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httk 2.4.0

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@jfwambaugh jfwambaugh released this 07 Jan 22:30
· 156 commits to main since this release
v2.4.0
c6d7afd

httk 2.4.0 (2024-8-14)

This release accompanies the submission of the new manuscript "Enabling Transparent Toxicokinetic Modeling for Public Health Risk Assessment" and includes changes intended to better facilitate development of new HTTK models through improved model clarity.

In addition we have incorporated comments received on manuscript "Impact of Gut Permeability on Estimation of Oral Bioavailability for Chemicals in Commerce and the Environment" provided by reviewers at ALTEX.

Bug Fixes

  • Cleaned up functions for model 3compartment
  • Corrected error where non-restrictive clearance option was not working for model pbtk
  • Set restrictive.clearance=TRUE by defailt in 'calc_hep_clearance' when model = "unscaled"
  • Corrected compartment names for model "gas_pbk" -- "Calv", "Cendexh", and "Cmixexh" were being returned in ppmv units, while "Calvppmv", "Cendexhppmv", and "Cmixexhppmv" were in uM
  • Calculation of Fabs corrected for non-human species to follow Yu and Amidon (1999) using small intestine mean residence time and radius. (Thank you ALTEX reviewers)
  • Intestinal flow rate correction to the Qgut model now scales with body weight (rodent Fgut was being predicted way too low)
  • Corrected units of Peff in calculation of Fabs by 'calc_fabs.oral'-- calculations now indicate that more chemicals are poorly absorbed.
  • Revised 'calc_css' to handle models with no specified analytic solution
  • Revised ionization code in 'armitage_eval' so that pka_donor and pka_accept values now correctly used (thank you Meredith Scherer)
  • Corrected bug in 'solve_model' when only specific times requesed and plots=TRUE (thank you Kimberly Troung)
  • Corrected bug with 'get_chem_id' when using 'add_chemtable' without DTXSIDs (thank you Marc Beal and Miyuki Breen)
  • Corrected bug with 'create_mc_samples' where arguments were not getting passed to 'invitro_mc' (thank you Hsing-Chieh Lin and Weihsueh Chiu)
  • Corrected bug in 'solve_model' where tsteps was ignored if times were specified

Enhancements

  • A physiology data table from 'httkpop_generate' can now be passed to 'calc_mc_css' and 'calc_mc_tk' (and 'calc_mc_css' via ...) so that a consistent populatin can be used across monte carlo runs. See argument httkpop.dt.
  • Physico-chemical properties are now retrieved from the CompTox Chemicals Dashboard programmatically using R package ctxR (Thank you Paul Kruse)
  • 'calc_fabs.oral' now calculates oral uptake rate kgutabs using Caco-2 permeability, according to method of Lennernas (1997) (Thank you ALTEX reviewers)
  • Revised and changed name of 'get_fabsgut' to 'get_fbio' and modified function to use 'calc_fbio.oral' rather than call oral bioavailability subfunctions directly
  • Replaced conversion of human effective gut permeability to rat using Wahajudin et al. (2011) regression (Thank you ALTEX reviewers)
  • Loading message displaying version now appears when package is loaded (thank you EPA NAMs class)
  • Cleaned up code for various ODE models to make them more consistent and better annotated (added more comments)
  • Reordered variables in modelinfo files for consistency so that diff can be used more easily to compare two models
  • Modified 'calc_kair' to only allow neutral chemical fraction to partition into air (thank you Jon Arnot)
  • Updated help files describing models
  • Default ODE solver tolerances increased to just below significant figures reported by HTTK (we report 4 sig figs, now require the solver to only converge to 5)
  • 'solve_[MODEL]' functions now exclusively pass arguments to deSolve through "..."
  • New modelinfo file variable default.solver.method can be set -- specifies the default ODE solver approach for deSolve if "lsoda" is not desired
  • Revised 'calc_css' to better calculate the day on which steady-state is reached
  • Added internal function 'check_model' to provide more informative error messages when key model parameters are missing
  • Updated scoping on several functions so that data.tables are handled locally within the functions and not passed by reference.
  • Precision of time points added by tsteps argument in 'solve_model' now limited to ten times higher than small.time
  • Additional time points now reported in 'solve_model' immediately after dose events to improve plotting
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