# Get all registered interval columns (parameters)
cols <- get.interval.cols()
# Build edge list from the 'depends' field
edges <- lapply(names(cols), function(param) {
deps <- cols[[param]]$depends
if (length(deps) == 0) return(NULL)
data.frame(from = deps, to = param, stringsAsFactors = FALSE)
}) |>
bind_rows()
# All unique nodes
all_nodes <- unique(c(edges$from, edges$to, names(cols)))
# Assign category for coloring
categorize <- function(name) {
case_when(
grepl("^auc", name) ~ "AUC",
grepl("^lambda|half\\.life|r\\.squared", name) ~ "Half-life / λz",
grepl("^cl\\.|^vz\\.|^vss", name) ~ "CL / Volume",
grepl("^mrt", name) ~ "MRT",
grepl("^c(max|min|0|last|first)|^t(max|min|last|first|lag)|^clast", name) ~ "Cmax / Tmax",
grepl("^f$|bioavail|^ae|^fe|^clr|^vd", name) ~ "Bioavailability / Renal",
grepl("^tss", name) ~ "Steady-state",
TRUE ~ "Other"
)
}
category_colors <- c(
"AUC" = "#4e79a7",
"Half-life / λz" = "#f28e2b",
"CL / Volume" = "#e15759",
"MRT" = "#76b7b2",
"Cmax / Tmax" = "#59a14f",
"Bioavailability / Renal"= "#edc948",
"Steady-state" = "#b07aa1",
"Other" = "#aaaaaa"
)
nodes <- data.frame(
id = all_nodes,
label = all_nodes,
group = categorize(all_nodes),
stringsAsFactors = FALSE
)
graph <- visNetwork(nodes, edges,
width = "100%", height = "700px",
main = "PKNCA NCA Parameter Dependencies") |>
visNodes(shape = "dot", size = 14,
font = list(size = 12),
borderWidth = 2) |>
visEdges(arrows = "to",
color = list(color = "#aaaaaa", highlight = "#333333"),
smooth = list(type = "cubicBezier")) |>
visOptions(
highlightNearest = list(enabled = TRUE, degree = 2, hover = TRUE),
nodesIdSelection = list(enabled = TRUE, main = "Select parameter")
) |>
visLegend(useGroups = TRUE, position = "right") |>
visPhysics(stabilization = list(iterations = 200)) |>
visLayout(randomSeed = 42)
# Register each category as a visNetwork group: nodes and legend swatches both
# take their color from the group definition, so they always match
for (grp in names(category_colors)) {
graph <- visGroups(graph, groupname = grp, color = category_colors[[grp]])
}
graph22 NCA Parameter Dependencies
PKNCA resolves parameter dependencies automatically: when you request aucinf.obs, PKNCA internally ensures lambda.z is computed first because aucinf.obs depends on it. These dependencies are declared at registration time — every NCA parameter is registered via add.interval.col() with a depends vector naming the parameters that must be computed before it, and the full registry is accessible via get.interval.cols(). The graph below makes the whole dependency network explicit.
22.1 Interactive dependency graph
How to use this graph:
- Click a parameter node to highlight its immediate dependencies and dependents
- The “Select parameter” dropdown jumps to a specific node
- Drag nodes to rearrange; scroll to zoom
- Colors indicate parameter family (see legend)
22.2 Dependency table
For a text-based reference:
dep_table <- lapply(names(cols), function(param) {
data.frame(
parameter = param,
depends_on = if (length(cols[[param]]$depends) == 0) "(none)"
else paste(cols[[param]]$depends, collapse = ", "),
stringsAsFactors = FALSE
)
}) |>
bind_rows() |>
arrange(parameter)
knitr::kable(dep_table, col.names = c("Parameter", "Depends on"))| Parameter | Depends on |
|---|---|
| adj.r.squared | half.life |
| adj_tobit_residual | half.life |
| ae | (none) |
| aucabove.predose.all | cstart |
| aucabove.trough.all | ctrough |
| aucall | (none) |
| aucall.dn | aucall |
| aucinf.obs | lambda.z, clast.obs |
| aucinf.obs.dn | aucinf.obs |
| aucinf.pred | lambda.z, clast.pred |
| aucinf.pred.dn | aucinf.pred |
| aucint.all | (none) |
| aucint.all.dose | (none) |
| aucint.inf.obs | lambda.z, clast.obs |
| aucint.inf.obs.dose | lambda.z, clast.obs |
| aucint.inf.pred | lambda.z, clast.pred |
| aucint.inf.pred.dose | lambda.z, clast.pred |
| aucint.last | (none) |
| aucint.last.dose | (none) |
| aucivall | aucall, c0 |
| aucivinf.obs | aucinf.obs, c0 |
| aucivinf.pred | aucinf.pred, c0 |
| aucivint.all | aucint.all, c0 |
| aucivint.last | aucint.last, c0 |
| aucivlast | auclast, c0 |
| aucivpbextall | aucall, aucivall |
| aucivpbextinf.obs | aucinf.obs, aucivinf.obs |
| aucivpbextinf.pred | aucinf.pred, aucivinf.pred |
| aucivpbextint.all | aucint.all, aucivint.all |
| aucivpbextint.last | aucint.last, aucivint.last |
| aucivpbextlast | auclast, aucivlast |
| auclast | (none) |
| auclast.dn | auclast |
| aucpext.obs | auclast, aucinf.obs |
| aucpext.pred | auclast, aucinf.pred |
| aumcall | (none) |
| aumcall.dn | aumcall |
| aumcinf.obs | lambda.z, clast.obs |
| aumcinf.obs.dn | aumcinf.obs |
| aumcinf.pred | lambda.z, clast.pred |
| aumcinf.pred.dn | aumcinf.pred |
| aumcint.all | (none) |
| aumcint.all.dose | (none) |
| aumcint.inf.obs | lambda.z, clast.obs |
| aumcint.inf.obs.dose | lambda.z, clast.obs |
| aumcint.inf.pred | lambda.z, clast.pred |
| aumcint.inf.pred.dose | lambda.z, clast.pred |
| aumcint.last | (none) |
| aumcint.last.dose | (none) |
| aumcivall | aumcall, c0 |
| aumcivinf.obs | aumcinf.obs, c0 |
| aumcivinf.pred | aumcinf.pred, c0 |
| aumcivint.all | aumcint.all, c0 |
| aumcivint.last | aumcint.last, c0 |
| aumcivlast | aumclast, c0 |
| aumclast | (none) |
| aumclast.dn | aumclast |
| c0 | (none) |
| cav | auclast |
| cav.dn | cav |
| cav.int.all | aucint.all |
| cav.int.inf.obs | aucint.inf.obs |
| cav.int.inf.pred | aucint.inf.pred |
| cav.int.last | aucint.last |
| ceoi | (none) |
| cl.all | aucall |
| cl.int.all | aucint.all |
| cl.int.inf.obs | aucint.inf.obs |
| cl.int.inf.pred | aucint.inf.pred |
| cl.int.last | aucint.last |
| cl.iv.all | aucivall |
| cl.iv.last | aucivlast |
| cl.iv.obs | aucivinf.obs |
| cl.iv.pred | aucivinf.pred |
| cl.ivint.all | aucivint.all |
| cl.ivint.last | aucivint.last |
| cl.last | auclast |
| cl.obs | aucinf.obs |
| cl.pred | aucinf.pred |
| cl.sparse.last | sparse_auclast |
| clast.obs | (none) |
| clast.obs.dn | clast.obs |
| clast.pred | half.life |
| clast.pred.dn | clast.pred |
| clr.last | ae |
| clr.last.dn | clr.last |
| clr.obs | ae |
| clr.obs.dn | clr.obs |
| clr.pred | ae |
| clr.pred.dn | clr.pred |
| cmax | (none) |
| cmax.dn | cmax |
| cmin | (none) |
| cmin.dn | cmin |
| count_conc | (none) |
| count_conc_measured | (none) |
| cstart | (none) |
| ctrough | (none) |
| ctrough.dn | ctrough |
| deg.fluc | cmax, cmin, cav |
| end | (none) |
| ermax | (none) |
| ertlst | (none) |
| ertmax | (none) |
| f | (none) |
| fe | ae |
| half.life | tmax, tlast |
| kel.all | mrt.all |
| kel.int.all | mrt.int.all |
| kel.int.inf.obs | mrt.int.inf.obs |
| kel.int.inf.pred | mrt.int.inf.pred |
| kel.int.last | mrt.int.last |
| kel.iv.all | mrt.iv.all |
| kel.iv.last | mrt.iv.last |
| kel.iv.obs | mrt.iv.obs |
| kel.iv.pred | mrt.iv.pred |
| kel.ivint.all | mrt.ivint.all |
| kel.ivint.last | mrt.ivint.last |
| kel.last | mrt.last |
| kel.obs | mrt.obs |
| kel.pred | mrt.pred |
| kel.sparse.last | mrt.sparse.last |
| lambda.z | half.life |
| lambda.z.corrxy | half.life |
| lambda.z.n.points | half.life |
| lambda.z.n.points_blq | half.life |
| lambda.z.time.first | half.life |
| lambda.z.time.last | half.life |
| mrt.all | aucall, aumcall |
| mrt.int.all | aucint.all, aumcint.all |
| mrt.int.inf.obs | aucint.inf.obs, aumcint.inf.obs |
| mrt.int.inf.pred | aucint.inf.pred, aumcint.inf.pred |
| mrt.int.last | aucint.last, aumcint.last |
| mrt.iv.all | aucivall, aumcivall |
| mrt.iv.last | auclast, aumclast |
| mrt.iv.obs | aucinf.obs, aumcinf.obs |
| mrt.iv.pred | aucinf.pred, aumcinf.pred |
| mrt.ivint.all | aucivint.all, aumcivint.all |
| mrt.ivint.last | aucivint.last, aumcivint.last |
| mrt.last | auclast, aumclast |
| mrt.md.obs | auclast, aumclast, aucinf.obs |
| mrt.md.pred | auclast, aumclast, aucinf.pred |
| mrt.obs | aucinf.obs, aumcinf.obs |
| mrt.pred | aucinf.pred, aumcinf.pred |
| mrt.sparse.last | sparse_auclast, sparse_aumclast |
| ptr | cmax, ctrough |
| r.squared | half.life |
| span.ratio | half.life |
| sparse_auc_df | sparse_auclast |
| sparse_auc_se | sparse_auclast |
| sparse_auclast | (none) |
| sparse_aumc_df | sparse_aumclast |
| sparse_aumc_se | sparse_aumclast |
| sparse_aumclast | sparse_auclast |
| start | (none) |
| swing | cmax, cmin |
| tfirst | (none) |
| thalf.eff.iv.last | mrt.iv.last |
| thalf.eff.iv.obs | mrt.iv.obs |
| thalf.eff.iv.pred | mrt.iv.pred |
| thalf.eff.last | mrt.last |
| thalf.eff.obs | mrt.obs |
| thalf.eff.pred | mrt.pred |
| time_above | (none) |
| tlag | (none) |
| tlast | (none) |
| tmax | (none) |
| tmin | (none) |
| tobit_residual | half.life |
| totdose | (none) |
| volpk | (none) |
| vss.all | cl.all, mrt.all |
| vss.int.all | cl.int.all, mrt.int.all |
| vss.int.inf.obs | cl.int.inf.obs, mrt.int.inf.obs |
| vss.int.inf.pred | cl.int.inf.pred, mrt.int.inf.pred |
| vss.int.last | cl.int.last, mrt.int.last |
| vss.iv.all | cl.iv.all, mrt.iv.all |
| vss.iv.last | cl.last, mrt.iv.last |
| vss.iv.obs | cl.obs, mrt.iv.obs |
| vss.iv.pred | cl.pred, mrt.iv.pred |
| vss.ivint.all | cl.ivint.all, mrt.ivint.all |
| vss.ivint.last | cl.ivint.last, mrt.ivint.last |
| vss.last | cl.last, mrt.last |
| vss.md.obs | cl.last, mrt.md.obs |
| vss.md.pred | cl.last, mrt.md.pred |
| vss.obs | cl.obs, mrt.obs |
| vss.pred | cl.pred, mrt.pred |
| vss.sparse.last | cl.sparse.last, mrt.sparse.last |
| vz.all | cl.all, lambda.z |
| vz.int.all | cl.int.all, lambda.z |
| vz.int.inf.obs | cl.int.inf.obs, lambda.z |
| vz.int.inf.pred | cl.int.inf.pred, lambda.z |
| vz.int.last | cl.int.last, lambda.z |
| vz.iv.all | cl.iv.all, lambda.z |
| vz.iv.last | cl.iv.last, lambda.z |
| vz.iv.obs | cl.iv.obs, lambda.z |
| vz.iv.pred | cl.iv.pred, lambda.z |
| vz.ivint.all | cl.ivint.all, lambda.z |
| vz.ivint.last | cl.ivint.last, lambda.z |
| vz.last | cl.last, lambda.z |
| vz.obs | cl.obs, lambda.z |
| vz.pred | cl.pred, lambda.z |
| vz.sparse.last | cl.sparse.last, kel.sparse.last |
22.3 Parameter-to-function mapping
Every interval parameter is computed by a function registered alongside it — usually named pk.calc.*() — and the registry entry returned by get.interval.cols() records that function name in its $FUN field, together with the parameter’s unit type and description. Where $FUN is NA, the parameter has no dedicated function: it is either produced as part of another function’s output (for example, r.squared and lambda.z.time.first are returned by the same half-life fit that produces half.life) or it is an interval boundary (start, end).
The table below is the complete index of the calculation API: every registered parameter, the function that computes it, its unit type, and its description. To add your own parameter to this registry, see the Writing Custom Parameters chapter and the vignette Writing PKNCA Parameter Functions.
cols <- get.interval.cols()
fun_map <- data.frame(
parameter = names(cols),
# $FUN is a character function name, or logical NA when the parameter has no
# dedicated function; as.character() coerces both to character
fun = vapply(cols, function(x) as.character(x$FUN), character(1)),
unit_type = vapply(cols, function(x) x$unit_type, character(1)),
desc = vapply(cols, function(x) x$desc, character(1)),
stringsAsFactors = FALSE
) |>
arrange(parameter)
knitr::kable(
fun_map,
row.names = FALSE,
col.names = c("Parameter", "Function", "Unit type", "Description")
)| Parameter | Function | Unit type | Description |
|---|---|---|---|
| adj.r.squared | NA | unitless | The adjusted r^2 value of the half-life calculation |
| adj_tobit_residual | NA | unitless | The adjusted Tobit residual standard deviation (analogous to adjusted r-squared; penalizes smaller windows) |
| ae | pk.calc.ae | amount | The amount excreted (typically into urine or feces) |
| aucabove.predose.all | pk.calc.aucabove | auc | The area under the concentration time the beginning of the interval to the last concentration above the limit of quantification plus the triangle from that last concentration to 0 at the first concentration below the limit of quantification, with a concentration subtracted from all concentrations and values below zero after subtraction set to zero |
| aucabove.trough.all | pk.calc.aucabove | auc | The area under the concentration time the beginning of the interval to the last concentration above the limit of quantification plus the triangle from that last concentration to 0 at the first concentration below the limit of quantification, with a concentration subtracted from all concentrations and values below zero after subtraction set to zero |
| aucall | pk.calc.auc.all | auc | The area under the concentration time curve from the beginning of the interval to the last concentration above the limit of quantification plus the triangle from that last concentration to 0 at the first concentration below the limit of quantification |
| aucall.dn | pk.calc.dn | auc_dosenorm | Dose normalized aucall |
| aucinf.obs | pk.calc.auc.inf.obs | auc | The area under the concentration time curve from the beginning of the interval to infinity with extrapolation to infinity from the observed Clast |
| aucinf.obs.dn | pk.calc.dn | auc_dosenorm | Dose normalized aucinf.obs |
| aucinf.pred | pk.calc.auc.inf.pred | auc | The area under the concentration time curve from the beginning of the interval to infinity with extrapolation to infinity from the predicted Clast |
| aucinf.pred.dn | pk.calc.dn | auc_dosenorm | Dose normalized aucinf.pred |
| aucint.all | pk.calc.aucint.all | auc | The area under the concentration time curve in the interval extrapolating from Tlast to infinity with the triangle from Tlast to the next point and zero thereafter (matching AUCall) |
| aucint.all.dose | pk.calc.aucint.all | auc | The area under the concentration time curve in the interval extrapolating from Tlast to infinity with the triangle from Tlast to the next point and zero thereafter (matching AUCall) with dose-aware interpolation/extrapolation of concentrations |
| aucint.inf.obs | pk.calc.aucint.inf.obs | auc | The area under the concentration time curve in the interval extrapolating from Tlast to infinity with zeros (matching AUClast) |
| aucint.inf.obs.dose | pk.calc.aucint.inf.obs | auc | The area under the concentration time curve in the interval extrapolating from Tlast to infinity with zeros (matching AUClast) with dose-aware interpolation/extrapolation of concentrations |
| aucint.inf.pred | pk.calc.aucint.inf.pred | auc | The area under the concentration time curve in the interval extrapolating from Tlast to infinity with the triangle from Tlast to the next point and zero thereafter (matching AUCall) |
| aucint.inf.pred.dose | pk.calc.aucint.inf.pred | auc | The area under the concentration time curve in the interval extrapolating from Tlast to infinity with the triangle from Tlast to the next point and zero thereafter (matching AUCall) with dose-aware interpolation/extrapolation of concentrations |
| aucint.last | pk.calc.aucint.last | auc | The area under the concentration time curve in the interval extrapolating from Tlast to infinity with zeros (matching AUClast) |
| aucint.last.dose | pk.calc.aucint.last | auc | The area under the concentration time curve in the interval extrapolating from Tlast to infinity with zeros (matching AUClast) with dose-aware interpolation/extrapolation of concentrations |
| aucivall | pk.calc.auciv | auc | The AUCall calculated with back-extrapolation for intravenous dosing using extrapolated C0 |
| aucivinf.obs | pk.calc.auciv | auc | The AUCinf,obs calculated with back-extrapolation for intravenous dosing using extrapolated C0 |
| aucivinf.pred | pk.calc.auciv | auc | The AUCinf,pred calculated with back-extrapolation for intravenous dosing using extrapolated C0 |
| aucivint.all | pk.calc.auciv | auc | The AUCint,all calculated with back-extrapolation for intravenous dosing using extrapolated C0 |
| aucivint.last | pk.calc.auciv | auc | The AUCint,last calculated with back-extrapolation for intravenous dosing using extrapolated C0 |
| aucivlast | pk.calc.auciv | auc | The AUClast calculated with back-extrapolation for intravenous dosing using extrapolated C0 |
| aucivpbextall | pk.calc.auciv_pbext | % | The back-extrapolation percent for intravenous dosing based on AUCall |
| aucivpbextinf.obs | pk.calc.auciv_pbext | % | The back-extrapolation percent for intravenous dosing based on AUCinf,obs |
| aucivpbextinf.pred | pk.calc.auciv_pbext | % | The back-extrapolation percent for intravenous dosing based on AUCinf,pred |
| aucivpbextint.all | pk.calc.auciv_pbext | % | The back-extrapolation percent for intravenous dosing based on AUCint,all |
| aucivpbextint.last | pk.calc.auciv_pbext | % | The back-extrapolation percent for intravenous dosing based on AUCint,last |
| aucivpbextlast | pk.calc.auciv_pbext | % | The back-extrapolation percent for intravenous dosing based on AUClast |
| auclast | pk.calc.auc.last | auc | The area under the concentration time curve from the beginning of the interval to the last concentration above the limit of quantification |
| auclast.dn | pk.calc.dn | auc_dosenorm | Dose normalized auclast |
| aucpext.obs | pk.calc.aucpext | % | Percent of the AUCinf that is extrapolated after Tlast calculated from the observed Clast |
| aucpext.pred | pk.calc.aucpext | % | Percent of the AUCinf that is extrapolated after Tlast calculated from the predicted Clast |
| aumcall | pk.calc.aumc.all | aumc | The area under the concentration time moment curve from the beginning of the interval to the last concentration above the limit of quantification plus the moment of the triangle from that last concentration to 0 at the first concentration below the limit of quantification |
| aumcall.dn | pk.calc.dn | aumc_dosenorm | Dose normalized aumcall |
| aumcinf.obs | pk.calc.aumc.inf.obs | aumc | The area under the concentration time moment curve from the beginning of the interval to infinity with extrapolation to infinity from the observed Clast |
| aumcinf.obs.dn | pk.calc.dn | aumc_dosenorm | Dose normalized aumcinf.obs |
| aumcinf.pred | pk.calc.aumc.inf.pred | aumc | The area under the concentration time moment curve from the beginning of the interval to infinity with extrapolation to infinity from the predicted Clast |
| aumcinf.pred.dn | pk.calc.dn | aumc_dosenorm | Dose normalized aumcinf.pred |
| aumcint.all | pk.calc.aumcint.all | aumc | The area under the moment curve in the interval extrapolating from Tlast to infinity with the triangle from Tlast to the next point and zero thereafter (matching AUMCall) |
| aumcint.all.dose | pk.calc.aumcint.all | aumc | The area under the moment curve in the interval extrapolating from Tlast to infinity with the triangle from Tlast to the next point and zero thereafter (matching AUMCall) with dose-aware interpolation/extrapolation of concentrations |
| aumcint.inf.obs | pk.calc.aumcint.inf.obs | aumc | The area under the moment curve in the interval extrapolating from Tlast to infinity with zeros (matching AUMClast) |
| aumcint.inf.obs.dose | pk.calc.aumcint.inf.obs | aumc | The area under the moment curve in the interval extrapolating from Tlast to infinity with zeros (matching AUMClast) with dose-aware interpolation/extrapolation of concentrations |
| aumcint.inf.pred | pk.calc.aumcint.inf.pred | aumc | The area under the moment curve in the interval extrapolating from Tlast to infinity with the triangle from Tlast to the next point and zero thereafter (matching AUMCall) |
| aumcint.inf.pred.dose | pk.calc.aumcint.inf.pred | aumc | The area under the moment curve in the interval extrapolating from Tlast to infinity with the triangle from Tlast to the next point and zero thereafter (matching AUMCall) with dose-aware interpolation/extrapolation of concentrations |
| aumcint.last | pk.calc.aumcint.last | aumc | The area under the moment curve in the interval extrapolating from Tlast to infinity with zeros (matching AUMClast) |
| aumcint.last.dose | pk.calc.aumcint.last | aumc | The area under the moment curve in the interval extrapolating from Tlast to infinity with zeros (matching AUMClast) with dose-aware interpolation/extrapolation of concentrations |
| aumcivall | pk.calc.aumciv | aumc | The AUMCall calculated with back-extrapolation for intravenous dosing using extrapolated C0 |
| aumcivinf.obs | pk.calc.aumciv | aumc | The AUMCinf,obs calculated with back-extrapolation for intravenous dosing using extrapolated C0 |
| aumcivinf.pred | pk.calc.aumciv | aumc | The AUMCinf,pred calculated with back-extrapolation for intravenous dosing using extrapolated C0 |
| aumcivint.all | pk.calc.aumciv | aumc | The AUMCint,all calculated with back-extrapolation for intravenous dosing using extrapolated C0 |
| aumcivint.last | pk.calc.aumciv | aumc | The AUMCint,last calculated with back-extrapolation for intravenous dosing using extrapolated C0 |
| aumcivlast | pk.calc.aumciv | aumc | The AUMClast calculated with back-extrapolation for intravenous dosing using extrapolated C0 |
| aumclast | pk.calc.aumc.last | aumc | The area under the concentration time moment curve from the beginning of the interval to the last concentration above the limit of quantification |
| aumclast.dn | pk.calc.dn | aumc_dosenorm | Dose normalized aumclast |
| c0 | pk.calc.c0 | conc | Initial concentration after an IV bolus |
| cav | pk.calc.cav | conc | The average concentration during an interval (calculated with AUClast) |
| cav.dn | pk.calc.dn | conc_dosenorm | Dose normalized cav |
| cav.int.all | pk.calc.cav | conc | The average concentration during an interval (calculated with AUCint.all) |
| cav.int.inf.obs | pk.calc.cav | conc | The average concentration during an interval (calculated with AUCint.inf.obs) |
| cav.int.inf.pred | pk.calc.cav | conc | The average concentration during an interval (calculated with AUCint.inf.pred) |
| cav.int.last | pk.calc.cav | conc | The average concentration during an interval (calculated with AUCint.last) |
| ceoi | pk.calc.ceoi | conc | Concentration at the end of infusion |
| cl.all | pk.calc.cl | clearance | Clearance or observed oral clearance calculated with AUCall |
| cl.int.all | pk.calc.cl | clearance | Clearance or observed oral clearance calculated with AUCint.all |
| cl.int.inf.obs | pk.calc.cl | clearance | Clearance or observed oral clearance calculated with AUCint.inf.obs |
| cl.int.inf.pred | pk.calc.cl | clearance | Clearance or observed oral clearance calculated with AUCint.inf.pred |
| cl.int.last | pk.calc.cl | clearance | Clearance or observed oral clearance calculated with AUCint.last |
| cl.iv.all | pk.calc.cl | clearance | Clearance for intravenous dosing calculated with AUCall |
| cl.iv.last | pk.calc.cl | clearance | Clearance for intravenous dosing calculated with AUClast |
| cl.iv.obs | pk.calc.cl | clearance | Clearance for intravenous dosing calculated with AUCinf,obs |
| cl.iv.pred | pk.calc.cl | clearance | Clearance for intravenous dosing calculated with AUCinf,pred |
| cl.ivint.all | pk.calc.cl | clearance | Clearance for intravenous dosing calculated with interval AUCint.all |
| cl.ivint.last | pk.calc.cl | clearance | Clearance for intravenous dosing calculated with interval AUCint.last |
| cl.last | pk.calc.cl | clearance | Clearance or observed oral clearance calculated to Clast |
| cl.obs | pk.calc.cl | clearance | Clearance or observed oral clearance calculated with observed Clast |
| cl.pred | pk.calc.cl | clearance | Clearance or observed oral clearance calculated with predicted Clast |
| cl.sparse.last | pk.calc.cl | clearance | Clearance from sparse sampling calculated with population AUClast |
| clast.obs | pk.calc.clast.obs | conc | The last concentration observed above the limit of quantification |
| clast.obs.dn | pk.calc.dn | conc_dosenorm | Dose normalized clast.obs |
| clast.pred | NA | conc | The concentration at Tlast as predicted by the half-life |
| clast.pred.dn | pk.calc.dn | conc_dosenorm | Dose normalized clast.pred |
| clr.last | pk.calc.clr | renal_clearance | The renal clearance calculated using AUClast |
| clr.last.dn | pk.calc.dn | renal_clearance_dosenorm | Dose normalized clr.last |
| clr.obs | pk.calc.clr | renal_clearance | The renal clearance calculated using AUCinf,obs |
| clr.obs.dn | pk.calc.dn | renal_clearance_dosenorm | Dose normalized clr.obs |
| clr.pred | pk.calc.clr | renal_clearance | The renal clearance calculated using AUCinf,pred |
| clr.pred.dn | pk.calc.dn | renal_clearance_dosenorm | Dose normalized clr.pred |
| cmax | pk.calc.cmax | conc | Maximum observed concentration |
| cmax.dn | pk.calc.dn | conc_dosenorm | Dose normalized cmax |
| cmin | pk.calc.cmin | conc | Minimum observed concentration |
| cmin.dn | pk.calc.dn | conc_dosenorm | Dose normalized cmin |
| count_conc | pk.calc.count_conc | count | Number of non-missing concentrations for an interval |
| count_conc_measured | pk.calc.count_conc_measured | count | Number of measured and non BLQ/ALQ concentrations for an interval |
| cstart | pk.calc.cstart | conc | The predose concentration |
| ctrough | pk.calc.ctrough | conc | The trough (end of interval) concentration |
| ctrough.dn | pk.calc.dn | conc_dosenorm | Dose normalized ctrough |
| deg.fluc | pk.calc.deg.fluc | % | Degree of fluctuation |
| end | NA | time | Ending time of the interval (potentially infinity) |
| ermax | pk.calc.ermax | amount_time | The maximum excretion rate (typically in urine or feces) |
| ertlst | pk.calc.ertlst | time | The midpoint collection time of the last measurable excretion rate (typically in urine or feces) |
| ertmax | pk.calc.ertmax | time | The midpoint collection time of the maximum excretion rate (typically in urine or feces) |
| f | pk.calc.f | fraction | Bioavailability or relative bioavailability |
| fe | pk.calc.fe | amount_dose | The fraction of the dose excreted |
| half.life | pk.calc.half.life | time | The (terminal) half-life |
| kel.all | pk.calc.kel | inverse_time | Elimination rate (as calculated from the MRTall) |
| kel.int.all | pk.calc.kel | inverse_time | Elimination rate (as calculated from the MRTint.all) |
| kel.int.inf.obs | pk.calc.kel | inverse_time | Elimination rate (as calculated from the MRTint.inf.obs) |
| kel.int.inf.pred | pk.calc.kel | inverse_time | Elimination rate (as calculated from the MRTint.inf.pred) |
| kel.int.last | pk.calc.kel | inverse_time | Elimination rate (as calculated from the MRTint.last) |
| kel.iv.all | pk.calc.kel | inverse_time | Elimination rate (as calculated from the MRTiv.all)) |
| kel.iv.last | pk.calc.kel | inverse_time | Elimination rate (as calculated from the intravenous MRTlast) |
| kel.iv.obs | pk.calc.kel | inverse_time | Elimination rate (as calculated from the intravenous MRTobs) |
| kel.iv.pred | pk.calc.kel | inverse_time | Elimination rate (as calculated from the intravenous MRTpred) |
| kel.ivint.all | pk.calc.kel | inverse_time | Elimination rate (as calculated from the MRTivint.all) |
| kel.ivint.last | pk.calc.kel | inverse_time | Elimination rate (as calculated from the MRTivint.last) |
| kel.last | pk.calc.kel | inverse_time | Elimination rate (as calculated from the MRT using AUClast) |
| kel.obs | pk.calc.kel | inverse_time | Elimination rate (as calculated from the MRT with observed Clast) |
| kel.pred | pk.calc.kel | inverse_time | Elimination rate (as calculated from the MRT with predicted Clast) |
| kel.sparse.last | pk.calc.kel | inverse_time | Elimination rate (as calculated from the MRTsparse.last) |
| lambda.z | NA | inverse_time | The elimination rate of the terminal half-life |
| lambda.z.corrxy | NA | unitless | Correlation between time and log-concentration for lambda.z points |
| lambda.z.n.points | NA | count | The number of points used for the calculation of half-life |
| lambda.z.n.points_blq | NA | count | The number of BLQ points included in the Tobit half-life calculation |
| lambda.z.time.first | NA | time | The first time point used for the calculation of half-life |
| lambda.z.time.last | NA | time | The last time point used for the calculation of half-life |
| mrt.all | pk.calc.mrt | time | Mean residence time calculated with AUCall/AUMCall |
| mrt.int.all | pk.calc.mrt | time | Mean residence time over interval calculated with AUCint.all/AUMCint.all |
| mrt.int.inf.obs | pk.calc.mrt | time | Mean residence time over interval calculated with AUCint.inf.obs/AUMCint.inf.obs |
| mrt.int.inf.pred | pk.calc.mrt | time | Mean residence time over interval calculated with AUCint.inf.pred/AUMCint.inf.pred |
| mrt.int.last | pk.calc.mrt | time | Mean residence time over interval calculated with AUCint.last/AUMCint.last |
| mrt.iv.all | pk.calc.mrt.iv | time | Mean residence time for IV dosing calculated with AUCall/AUMCall |
| mrt.iv.last | pk.calc.mrt.iv | time | The mean residence time to the last observed concentration above the LOQ correcting for dosing duration |
| mrt.iv.obs | pk.calc.mrt.iv | time | The mean residence time to infinity using observed Clast correcting for dosing duration |
| mrt.iv.pred | pk.calc.mrt.iv | time | The mean residence time to infinity using predicted Clast correcting for dosing duration |
| mrt.ivint.all | pk.calc.mrt.iv | time | Mean residence time for IV interval calculated with AUCint.all/AUMCint.all |
| mrt.ivint.last | pk.calc.mrt.iv | time | Mean residence time for IV interval calculated with AUCint.last/AUMCint.last |
| mrt.last | pk.calc.mrt | time | The mean residence time to the last observed concentration above the LOQ |
| mrt.md.obs | pk.calc.mrt.md | time | The mean residence time with multiple dosing and nonlinear kinetics using observed Clast |
| mrt.md.pred | pk.calc.mrt.md | time | The mean residence time with multiple dosing and nonlinear kinetics using predicted Clast |
| mrt.obs | pk.calc.mrt | time | The mean residence time to infinity using observed Clast |
| mrt.pred | pk.calc.mrt | time | The mean residence time to infinity using predicted Clast |
| mrt.sparse.last | pk.calc.mrt | time | Mean residence time from sparse sampling |
| ptr | pk.calc.ptr | fraction | Peak-to-Trough ratio (fraction) |
| r.squared | NA | unitless | The r^2 value of the half-life calculation |
| span.ratio | NA | fraction | The ratio of the half-life to the duration used for half-life calculation |
| sparse_auc_df | NA | count | For sparse PK sampling, the standard error degrees of freedom of the area under the concentration time curve from the beginning of the interval to the last concentration above the limit of quantification |
| sparse_auc_se | NA | auc | For sparse PK sampling, the standard error of the area under the concentration time curve from the beginning of the interval to the last concentration above the limit of quantification |
| sparse_auclast | pk.calc.sparse_auclast | auc | For sparse PK sampling, the area under the concentration time curve from the beginning of the interval to the last concentration above the limit of quantification |
| sparse_aumc_df | NA | count | For sparse PK sampling, the degrees of freedom for the AUMC variance estimate |
| sparse_aumc_se | NA | aumc | For sparse PK sampling, the standard error of the area under the moment curve |
| sparse_aumclast | pk.calc.sparse_aumclast | aumc | For sparse PK sampling, the area under the moment curve from the beginning of the interval to the last concentration above the limit of quantification |
| start | NA | time | Starting time of the interval |
| swing | pk.calc.swing | % | Swing relative to Cmin |
| tfirst | pk.calc.tfirst | time | Time of the first concentration above the limit of quantification |
| thalf.eff.iv.last | pk.calc.thalf.eff | time | The effective half-life (as determined from the intravenous MRTlast) |
| thalf.eff.iv.obs | pk.calc.thalf.eff | time | The effective half-life (as determined from the intravenous MRTobs) |
| thalf.eff.iv.pred | pk.calc.thalf.eff | time | The effective half-life (as determined from the intravenous MRTpred) |
| thalf.eff.last | pk.calc.thalf.eff | time | The effective half-life (as determined from the MRTlast) |
| thalf.eff.obs | pk.calc.thalf.eff | time | The effective half-life (as determined from the MRTobs) |
| thalf.eff.pred | pk.calc.thalf.eff | time | The effective half-life (as determined from the MRTpred) |
| time_above | pk.calc.time_above | time | Time above a given concentration |
| tlag | pk.calc.tlag | time | Lag time |
| tlast | pk.calc.tlast | time | Time of the last concentration observed above the limit of quantification |
| tmax | pk.calc.tmax | time | Time of the maximum observed concentration |
| tmin | pk.calc.tmin | time | Time of the minimum observed concentration |
| tobit_residual | NA | unitless | The estimated residual standard deviation (on the log-concentration scale) from the Tobit half-life fit |
| totdose | pk.calc.totdose | dose | Total dose administered during an interval |
| volpk | pk.calc.volpk | volume | The sum of urine volumes for the interval |
| vss.all | pk.calc.vss | volume | Steady-state volume of distribution calculated with AUCall-based CL and MRT |
| vss.int.all | pk.calc.vss | volume | Steady-state volume of distribution using interval AUCint.all |
| vss.int.inf.obs | pk.calc.vss | volume | Steady-state volume of distribution using interval AUCint.inf.obs |
| vss.int.inf.pred | pk.calc.vss | volume | Steady-state volume of distribution using interval AUCint.inf.pred |
| vss.int.last | pk.calc.vss | volume | Steady-state volume of distribution using interval AUCint.last |
| vss.iv.all | pk.calc.vss | volume | Steady-state volume of distribution for IV dosing using AUCall |
| vss.iv.last | pk.calc.vss | volume | The steady-state volume of distribution with intravenous infusion calculating through Tlast |
| vss.iv.obs | pk.calc.vss | volume | The steady-state volume of distribution with intravenous infusion using observed Clast |
| vss.iv.pred | pk.calc.vss | volume | The steady-state volume of distribution with intravenous infusion using predicted Clast |
| vss.ivint.all | pk.calc.vss | volume | Steady-state volume of distribution for IV interval using AUCint.all |
| vss.ivint.last | pk.calc.vss | volume | Steady-state volume of distribution for IV interval using AUCint.last |
| vss.last | pk.calc.vss | volume | The steady-state volume of distribution calculating through Tlast |
| vss.md.obs | pk.calc.vss | volume | The steady-state volume of distribution for nonlinear multiple-dose data using observed Clast |
| vss.md.pred | pk.calc.vss | volume | The steady-state volume of distribution for nonlinear multiple-dose data using predicted Clast |
| vss.obs | pk.calc.vss | volume | The steady-state volume of distribution using observed Clast |
| vss.pred | pk.calc.vss | volume | The steady-state volume of distribution using predicted Clast |
| vss.sparse.last | pk.calc.vss | volume | Steady-state volume of distribution from sparse sampling |
| vz.all | pk.calc.vz | volume | Terminal volume of distribution calculated with AUCall-based CL |
| vz.int.all | pk.calc.vz | volume | Terminal volume of distribution using interval AUCint.all |
| vz.int.inf.obs | pk.calc.vz | volume | Terminal volume of distribution using interval AUCint.inf.obs |
| vz.int.inf.pred | pk.calc.vz | volume | Terminal volume of distribution using interval AUCint.inf.pred |
| vz.int.last | pk.calc.vz | volume | Terminal volume of distribution using interval AUCint.last |
| vz.iv.all | pk.calc.vz | volume | Terminal volume of distribution for IV dosing using AUCall |
| vz.iv.last | pk.calc.vz | volume | Terminal volume of distribution for IV dosing using AUClast |
| vz.iv.obs | pk.calc.vz | volume | Terminal volume of distribution for IV dosing using observed AUCinf |
| vz.iv.pred | pk.calc.vz | volume | Terminal volume of distribution for IV dosing using predicted AUCinf |
| vz.ivint.all | pk.calc.vz | volume | Terminal volume of distribution for IV interval using AUCint.all |
| vz.ivint.last | pk.calc.vz | volume | Terminal volume of distribution for IV interval using AUCint.last |
| vz.last | pk.calc.vz | volume | Terminal volume of distribution calculated with AUClast-based CL |
| vz.obs | pk.calc.vz | volume | The terminal volume of distribution using observed Clast |
| vz.pred | pk.calc.vz | volume | The terminal volume of distribution using predicted Clast |
| vz.sparse.last | pk.calc.vz | volume | Terminal volume of distribution from sparse sampling |
22.4 Dependency resolution
When you call pk.nca(), PKNCA sorts the registry internally with PKNCA:::sort_interval_cols() (unexported) to produce a topologically sorted execution order — parameters with no dependencies run first, then those that depend on already-computed values.
# Count the direct dependencies of each parameter
cols <- get.interval.cols()
dep_counts <- sapply(cols, function(x) length(x$depends))
all_deps <- data.frame(
parameter = names(dep_counts),
n_depends = unname(dep_counts)
) |>
arrange(n_depends, parameter)
cat(sprintf("%d parameters have no dependencies (base parameters).\n", sum(all_deps$n_depends == 0)))37 parameters have no dependencies (base parameters).cat(sprintf("%d parameters have at least one dependency (derived parameters).\n\n", sum(all_deps$n_depends > 0)))166 parameters have at least one dependency (derived parameters).# Show only derived parameters
all_deps |>
filter(n_depends > 0) |>
knitr::kable(
col.names = c("Parameter", "N dependencies"),
caption = "Derived parameters ordered by number of direct dependencies"
)| Parameter | N dependencies |
|---|---|
| adj.r.squared | 1 |
| adj_tobit_residual | 1 |
| aucabove.predose.all | 1 |
| aucabove.trough.all | 1 |
| aucall.dn | 1 |
| aucinf.obs.dn | 1 |
| aucinf.pred.dn | 1 |
| auclast.dn | 1 |
| aumcall.dn | 1 |
| aumcinf.obs.dn | 1 |
| aumcinf.pred.dn | 1 |
| aumclast.dn | 1 |
| cav | 1 |
| cav.dn | 1 |
| cav.int.all | 1 |
| cav.int.inf.obs | 1 |
| cav.int.inf.pred | 1 |
| cav.int.last | 1 |
| cl.all | 1 |
| cl.int.all | 1 |
| cl.int.inf.obs | 1 |
| cl.int.inf.pred | 1 |
| cl.int.last | 1 |
| cl.iv.all | 1 |
| cl.iv.last | 1 |
| cl.iv.obs | 1 |
| cl.iv.pred | 1 |
| cl.ivint.all | 1 |
| cl.ivint.last | 1 |
| cl.last | 1 |
| cl.obs | 1 |
| cl.pred | 1 |
| cl.sparse.last | 1 |
| clast.obs.dn | 1 |
| clast.pred | 1 |
| clast.pred.dn | 1 |
| clr.last | 1 |
| clr.last.dn | 1 |
| clr.obs | 1 |
| clr.obs.dn | 1 |
| clr.pred | 1 |
| clr.pred.dn | 1 |
| cmax.dn | 1 |
| cmin.dn | 1 |
| ctrough.dn | 1 |
| fe | 1 |
| kel.all | 1 |
| kel.int.all | 1 |
| kel.int.inf.obs | 1 |
| kel.int.inf.pred | 1 |
| kel.int.last | 1 |
| kel.iv.all | 1 |
| kel.iv.last | 1 |
| kel.iv.obs | 1 |
| kel.iv.pred | 1 |
| kel.ivint.all | 1 |
| kel.ivint.last | 1 |
| kel.last | 1 |
| kel.obs | 1 |
| kel.pred | 1 |
| kel.sparse.last | 1 |
| lambda.z | 1 |
| lambda.z.corrxy | 1 |
| lambda.z.n.points | 1 |
| lambda.z.n.points_blq | 1 |
| lambda.z.time.first | 1 |
| lambda.z.time.last | 1 |
| r.squared | 1 |
| span.ratio | 1 |
| sparse_auc_df | 1 |
| sparse_auc_se | 1 |
| sparse_aumc_df | 1 |
| sparse_aumc_se | 1 |
| sparse_aumclast | 1 |
| thalf.eff.iv.last | 1 |
| thalf.eff.iv.obs | 1 |
| thalf.eff.iv.pred | 1 |
| thalf.eff.last | 1 |
| thalf.eff.obs | 1 |
| thalf.eff.pred | 1 |
| tobit_residual | 1 |
| aucinf.obs | 2 |
| aucinf.pred | 2 |
| aucint.inf.obs | 2 |
| aucint.inf.obs.dose | 2 |
| aucint.inf.pred | 2 |
| aucint.inf.pred.dose | 2 |
| aucivall | 2 |
| aucivinf.obs | 2 |
| aucivinf.pred | 2 |
| aucivint.all | 2 |
| aucivint.last | 2 |
| aucivlast | 2 |
| aucivpbextall | 2 |
| aucivpbextinf.obs | 2 |
| aucivpbextinf.pred | 2 |
| aucivpbextint.all | 2 |
| aucivpbextint.last | 2 |
| aucivpbextlast | 2 |
| aucpext.obs | 2 |
| aucpext.pred | 2 |
| aumcinf.obs | 2 |
| aumcinf.pred | 2 |
| aumcint.inf.obs | 2 |
| aumcint.inf.obs.dose | 2 |
| aumcint.inf.pred | 2 |
| aumcint.inf.pred.dose | 2 |
| aumcivall | 2 |
| aumcivinf.obs | 2 |
| aumcivinf.pred | 2 |
| aumcivint.all | 2 |
| aumcivint.last | 2 |
| aumcivlast | 2 |
| half.life | 2 |
| mrt.all | 2 |
| mrt.int.all | 2 |
| mrt.int.inf.obs | 2 |
| mrt.int.inf.pred | 2 |
| mrt.int.last | 2 |
| mrt.iv.all | 2 |
| mrt.iv.last | 2 |
| mrt.iv.obs | 2 |
| mrt.iv.pred | 2 |
| mrt.ivint.all | 2 |
| mrt.ivint.last | 2 |
| mrt.last | 2 |
| mrt.obs | 2 |
| mrt.pred | 2 |
| mrt.sparse.last | 2 |
| ptr | 2 |
| swing | 2 |
| vss.all | 2 |
| vss.int.all | 2 |
| vss.int.inf.obs | 2 |
| vss.int.inf.pred | 2 |
| vss.int.last | 2 |
| vss.iv.all | 2 |
| vss.iv.last | 2 |
| vss.iv.obs | 2 |
| vss.iv.pred | 2 |
| vss.ivint.all | 2 |
| vss.ivint.last | 2 |
| vss.last | 2 |
| vss.md.obs | 2 |
| vss.md.pred | 2 |
| vss.obs | 2 |
| vss.pred | 2 |
| vss.sparse.last | 2 |
| vz.all | 2 |
| vz.int.all | 2 |
| vz.int.inf.obs | 2 |
| vz.int.inf.pred | 2 |
| vz.int.last | 2 |
| vz.iv.all | 2 |
| vz.iv.last | 2 |
| vz.iv.obs | 2 |
| vz.iv.pred | 2 |
| vz.ivint.all | 2 |
| vz.ivint.last | 2 |
| vz.last | 2 |
| vz.obs | 2 |
| vz.pred | 2 |
| vz.sparse.last | 2 |
| deg.fluc | 3 |
| mrt.md.obs | 3 |
| mrt.md.pred | 3 |
22.5 Querying dependents: get.parameter.deps()
get.parameter.deps() is the reverse lookup: given a parameter name, it returns that parameter and every parameter downstream of it — the ones whose results would be affected if you excluded or modified it.
get.parameter.deps("auclast") [1] "aucivlast" "aucivpbextlast" "auclast"
[4] "auclast.dn" "aucpext.obs" "aucpext.pred"
[7] "cav" "cav.dn" "cl.iv.last"
[10] "cl.last" "deg.fluc" "kel.iv.last"
[13] "kel.last" "mrt.iv.last" "mrt.last"
[16] "mrt.md.obs" "mrt.md.pred" "thalf.eff.iv.last"
[19] "thalf.eff.last" "vss.iv.last" "vss.last"
[22] "vss.md.obs" "vss.md.pred" "vz.iv.last"
[25] "vz.last"