Nothing
inst/doc/Introducing_nhanesA.R
In nhanesA: NHANES Data Retrieval
## ----nhanestables, eval=FALSE-------------------------------------------------
# library(nhanesA)
# nhanesTables('EXAM', 2005)
## ----nhanestables1, echo=FALSE------------------------------------------------
df <- data.frame(matrix(1,nrow=13,ncol=2))
names(df) <- c('Data.File.Name', 'Data.File.Description')
df[1,] <- list('BPX_D', 'Blood Pressure')
df[2,] <- list('BMX_D', 'Body Measures')
df[3,] <- list('AUX_D', 'Audiometry')
df[4,] <- list('AUXTYM_D', 'Audiometry - Tympanometry')
df[5,] <- list('DXXFEM_D', 'Dual Energy X-ray Absorptiometry - Femur')
df[6,] <- list('OPXFDT_D', 'Ophthalmology - Frequency Doubling Technology')
df[7,] <- list('OHX_D', 'Oral Health')
df[8,] <- list('PAXRAW_D', 'Physical Activity Monitor')
df[9,] <- list('VIX_D', 'Vision')
df[10,] <- list('DXXAG_D', 'Dual Energy X-ray Absorptiometry - Android/Gynoid')
df[11,] <- list( 'AUXAR_D', 'Audiometry - Acoustic Reflex')
df[12,] <- list('OPXRET_D', 'Ophthalmology - Retinal Imaging')
df[13,] <- list('DXXSPN_D', 'Dual Energy X-ray Absorptiometry - Spine')
df
## ----nhanestablevars, eval=FALSE----------------------------------------------
# nhanesTableVars('EXAM', 'BMX_D')
## ----nhanestablevars1, echo=FALSE---------------------------------------------
df <- data.frame(matrix(1,nrow=27,ncol=2))
names(df) <- c('Variable.Name', 'Variable.Description')
df[1,] <- list('BMDSTATS', 'Body Measures Component status Code')
df[2,] <- list('BMIARMC', 'Arm Circumference Comment')
df[3,] <- list('BMIARML', 'Upper Arm Length Comment')
df[4,] <- list('BMICALF', ' Maximal Calf Comment')
df[5,] <- list('BMIHEAD', 'Head Circumference Comment')
df[6,] <- list('BMIHT', 'Standing Height Comment')
df[7,] <- list('BMILEG', 'Upper Leg Length Comment')
df[8,] <- list('BMIRECUM', 'Recumbent Length Comment')
df[9,] <- list('BMISUB', 'Subscapular Skinfold Comment')
df[10,] <- list('BMITHICR', 'Thigh Circumference Comment')
df[11,] <- list('BMITRI', 'Triceps Skinfold Comment')
df[12,] <- list('BMIWAIST', 'Waist Circumference Comment')
df[13,] <- list('BMIWT', 'Weight Comment')
df[14,] <- list('BMXARMC', 'Arm Circumference (cm)')
df[15,] <- list('BMXARML', 'Upper Arm Length (cm)')
df[16,] <- list('BMXBMI', 'Body Mass Index (kg/m**2)')
df[17,] <- list('BMXCALF', 'Maximal Calf Circumference (cm)')
df[18,] <- list('BMXHEAD', 'Head Circumference (cm)')
df[19,] <- list('BMXHT', 'Standing Height (cm)')
df[20,] <- list('BMXLEG', 'Upper Leg Length (cm)')
df[21,] <- list('BMXRECUM', 'Recumbent Length (cm)')
df[22,] <- list('BMXSUB', 'Subscapular Skinfold (mm)')
df[23,] <- list('BMXTHICR', 'Thigh Circumference (cm)')
df[24,] <- list('BMXTRI', 'Triceps Skinfold (mm)')
df[25,] <- list('BMXWAIST', 'Waist Circumference (cm)')
df[26,] <- list('BMXWT', 'Weight (kg)')
df[27,] <- list('SEQN', 'Respondent sequence number.')
df
## ----nhanes, eval=FALSE-------------------------------------------------------
# bmx_d <- nhanes('BMX_D')
# demo_d <- nhanes('DEMO_D')
## ----bmd1, eval=FALSE---------------------------------------------------------
# bmx_demo <- merge(demo_d, bmx_d)
# options(digits=4)
# select_cols <- c('RIAGENDR', 'BMXHT', 'BMXWT', 'BMXLEG', 'BMXCALF', 'BMXTHICR')
# print(bmx_demo[5:8,select_cols], row.names=FALSE)
## ----bmx0, echo=FALSE---------------------------------------------------------
df <- data.frame(matrix(1,nrow=4,ncol=6))
names(df) <- c('RIAGENDR', 'BMXHT', 'BMXWT', 'BMXLEG', 'BMXCALF', 'BMXTHICR')
df[1,] <- list(2, 156.0, 75.2, 38.0, 36.6, 53.7)
df[2,] <- list(1, 167.6, 69.5, 40.4, 35.6, 48.0)
df[3,] <- list(2, 163.7, 45.0, 39.2, 31.7, 41.3)
df[4,] <- list(1, 182.4, 101.9, 41.5, 42.6, 50.5)
print(df,row.names=FALSE)
## ----nhanescodebook, eval=FALSE-----------------------------------------------
# nhanesCodebook('DEMO_D', 'RIAGENDR')
## ----translate1, echo=FALSE---------------------------------------------------
df <- data.frame(matrix(1,nrow=3,ncol=5))
names(df) <- c("Code.or.Value", "Value.Description", "Count", "Cumulative", "Skip to Item")
df[1,] <- list(1, 'Male', 5080, 5080, NA)
df[2,] <- list(2, 'Female', 5268, 10348, NA)
df[3,] <- list('.', 'Missing', 0, 10348, NA)
codelist <- list("RIAGENDR", "Gender", "Gender of the sample person",
"Both males and females 0 YEARS -\r 150 YEARS", df)
names(codelist) <- c('Variable Name', 'SAS Label', 'English Text', 'Target', 'RIAGENDR')
codelist
## ----bmx1, eval=FALSE---------------------------------------------------------
# demo_d <- nhanesTranslate('DEMO_D', 'RIAGENDR', data=demo_d)
## ----bmx_m1, echo=FALSE-------------------------------------------------------
message("Translated columns: RIAGENDR")
## ----bmx2, eval=FALSE---------------------------------------------------------
# bmx_demo <- merge(demo_d, bmx_d)
## ----bmx3, echo=FALSE---------------------------------------------------------
#bmx_demo$RIAGENDR[bmx_demo$RIAGENDR==1] <- 'Male'
#bmx_demo$RIAGENDR[bmx_demo$RIAGENDR==2] <- 'Female'
## ----bmx_final_result, eval=FALSE---------------------------------------------
# print(bmx_demo[5:8,select_cols], row.names=FALSE)
## ----bmx4, echo=FALSE---------------------------------------------------------
df <- data.frame(matrix(1,nrow=4,ncol=6))
names(df) <- c('RIAGENDR', 'BMXHT', 'BMXWT', 'BMXLEG', 'BMXCALF', 'BMXTHICR')
df[1,] <- list('Female', 156.0, 75.2, 38.0, 36.6, 53.7)
df[2,] <- list('Male', 167.6, 69.5, 40.4, 35.6, 48.0)
df[3,] <- list('Female', 163.7, 45.0, 39.2, 31.7, 41.3)
df[4,] <- list('Male', 182.4, 101.9, 41.5, 42.6, 50.5)
print(df,row.names=FALSE)
## ----nhanestranslate1, eval=FALSE---------------------------------------------
# bpx_d <- nhanes('BPX_D')
# head(bpx_d[,6:11])
## ----simpletranslate1, echo=FALSE---------------------------------------------
df <- data.frame(matrix(1,nrow=6,ncol=6))
names(df) <- c("BPQ150A", "BPQ150B", "BPQ150C", "BPQ150D", "BPAARM", "BPACSZ")
df[2:6,1:4] <- 2
df[3,1] <- 1
df[3:6,6] <- 4
df[2,6] <- 3
df[4,6] <- 3
df[1,] <- NA
df
## ----nhanestranslate2, eval=FALSE---------------------------------------------
# bpx_d_vars <- nhanesTableVars('EXAM', 'BPX_D', namesonly=TRUE)
# #Alternatively may use bpx_d_vars = names(bpx_d)
# bpx_d <- nhanesTranslate('BPX_D', bpx_d_vars, data=bpx_d)
## ----simpletranslate2, echo=FALSE---------------------------------------------
translated <- c('BPAARM', 'BPACSZ', 'BPAEN2', 'BPAEN3', 'BPAEN4', 'BPQ150A', 'BPQ150B', 'BPQ150C', 'BPQ150D', 'BPXPTY', 'BPXPULS', 'PEASCCT1', 'PEASCST1')
message(paste(c("Translated columns:", translated), collapse = ' '))
## ----nhanestranslate3, eval=FALSE---------------------------------------------
# head(bpx_d[,6:11])
## ----simpletranslate3, echo=FALSE---------------------------------------------
df$BPAARM[df$BPAARM==1] <- 'Right'
df[df==1] <- 'Yes'
df[df==2] <- 'No'
df[df==3] <- 'Adult (12X22)'
df[df==4] <- 'Large (15X32)'
df
## ----nhaneslapplytables, eval=FALSE-------------------------------------------
# q2007names <- nhanesTables('Q', 2007, namesonly=TRUE)
# q2007tables <- lapply(q2007names, nhanes)
# names(q2007tables) <- q2007names
## ----prepan, eval=FALSE-------------------------------------------------------
# #List all pre-pandemic tables
# nhanesSearchTableNames('^P_')
# #List table variables
# nhanesTableVars('EXAM', 'P_AUX', namesonly=TRUE)
# #List pre-pandemic EXAM tables
# nhanesTables('EXAM', 'P')
# #Table import, variable translation, and codebook display operate as usual
# p_dxxfem <- nhanes('P_DXXFEM')
# nhanesTranslate('P_BMX', 'BMDSTATS')
# nhanesCodebook('P_INS', 'LBDINSI')
## ----nhanesdxa, eval=FALSE----------------------------------------------------
# #Import into R
# dxx_b <- nhanesDXA(2001)
# #Save to file
# nhanesDXA(2001, destfile="dxx_b.xpt")
# #Import supplemental data
# dxx_c_s <- nhanesDXA(2003, suppl=TRUE)
# #Apply code translations
# dxalist <- c('DXAEXSTS', 'DXIHE')
# dxx_b <- nhanesTranslate(colnames=dxalist, data=dxx_b, dxa=TRUE)
## ----nnyfs, eval=FALSE--------------------------------------------------------
# #List NNYFS EXAM tables
# nhanesTables('EXAM', 'Y')
# #Table import and variable translation operate as usual
# y_cvx <- nhanes('Y_CVX')
# nhanesTranslate('Y_CVX','CVXPARC')
## ----nhanessearch, eval=FALSE-------------------------------------------------
# # nhanesSearch use examples
# #
# # Search on the word bladder, restrict to the 2001-2008 surveys,
# # print out 50 characters of the variable description
# nhanesSearch("bladder", ystart=2001, ystop=2008, nchar=50)
# #
# # Search on "urin" (will match urine, urinary, etc), from 1999-2010, return table names only
# nhanesSearch("urin", ignore.case=TRUE, ystop=2010, namesonly=TRUE)
# #
# # Search on "urin", exclude "During", search surveys from 1999-2010, return table names only
# nhanesSearch("urin", exclude_terms="during", ignore.case=TRUE, ystop=2010, namesonly=TRUE)
# #
# # Restrict search to 'EXAM' and 'LAB' data groups. Explicitly list matching and exclude terms, leave ignore.case set to default value of FALSE. Search surveys from 2009 to present.
# nhanesSearch(c("urin", "Urin"), exclude_terms=c("During", "eaten during", "do during"), data_group=c('EXAM', 'LAB'), ystart=2009)
# #
# # Search on "tooth" or "teeth", all years
# nhanesSearch(c("tooth", "teeth"), ignore.case=TRUE)
# #
# # Search for variables where the variable description begins with "Tooth"
# nhanesSearch("^Tooth")
## ----nhanessearchvarname1, eval=FALSE-----------------------------------------
# #nhanesSearchVarName use examples
# nhanesSearchVarName('BPXPULS')
## ----nhanessearchvarname2, echo=FALSE-----------------------------------------
bpxtables <- c("BPX_D", "BPX_E", "BPX", "BPX_C", "BPX_B", "BPX_F", "BPX_G", "BPX_H", "BPX_I", "BPX_J")
bpxtables
## ----nhanessearchvarname3, eval=FALSE-----------------------------------------
# nhanesSearchVarName('CSQ260i', includerdc=TRUE, nchar=38, namesonly=FALSE)
## ----nhanessearchvarname4, echo=FALSE-----------------------------------------
df <- data.frame(Variable.Name=character(2),
Variable.Description=character(2),
Data.File.Name=character(2),
Data.File.Description=character(2),
Begin.Year=integer(2),
EndYear=integer(2),
Component=character(2),
Use.Constraints=character(2))
df[1,] <- list('CSQ260i', 'Do you now have any of the following p','CSX_G_R','Taste & Smell',
2012,2012,'Examination', 'RDC Only')
df[2,] <- list('CSQ260i', 'Do you now have any of the following p','CSX_H','Taste & Smell',
2013, 2014, 'Examination', 'None')
df
## ----nhanessearchtablenames1, eval=FALSE--------------------------------------
# # nhanesSearchTableNames use examples
# nhanesSearchTableNames('BMX')
## ----nhanessearchtablename2, echo=FALSE---------------------------------------
bpxtables <- c("BMX_D", "BMX", "BMX_E", "BMX_C", "BMX_B", "BMX_F", "BMX_H", "BMX_G", "BMX_I", "BMX_J", "P_BMX")
bpxtables
## ----nhanessearchtablenames3, eval=FALSE--------------------------------------
# nhanesSearchTableNames('HPVS', includerdc=TRUE, nchar=42, details=TRUE)
## ----nhanessearchtablenames4, echo=FALSE--------------------------------------
df <- data.frame(
Years=character(),
Data.File.Name=character(),
Doc.File=character(),
Data.File=character(),
Date.Published=character())
df[1,] <- list('2009-2010', 'Human Papillomavirus (HPV) - 6, 11, 16 & 1', 'HPVSER_F Doc', 'HPVSER_F Data [XPT - 171.6 KB]','November 2013')
df[2,] <- list('2005-2006', 'Human Papillomavirus (HPV) - 6, 11, 16 & 1', 'HPVS_D_R Doc', 'RDC Only', 'July 2013')
df[3,] <- list('2007-2008', 'Human Papillomavirus (HPV) - 6, 11, 16 & 1', 'HPVSER_E Doc', 'HPVSER_E Data [XPT - 155.7 KB] November 2013')
df[4,] <- list('2005-2006', 'Human Papillomavirus (HPV) - 6, 11, 16 & 1', 'HPVSER_D Doc', 'HPVSER_D Data [XPT - 151.6 KB] July 2013')
df[5,] <- list('2005-2006', 'Human Papillomavirus (HPV) - Multiplexed 6', 'HPVSRM_D Doc', 'HPVSRM_D Data [XPT - 302.6 KB] January 2015')
df[6,] <- list('2005-2006', 'Human Papillomavirus (HPV) DNA - Vaginal S', 'HPVSWR_D Doc', 'HPVSWR_D Data [XPT - 694.4 KB] November 2010')
df[7,] <- list('2007-2008', 'Human Papillomavirus (HPV) DNA - Vaginal S', 'HPVSWR_E Doc', 'HPVSWR_E Data [XPT - 677.9 KB] August 2012')
df[8,] <- list('2009-2010', 'Human Papillomavirus (HPV) DNA - Vaginal S', 'HPVSWR_F Doc', 'HPVSWR_F Data [XPT - 725.2 KB] August 2012')
df[9,] <- list('2011-2012', 'Human Papillomavirus (HPV) DNA - Vaginal S', 'HPVSWR_G Doc', 'HPVSWR_G Data [XPT - 661.1 KB] March 2015')
df[10,] <- list('2005-2006', 'Human Papillomavirus (HPV) DNA - Vaginal S', 'HPVSWR_D Doc', 'HPVSWR_D Data [XPT - 694.4 KB] Updated November 2018')
df[11,] <- list('2009-2010', 'Human Papillomavirus (HPV) DNA - Vaginal S', 'HPVS_F_R Doc', 'RDC Only', 'August 2012')
df[12,] <- list('2011-2012', 'Human Papillomavirus (HPV) DNA - Vaginal S', 'HPVS_G_R Doc', 'RDC Only', 'March 2015')
df[13,] <- list('2013-2014', 'Human Papillomavirus (HPV) DNA - Vaginal S', 'HPVSWR_H Doc', 'HPVSWR_H Data [XPT - 716.6 KB] December 2016')
df[14,] <- list('2013-2014', 'Human Papillomavirus (HPV) DNA - Vaginal S', 'HPVS_H_R Doc', 'RDC Only', 'December 2016')
df[15,] <- list('2015-2016', 'Human Papillomavirus (HPV) DNA - Vaginal S', 'HPVSWC_I Doc', 'HPVSWC_I Data [XPT - 33.3 KB] November 2018')
df[16,] <- list('2015-2016', 'Human Papillomavirus (HPV) DNA - Vaginal S', 'HPVSWR_I Doc', 'HPVSWR_I Data [XPT - 667.5 KB] November 2018')
df[17,] <- list('2015-2016', 'Human Papillomavirus (HPV) DNA - Vaginal S', 'HPVS_I_R Doc', 'RDC Only', 'November 2018')
df[18,] <- list('2017-2018', 'Human Papillomavirus (HPV) DNA - Vaginal S', 'HPVS_J_R Doc', 'RDC Only', 'December 2020')
df
Try the nhanesA package in your browser
Any scripts or data that you put into this service are public.
nhanesA documentation built on July 26, 2023, 5:41 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
## ----nhanestables, eval=FALSE-------------------------------------------------
# library(nhanesA)
# nhanesTables('EXAM', 2005)
## ----nhanestables1, echo=FALSE------------------------------------------------
df <- data.frame(matrix(1,nrow=13,ncol=2))
names(df) <- c('Data.File.Name', 'Data.File.Description')
df[1,] <- list('BPX_D', 'Blood Pressure')
df[2,] <- list('BMX_D', 'Body Measures')
df[3,] <- list('AUX_D', 'Audiometry')
df[4,] <- list('AUXTYM_D', 'Audiometry - Tympanometry')
df[5,] <- list('DXXFEM_D', 'Dual Energy X-ray Absorptiometry - Femur')
df[6,] <- list('OPXFDT_D', 'Ophthalmology - Frequency Doubling Technology')
df[7,] <- list('OHX_D', 'Oral Health')
df[8,] <- list('PAXRAW_D', 'Physical Activity Monitor')
df[9,] <- list('VIX_D', 'Vision')
df[10,] <- list('DXXAG_D', 'Dual Energy X-ray Absorptiometry - Android/Gynoid')
df[11,] <- list( 'AUXAR_D', 'Audiometry - Acoustic Reflex')
df[12,] <- list('OPXRET_D', 'Ophthalmology - Retinal Imaging')
df[13,] <- list('DXXSPN_D', 'Dual Energy X-ray Absorptiometry - Spine')
df
## ----nhanestablevars, eval=FALSE----------------------------------------------
# nhanesTableVars('EXAM', 'BMX_D')
## ----nhanestablevars1, echo=FALSE---------------------------------------------
df <- data.frame(matrix(1,nrow=27,ncol=2))
names(df) <- c('Variable.Name', 'Variable.Description')
df[1,] <- list('BMDSTATS', 'Body Measures Component status Code')
df[2,] <- list('BMIARMC', 'Arm Circumference Comment')
df[3,] <- list('BMIARML', 'Upper Arm Length Comment')
df[4,] <- list('BMICALF', ' Maximal Calf Comment')
df[5,] <- list('BMIHEAD', 'Head Circumference Comment')
df[6,] <- list('BMIHT', 'Standing Height Comment')
df[7,] <- list('BMILEG', 'Upper Leg Length Comment')
df[8,] <- list('BMIRECUM', 'Recumbent Length Comment')
df[9,] <- list('BMISUB', 'Subscapular Skinfold Comment')
df[10,] <- list('BMITHICR', 'Thigh Circumference Comment')
df[11,] <- list('BMITRI', 'Triceps Skinfold Comment')
df[12,] <- list('BMIWAIST', 'Waist Circumference Comment')
df[13,] <- list('BMIWT', 'Weight Comment')
df[14,] <- list('BMXARMC', 'Arm Circumference (cm)')
df[15,] <- list('BMXARML', 'Upper Arm Length (cm)')
df[16,] <- list('BMXBMI', 'Body Mass Index (kg/m**2)')
df[17,] <- list('BMXCALF', 'Maximal Calf Circumference (cm)')
df[18,] <- list('BMXHEAD', 'Head Circumference (cm)')
df[19,] <- list('BMXHT', 'Standing Height (cm)')
df[20,] <- list('BMXLEG', 'Upper Leg Length (cm)')
df[21,] <- list('BMXRECUM', 'Recumbent Length (cm)')
df[22,] <- list('BMXSUB', 'Subscapular Skinfold (mm)')
df[23,] <- list('BMXTHICR', 'Thigh Circumference (cm)')
df[24,] <- list('BMXTRI', 'Triceps Skinfold (mm)')
df[25,] <- list('BMXWAIST', 'Waist Circumference (cm)')
df[26,] <- list('BMXWT', 'Weight (kg)')
df[27,] <- list('SEQN', 'Respondent sequence number.')
df
## ----nhanes, eval=FALSE-------------------------------------------------------
# bmx_d <- nhanes('BMX_D')
# demo_d <- nhanes('DEMO_D')
## ----bmd1, eval=FALSE---------------------------------------------------------
# bmx_demo <- merge(demo_d, bmx_d)
# options(digits=4)
# select_cols <- c('RIAGENDR', 'BMXHT', 'BMXWT', 'BMXLEG', 'BMXCALF', 'BMXTHICR')
# print(bmx_demo[5:8,select_cols], row.names=FALSE)
## ----bmx0, echo=FALSE---------------------------------------------------------
df <- data.frame(matrix(1,nrow=4,ncol=6))
names(df) <- c('RIAGENDR', 'BMXHT', 'BMXWT', 'BMXLEG', 'BMXCALF', 'BMXTHICR')
df[1,] <- list(2, 156.0, 75.2, 38.0, 36.6, 53.7)
df[2,] <- list(1, 167.6, 69.5, 40.4, 35.6, 48.0)
df[3,] <- list(2, 163.7, 45.0, 39.2, 31.7, 41.3)
df[4,] <- list(1, 182.4, 101.9, 41.5, 42.6, 50.5)
print(df,row.names=FALSE)
## ----nhanescodebook, eval=FALSE-----------------------------------------------
# nhanesCodebook('DEMO_D', 'RIAGENDR')
## ----translate1, echo=FALSE---------------------------------------------------
df <- data.frame(matrix(1,nrow=3,ncol=5))
names(df) <- c("Code.or.Value", "Value.Description", "Count", "Cumulative", "Skip to Item")
df[1,] <- list(1, 'Male', 5080, 5080, NA)
df[2,] <- list(2, 'Female', 5268, 10348, NA)
df[3,] <- list('.', 'Missing', 0, 10348, NA)
codelist <- list("RIAGENDR", "Gender", "Gender of the sample person",
"Both males and females 0 YEARS -\r 150 YEARS", df)
names(codelist) <- c('Variable Name', 'SAS Label', 'English Text', 'Target', 'RIAGENDR')
codelist
## ----bmx1, eval=FALSE---------------------------------------------------------
# demo_d <- nhanesTranslate('DEMO_D', 'RIAGENDR', data=demo_d)
## ----bmx_m1, echo=FALSE-------------------------------------------------------
message("Translated columns: RIAGENDR")
## ----bmx2, eval=FALSE---------------------------------------------------------
# bmx_demo <- merge(demo_d, bmx_d)
## ----bmx3, echo=FALSE---------------------------------------------------------
#bmx_demo$RIAGENDR[bmx_demo$RIAGENDR==1] <- 'Male'
#bmx_demo$RIAGENDR[bmx_demo$RIAGENDR==2] <- 'Female'
## ----bmx_final_result, eval=FALSE---------------------------------------------
# print(bmx_demo[5:8,select_cols], row.names=FALSE)
## ----bmx4, echo=FALSE---------------------------------------------------------
df <- data.frame(matrix(1,nrow=4,ncol=6))
names(df) <- c('RIAGENDR', 'BMXHT', 'BMXWT', 'BMXLEG', 'BMXCALF', 'BMXTHICR')
df[1,] <- list('Female', 156.0, 75.2, 38.0, 36.6, 53.7)
df[2,] <- list('Male', 167.6, 69.5, 40.4, 35.6, 48.0)
df[3,] <- list('Female', 163.7, 45.0, 39.2, 31.7, 41.3)
df[4,] <- list('Male', 182.4, 101.9, 41.5, 42.6, 50.5)
print(df,row.names=FALSE)
## ----nhanestranslate1, eval=FALSE---------------------------------------------
# bpx_d <- nhanes('BPX_D')
# head(bpx_d[,6:11])
## ----simpletranslate1, echo=FALSE---------------------------------------------
df <- data.frame(matrix(1,nrow=6,ncol=6))
names(df) <- c("BPQ150A", "BPQ150B", "BPQ150C", "BPQ150D", "BPAARM", "BPACSZ")
df[2:6,1:4] <- 2
df[3,1] <- 1
df[3:6,6] <- 4
df[2,6] <- 3
df[4,6] <- 3
df[1,] <- NA
df
## ----nhanestranslate2, eval=FALSE---------------------------------------------
# bpx_d_vars <- nhanesTableVars('EXAM', 'BPX_D', namesonly=TRUE)
# #Alternatively may use bpx_d_vars = names(bpx_d)
# bpx_d <- nhanesTranslate('BPX_D', bpx_d_vars, data=bpx_d)
## ----simpletranslate2, echo=FALSE---------------------------------------------
translated <- c('BPAARM', 'BPACSZ', 'BPAEN2', 'BPAEN3', 'BPAEN4', 'BPQ150A', 'BPQ150B', 'BPQ150C', 'BPQ150D', 'BPXPTY', 'BPXPULS', 'PEASCCT1', 'PEASCST1')
message(paste(c("Translated columns:", translated), collapse = ' '))
## ----nhanestranslate3, eval=FALSE---------------------------------------------
# head(bpx_d[,6:11])
## ----simpletranslate3, echo=FALSE---------------------------------------------
df$BPAARM[df$BPAARM==1] <- 'Right'
df[df==1] <- 'Yes'
df[df==2] <- 'No'
df[df==3] <- 'Adult (12X22)'
df[df==4] <- 'Large (15X32)'
df
## ----nhaneslapplytables, eval=FALSE-------------------------------------------
# q2007names <- nhanesTables('Q', 2007, namesonly=TRUE)
# q2007tables <- lapply(q2007names, nhanes)
# names(q2007tables) <- q2007names
## ----prepan, eval=FALSE-------------------------------------------------------
# #List all pre-pandemic tables
# nhanesSearchTableNames('^P_')
# #List table variables
# nhanesTableVars('EXAM', 'P_AUX', namesonly=TRUE)
# #List pre-pandemic EXAM tables
# nhanesTables('EXAM', 'P')
# #Table import, variable translation, and codebook display operate as usual
# p_dxxfem <- nhanes('P_DXXFEM')
# nhanesTranslate('P_BMX', 'BMDSTATS')
# nhanesCodebook('P_INS', 'LBDINSI')
## ----nhanesdxa, eval=FALSE----------------------------------------------------
# #Import into R
# dxx_b <- nhanesDXA(2001)
# #Save to file
# nhanesDXA(2001, destfile="dxx_b.xpt")
# #Import supplemental data
# dxx_c_s <- nhanesDXA(2003, suppl=TRUE)
# #Apply code translations
# dxalist <- c('DXAEXSTS', 'DXIHE')
# dxx_b <- nhanesTranslate(colnames=dxalist, data=dxx_b, dxa=TRUE)
## ----nnyfs, eval=FALSE--------------------------------------------------------
# #List NNYFS EXAM tables
# nhanesTables('EXAM', 'Y')
# #Table import and variable translation operate as usual
# y_cvx <- nhanes('Y_CVX')
# nhanesTranslate('Y_CVX','CVXPARC')
## ----nhanessearch, eval=FALSE-------------------------------------------------
# # nhanesSearch use examples
# #
# # Search on the word bladder, restrict to the 2001-2008 surveys,
# # print out 50 characters of the variable description
# nhanesSearch("bladder", ystart=2001, ystop=2008, nchar=50)
# #
# # Search on "urin" (will match urine, urinary, etc), from 1999-2010, return table names only
# nhanesSearch("urin", ignore.case=TRUE, ystop=2010, namesonly=TRUE)
# #
# # Search on "urin", exclude "During", search surveys from 1999-2010, return table names only
# nhanesSearch("urin", exclude_terms="during", ignore.case=TRUE, ystop=2010, namesonly=TRUE)
# #
# # Restrict search to 'EXAM' and 'LAB' data groups. Explicitly list matching and exclude terms, leave ignore.case set to default value of FALSE. Search surveys from 2009 to present.
# nhanesSearch(c("urin", "Urin"), exclude_terms=c("During", "eaten during", "do during"), data_group=c('EXAM', 'LAB'), ystart=2009)
# #
# # Search on "tooth" or "teeth", all years
# nhanesSearch(c("tooth", "teeth"), ignore.case=TRUE)
# #
# # Search for variables where the variable description begins with "Tooth"
# nhanesSearch("^Tooth")
## ----nhanessearchvarname1, eval=FALSE-----------------------------------------
# #nhanesSearchVarName use examples
# nhanesSearchVarName('BPXPULS')
## ----nhanessearchvarname2, echo=FALSE-----------------------------------------
bpxtables <- c("BPX_D", "BPX_E", "BPX", "BPX_C", "BPX_B", "BPX_F", "BPX_G", "BPX_H", "BPX_I", "BPX_J")
bpxtables
## ----nhanessearchvarname3, eval=FALSE-----------------------------------------
# nhanesSearchVarName('CSQ260i', includerdc=TRUE, nchar=38, namesonly=FALSE)
## ----nhanessearchvarname4, echo=FALSE-----------------------------------------
df <- data.frame(Variable.Name=character(2),
Variable.Description=character(2),
Data.File.Name=character(2),
Data.File.Description=character(2),
Begin.Year=integer(2),
EndYear=integer(2),
Component=character(2),
Use.Constraints=character(2))
df[1,] <- list('CSQ260i', 'Do you now have any of the following p','CSX_G_R','Taste & Smell',
2012,2012,'Examination', 'RDC Only')
df[2,] <- list('CSQ260i', 'Do you now have any of the following p','CSX_H','Taste & Smell',
2013, 2014, 'Examination', 'None')
df
## ----nhanessearchtablenames1, eval=FALSE--------------------------------------
# # nhanesSearchTableNames use examples
# nhanesSearchTableNames('BMX')
## ----nhanessearchtablename2, echo=FALSE---------------------------------------
bpxtables <- c("BMX_D", "BMX", "BMX_E", "BMX_C", "BMX_B", "BMX_F", "BMX_H", "BMX_G", "BMX_I", "BMX_J", "P_BMX")
bpxtables
## ----nhanessearchtablenames3, eval=FALSE--------------------------------------
# nhanesSearchTableNames('HPVS', includerdc=TRUE, nchar=42, details=TRUE)
## ----nhanessearchtablenames4, echo=FALSE--------------------------------------
df <- data.frame(
Years=character(),
Data.File.Name=character(),
Doc.File=character(),
Data.File=character(),
Date.Published=character())
df[1,] <- list('2009-2010', 'Human Papillomavirus (HPV) - 6, 11, 16 & 1', 'HPVSER_F Doc', 'HPVSER_F Data [XPT - 171.6 KB]','November 2013')
df[2,] <- list('2005-2006', 'Human Papillomavirus (HPV) - 6, 11, 16 & 1', 'HPVS_D_R Doc', 'RDC Only', 'July 2013')
df[3,] <- list('2007-2008', 'Human Papillomavirus (HPV) - 6, 11, 16 & 1', 'HPVSER_E Doc', 'HPVSER_E Data [XPT - 155.7 KB] November 2013')
df[4,] <- list('2005-2006', 'Human Papillomavirus (HPV) - 6, 11, 16 & 1', 'HPVSER_D Doc', 'HPVSER_D Data [XPT - 151.6 KB] July 2013')
df[5,] <- list('2005-2006', 'Human Papillomavirus (HPV) - Multiplexed 6', 'HPVSRM_D Doc', 'HPVSRM_D Data [XPT - 302.6 KB] January 2015')
df[6,] <- list('2005-2006', 'Human Papillomavirus (HPV) DNA - Vaginal S', 'HPVSWR_D Doc', 'HPVSWR_D Data [XPT - 694.4 KB] November 2010')
df[7,] <- list('2007-2008', 'Human Papillomavirus (HPV) DNA - Vaginal S', 'HPVSWR_E Doc', 'HPVSWR_E Data [XPT - 677.9 KB] August 2012')
df[8,] <- list('2009-2010', 'Human Papillomavirus (HPV) DNA - Vaginal S', 'HPVSWR_F Doc', 'HPVSWR_F Data [XPT - 725.2 KB] August 2012')
df[9,] <- list('2011-2012', 'Human Papillomavirus (HPV) DNA - Vaginal S', 'HPVSWR_G Doc', 'HPVSWR_G Data [XPT - 661.1 KB] March 2015')
df[10,] <- list('2005-2006', 'Human Papillomavirus (HPV) DNA - Vaginal S', 'HPVSWR_D Doc', 'HPVSWR_D Data [XPT - 694.4 KB] Updated November 2018')
df[11,] <- list('2009-2010', 'Human Papillomavirus (HPV) DNA - Vaginal S', 'HPVS_F_R Doc', 'RDC Only', 'August 2012')
df[12,] <- list('2011-2012', 'Human Papillomavirus (HPV) DNA - Vaginal S', 'HPVS_G_R Doc', 'RDC Only', 'March 2015')
df[13,] <- list('2013-2014', 'Human Papillomavirus (HPV) DNA - Vaginal S', 'HPVSWR_H Doc', 'HPVSWR_H Data [XPT - 716.6 KB] December 2016')
df[14,] <- list('2013-2014', 'Human Papillomavirus (HPV) DNA - Vaginal S', 'HPVS_H_R Doc', 'RDC Only', 'December 2016')
df[15,] <- list('2015-2016', 'Human Papillomavirus (HPV) DNA - Vaginal S', 'HPVSWC_I Doc', 'HPVSWC_I Data [XPT - 33.3 KB] November 2018')
df[16,] <- list('2015-2016', 'Human Papillomavirus (HPV) DNA - Vaginal S', 'HPVSWR_I Doc', 'HPVSWR_I Data [XPT - 667.5 KB] November 2018')
df[17,] <- list('2015-2016', 'Human Papillomavirus (HPV) DNA - Vaginal S', 'HPVS_I_R Doc', 'RDC Only', 'November 2018')
df[18,] <- list('2017-2018', 'Human Papillomavirus (HPV) DNA - Vaginal S', 'HPVS_J_R Doc', 'RDC Only', 'December 2020')
df
Try the nhanesA package in your browser
Any scripts or data that you put into this service are public.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.