Package: transplantr 0.2.0

transplantr: Audit and Research Functions for Transplantation

A set of vectorised functions to calculate medical equations used in transplantation, focused mainly on transplantation of abdominal organs. These functions include donor and recipient risk indices as used by NHS Blood & Transplant, OPTN/UNOS and Eurotransplant, tools for quantifying HLA mismatches, functions for calculating estimated glomerular filtration rate (eGFR), a function to calculate the APRI (AST to platelet ratio) score used in initial screening of suitability to receive a transplant from a hepatitis C seropositive donor and some biochemical unit converter functions. All functions are designed to work with either US or international units. References for the equations are provided in the vignettes and function documentation.

Authors:John Asher [aut, cre]

transplantr_0.2.0.tar.gz
transplantr_0.2.0.zip(r-4.7)transplantr_0.2.0.zip(r-4.6)transplantr_0.2.0.zip(r-4.5)
transplantr_0.2.0.tgz(r-4.6-any)transplantr_0.2.0.tgz(r-4.5-any)
transplantr_0.2.0.tar.gz(r-4.7-any)transplantr_0.2.0.tar.gz(r-4.6-any)
transplantr_0.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
transplantr/json (API)

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

Bug tracker:https://github.com/johnasher/transplantr/issues

Pkgdown/docs site:https://transplantr.txtools.net

Datasets:
  • kidney.donors - Simulated dataset of donors to illustrate KDRI vignette.
  • liver.pts - Simulated dataset to illustrate MELD calculator vignette.
  • mismatches - Simulated dataset to illustrate mismatches for HLA vignette.
  • results - Simulated dataset to illustrate eGFR calculator vignette.
  • results_US - Simulated dataset to illustrate eGFR calculator vignette.
  • serial.results - Simulated dataset to illustrate serial results eGFR calculator vignette.

On CRAN:

Conda:

5.33 score 3 stars 36 scripts 207 downloads 58 exports 0 dependencies

Last updated from:9662038338. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK117
source / vignettesOK173
linux-release-x86_64OK116
macos-release-arm64OK143
macos-oldrel-arm64OK168
windows-develOK82
windows-releaseOK98
windows-oldrelOK76
wasm-releaseOK92

Exports:apribar_scorebilirubin_to_SIbilirubin_to_USbun_to_ureachi2dobckd_epickd_epi_UScockcroftcockcroft_UScreatinine_to_SIcreatinine_to_USeptsepts_lookupet_drihla_mm_levelhla_mm_level_stribwkdpikdpi_lookupkdpi_USliver_drimdrdmdrd_USmeldmeld_nameld_na_USmeld_USnankivellnankivell_spknankivell_spk_USnankivell_USp_passp_softp_soft_USpdripedi_softpeldpeld_USraw_eptsschwartzschwartz_USsoftsoft_USsoft2soft2_USukeldukeld_USukkdriukkdri_qukkrriukkrri_qurea_to_bunuskdriuskdri_USwalserwalser_USwatson_ukkdri

Dependencies:

Estimated GFR
Introduction | CKD-EPI formula | Calculating serial eGFR Results | Abbreviated MDRD formula | Schwartz formula | Cockcroft-Gault formula | Formulae to be added in future | References
Rendered fromegfr.Rmdusingknitr::rmarkdown

Last update: 2020-02-28
Started: 2019-12-10

Liver transplant risk stratification
Introduction | Adult risk stratification | Risk stratification in children | MELD and MELD-Na scores | UKELD score | SOFT score | DRI and ET-DRI | PELD score | Pedi-SOFT | References
Rendered fromliver_recipient_scoring.Rmdusingknitr::rmarkdown

Last update: 2020-02-27
Started: 2019-12-10

Kidney Donor and Recipient Risk Index
Introduction | UK Kidney Donor and Recipient Risk Indices (2019) | UK Kidney Donor Risk Index | UK Recipient Risk Index | UK Kidney Donor Risk Index (2012) | US Kidney Donor Risk Index | US KDPI | Estimated Post-Transplant Survival Score (EPTS) | References
Rendered fromkidney_risk_scores.Rmdusingknitr::rmarkdown

Last update: 2020-01-06
Started: 2019-12-04

HLA Mismatch Level
Introduction | Using hla_mm_level() | Using hla_mm_level_str() | References
Rendered fromhla_mismatch_grade.Rmdusingknitr::rmarkdown

Last update: 2019-12-28
Started: 2019-12-16

Readme and manuals

Help Manual

Help pageTopics
AST to Platelet Ratio (APRI)apri
BAR (Balance of Risk) score in liver transplantationbar_score
Bilirubin unit converter (mg/dl -> µmol/l)bilirubin_to_SI
Bilirubin unit converter (µmol/l -> mg/dl)bilirubin_to_US
Convert BUN to ureabun_to_urea
Convert CHI number to date of birthchi2dob
eGFR by CKD-EPI equationckd_epi
eGFR by CKD-EPI equation (US units)ckd_epi_US
Creatinine clearance by Cockcroft-Gault equationcockcroft
Creatinine clearance by Cockcroft-Gault equation (US units)cockcroft_US
Creatinine unit converter (mg/dl -> µmol/l)creatinine_to_SI
Creatinine unit converter (µmol/l -> mg/dl)creatinine_to_US
Estimated Post-Transplant Survival Score (EPTS)epts
EPTS lookup functionepts_lookup
Eurotransplant Donor Risk Index in Liver Transplantation (ET-DRI)et_dri
HLA mismatch levelhla_mm_level
HLA mismatch level from stringhla_mm_level_str
Ideal body weightibw
US KDPIkdpi
US KDPI lookup functionkdpi_lookup
US KDPI (US units)kdpi_US
Simulated dataset of donors to illustrate KDRI vignette.kidney.donors
Liver Donor Risk Index (DRI)liver_dri
Simulated dataset to illustrate MELD calculator vignette.liver.pts
eGFR by abbreviated MDRD equationmdrd
eGFR by abbreviated MDRD equation (US units)mdrd_US
MELD scoremeld
MELD-Na scoremeld_na
MELD-Na score (US units)meld_na_US
MELD score (US units)meld_US
Simulated dataset to illustrate mismatches for HLA vignette.mismatches
eGFR using Nankivell formulanankivell
eGFR using the Nankivell-SPK formulanankivell_spk
eGFR using the Nankivell-SPK formula (US units)nankivell_spk_US
eGFR using Nankivell formula (US units)nankivell_US
P-PASS pre-procurement pancreas suitability scorep_pass
P-SOFT Scorep_soft
P-SOFT Score (US units)p_soft_US
Pancreas donor risk indexpdri
Pedi-SOFT Scorepedi_soft
PELD scorepeld
PELD score (US units)peld_US
Estimated Post-Transplant Survival Score (EPTS)raw_epts
Simulated dataset to illustrate eGFR calculator vignette.results
Simulated dataset to illustrate eGFR calculator vignette.results_US
eGFR by bedside Schwartz formulaschwartz
eGFR by bedside Schwartz formula (US units)schwartz_US
Simulated dataset to illustrate serial results eGFR calculator vignette.serial.results
SOFT score (Survival Outcomes Following Liver Transplantation)soft
SOFT score (Survival Outcomes Following Liver Transplantation) (US units)soft_US
SOFT score from P-SOFTsoft2
SOFT score from P-SOFT (US units)soft2_US
UKELD scoreukeld
UKELD score (US units)ukeld_US
UK Kidney Donor Risk Index (NHSBT, 2019 version)ukkdri
UK Kidney Donor Risk Index Quartile (2019)ukkdri_q
UK Kidney Recipient Risk Index (NHSBT, 2019 version)ukkrri
UK Kidney Recipient Risk Index Quartile (2019)ukkrri_q
Convert urea to BUNurea_to_bun
US Kidney Donor Risk Indexuskdri
US Kidney Donor Risk Index (US units)uskdri_US
eGFR using the Walser formulawalser
eGFR using the Walser formula (US units)walser_US
UK Kidney Donor Risk Index (2012 version)watson_ukkdri