Tables in DB missing from metadata

[deepayan]

The following tables are in the database (can be retrieved using nhanes(name)) but do not appear in the metadata table Metadata.QuestionnaireDescriptions.

The commonality seems to be that their nhanesCodebook() is also broken.

• RXQ_DRUG - drug table (no SEQN)
• DRXFMT_B - TOC has no codebook
• DRXFMT - TOC has no codebook
• DRXFCD_J - TOC has no codebook
• DRXFCD_I - TOC has no codebook
• SSNH4THY - wrong auto-generated URL, should have had suffix _B
• SSHCV_E - looks OK (except variable SSASCR3?)
• SSDFS_A - looks OK
• POOLTF_E - TOC has no codebook
• POOLTF_D - TOC has no codebook
• SSCMVG_A - looks OK
• SSCARD_A - looks OK
• SSBNP_A - looks OK
• SSANA2_A - looks OK
• SSANA_A - looks OK
• SSAGP_J - looks OK
• SSAGP_I - looks OK
• PFC_POOL - page missing
• DSPI - looks OK, but no SEQN
• FOODLK_D - TOC has no codebook
• DSII - looks OK
• FOODLK_C - ?? (lookup table)
• DSBI - looks OK, but no SEQN
• VARLK_D - ?? (lookup table)
• VARLK_C - ?? (lookup table)
• SSUCSH_A - looks OK
• SSTROP_A - looks OK

[rsgoncalves]

What seems to be happening with these is that nhanesA::nhanesTables() isn't returning them—a bug in nhanesA likely.

For example, the table SSANA_A isn't among the 1999-2000 survey tables obtained via:

tables_99 <- nhanesTables(data_group="LAB", year=1999, details=TRUE, includerdc=TRUE)

[deepayan]

Thanks, I'll take a closer look. Interestingly,

nhanesTables(data_group="LAB", year=1999, details=TRUE, includerdc=TRUE)

run without the DB finds a few more tables, but none of the ones listed above:

"LAB05"    "L11_2_R"  "L09RDC_A" "L05RDC_A" "L06_2_00" "VID_2_00" "L10_2_00" "L18_2_00" "L13_2_R"  "L19_2_R" "L16_2_R"  "L25_2_R"  "VIT_2_R"

[deepayan]

So, it looks like

nhanesTables(data_group="LAB", year=1999, details=TRUE, includerdc=TRUE)

doesn't include SSANA_A because it and its variables are not included in

https://wwwn.cdc.gov/Nchs/Nhanes/search/variablelist.aspx?Component=Laboratory&CycleBeginYear=1999

which is where nhanesTables() looks. This looks like a bug in the NHANES website.

I am not sure how we can work around this. Changing nhanesTables() doesn't really make sense. We probably need to work off a different source of tables (like the nhanesA::nhanesManifest() recently added by @rgentlem).

[rsgoncalves]

Thank you @deepayan. Using nhaneManifest() we now have all the listed tables in the metadata release https://github.com/ccb-hms/NHANES-metadata/releases/tag/v3.8.0 (to be included in the NHANES DB in the next iteration).