compare_mgfr_summary: Compare Iohexol mGFR results using available methods
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compare_mgfr_summary

R Documentation

Compare Iohexol mGFR results using available methods

Description

Two functions are provided to to summarize available options and analyze outlier or inconsistent results. Most variation occurs due to poor fitting or variability in early timepoints (<90min), although the late time points account for ~90 clearance. Further discussion and details regarding methods of fitting the 2-compartment models can be found at Pottel et al. The summary provides estimates of kinetic parameters (k10, k21, k12) which can be used in ODE models, but is not implemented here.

Usage

compare_mgfr_summary(time, iohexol_conc, t_early = 100, t_late = 120, ...)

compare_mgfr_plot(
  time,
  iohexol_conc,
  t_early = 100,
  t_late = 120,
  mfr = c(2, 3),
  ...
)

Arguments

`time`	A vector of time values (minutes)
`iohexol_conc`	A vector of Iohexol plasma measurements (ug/mL)
`t_early`	Last Time point (minutes) to use in the "Early" distribution phase, defaults to `100`
`t_late`	First Time point (minutes) to use in the "Late" elimination phase, defaults to `120`
`...`	Inherits from named 'calculate_mgfr_2c' paramaters. Any arguments can be added, but must be named (eg 'ioh_inj_vol = 5.1').
`mfr`	Plot layout. defaults to c(2,3) for 2 rows, 3 columns

Value

'compare_mgfr_summary()' Returns a table of mGFR summary parameters, and 'compare_mgfr_plot()' returns a panel of plots using a combination of available methods. The single sample method result is not included but can be called separately using ‘calculate_mgfr_ss'. ’

Examples

library(tabletools)
# PUBLISHED IOHEXOL DATA ----
# data available in package by calling
## ├ Schwartz Data ----
# Data extracted from Schwartz Fig1 https://pubmed.ncbi.nlm.nih.gov/16612328/
# Iohexol 5mL IV injection (Omnipaque 300, 5mL ~3235mg Iohexol)
# sampling at 10, 20, 30, 60, 120, 240, 300, 360 min
# time (minutes)
# Iohexol (ug/ml)
# age, height, weight not known for the example
dat_schwartz

## ├ Pottel data ----
# from Supplemental document in https://pubmed.ncbi.nlm.nih.gov/33952185/
dat10
dat17

## ├ Tondel data ----
# full example data provided by Tondel in Table 2: https://pubmed.ncbi.nlm.nih.gov/29134449/
dat_tondel

compare_mgfr_summary(dat_tondel$time, dat_tondel$iohexol, ioh_inj_vol = 2.08, weight = 13, height = 0.9)
compare_mgfr_plot(dat_tondel$time, dat_tondel$iohexol, ioh_inj_vol = 2.08, weight = 13, height = 0.9, id="dat_tondel")

# Comparisons of available methods: published studies
# Schwartz data in kids; note don't have subject details (height, weight, inj_vol)
compare_mgfr_summary(dat_schwartz$time, dat_schwartz$iohexol_ug_ml, height = 0.8, weight = 13, ioh_inj_vol = 2.08)
compare_mgfr_plot(dat_schwartz$time, dat_schwartz$iohexol_ug_ml, height = 0.8, weight = 13, ioh_inj_vol = 2.08, id="dat_schwartz")

# Pottel ID#10 Difficult fit
# Negative value using unconstrained parameters (NLLS-base-unweighted)
# caused by early outlier data points (t=60 most likely)
compare_mgfr_summary(dat10$time, dat10$iohexol, height = 1.67, weight = 70)
compare_mgfr_plot(dat10$time, dat10$iohexol, height = 1.67, weight = 70, id="dat10")

# Pottel ID#17 Difficult fit
compare_mgfr_summary(dat17$time, dat17$iohexol, height = 1.67, weight = 70, id="dat17")
compare_mgfr_plot(dat17$time, dat17$iohexol, height = 1.67, weight = 70, id="dat17")

# ODE MODEL FOR COMPARISON;
# Example only to verify ODE parameter estimates, not required for GFR calculation
# This model uses solution from the nls model to get the kinetic parameters
library(deSolve)
m2c <- function(Time, State, Pars) {
  with(as.list(c(State, Pars)), {
    dIohexol <- -k10*Iohexol - k12*Iohexol + k21*C2 # Central Conc
    dC2 <-  k12*Iohexol - k21*C2                    # Peripheral Conc
    return(list(c(dIohexol, dC2)))
  })
}
# get parameters from nls model
ioh_nlfit <- calculate_mgfr_2c(dat_schwartz$time, dat_schwartz$iohexol_ug_ml, height = 1.67, weight = 70, ioh_inj_vol = 5)
pars  <- c(k10 = ioh_nlfit$k10, k21 = ioh_nlfit$k21, k12 = ioh_nlfit$k12)
# plug into the ODE model solution
yini  <- c(Iohexol = ioh_nlfit$A+ioh_nlfit$B, C2=0)
times <- seq(0, 360, by = 1)
out   <- ode(yini, times, m2c, pars)
out_df <- as.data.frame(out)
# Plot to verfiy kinetic parameters vs nls model
calculate_mgfr_2c(dat_schwartz$time, dat_schwartz$iohexol_ug_ml, height = 1.67, weight = 70, ioh_inj_vol = 5, output="plot")
lines(out_df$time, out_df$Iohexol, lty=2)

JMLuther/tabletools documentation built on April 14, 2025, 3:09 a.m.