recalc_PK: Recalculate the PK for specific concentration-time profiles...

In shirewoman2/Consultancy: Standardized tools for using R within the Simcyp Consultancy Team

Recalculate the PK for specific concentration-time profiles after running calc_PK

Description

recalc_PK takes as input the output from calc_PK and recalculates the PK for any concentration-time profiles specified. A few notes about the output and calculations:

1. Aggregated PK will be recalculated to include the newly calculated individual PK parameters.

2. Graphs show the time since the start of the dosing interval on the x axis rather than the time since the first dose.

3. The ID you'll see listed on graphs or in the console if you ask for all of the progress to be shown is the compound ID, any perpetrator present, the tissue, the individual, the trial, whether the data were simulated or observed, the file name, the observed file name, and the dose number.

Usage

recalc_PK(
  ct_dataframe,
  which_dose = c("first", "last"),
  compound_name = NA,
  perpetrator_name = NA,
  existing_PK,
  existing_exp_details = NA,
  ID_match = NA,
  compoundID_match = NA,
  inhibitor_match = NA,
  tissue_match = NA,
  individual_match = NA,
  trial_match = NA,
  simulated_match = NA,
  file_match = NA,
  obsfile_match = NA,
  dosenum_match = NA,
  first_dose_time = NA,
  last_dose_time = NA,
  dosing_interval = NA,
  trapezoidal_method = "LULD",
  fit_points_after_x_time = NA,
  fit_last_x_number_of_points = NA,
  add_t0_point = TRUE,
  omit_0_concs = TRUE,
  weights = NULL,
  effort_to_get_elimination_rate = "try really hard",
  report_progress = "some",
  returnAggregateOrIndiv = "both",
  return_graphs_of_fits = TRUE,
  save_graphs_of_fits = FALSE,
  ncol = NULL,
  nrow = NULL,
  fig_width = 8.5,
  fig_height = 11
)

Arguments

ct_dataframe	a data.frame of concentration-time data in the same format as those created by running extractConcTime, extractConcTime_mult, extractObsConcTime, or extractObsConcTime_mult.
which_dose	character vector specifying which dose you want the PK for. Default is which_dose = c("first", "last") to get the PK for the first and last doses. If you only want one of those, just specify the one you want. If you want a specific interval that may or may not match the first or last dose, then you can specify it here and everything in that dosing interval will be integrated. For example, say you want PK for the first dose, the last dose, and also the interval from 24 to 36 hours. Here's how you would specify that: which_dose = c("first", "last", "24 to 36").
compound_name	the name of the compound for which PK are being calculated, e.g., "midazolam". If you already have a column titled "Compound" in ct_dataframe, leaving this as NA will retain that compound name. If you have more than one compound that you want to specify – for example, you're calculating the PK for both the substrate and for primary metabolite 1 – you can specify them with a named character vector like this: compound_name = c("substrate" = "midazolam", "primary metabolite 1" = "OH-midazolam"). All possible compound IDs permissible here: "substrate", "primary metabolite 1", "primary metabolite 2", "secondary metabolite", "inhibitor 1", "inhibitor 2", or "inhibitor 1 metabolite". This will not affect how any calculations are performed but will be included in the output data so that you have a record of which compound the data pertain to.
perpetrator_name	the name of the perpetrator, where applicable, e.g., "itraconazole". If you already have a column titled "Inhibitor" in ct_dataframe, leaving this as NA will retain that perpetrator name. This will not affect how any calculations are performed but will be included in the output data so that you have a record of which compound the data pertain to.
existing_PK	the output from calc_PK
existing_exp_details	optionally include the output from runningextractExpDetails_mult if these data are simulated. If you include this, we'll use existing_exp_details to do some data checking, including checking when each dose starts, what the dosing interval is, and making sure that, if you ask for the last-dose PK, you only get PK for that dosing interval and not any washout period that may also have been included in the data. This is not yet set up to check observed data in this manner.
ID_match	match specific data set IDs. These are the labels that show up in graphs of fitted data, e.g., "substrate none plasma 22 10 simulated abc1a-10mg-xlsx obsdatafile.xlsx NA 1". That ID is, in order, compound ID, what perpetrator was present, tissue, individual, trial, simulated or observed data, Simulator file name, observed data file name, and the dose number. Presumably, you're recalculating PK because you want to use different points for determining the terminal elimination rate, so the dose number will probably always be 1 here.
compoundID_match	any values in the CompoundID column to match in the data; matching PK profiles will be recalculated
inhibitor_match	any values in the Inhibitor column to match in the data; matching PK profiles will be recalculated
tissue_match	any values in the Tissue column to match in the data; matching PK profiles will be recalculated
individual_match	any values in the Individual column to match in the data; matching PK profiles will be recalculated
trial_match	any values in the Trial column to match in the data; matching PK profiles will be recalculated
simulated_match	any values in the Simulated column to match in the data; matching PK profiles will be recalculated
file_match	any values in the File column to match in the data; matching PK profiles will be recalculated
obsfile_match	any values in the ObsFile column to match in the data; matching PK profiles will be recalculated
dosenum_match	any values in the DoseNum column to match in the data; matching PK profiles will be recalculated
first_dose_time	the time at which the first dose was administered. If this is left as NA, the default value, this will be set to the minimum time included in your data where concentrations were above 0 unless you have supplied something for existing_exp_details (only applicable with simulated data). When that's the case and you leave this as NA, we'll get the start time for each compound from that information. If you're not supplying simulated data and something for existing_exp_details, we strongly recommend filling in this value rather than letting us estimate it. You'll get more consistent results when we know for sure when to start integrating.
last_dose_time	the time at which the last dose was administered. If this is left as NA, the default value, we'll assume that the last dose was administered at the earliest time included in the data for the highest dose number included in the data unless you have supplied something for existing_exp_details (only applicable with simulated data). When that's the case and you leave this as NA, we'll calculate the last-dose time for each compound from that information. If you're not supplying simulated data and something for existing_exp_details, we strongly recommend filling in this value rather than letting us estimate it. You'll get more consistent results when we know for sure when to start integrating.
dosing_interval	the dosing interval; default is NA which assumes that all data assigned with a given dose number should be used in calculating PK values. Cases where this wouldn't necessarily be true: When there's a washout period included in the data that is longer than the dosing interval. In that situation, this will assume that only data within the dosing interval should be used. For example, say that the last QD dose occurred at 168 h but the washout period lasted until 336 h. For calculating the last-dose AUCtau, you'd only want the time from 168 to 192 h, so if you set dosing_interval = 24, that will only calculate AUCtau using data from 168 to 192 h rather than from 168 to 336 h. This is only set up to accommodate a single dosing interval and not custom dosing regimens.
trapezoidal_method	which trapezoidal method should be used for calculating the AUC? Options are "LULD" (default) for "linear up/log down" or "linear".
fit_points_after_x_time	optionally specify that you want to fit only points after a certain time after the most-recent dose. Default of NA means that we'll fit all the data after tmax. Keep in mind that this will apply to ALL profiles.
fit_last_x_number_of_points	optionally specify that you want to fit the last X number of points for each dose (replace with whatever number makes sense for your situation). Default of NA means that we'll fit all the data after tmax. Keep in mind that this will apply to ALL profiles. An important note for fitting simulated data: If you supply simulated data with a lot of points, we will only use 100 of those concentration-time points to describe each dosing interval because performing, say, 10 trials x 10 subjects = 100 nonlinear regressions with a thousand points for each dose number requires excessive computing time needlessly because the regression must minimize the distance between the fitted curve and every one of those points. Simulated data are pretty predictable; your fitted parameters will not be less accurate with this approach. If you supply simulated data, it will probably be less confusing and yield more predictable results if you specify a value for fit_points_after_x_time rather than fit_last_x_number_of_points.
add_t0_point	TRUE (default) or FALSE for whether to add a point a t = 0 with a concentration of 0 to the data to be integrated. This ONLY applies to dose 1 data. If your data did not include a t0 point and you leave this off, you will miss the initial part of the AUC. If there is already a point at t = 0, this will be ignored and nothing in your data will change.
omit_0_concs	TRUE (default) or FALSE for whether to omit any points where the concentration = 0 since A) they were presumably below the LLOQ and B) they will mess up weighting should you choose to use a "1/y" or "1/y^2" weighting scheme. Concentrations of 0 at t0 will be retained, though, to allow for a more accurate calculation of the absorption-phase contribution to AUCinf and since 0 values at t0 would not be included in any regression of the elimination phase anyway.
weights	Weighting scheme to use for the regression. User may supply a numeric vector of weights to use or choose from "1/x", "1/x^2", "1/y" or "1/y^2". If left as NULL, no weighting scheme will be used. Be careful that you don't have any infinite values or this will fail!
effort_to_get_elimination_rate	How hard should we try to get the terminal elimination rate for dose 1? Default, "try really hard", means that we'll first try a nonlinear regression using the base R function nls, then, if that fails, we'll try expanding the boundaries for the regression and use the nls2 package function nls2 and we'll attempt that twice – the second time with some minor variations. That takes a while to run, so, if you don't want us to try that hard, other options are "try hard" (we'll only try the regular nls fit and then one variation on the nls2 fit), "try" (we'll only try the regular nls fit and then give up if it doesn't work), or "don't try" to just not get the AUCinf or terminal elimination rates at all.
report_progress	"yes", "no", or "some" (default) for whether to print messages saying when each combination of file, observed file, trial, individual, perpetrator, etc. has been completed. Setting this to "yes" can fill up your console pretty rapidly but can also be reassuring that things are, in fact, progressing.
returnAggregateOrIndiv	return aggregate and/or individual PK parameters? Options are "aggregate", "individual", or "both" (default).
return_graphs_of_fits	TRUE (default) or FALSE for whether to return a list of the graphs showing the fitted data any time the dose 1 AUC was extrapolated to infinity.
save_graphs_of_fits	TRUE or FALSE (default) for whether to save png files of graphs showing the fitted data for any time the dose 1 AUC was extrapolated to infinity. This will save one png per set of file, compoundID, inhibitor, and tissue. Note: This isn't quite working, so you may want to just look at the graphs rather than saving them until I figure out the problem. It's not saving all the graphs it should. -LSh
ncol	number of columns to use for graphing the fitted data
nrow	number of rows to use for graphing the fitted data
fig_width	figure width in inches for saving graphs of fits (you may want this to be huge if there are a lot of profiles). Defaults to 8.5.
fig_height	figure height in inches for saving graphs of fits (you may want this to be huge if there are a lot of profiles). Defaults to 11.

Value

returns a list of individual and/or aggregate PK data

Examples

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shirewoman2/Consultancy documentation built on Feb. 18, 2025, 10 p.m.