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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 0.10.2
- A minor change to
pk.calc.aucpext()
was made so that it
now returns NA_real_
instead of NaN
.
- A minor change was made so that AUC and amount excreted (ae)
calculations will provide an exclusion reason the result is
NA
.
- A minor new feature makes the specification of imputation easier.
You can give the imputation with or without the “PKNCA_impute_method_”
prefix. So, “PKNCA_impute_method_start_predose” and “start_predose” are
equivalent.
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
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.