Package: parseRPDR 1.1.1

parseRPDR: Parse and Manipulate Research Patient Data Registry ('RPDR') Text Queries

Functions to load Research Patient Data Registry ('RPDR') text queries from Partners Healthcare institutions into R. The package also provides helper functions to manipulate data and execute common procedures such as finding the closest radiological exams considering a given timepoint, or creating a DICOM header database from the downloaded images. All functionalities are parallelized for fast and efficient analyses.

Authors:Marton Kolossvary [aut, cre]

parseRPDR_1.1.1.tar.gz
parseRPDR_1.1.1.zip(r-4.5)parseRPDR_1.1.1.zip(r-4.4)parseRPDR_1.1.1.zip(r-4.3)
parseRPDR_1.1.1.tgz(r-4.4-any)parseRPDR_1.1.1.tgz(r-4.3-any)
parseRPDR_1.1.1.tar.gz(r-4.5-noble)parseRPDR_1.1.1.tar.gz(r-4.4-noble)
parseRPDR_1.1.1.tgz(r-4.4-emscripten)parseRPDR_1.1.1.tgz(r-4.3-emscripten)
parseRPDR.pdf |parseRPDR.html✨
parseRPDR/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/martonkolossvary/parserpdr/issues

On CRAN:

4.57 score 10 stars 37 scripts 387 downloads 38 exports 39 dependencies

Last updated 7 months agofrom:7ad2147479. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 22 2024
R-4.5-winOKOct 22 2024
R-4.5-linuxOKOct 22 2024
R-4.4-winOKOct 22 2024
R-4.4-macOKOct 22 2024
R-4.3-winOKOct 22 2024
R-4.3-macOKOct 22 2024

Exports:all_ids_mi2b2convert_diaconvert_encconvert_labconvert_medconvert_notesconvert_phyconvert_prcconvert_rfvcreate_img_dbexport_notesfind_examload_allload_all_dataload_bibload_conload_demload_dem_oldload_diaload_encload_labload_lnoload_mcmload_medload_micload_mrnload_notesload_phyload_prcload_prvload_ptdload_rdtload_rfvload_trnpretty_mrnpretty_numberspretty_textremove_column

Dependencies:bitbit64clicliprcodetoolscpp11crayondata.tabledigestdoFuturefansiforeachfuturefuture.applyglobalsgluehmsiteratorslifecyclelistenvmagrittrparallellypillarpkgconfigprettyunitsprogressprogressrR6readrrlangstringistringrtibbletidyselecttzdbutf8vctrsvroomwithr

Readme and manuals

Help Manual

Help pageTopics
Legacy function to create a vector of all possible IDs for mi2b2 workbenchall_ids_mi2b2
Searches diagnosis columns for given diseases.convert_dia
Searches columns for given diseases defined by ICD codes.convert_enc
Converts lab results to normal/abnormal based-on reference values.convert_lab
Adds boolean columns corresponding to a group of medications whether it is present in the given row.convert_med
Extracts information from notes free text.convert_notes
Searches health history data for given codesconvert_phy
Searches procedures columns for given procedures.convert_prc
Searches columns for given reason for visit defined by ERFV codes.convert_rfv
Create a database of DICOM headers.create_img_db
Exports free text notes to individual text files.export_notes
Find exam data within a given timeframe using parallel CPU computing.find_exam
Loads allergy data information into R.load_all
Loads all RPDR text outputs into R.load_all_data
Loads BiobankFile data into R.load_bib
Loads contact information into R.load_con
Loads demographic information into R for new demographic tables following changes in the beginning of 2022.load_dem
Loads demographic information into R for demographics tables before 2022.load_dem_old
Loads diagnoses into R.load_dia
Loads encounter information into R.load_enc
Loads laboratory results into R.load_lab
Loads LMR note documents into R.load_lno
Loads match control data into R.load_mcm
Loads medication order detail into R.load_med
Loads microbiology results into R.load_mic
Loads MRN data into R.load_mrn
Loads note documents into R.load_notes
Loads helath history information into R.load_phy
Loads procedures into R.load_prc
Loads providers information into R.load_prv
Loads patient data information into R.load_ptd
Loads radiology procedures data into R.load_rdt
Loads reason for visit data into R.load_rfv
Loads transfusion results into R.load_trn
Converts MRN integer to string compatible with RPDR.pretty_mrn
Converts numerical codes to universal format specified by length.pretty_numbers
Removes spaces, special characters and capitals from string vector.pretty_text
Delete columns with all NA or all identical data.remove_column