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Changelog

Source: NEWS.md

clinPK 0.14.0 (development version)

Major changes

  • Refactored pct_*_for_*() functions. As input, they now accept vectors of values. They now return either a vector of percentiles for the given physical measurement, or a data frame with the observed percentile for the given physical measurement, along with a select distribution of physical measurements at particular percentiles. These functions also use updated CDC growth charts instead of WHO growth charts.
  • Added median_*_for_*() functions for calculating median growth values for infants and children. These functions replace the now-deprecated return_median argument in the pct_*_for_*() functions.
  • Added CDC growth chart data sets as package data (see ?"growth-charts").
  • Removed read_who_table() function, as part of the refactor for the pct_*_for_*() functions.
  • Added calc_treosulfan_success() function.
  • Added calc_egfr_combined() function for estimating eGFR from both creatinine and cystatin C, supporting the CKD-EPI (2021, without race) and EKFC equations.
  • Added European Kidney Function Consortium (EKFC) eGFR equations: creatinine-based (calc_egfr(method = "ekfc")), cystatin C-based (calc_egfr_cystatin(method = "ekfc")), and the mean of both (calc_egfr_combined(method = "ekfc")).
  • Added CKD-EPI cystatin C equation (2012) (calc_egfr_cystatin(method = "ckd_epi")). calc_egfr_cystatin() gains age, sex, and verbose arguments.

Minor updates

  • Activated roxygen’s markdown parser for improved function documentation
  • calc_egfr_cystatin() now errors if cystatin_unit is not mg/L. Previously, other units were silently ignored.
  • calc_egfr() now validates method with match.arg(), so the available methods are listed in its usage. Unrecognized methods now give match.arg()’s error message, and unambiguous partial method names are accepted.
  • egfr_cov_reqs() now returns the canonical method name ("malmo_lund_revised") for Lund-Malmo aliases.
  • calc_egfr() now supports vectors of race for the CKD-EPI and MDRD methods, and vectors of age for the bedside Schwartz method. Previously these errored.
  • calc_egfr() and calc_egfr_combined() now error if unit_out is not one of "mL/min", "mL/hr", "L/min", or "L/hr". Previously, unrecognized units were silently treated as mL/min.
  • calc_egfr_cystatin()’s unit_out now defaults to NULL, which picks "ml/min" for the Larsson method, and "ml/min/1.73m2" for the Grubb, Hoek, EKFC, and CKD-EPI methods. Previously, the Hoek method errored unless unit_out was set.
  • Breaking change: calc_egfr() now handles absolute and relative (per 1.73 m2) eGFR correctly for the Jelliffe and Wright methods. Previously, all methods other than Cockcroft-Gault were assumed to report values per 1.73 m2.
    • method = "wright" and method = "jelliffe_unstable" report absolute values (mL/min), as in the original publications. They now default to relative = FALSE (like Cockcroft-Gault) and are labelled correctly. Previously, they were labelled as per 1.73 m2, and relative = FALSE scaled them by BSA a second time. This also affected calc_carboplatin_calvert() with these methods, which overestimated doses.
    • method = "jelliffe" now reports values per 1.73 m2, as in the original publication (Jelliffe, 1973). Previously, values were multiplied by BSA/1.73 but labelled as per 1.73 m2, and relative = FALSE scaled them by BSA a second time. BSA is now only required when relative = FALSE.
    • method = "jelliffe" now uses a factor of 0.9 for females, as in the original publication. Previously, it used 0.99.
  • Breaking change: calc_egfr_cystatin(method = "grubb") now reports eGFR in mL/min/1.73m2, as in the original publication (Grubb et al., Clinical Chemistry, 2005). Previously, it was labelled as absolute eGFR (mL/min) and could be converted to other absolute units, which was incorrect. The calculated values are unchanged, but the Grubb method now only supports unit_out = "ml/min/1.73m2".
  • Added references for the Grubb, Larsson, and Hoek methods to the calc_egfr_cystatin() documentation, along with a note that these equations were developed with cystatin C assays calibrated before international standardization.
  • calc_egfr_cystatin() now warns when the Grubb or CKD-EPI methods are used for patients < 18 years of age, since these equations were developed in adults. For the Grubb method, age is optional and only used for this warning.

clinPK 0.13.0

CRAN release: 2024-02-23

Major changes

  • Added support for converting bilirubin and albumin units
  • Added support for Calvert equation for carboplatin
  • Added function for grading neutropenia

Minor updates

  • Added support for Hoek eGFR method
  • Vectorize weight2kg() over both units and values

clinPK 0.11.1

CRAN release: 2022-05-09

Major changes

  • various corrections in nca() function
  • various updates to AKI staging equations: MDRD equation (use 2006 publication), kDIGO and PRIFLE
  • added equations of MDRD and CKD-EPI without race

Minor updates

  • refactor of calc_ibw()
  • fixed Boyd equation in calc_bsa()
  • added function to convert flow units
  • updates to 2-sample equation
  • added Cockcroft-Gault equation for spinal cord injury patients
  • consistent handling of missing/unrecognized data in calc_ibw()/calc_ffm()/calc_egfr()
  • various minor fixes and updates
  • various documentation updates
  • added many unit tests, increase overall coverage to >86%

clinPK 0.9.0

CRAN release: 2017-06-19

Initial CRAN version.