov/nchs/nhanes/nhanesi.htm
NHANES II: http://www.cdc.gov/nchs/nhanes/nhanesii.htm
## Load SAScii
library(SAScii)
## Import using read.SAScii # It takes time.
nhanesii.allergy <-
read.SAScii(fn = "ftp://ftp.cdc.gov/pub/Health_Statistics/NCHS/nhanes/nhanesii/DU5309.txt",
sas_ri = "ftp://ftp.cdc.gov/pub/Health_Statistics/NCHS/nhanes/nhanesii/DU5309_F.sas")
Only the values are imported. No labeling by converting to factors.
head(nhanesii.allergy)
SEQN N2AL0006 N2AL0010 N2AL0011 N2AL0012 N2AL0013 N2AL0024 N2AL0025 N2AL0026 N2AL0027 N2AL0028 N2AL0029 N2AL0030
1 37 5371 NA 2 2 NA 1 1 9 9 9 NA 6
2 38 5371 NA 2 2 NA 1 1 9 9 9 NA 9
3 44 5371 NA 2 1 NA 1 1 9 9 9 NA 6
4 45 5371 NA 2 2 NA 1 1 9 9 9 NA 3
5 48 5371 NA 2 2 NA 1 1 9 9 9 NA 3
6 49 5371 NA 2 2 NA 1 1 9 9 9 NA 6
N2AL0032 N2AL0034 N2AL0035 N2AL0036 N2AL0037 N2AL0042 N2AL0047 N2AL0049 N2AL0051 N2AL0053 N2AL0055 N2AL0056
1 2 NA 4 1 103 NA 6 NA 2 70 1 1
2 3 NA 5 1 302 NA 11 NA 10 64 1 1
3 1 NA 4 1 46 NA 8 NA 1 68 2 3
4 1 NA 4 1 231 NA 11 NA 9 64 1 1
5 2 NA 4 1 241 NA 10 NA 7 65 2 2
6 2 NA 4 1 254 NA 9 NA 11 66 1 2
N2AL0057 N2AL0059 N2AL0060 N2AL0062 N2AL0064 N2AL0065 N2AL0066 N2AL0067 N2AL0068 N2AL0069 N2AL0070 N2AL0071
1 12 1 8 0 NA NA NA NA NA NA NA NA
2 12 1 9 25 2 NA NA NA NA NA NA NA
3 12 1 7 22 2 NA NA NA NA NA NA NA
4 95 1 13 26 2 NA NA NA NA NA NA NA
5 13 1 10 25 2 NA NA NA NA NA NA NA
6 12 1 10 24 2 NA NA NA NA NA NA NA
N2AL0072 N2AL0073 N2AL0076 N2AL0079 N2AL0080 N2AL0081 N2AL0082 N2AL0091 N2AL0092 N2AL0093 N2AL0094 N2AL0095
1 NA NA NA NA NA NA NA 8 4 NA 1 NA
2 NA NA NA NA NA NA NA 9 5 NA 1 NA
3 NA NA NA NA NA NA NA 4 2 NA 1 NA
4 NA NA NA NA NA NA NA 3 1 NA 1 NA
5 NA NA NA NA NA NA NA 3 1 NA 1 NA
6 NA NA NA NA NA NA NA 4 2 NA 1 NA
N2AL0096 N2AL0097 N2AL0098 N2AL0099 N2AL0100 N2AL0101 N2AL0103 N2AL0104 N2AL0105 N2AL0106 N2AL0107 N2AL0109
1 NA NA NA NA 2 12 2 2 2 9 21 NA
2 NA NA NA NA 2 16 1 2 2 9 18 NA
3 NA NA NA NA 2 18 1 0 1 5 16 5500
4 NA NA NA NA 2 19 1 0 1 7 18 NA
5 NA NA NA NA 2 19 3 0 2 9 12 0
6 NA NA NA NA 2 11 3 0 2 9 15 2000
N2AL0113 N2AL0114 N2AL0115 N2AL0119 N2AL0120 N2AL0121 N2AL0125 N2AL0126 N2AL0127 N2AL0131 N2AL0132 N2AL0133
1 NA NA NA NA NA NA NA NA NA NA NA NA
2 NA NA NA NA NA NA NA NA NA NA NA NA
3 2 NA NA 2 NA NA 2 NA NA 2 NA NA
4 NA NA NA NA NA NA NA NA NA NA NA NA
5 2 NA NA 1 NA 1728 2 NA NA 2 NA NA
6 2 NA NA 1 NA 2664 2 NA NA 2 NA NA
N2AL0137 N2AL0138 N2AL0139 N2AL0143 N2AL0144 N2AL0145 N2AL0149 N2AL0150 N2AL0151 N2AL0155 N2AL0156 N2AL0157
1 NA NA NA NA NA NA NA NA NA NA NA NA
2 NA NA NA NA NA NA NA NA NA NA NA NA
3 2 NA NA 2 NA NA 2 NA NA 2 NA NA
4 NA NA NA NA NA NA NA NA NA NA NA NA
5 2 NA NA 2 NA NA 2 NA NA 2 NA NA
6 2 NA NA 2 NA NA 2 NA NA 2 NA NA
N2AL0161 N2AL0162 N2AL0163 N2AL0167 N2AL0168 N2AL0169 N2AL0173 N2AL0177 N2AL0178 N2AL0179 N2AL0180 N2AL0181
1 NA NA NA NA NA NA NA 2 2 NA NA NA
2 NA NA NA NA NA NA NA 2 2 NA NA NA
3 2 NA NA 2 NA NA 5500 2 1 1 NA NA
4 NA NA NA NA NA NA NA 2 2 NA NA NA
5 1 NA 40 2 NA NA 1768 2 1 1 NA NA
6 2 NA NA 2 NA NA 4664 2 1 1 NA NA
N2AL0182 N2AL0183 N2AL0184 N2AL0186 N2AL0188 N2AL0190 N2AL0192 N2AL0206 N2AL0207 N2AL0208 N2AL0209 N2AL0210
1 NA NA 2 25 76 6 NA 1 2 1 3 290
2 NA NA 2 24 76 11 NA 1 2 1 3 91
3 NA NA 2 20 76 8 NA 6 2 1 3 71
4 NA NA 3 11 76 11 NA 1 2 1 3 193
5 NA NA 2 25 76 10 NA 5 2 1 3 40
6 NA NA 2 28 76 9 NA 2 2 1 3 61
N2AL0213 N2AL0247 N2AL0249 N2AL0251 N2AL0253 N2AL0255 N2AL0256 N2AL0257 N2AL0259 N2AL0260 N2AL0262 N2AL0264
1 NA 44 NA 8 31 1 1 12 2 8 44 1
2 NA 63 NA 6 12 2 1 13 3 9 33 2
3 NA 37 NA 3 38 1 3 72 2 7 21 1
4 NA 37 NA 8 38 2 1 95 4 9 28 1
5 NA 32 NA 7 43 2 2 13 4 10 28 1
6 NA 28 NA 4 47 2 2 13 4 10 31 2
N2AL0265 N2AL0266 N2AL0267 N2AL0268 N2AL0269 N2AL0270 N2AL0271 N2AL0272 N2AL0273 N2AL0276 N2AL0279 N2AL0280
1 1 NA NA 1 1 NA NA NA 717 233 1 1
2 1 NA NA 1 1 NA NA NA 857 230 4 2
3 1 NA NA 1 1 NA NA NA 278 715 1 2
4 1 NA NA 1 1 NA NA NA 707 394 1 2
5 2 NA 2 NA NA 2 2 NA NA NA NA 2
6 2 NA 1 2 1 NA NA NA 769 984 1 2
N2AL0281 N2AL0282 N2AL0288 N2AL0294 N2AL0300 N2AL0306 N2AL0312 N2AL0318 N2AL0324 N2AL0326 N2AL0327 N2AL0328
1 2 21910 18948 0 22813 0 0 NA 1 1 1 NA
2 NA 8210 7345 0 0 17097 0 NA 1 1 2 NA
3 NA 7169 6478 0 0 14543 0 NA 1 1 2 NA
4 NA 8210 7345 0 16210 0 0 NA 1 1 2 NA
5 NA 8271 7511 0 0 12701 0 NA 1 1 2 NA
6 NA 10429 9216 0 22220 0 0 NA 1 1 2 NA
N2AL0401 N2AL0405 N2AL0406 N2AL0409 N2AL0411 N2AL0412 N2AL0414 N2AL0416 N2AL0418 N2AL0419 N2AL0421 N2AL0423
1 5309 0 NA 2 3 NA 0 0 2 0 0 10
2 5309 0 NA 9 3 NA 0 0 2 0 0 10
3 5309 1 NA 88 3 NA 88 88 8 88 88 88
4 5309 0 NA 9 3 NA 0 0 2 0 0 10
5 5309 0 NA 7 3 NA 0 0 2 0 0 10
6 5309 0 NA 7 3 NA 0 0 2 0 0 10
N2AL0425 N2AL0427 N2AL0429 N2AL0431 N2AL0432 N2AL0434 N2AL0436 N2AL0438 N2AL0440 N2AL0442 N2AL0444 N2AL0445
1 10 0 0 2 0 0 20 10 0 0 2 0
2 10 0 0 2 0 0 20 10 0 0 2 0
3 88 88 88 8 88 88 88 88 88 88 8 88
4 10 0 0 2 0 0 20 19 0 0 2 0
5 10 0 0 2 0 0 20 10 0 0 2 0
6 10 0 0 2 0 0 20 10 0 0 2 0
N2AL0447 N2AL0449 N2AL0451 N2AL0453 N2AL0455 N2AL0457 N2AL0458 N2AL0460 N2AL0462 N2AL0464 N2AL0466 N2AL0468
1 0 10 10 0 0 2 0 0 20 10 0 0
2 0 10 10 0 0 2 0 0 20 10 0 0
3 88 88 88 88 88 8 88 88 88 88 88 88
4 0 10 10 0 0 2 0 0 20 19 0 0
5 0 10 10 0 0 2 0 0 20 10 0 0
6 0 10 10 0 0 2 0 0 20 10 0 0
N2AL0470 N2AL0471 N2AL0473 N2AL0475 N2AL0477 N2AL0479 N2AL0481 N2AL0483 N2AL0484 N2AL0486 N2AL0488 N2AL0490
1 2 0 0 10 10 0 0 2 0 0 20 10
2 2 0 0 10 10 0 0 2 0 0 20 10
3 8 88 88 88 88 88 88 8 88 88 88 88
4 2 0 0 10 10 0 0 2 0 0 20 19
5 2 0 0 10 10 0 0 2 0 0 20 10
6 2 0 0 10 10 0 0 2 0 0 20 10
N2AL0492 N2AL0494 N2AL0496 N2AL0497 N2AL0499 N2AL0501 N2AL0503 N2AL0505 N2AL0507 N2AL0509 N2AL0510 N2AL0512
1 0 0 2 0 0 10 10 0 0 2 0 0
2 0 0 2 0 0 10 10 0 0 2 0 0
3 88 88 8 88 88 88 88 88 88 8 88 88
4 0 0 2 0 0 10 10 0 0 2 0 0
5 0 0 2 0 0 10 10 0 0 2 0 0
6 0 0 2 0 0 10 10 0 0 2 0 0
N2AL0514 N2AL0516 N2AL0518 N2AL0520 N2AL0522 N2AL0523 N2AL0525 N2AL0527 N2AL0529 N2AL0531 N2AL0533 N2AL0535
1 20 10 0 0 2 0 0 10 10 0 0 2
2 20 10 0 0 2 0 0 10 10 0 0 2
3 88 88 88 88 8 88 88 88 88 88 88 8
4 20 19 0 0 2 0 0 10 10 0 0 2
5 20 10 0 0 2 0 0 10 10 0 0 2
6 20 10 0 0 2 0 0 10 10 0 0 2
N2AL0536 N2AL0538 N2AL0540 N2AL0542 N2AL0544 N2AL0546 N2AL0548 N2AL0549 N2AL0551 N2AL0553 N2AL0555 N2AL0557
1 0 0 20 10 0 0 2 0 0 10 10 0
2 0 0 20 10 0 0 2 0 0 10 10 0
3 88 88 88 88 88 88 8 88 88 88 88 88
4 0 0 20 19 0 0 2 0 0 10 10 0
5 0 0 20 10 0 0 2 0 0 10 10 0
6 0 0 20 10 0 0 2 0 0 10 10 0
N2AL0559 N2AL0561 N2AL0562 N2AL0564 N2AL0566 N2AL0568 N2AL0570 N2AL0572 N2AL0574 N2AL0575 N2AL0577 N2AL0579
1 0 2 0 0 20 10 0 0 2 0 0 10
2 0 2 0 0 20 10 0 0 2 0 0 10
3 88 8 88 88 88 88 88 88 8 88 88 88
4 0 2 0 0 20 19 0 0 2 0 0 10
5 0 2 0 0 20 10 0 0 2 0 0 10
6 0 2 0 0 20 10 0 0 2 0 0 10
N2AL0581 N2AL0583 N2AL0585 N2AL0587 N2AL0588 N2AL0590 N2AL0592 N2AL0594 N2AL0596 N2AL0598 N2AL0600 N2AL0601
1 10 0 0 2 0 0 20 10 0 0 2 0
2 10 0 0 2 0 0 20 10 0 0 2 0
3 88 88 88 8 88 88 88 88 88 88 8 88
4 10 0 0 2 0 0 20 19 0 0 2 0
5 10 0 0 2 0 0 20 10 0 0 2 0
6 10 0 0 2 0 0 20 10 0 0 2 0
N2AL0603 N2AL0605 N2AL0607 N2AL0609 N2AL0611 N2AL0613 N2AL0614 N2AL0616 N2AL0618 N2AL0620 N2AL0622 N2AL0624
1 0 10 10 0 0 2 0 0 20 10 0 0
2 0 10 10 0 0 2 0 0 20 10 0 0
3 88 88 88 88 88 8 88 88 88 88 88 88
4 0 10 10 0 0 2 0 0 20 19 0 0
5 0 10 10 0 0 2 0 0 20 10 0 0
6 0 10 10 0 0 2 0 0 20 10 0 0
N2AL0626 N2AL0627 N2AL0629 N2AL0631 N2AL0633 N2AL0635 N2AL0637 N2AL0639 N2AL0640 N2AL0642 N2AL0644 N2AL0646
1 2 0 0 10 10 0 0 2 0 0 20 10
2 2 0 0 10 10 0 0 2 0 0 20 10
3 8 88 88 88 88 88 88 8 88 88 88 88
4 2 0 0 10 10 0 0 2 0 0 20 10
5 2 0 0 10 10 0 0 2 0 0 20 10
6 2 0 0 10 10 0 0 2 0 0 20 10
N2AL0648 N2AL0650 N2AL0652 N2AL0653 N2AL0655 N2AL0657 N2AL0659 N2AL0661 N2AL0663 N2AL0665 N2AL0666 N2AL0668
1 0 0 2 0 0 10 10 0 0 2 0 0
2 88 88 8 12 12 10 11 88 88 8 12 12
3 88 88 8 88 88 88 88 88 88 8 88 88
4 88 88 8 88 88 88 16 88 88 8 88 88
5 0 0 2 0 0 10 10 0 0 2 0 0
6 0 0 2 0 0 10 10 0 0 2 0 0
N2AL0670 N2AL0672 N2AL0674 N2AL0675 N2AL0676 N2AL0677 N2AL0678 N2AL0679 N2AL0680 N2AL0681 N2AL0682 N2AL0683
1 20 10 NA 0 0 0 0 0 0 0 0 0
2 20 11 NA 0 0 0 0 0 0 0 0 0
3 88 88 NA 0 0 0 0 0 0 0 0 0
4 88 16 NA 0 0 0 0 0 0 0 0 0
5 20 10 NA 0 0 0 0 0 0 0 0 0
6 20 10 NA 0 0 0 0 0 0 0 0 0
N2AL0684 N2AL0685 N2AL0686 N2AL0687 N2AL0688 N2AL0689 N2AL0690 N2AL0691 N2AL0692 N2AL0693 N2AL0694 N2AL0695
1 0 0 0 0 0 0 0 0 0 0 0 NA
2 0 0 0 0 0 0 0 0 0 0 0 NA
3 0 0 0 0 0 0 0 0 0 0 0 NA
4 0 0 0 0 0 0 0 0 0 0 0 NA
5 0 0 0 0 0 0 0 0 0 0 0 NA
6 0 0 0 0 0 0 0 0 0 0 0 NA