Note that backward compatibility of function arguments will not be (near-)guaranteed until version 1.0. Argument and function changes will continue until then. These will be especially noticeable around the inclusion of IV NCA parameters and additional specifications of the dosing including dose amount and route.

PKNCA 0.10.1

• A new parameter aucabove.trough.all was added to calculate the NCA above the trough concentration.
• Testing updates were made to work with dplyr version 1.1.0 (fix #198)
• Internal changes to how columns are identified were made, and the parseFormula function was subsequently removed (parseFormula was never intended for external use).

PKNCA 0.10.0

Bugs Fixed

• When calculating AUC with only a single concentration measurement, NA is now returned instead of 0. (fix #176)

New Features

• Initial support for unit assignment and conversion has been added. See the units argument to the PKNCAdata() function and the function pknca_units_table().
• Initial support for imputation has been added. See the impute argument to the PKNCAdata() function and the Data Imputation vignette.
• With the addition of units, several outputs now will differ, if units are used:
  • summary() on a PKNCAresults object shows the units in the column heading.
  • When running as.data.frame() on a PKNCAresults object with the argument out.format="wide", if standardized units values are available, they will be used. And if any unit are available, they will be in the column names.
• Summary tables with units use the “pretty_name” for a parameter which is intended for clearer representation in reports. “pretty_name” use can be controlled with the “pretty_names” argument to summary().
  • Note that the pretty names themselves may be modified to help clarify and/or shorten the names to make the table heading more useful. If you intend to modify column headers programmatically, set pretty_names=FALSE when calling the summary() function.
• New, IV AUC calculation methods have been added.
• pk.calc.time_above() now uses the default AUC calculation method for interpolation of time above. And, it can use ‘lin up/log down’ interpolation.
• PKNCA can now calculate parameters that require extra information by adding the extra information to the intervals data.frame. For example, add conc_above as a column to the intervals to allow calculation of time_above. With this change, the “conc_above” PKNCA.options() value has been removed.
• Added dplyr joins, filter, mutate, group_by, and ungroup to allow modification of PKNCA objects after creation. (Note that these functions will make the provenance no longer match for PKNCAresults objects.)

Breaking Changes

• Some functions that were intended to be internal were removed:
  • All getData() functions were removed.
  • The getDataName() function for PKNCAdata objects was removed.
• interpolate.conc() and interp.extrap.conc() now give more errors with missing (NA) input. This should not affect typical NCA (where NA values are dropped), but it may affect direct calls to the functions themselves.

Internal Breaking Changes (these should not affect PKNCA users)

• print.parseFormula() was removed from the package.

PKNCA 0.9.5

• The internals of how PKNCA performs calculations had a significant update. The only user-visible change should be that PKNCA does not perform parallel computations as of this version. Parallel computation is planned to return in the near future.
  • Breaking change: As part of this change, the split methods for PKNCAconc and PKNCAdose objects were removed along with the merge.splitList function.
• Single-subject (ungrouped) analysis works without creating a dummy group (#74)
• PKNCAconc objects are checked earlier for valid data (#154)
• Add time_above parameter to calculate time above a given concentration.
• Fix numeric BLQ replacement when the value is a number and different values are given for first, middle, and last (related to #145). This only affects datasets where BLQ is being replaced with a nonzero value (not a common scenario).
• Fix issue where intervals could not be tibbles (#141)
• Fix minor issue where only the first exclusion reason would show in the exclusion column and other reasons would be ignored (#113). Note that the impact of this bug is minimal as the result would have been excluded from summaries for the first reason found, but if there were multiple reasons for exclusion the subsequent reasons would not be recorded.

PKNCA 0.9.4

• Additional changes required for compatibility dplyr version 1.0 and CRAN checks. No functionality changed.
• Minor typographical and documentation consistency cleanups throughout.

PKNCA 0.9.3

• Changes required for compatibility dplyr version 1.0. No functionality changed.

PKNCA 0.9.2

• New feature: the time_calc() function will help convert time values to be relative to events (such as calculating time after and before doses)
• Fix issue summarizing results when “start” and “end” are dropped and there are multiple interval rows matched for a single group.
• Enable exclusions to be prevented when the input arguments suggest exclusion, but the parameter calculating function may be aware of better information about exclusion.
• Ensure that exclusions are maintained if an earlier parameter is excluded during the initial parameter calculations (Fix #112).
• Two-point half-life calculation works and adjusted r-squared gives a warning instead of an error with 2 points (Fix #114).
• Half-life calculation time was decreased by using .lm.fit() instead of lm() decreasing time for a full NCA run by ~30% (and half-life by ~50%).
• For R version 4.0, much more care was taken not to create factors from strings unless required (see https://developer.r-project.org/Blog/public/2020/02/16/stringsasfactors/index.html)

PKNCA 0.9.1

• Correct vignette building.

PKNCA 0.9.0

• Breaking Change: plot.PKNCAconc() was moved to the pknca.reporting package (https://github.com/billdenney/pknca.reporting)
• Breaking Change: summary.PKNCAresults() now provides a caption including the summary method for each parameter. If you change summary functions using PKNCA.set.summary(), you must now use the description option to set the description of the summary.
• Breaking Change: ptr now accurately uses ctrough instead of cmin (fix #106)
• Issue fixed where aucint* calculations now respect BLQ and NA rules like other calculations. (#104)
• When half.life is not calculated due to insufficient number of points (default < 3), an exclusion reason is added. (#102)
• tibbles now work as the interval argument for PKNCAdata() (fix #72)
• Issue fixed with summarization of data that has exclusions. Exclusions are now correctly handled as missing instead of never calculated.
• parseFormula now internally uses NULL for no-group formula definitions.
• signifString and roundString now have sci_range (deprecating si_range) and sci_sep arguments.
• Documentation is improved, especially around the selection of parameters for intervals.
• Multiple dose data with a single concentration measurement no longer generates an error (fixes #84).
• The “start” and “end” columns may now be dropped from the summary of PKNCAresults objects.
• PKNCAdata() is more restrictive on unknown arguments issuing an error when unknown arguments are present.
• intervals argument to PKNCAdata() may now be a tibble (fixes #72).
• Documentation has been extensively updated (fixes #81).
• CRAN changes: Vignettes now better respect not loading suggested packages. Tests are now more permissive in timing.

PKNCA 0.8.5

• Cleaned AUCint names
• Added dose-count within interval (to warn of multiple doses within an interval)
• Various documentation updates
• signifString and roundString now by default use scientific notation for values >=1e6 and <=1e-6
• Fix bug in option handling within pk.nca (Fix #68)

PKNCA 0.8.4

• Added AUCint flavors
• Parameter names for NCA parameters will likely be changing in the next version; code will still work, but some calculation methods and therefore results may be subtly different. These changes will be fully documented.)

PKNCA 0.8.2

• BACKWARD INCOMPATIBILITY: The function supplied to the exclude argument ‘FUN’ now requires two arguments and operates on the level of a single group rather than the full object. The function can also return the reason as a character string instead of a logical mask of when to exclude data.

• BACKWARD INCOMPATIBILITY: Added back-end functionality to only require one function to handle many NCA parameters that are related (e.g. combine pk.calc.aucpext, pk.calc.aucpext.obs, pk.calc.aucpext.pred, etc.). If your current code calls a specific function (like pk.calc.aucpext.pred), you must change to using the generic function (like pk.calc.aucpext)

• BACKWARD INCOMPATIBILITY: Functions that previously may have returned Infinity due to dividing by zero (e.g. when AUC=0 calculating clearance) now return NA.

• Added Validation vignette.

• Corrected issue where time to steady-state with a single estimate may have given more than one estimated time to steady-state.

• Corrected issue with exclude handling where now a blank string is also accepted as included (not excluded).

• PKNCAconc now accepts a “volume” argument and pk.nca can now calculate urine/feces-related parameters (fe, ae, clr)

• exclude_nca* functions added (Fixes issue #20)

• Add manual half-life point selection (Fixes issue #18)

• Improved summary settings (Fixes issue #54)

• Add parameters for Ceoi and intravenous MRT

• Updated vignettes to improve clarity

• Added dose-normalized PK parameters (Fixes issue #41)

• Added checks to confirm that concentration and time are numeric (Fixes feature request #40)

• Improved test coverage

PKNCA 0.8.1

• A PKNCAdose is no longer required for calculations.
• Data may now be excluded from calculations.

PKNCA 0.8

This release is not backward compatible. The switch to observed and predicted-related NCA parameters (like aucinf.obs and aucinf.pred) changed the format of the intervals specification.

• Remove dependency on doBy library
• Dose-aware interpolation and extrapolation was added with the interp.extrap.conc.dose function.
• Added Clast.pred related NCA calculations
• Added N to summary of PKNCAresults
• Added parameter selection between Clast,observed and Clast,predicted across all parameters
• Enabled PKNCAdose to be specified with one-sided formula
• Improved error reporting so that the group and time (interval specification) is reported in addition to the error.
• PKNCAdose now allows route of administration and IV infusion parameters of rate/duration to be specified

PKNCA 0.7.1

• Updated vignettes
• Standardize rounding and significance with missing values in signifString and roundString
• Enable wide data output with as.data.frame(PKNCAresults, out.format=“wide”)
• Correct calculation of Vz
• Various CRAN-related cleanups

PKNCA 0.7

• Features added
  • Additional PK parameters to support IV dosing added
  • Fix #11, Intervals can be specified manually, and will apply across appropriate parts of the grouping variables
  • Enable dose and dose.time as parameters to NCA calculations
  • More NCA parameters are calculated, especially related to IV dosing
  • Fix #8, Reporting times for time-based parameters are now within the current interval rather than since first dose (e.g. Tmax on day 14 should be between 0 and 24 not 2724+c(0, 24))
  • Added several vignettes
• Bugs fixed
  • Dosing without concentration is probably placebo; warn and continue
  • Fix #6, make merge.splitByData work with more than one dosing level
  • Export some generic classes that were not previously exported to simplify their use
  • Superposition extensions when lambda.z cannot be calculated
  • Significance rounding into character strings works when the rounding moves up one order of magnitude.
  • Fix #9, summarization of parameters that are not calculated show not calculated instead of missing.

PKNCA 0.6

First release targeting CRAN