News for R package httk

Changes in version 1.9.2 (April 22, 2019)
Updated tests to reflect correct model predictions.
Greg Honda fixed errors that was causing the 3compartmentss and 1compartment 
models to not work with Monte Carlo.

Changes in version 1.9.1 (April 15, 2019)

Greg Honda fixed signficant errors in calc_analytic_css that was causeing Css to
  be over-estimated roughly 10x, therefore reducing the oral equivalent dose 10x
  (thank you Nisha Sipes for bug report)
   
Changes in version 1.9 (February, 2019)

This version is consistent with the submitted version of Honda et al. 
  "Using the Concordance of In Vitro and In Vivo Data to Evaluate Extrapolation 
  Assumptions"
New rat-specific in vitro TK data provided for 65 chemicals 
New functions for calculating in vitro disposition armitage_eval, 
  armitage_estimate_sarea (thank you James Armitage)
Added arguments to IVIVE functions (e.g., calc_mc_css) to use sets of 
  assumptions identified by Honda et al. (e.g., IVIVE="Honda1")
  (thank you Katie Paul-Friedman)
Changed all model parameter sets to include physico-chemical properties to
  better facilitate Monte Carlo analysis
Updated load_sipes2017 to be much faster by loading an image by default
Updated help files for Sipes2017 and load_sipes2017.
get_wetmore functions changed to get_lit
httkpop_bio exported to user functions
Corrected mistake in get_cheminfo help file: exlude.fub.zero defaults to 
  FALSE for 3compartmentss and TRUE for others
Corrected (thank you Jason Phillips), updated, and added pKa values from 
  Strope et al., 2018
For time point after first dose: bug now corrected when not starting at time 0
  (thank you Xiaoqing Chang)
Corrected calc_mc_css bug: species passed to monte_carlo function
Added figures to help files of solve functions
Added hematocrit argument to calc_rblood2plasma
Made amounts in 1comp model not scaled by body weight, adding BW to parameters
  for that model thank you Tom Moxon)
Converted all phys-chem properties except pKa to values predicted by OPERA 
  (Mansouri et al., 2018)
Added missing logP and MW for some chemicals from OPERA
Renamed and added vignettes
Moved code base to Bitbucket internally (thank you Sean Watford and Jeremy 
      Dunne)

Changes in version 1.8

This version is consistent with the published version of Pearce et al. 
  "Evaluation and calibration of high-throughput predictions of chemical 
  distribution to tissues". This version containins calibrations for 
  tisse:plasma partition coefficient calibration predictions. 
Added arguments for whether or not to use new calibration regressions 
  (regression) and adjusted Funbound.plasma (adjusted.Funbound.plasma).
Data from ADMET used in Sipes et al. (2017) is now included as Sipes2017 and 
  can be added with the new function: load_sipes2017().
New data has been added from an IVIVE evaluation of toxicokinetics 
  (Wambaugh et al. 2018).
Funbound.plasma values from Wetmore 2012 and 2013 that were previously rounded 
  to 2 decimal places are now rounded to 3, resulting in additional compounds
  with measurable Funbound.plasma that were otherwise assumed to be below the 
  limit of detection.
pKa data is now readable when values are separated by a semicolon rather than a 
  comma. These values were previously misread as neutral.
Partition coefficients can now be predicted without calculating all of them, 
  using the tissues argument.
Calc_mc_css runs faster when not using httkpop and calculating Rblood2plasma, 
  now only calculated once.
New data are added to chem.invivo.PK.data and chem.invivo.PK.summary.data.
chem.lists is updated, and is.pharma has been added as a function.
A new table is included: chem.invivo.PK.aggregate data
Corrected calc_mc_css bug: daily.dose now working as an argument (previously 
  only running as 1).
calc_analytic_css does not recalculate all partition coefficients when 
  specifying a tissue.
logP values from EPISuite or valued NA have been replaced with predictions from 
  OPERA where available. 
hepatic.bioavailability is added as a parameter to the models 1compartment 
  (parameterize_1comp) and 3compartmentss (parameterize_steadystate) and now 
  used with these models (multiplied by the dose and Fgutabs).
kinhabs and kdermabs, both of which were unused in the models, are removed.
vLiverPBPK.c, the source file for the pbtk model, now has updated variable 
  names, and corresponding changes are made in solve_pbtk.
The time step immediately after addition of dose is added to better capture p
  eak concentration for iv dosing.
kgutabs default changed to 2.18.

Changes in version 1.7

This version is consistent with the JSS publication of Pearce et al. "httk: R 
  Package for High-Throughput Toxicokinetics".
Corrected minor bugs including: corrected intrinsic clearances for (about 10) 
  compounds from Brown 2007, corrected output message from calc_mc_css
Corrected Funbound.plasma used for predicting partitioning into interstitial 
  protein (negligible difference in predictions)
Corrected bug in calculating Rblood2plasma in calc_mc_css, and added faster 
  method for calculating Rblood2plasma for 3compartmentss.

changes in version 1.6

This version includes data and modifications as reported in the recently 
  submitted Pearce et al. paper "Evaluation and Calibration of High-Throughput 
  Predictions of Chemical Distribution to Tissues". 
The Schmitt (2008) method for partition coefficients has been modified and 
  calibrated using experimental data. 
The new method is now default, although the previous approach is available (set 
  regression=FALSE and Funbound.plasma.pc.correction=FALSE for other models).  
  The membrane affinity regression is new and always used in place of the old. 
Added function available_rblood2plasma
In vivo Rblood2plasma used when available
well-stirred blood correction and restrictive.clearance options added 
New in vitro data from Uchimura 2010, brown 2007 and Pirovano 2016, Gulden 2002
Tonnelier Funbound.plasma values of 0.005 changed to 0 in 
  chem.physical_and_invitro.data
New tissue.data table with Ruark 2014 that contains different formatting with 
  human and rat specific data
parameterize_schmitt: added force.human.fub argument
added plasma protein and neutral lipid volume fractions to physiology.data for 
  use in package
calc_mc_css: defaults to direct resampling. no longer coerces species to human 
  when httkpop=T. When another species is entered, a warning is thrown and the 
  function behaves as if httkpop=F.
updated help file references and examples
corrected parameterize_3comp default.to.human bug: always set to false
removed temperature from schmitt parameters
overwrite 0 values for Fubound.plasma when overwrite=F in add_chemtable
added vignette for generating partition coefficient plots
added dsstox info: new columns: "DSSTox_Substance_Id","Structure_Formula", or 
  "Substance_Type".  overwrote: MW and SMILES
added pc.data and obach2008 tables
httkpop option in calc_mc_css: well-stirred correction and new Funbound.plasma 
  used by default. New partition coefficients used with other models by default.

Changes in version 1.5

This version is consistent with  Ring et al. “Identifying populations sensitive 
  to environmental chemicals by simulating toxicokinetic variability”, which is 
  accepted for publication at Environment International. Revisions include 
  models, data, and vignettes for “httk-pop” functionality. “httk-pop” allows 
  Monte Carlo simulation of physiological variability using data from the 
  National Health and Nutrition Examination Survey. This new human variability 
  functionality is the new default, although the previous approach is available 
  (set httkpop=FALSE).
default.to.human argument added to calc_hepatic_clearance and calc_stats.
calc_hepatic_clearance and calc_total_clearance do not necessarily require all 
  parameters.
Argument "tissue" added to calc_analytic_css, calc_mc_css, and 
  calc_mc_oral_equiv, enabling tissue specific calculations in addition to 
  plasma.
Corrected minor bug for get_cheminfo.
calc_dow: fraction neutral argument changed to fraction charged, thus treating 
  zwitterions as neutrals
Corrected bug in monte_carlo: Upper bound placed at limit of detection for 
  censored params truncated normal distribution.  However, this has no impact on
  the default case where the limit of detection is .01 the mean .005 because of 
  the small standard deviation size (.0015). Only large coefficients of 
  variation or Funbound.plasma values close to the limit of detection would be 
  affected.
Multiple iv doses enabled in solve functions.
get_rblood2plasma function added to retrieve in vivo Rblood2plasma from 
  chem.physical_and_invitro.data.

Changes in version: 1.4

This revision incorporates changes suggested by the reviewers of Pearce et al. 
  "httk: R Package for High-Throughput Toxicokinetics", which was accepted, 
  pending minor revision, in the Journal of  Statistical Software (now included 
  in vignettes). 
Table name "PK.physiology.data" changed to "physiology.data".

Changes in version 1.3

This revision adds ~200 more chemicals (from two recent publications including 
  Wetmore et al. 2015) and make several small changes to improve usability and 
  stability. 

Changes in version 1.2

This version is consistent with a newly submitted article Pearce et al. 
  "httk: R Package for High-Throughput Toxicokinetics" to the Journal of 
  Statistical SoftwareJ describing use of this package. 
This revision changes some model parameter names to follow a more systematic 
  naming convention. 
Minor bugs have been corrected. 

Version 1.1

Initial public (CRAN) release (March 6, 2015).