Package: dbGaPCheckup 1.1.0

dbGaPCheckup: dbGaP Checkup

Contains functions that check for formatting of the Subject Phenotype data set and data dictionary as specified by the National Center for Biotechnology Information (NCBI) Database of Genotypes and Phenotypes (dbGaP) <https://www.ncbi.nlm.nih.gov/gap/docs/submissionguide/>.

Authors:Lacey W. Heinsberg [aut, cre], Daniel E. Weeks [aut], University of Pittsburgh [cph]

dbGaPCheckup_1.1.0.tar.gz
dbGaPCheckup_1.1.0.zip(r-4.5)dbGaPCheckup_1.1.0.zip(r-4.4)dbGaPCheckup_1.1.0.zip(r-4.3)
dbGaPCheckup_1.1.0.tgz(r-4.4-any)dbGaPCheckup_1.1.0.tgz(r-4.3-any)
dbGaPCheckup_1.1.0.tar.gz(r-4.5-noble)dbGaPCheckup_1.1.0.tar.gz(r-4.4-noble)
dbGaPCheckup_1.1.0.tgz(r-4.4-emscripten)dbGaPCheckup_1.1.0.tgz(r-4.3-emscripten)
dbGaPCheckup.pdf |dbGaPCheckup.html✨
dbGaPCheckup/json (API)
NEWS

# Install 'dbGaPCheckup' in R:
install.packages('dbGaPCheckup', repos = c('https://lwheinsberg.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/lwheinsberg/dbgapcheckup/issues

Datasets:

On CRAN:

43 exports 3 stars 1.38 score 104 dependencies 18 scripts 992 downloads

Last updated 11 months agofrom:163c17b44d. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 17 2024
R-4.5-winNOTESep 17 2024
R-4.5-linuxNOTESep 17 2024
R-4.4-winNOTESep 17 2024
R-4.4-macNOTESep 17 2024
R-4.3-winOKSep 17 2024
R-4.3-macOKSep 17 2024

Exports:add_missing_fieldscheck_reportcomplete_checkcreate_awareness_reportcreate_reportdat_functiondat_function_selecteddecimal_checkdescription_checkdictionary_searchdimension_checkdup_valueseval_functionfield_checkid_checkid_first_dataid_first_dictint_checkinteger_checklabel_dataminmax_checkmisc_format_checkmissing_value_checkmissingness_summarymm_precheckmv_precheckNA_checkNA_precheckname_checkname_correctname_precheckpkg_field_checkreorder_datareorder_dictionaryrow_checkshort_field_checkshort_prechecksuper_short_prechecktype_checkvalue_meaning_tablevalue_missing_tablevalues_checkvalues_precheck

Dependencies:base64encbitbit64bslibcachemcellrangerclassclassIntclicliprcolorspacecommonmarkcpp11crayondigestdplyre1071evaluatefansifarverfastmapfontawesomeforcatsformatRfsgenericsggplot2gluegridExtragtablehavenhighrhmshtmltoolshttpuvisobandjquerylibjsonliteKernSmoothknitrlabelinglabelledlaterlatticelifecyclemagrittrMASSMatrixmemoisemgcvmimeminiUImunsellnaniarnlmenormpanderpillarpkgconfigplyrprettyunitsprogresspromisesproxypurrrquestionrR.cacheR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppreadrreadxlrematchrlangrmarkdownrprojrootrstudioapisassscalesshinysourcetoolsstringistringrstylertibbletidyrtidyselecttinytextzdbUpSetRutf8vctrsviridisviridisLitevisdatvroomwithrxfunxtableyaml

dbGaPCheckup Quick Start

Lacey W. Heinsberg and Daniel E. Weeks

Rendered fromdbGaPCheckup.Rmdusingknitr::rmarkdownon Sep 17 2024.

Last update: 2023-02-13
Started: 2022-10-31

dbGaPCheckup Vignette

Lacey W. Heinsberg and Daniel E. Weeks

Rendered fromdbGaPCheckup_vignette.Rmdusingknitr::rmarkdownon Sep 17 2024.

Last update: 2023-02-13
Started: 2022-10-31

Readme and manuals

Help Manual

Help pageTopics
Add Missing Fieldsadd_missing_fields
Check Reportcheck_report
Complete Checkcomplete_check
Create Awareness Reportcreate_awareness_report
Create Reportcreate_report
Data Utility Functiondat_function
Data Selected Utility Functiondat_function_selected
DD.dict.ADD.dict.A
DD.dict.BDD.dict.B
DD.dict.CDD.dict.C
DD.dict.DDD.dict.D
DD.dict.EDD.dict.E
DD.dict.FDD.dict.F
DD.dict.GDD.dict.G
DD.dict.HDD.dict.H
DD.dict.IDD.dict.I
DD.dict.JDD.dict.J
DD.dict.KDD.dict.K
DD.dict.LDD.dict.L
DD.dict.MDD.dict.M
DD.dict.NDD.dict.N
DD.dict.QDD.dict.Q
DD.dict.RDD.dict.R
DD.dict.SDD.dict.S
Decimal Checkdecimal_check
Description Checkdescription_check
Data Dictionary Searchdictionary_search
Dimension Checkdimension_check
DS.data.ADS.data.A
DS.data.BDS.data.B
DS.data.CDS.data.C
DS.data.DDS.data.D
DS.data.EDS.data.E
DS.data.FDS.data.F
DS.data.GDS.data.G
DS.data.HDS.data.H
DS.data.IDS.data.I
DS.data.JDS.data.J
DS.data.KDS.data.K
DS.data.LDS.data.L
DS.data.MDS.data.M
DS.data.NDS.data.N
DS.data.ODS.data.O
DS.data.PDS.data.P
DS.data.QDS.data.Q
DS.data.RDS.data.R
DS.data.SDS.data.S
Duplicate Values Functiondup_values
Evaluation Utility Functioneval_function
ExampleAExampleA
ExampleBExampleB
ExampleCExampleC
ExampleDExampleD
ExampleEExampleE
ExampleFExampleF
ExampleGExampleG
ExampleHExampleH
ExampleIExampleI
ExampleJExampleJ
ExampleKExampleK
ExampleLExampleL
ExampleMExampleM
ExampleNExampleN
ExampleOExampleO
ExamplePExampleP
ExampleQExampleQ
ExampleRExampleR
ExampleSExampleS
Field Checkfield_check
ID Checkid_check
Relocate SUBJECT_ID to First Column of Data Setid_first_data
Relocate SUBJECT_ID to First Column of Data Dictionaryid_first_dict
Integer Check Base Functionint_check
Integer Checkinteger_check
Label the datalabel_data
Minimum and Maximum Values Checkminmax_check
Miscellaneous Format Checkmisc_format_check
Missing Value Checkmissing_value_check
Missingness Summarymissingness_summary
Min Max Required Pre-checksmm_precheck
Missing Values Required Pre-checksmv_precheck
Missing Value (NA) CheckNA_check
Min Max Required Pre-checksNA_precheck
Name Checkname_check
Name Correction Utility Functionname_correct
Name Pre-checksname_precheck
Package Required Field Checkpkg_field_check
Reorder Data Set Utility Functionreorder_data
Reorder Data Dictionary Utility Functionreorder_dictionary
Row Checkrow_check
Truncated Field Checkshort_field_check
Truncated Pre-checkshort_precheck
Very Truncated Pre-checksuper_short_precheck
Type Checktype_check
Value-Meaning Tablevalue_meaning_table
Values Missing Table Awareness Functionvalue_missing_table
Values Checkvalues_check
Values Pre-Checkvalues_precheck