clinPK

Description

Equations and tool for clinical pharmacokinetics

Author(s)

Ron Keizer ronkeizer@gmail.com

Greater-than-or-equal-to with a little room for floating point precision issues

Description

Greater-than-or-equal-to with a little room for floating point precision issues

Usage

x %>=% y

Arguments

Less-than-or-equal-to with a little room for floating point precision issues

Description

Less-than-or-equal-to with a little room for floating point precision issues

Usage

x %<=% y

Arguments

Convert quantity expressed in absolute units relative to normalized BSA

Description

Often used for eGFR estimates

Usage

absolute2relative_bsa(quantity, bsa = NULL, ...)

Arguments

Value

quantity expressed relative to /1.73m2

Examples

absolute2relative_bsa(quantity = 60, bsa = 1.6)
absolute2relative_bsa(quantity = 60, weight = 14, height = 90, method = "dubois")

Calculate accumulation ratio This is the ratio of drug concentration or AUC at steady state over concentrations after single dose

Description

Calculate accumulation ratio This is the ratio of drug concentration or AUC at steady state over concentrations after single dose

Usage

accumulation_ratio(kel = NULL, halflife = NULL, tau = 24)

Arguments

Examples

accumulation_ratio(halflife = 24, tau = 24)
accumulation_ratio(kel = 0.08, tau = 12)

Add residual variability to data

Description

Add residual variability to data

Usage

add_ruv(x, ruv = list())

Arguments

Examples

y <- pk_1cmt_inf()$y
y + add_ruv(y, list(prop = 0.1, add = 0.05))

factors or characters to numeric

Description

factors or characters to numeric

Usage

as.num(x)

Arguments

Convert AUCtau or AUCt to dose (for 1-compartment linear PK model)

Description

Convert AUCtau or AUCt to dose (for 1-compartment linear PK model)

Usage

auc2dose(auc, CL, V, t_auc = NA)

Arguments

Examples

auc2dose(450, CL = 5, V = 50)

Calculate adjusted body weight (ABW)

Description

Often used for chemotherapy calculations when actual weight > 120 Adjusted body weight is returned in units of kg.

Usage

calc_abw(weight = NULL, ibw = NULL, factor = 0.4, verbose = TRUE, ...)

Arguments

Value

adjusted body weight in kg

Examples

calc_abw(weight = 80, ibw = 60)
calc_abw(weight = 80, height = 160, sex = "male", age = 60)

Calculate AKI stage

Description

Calculate AKI class based on serum creatinine values over time, using various methods for children (pRIFLE) and adults (RIFLE, kDIGO)

Usage

calc_aki_stage(
  scr = NULL,
  times = NULL,
  method = "kdigo",
  baseline_scr = "median",
  baseline_egfr = NULL,
  first_dose_time = NULL,
  age = NULL,
  egfr = NULL,
  egfr_method = NULL,
  force_numeric = FALSE,
  override_prifle_baseline = FALSE,
  verbose = TRUE,
  return_object = TRUE,
  ...
)

Arguments

References

• pRIFLE: Ackan-Arikan et al. "Modified RIFLE criteria in critically ill children with acute kidney injury." Kidney Int. (2007)

• RIFLE: Bellomo et al. "Acute renal failure - definition, outcome measures, animal models, fluid therapy and information technology needs: the Second International Consensus Conference of the Acute Dialysis Quality Initiative (ADQI) Group." Critical Care. (2004)

• KDIGO: Khwaja. "KDIGO clinical practice guidelines for acute kidney injury." Nephron Clinical Practice. (2012)

• pRIFLE baseline eGFR: Soler et al. "pRIFLE (Pediatric Risk, Injury, Failure, Loss, End Stage Renal Disease) score identifies Acute Kidney Injury and predicts mortality in critically ill children : a prospective study." Pediatric Critical Care Medicine. (2014)

Examples

calc_aki_stage(
  scr = c(0.7, 0.9, 1.8, 1.5),
  t = c(0, 40, 100, 130),
  age = 50, weight = 60,
  height = 170, sex = "female")

Calculate the amounts in all compartments in a compartmental PK system based on a given concentration in the central compartment, and assuming steady state.

Description

Calculate the amounts in all compartments in a compartmental PK system based on a given concentration in the central compartment, and assuming steady state.

Usage

calc_amts_for_conc(conc = 10, parameters = NULL, n_cmt = 1)

Arguments

Examples

calc_amts_for_conc(conc = 10, parameters = list(CL = 5, V = 50), n_cmt = 1)
calc_amts_for_conc(
  conc = 10,
  parameters = list(CL = 5, V = 50, Q = 20, V2 = 100),
  n_cmt = 2)
calc_amts_for_conc(
  conc = 10,
  parameters = list(CL = 5, V = 50, Q = 20, V2 = 100, Q2 = 30, V3 = 200),
  n_cmt = 3)

Calculate baseline sCr

Description

Calculate baseline sCr

Usage

calc_baseline_scr(
  baseline_scr,
  scr,
  times,
  method,
  first_dose_time = NULL,
  verbose
)

Arguments

Calculate BMI

Description

Calculate BMI

Usage

calc_bmi(weight, height)

Arguments

Value

value of BMI in kg/m2

Examples

calc_bmi(weight = 70, height = 160)

Calculate body surface area

Description

Get an estimate of body-surface area (in m2) based on weight and height

Usage

calc_bsa(
  weight = NULL,
  height = NULL,
  method = c("dubois", "mosteller", "haycock", "gehan_george", "boyd")
)

Arguments

Value

Returns a list of the following elements:

Examples

calc_bsa(weight = 70, height = 170)
calc_bsa(weight = 70, height = 170, method = "gehan_george")

Calvert equation for carboplatin

Description

The Calvert equation calculates a dose expected to bring the patient to the target AUC given their glomerular filtration rate (GFR). The original equation was developed on a data set of 18 individuals with GFR of 33-136 ml/min.

Usage

calc_carboplatin_calvert(target_auc, gfr = NULL, ...)

Arguments

References

Calvert et al., Journal of Clinical Oncology (1976)

Examples

calc_carboplatin_calvert(5, 100)
calc_carboplatin_calvert(4, 30)
calc_carboplatin_calvert(2, sex = "male", age = 50, scr = 1.1, weight = 70)

Estimate serum creatinine

Description

Calculate an estimated serum creatinine. Function takes vectorized input as well.

Usage

calc_creat(sex = NULL, age = NULL, digits = 1)

Arguments

Details

Uses equations described in Ceriotti et al. Clin Chem. 2008, and Junge W et al. Clin Chim Acta. 2004. For age 15-18, a linear interpolation is used between equations for <15 and >18 years as described in Johanssen A et al. Ther Drug Monit 2011.

Examples

calc_creat(sex = "male", age = 40)
calc_creat(sex = "male", age = c(10, 17, 60))

Estimate serum creatinine in neonates

Description

Calculate an estimated serum creatinine. Function takes vectorized input as well.

Usage

calc_creat_neo(pma = NULL, digits = 1)

Arguments

Details

Uses equations described in Germovsek E et al. (http://www.ncbi.nlm.nih.gov/pubmed/27270281) based on data from Cuzzolin et al. (http://www.ncbi.nlm.nih.gov/pubmed/16773403) and Rudd et al. (http://www.ncbi.nlm.nih.gov/pubmed/6838252)

Examples

cr <- calc_creat_neo(pma = 36)
convert_creat_unit(cr$value, unit_in = cr$unit, unit_out = "mg/dL")

Calculate commonly used "dosing weight"

Description

Dosing weight is determined based on total (TBW), ideal (IBW), or adjusted (ABW) body weight in kg.

Usage

calc_dosing_weight(weight, height, age, sex, verbose = TRUE, ...)

Arguments

Details

This is derived using following: - In principle, use IBW - If total body weight (TBW) > 1.2*IBW, then use ABW - If TBW < IBW, use TBW

Value

Returns a list of the following elements:

Examples

calc_dosing_weight(weight = 50, height = 170, sex = "female", age = 50)

Calculate eGFR

Description

Calculate the estimated glomerular filtration rate (an indicator of renal function) based on measured serum creatinine using one of the following approaches:

• Cockcroft-Gault (using weight, ideal body weight, or adjusted body weight)

• C-G spinal cord injury (using correction factor of 0.7, representing median correction point reported in the original publication (parapalegic patients: 0.8; tetrapalegic patients: 0.6))

• Revised Lund-Malmo

• Modification of Diet in Renal Disease study (MDRD; with or without consideration of race, using either the original equation (published 2001) or the equation updated to reflect serum creatinine assay standardization (2006))

• CKD-EPI (with or without consideration of race, or 2021 re-fit without race)

• Schwartz

• Schwartz revised / bedside

• Jelliffe

• Jelliffe for unstable renal function. Note that the 15 P_adj recommended for hemodialysis patients is not included in this implementation.

• Wright equation for eGFR in cancer patients, with creatinine measured using the Jaffe assay.

Equations for estimation of eGFR from Cystatin C concentrations are available from the 'calc_egfr_cystatin()' function.

Usage

calc_egfr(
  method = "cockcroft_gault",
  sex = NULL,
  age = NULL,
  scr = NULL,
  scr_unit = NULL,
  race = "other",
  weight = NULL,
  height = NULL,
  bsa = NULL,
  preterm = FALSE,
  ckd = FALSE,
  times = NULL,
  bsa_method = "dubois",
  relative = NULL,
  unit_out = "mL/min",
  verbose = TRUE,
  min_value = NULL,
  max_value = NULL,
  fail = TRUE,
  ...
)

Arguments

Note

The MDRD and CKD-EPI equations use race as a factor in estimation of GFR. Racism has historically been and continues to be a problem in medicine, with racialized patients experiencing poorer outcomes. Given this context, the use of race in clinical algorithms should be considered carefully (Vyas et al., NEJM (2020)). Provided here are versions of the CKD-EPI and MDRD equations that do not consider the race of the patient. Removing race from GFR estimation may lead to worse outcomes for Black patients in some contexts (Casal et al., The Lancet (2021)). On the other hand, including race in GFR estimation may also prevent Black patients from obtaining procedures like kidney transplants (Zelnick, et al. JAMA Netw Open. (2021)). In 2021, the NKF/ASN Task Force on Reassessing the Inclusion of Race in Diagnosing Kidney Diseases published revised versions of the CKD-EPI equations refit on the original data but with race excluded, which may produce less biased estimates (Inker, et al., NEJM (2021)).

References

• Cockcroft-Gault: Cockcroft & Gault, Nephron (1976)

• Cockcroft-Gault for spinal cord injury: Mirahmadi et al., Paraplegia (1983)

• Revised Lund-Malmo: Nyman et al., Clinical Chemistry and Laboratory Medicine (2014)

• MDRD: Manjunath et al., Curr. Opin. Nephrol. Hypertens. (2001) and Levey et al., Clinical Chemistry (2007). (See Note.)

• CKD-EPI: Levey et al., Annals of Internal Medicine (2009). (See Note.)

• CKD-EPI (2021): Inker, et al., NEJM (2021).

• Schwartz: Schwartz et al., Pediatrics (1976)

• Schwartz revised / bedside: Schwartz et al., Journal of the American Society of Nephrology (2009)

• Jelliffe: Jelliffe, Annals of Internal Medicine (1973)

• Jelliffe for unstable renal function: Jelliffe, American Journal of Nephrology (2002)

• Wright: Wright et al., British Journal of Cancer (2001)

Examples

calc_egfr(sex = "male", age = 50, scr = 1.1, weight = 70)
calc_egfr(sex = "male", age = 50, scr = 1.1, weight = 70, unit_out = "L/hr")
calc_egfr(sex = "male", age = 50, scr = 1.1, weight = 70, bsa = 1.8, method = "ckd_epi")
calc_egfr(sex = "male", age = 50, scr = c(1.1, 0.8),
  weight = 70, height = 170, method = "jelliffe")
calc_egfr(sex = "male", age = 50, scr = c(1.1, 0.8),
  weight = 70, height = 170, method = "jelliffe_unstable")
calc_egfr(sex = "male", age = 50, scr = 1.1,
  weight = 70, bsa = 1.6, method = "malmo_lund_revised", relative = FALSE)

Calculate eGFR based on Cystatin C measurements

Description

Calculate eGFR based on Cystatin C measurements

Usage

calc_egfr_cystatin(
  cystatin = NULL,
  cystatin_unit = "mg/L",
  method = c("grubb", "larsson", "hoek"),
  unit_out = c("ml/min", "ml/hr", "l/min", "l/hr", "ml/min/1.73m2")
)

Arguments

Examples

calc_egfr_cystatin(1.0)
calc_egfr_cystatin(1.0, method = "larsson")
calc_egfr_cystatin(1.0, unit_out = "l/hr")

Calculate fat-free mass

Description

Get an estimate of fat-free mass (FFM, in kg) based on weight, height, and sex (and age for Storset equation).

Usage

calc_ffm(
  weight = NULL,
  bmi = NULL,
  sex = NULL,
  height = NULL,
  age = NULL,
  method = c("janmahasatian", "green", "al-sallami", "storset", "bucaloiu", "hume",
    "james", "garrow_webster"),
  digits = 1
)

Arguments

Details

References: 'janmahasatian', 'green': Janmahasatian et al. Clin Pharmacokinet. 2005;44(10):1051-65) 'al-sallami': Al-Sallami et al. Clin Pharmacokinet 2015 'storset': Storset E et al. TDM 2016 'bucaloiu': Bucaloiu ID et al. Int J of Nephrol Renovascular Dis. 2011 (Morbidly obese females) 'hume': Hume R. J Clin Pathol 1966 'james': James WPT et al. Research on obesity: a report of the DHSS/MRC Group 1976 ‘garrow_webster': Garrow JS, Webster J. Quetelet’s index (W/H2) as a measure of fatness. Int J Obesity 1984

Overview: - Sinha J, Duffull1 SB, Al-Sallami HS. Clin Pharmacokinet 2018. https://doi.org/10.1007/s40262-017-0622-5

Value

Returns a list of the following elements:

Examples

calc_ffm(weight = 70, bmi = 25, sex = "male")
calc_ffm(weight = 70, height = 180, age = 40, sex = "female", method = "storset")

Calculate ideal body weight in kg for children and adults

Description

Get an estimate of ideal body weight. This function allows several commonly used equations

Usage

calc_ibw(
  weight = NULL,
  height = NULL,
  age = NULL,
  sex = "male",
  method_children = "standard",
  method_adults = "devine"
)

ibw_standard(age, height = NULL, sex = NULL)

ibw_devine(age, height = NULL, sex = NULL)

Arguments

Details

Equations:

<1yo Use actual body weight

1-17 years old ('standard'): if height < 5ft: IBW= (height in cm2 x 1.65)/1000 if height > 5ft: IBW (male) = 39 + (2.27 x height in inches over 5 feet) IBW (female) = 42.2 + (2.27 x height in inches over 5 feet)

Methods not implemented yet: McLaren: IBW = - step1: x = 50th percentile height for given age - step2: IBW = 50th percentile weight for x on weight-for-height scale Moore: IBW = weight at percentile x for given age, where x is percentile of height for given age BMI: IBW = 50th percentile of BMI for given age x (height in m)^2 ADA: IBW = 50th percentile of WT for given age

>= 18 years old (Devine equation) IBW (male) = 50 + (2.3 x height in inches over 5 feet) IBW (female) = 45.5 + (2.3 x height in inches over 5 feet)

Examples

calc_ibw(weight = 70, height = 170, age = 40, sex = "female")
calc_ibw(weight = 30, height = 140, age = 10, sex = "female")

Calculate elimination rate when given two TDM samples

Description

Calculate elimination rate when given two TDM samples

Usage

calc_kel_double_tdm(
  dose = 1000,
  t = c(2, 11.5),
  dv = c(30, 10),
  tau = 12,
  t_inf = 1,
  V = NULL,
  steady_state = TRUE,
  return_parameters = FALSE
)

Arguments

Examples

calc_kel_double_tdm(dose = 1000, t = c(3, 18), dv = c(30, 10))

Calculate elimination rate when given a single TDM sample

Description

Using iterative k_el calculation, and based on given Volume

Usage

calc_kel_single_tdm(
  dose = 1000,
  V = 50,
  t = 10,
  dv = 10,
  tau = 12,
  t_inf = 1,
  kel_init = 0.1,
  n_iter = 25,
  learn_rate = 0.2
)

Arguments

Examples

calc_kel_single_tdm(dose = 1000, t = 18)

Calculate kinetic GFR

Description

Calculate the kinetic GFR based on a patients first two serum creatinine measurements. Kinetic GFR may be more predictive of future AKI for patients whose serum creatinine is changing quickly. Briefly, an increase in SCr over the course of a day indicates an effective GFR lower than the most recent SCr measurement may indicate if steadystate is assumed, while a decrease in SCr over a short time indicates a higher effective GFR than the most recent SCr would indicate. There are several ways of approximating maximum theoretical creatinine accumulation rate; here the method used by Pianta et al., (PLoS ONE, 2015) has been implemented.

Usage

calc_kgfr(
  scr1 = NULL,
  scr2 = NULL,
  scr_unit = "mg/dl",
  time_delay = NULL,
  weight = NULL,
  vd = NULL,
  egfr = NULL,
  egfr_method = NULL,
  sex = NULL,
  age = NULL,
  height = NULL,
  ...
)

Arguments

Value

kGFR, in ml/min

References

Pianta et al., PLoS ONE (2015)

Examples

calc_kgfr(weight = 100, scr1 = 150, scr2 = 200, scr_unit = 'umol/l',
         time_delay = 24, egfr = 30)
calc_kgfr(weight = 70, scr1 = 350, scr2 = 300, scr_unit = 'umol/l',
          time_delay = 24, egfr_method = 'mdrd', age = 70, sex = 'male')

Calculate lean body weight

Description

Get an estimate of lean body weight (LBW, in kg) based on weight, height, and sex.

Usage

calc_lbw(
  weight = NULL,
  bmi = NULL,
  sex = NULL,
  height = NULL,
  method = "green",
  digits = 1
)

Arguments

Details

Note: technically not the same as fat-free mass, although difference is small.

References: 'green': Green and Duffull. Clin Pharmacol Ther 2002; 'james': Absalom AR et al. Br J Anaesth 2009; 103:26-37. James W. Research on obesity. London: Her Majesty's Stationary Office, 1976. 'hume' : Hume R et al. J Clin Pathol. 1966 Jul; 19(4):389-91. 'boer' : Boer P et al. Am J Physiol 1984; 247: F632-5

Value

Returns a list of the following elements:

Examples

calc_lbw(weight = 80, height = 170, sex = "male")
calc_lbw(weight = 80, height = 170, sex = "male", method = "james")

Calculate neutropenia grade from ANC

Description

Assigns neutropenia grade based on the National Cancer Institute system. Note that while this system assigns a grade of 1 to an ANC between 1500-2000, the term neutropenia is usually reserved for a grade of 2 or higher (an ANC of <1500)

Usage

calc_neutropenia_grade(anc)

Arguments

References

• Neutropenia: US National Cancer Institute's Common Toxicity Criteria

Examples

calc_neutropenia_grade(
  anc = c(500, 1501)
)

Calculate half-life based on two points

Description

based on two sampling points (in same interval)

Usage

calc_t12(t1, t2, y1, y2)

Arguments

Examples

calc_t12(3, 24, 30, 10)

Checks whether required covariates for eGFR calculations are present

Description

returns true if all patient covs specified in required covs are non-null, non-NA and not a 0-character string. See 'is.nil' for missing data types checked. Returns TRUE if no covariates are required.

Usage

check_covs_available(
  cov_reqs = NULL,
  patient_covs = NULL,
  verbose = TRUE,
  fail = TRUE
)

Arguments

Examples

check_covs_available(
  egfr_cov_reqs('cockcroft_gault_ideal')[[1]],
  list(creat = 1, weight = 100, height = 160, sex = 'female', age = 90))

Convert cm to inch

Description

Convert cm to inch

Usage

cm2inch(cm)

Arguments

Examples

cm2inch(2.54)

Convert concentration to molar

Description

Convert concentration to molar

Usage

conc2mol(conc = NULL, unit_conc = NULL, mol_weight = NULL, unit_mol = NULL)

Arguments

Examples

conc2mol(100, unit_conc = "g/l", mol_weight = 180.15588)

Convert albumin from / to units

Description

Accepted units are "g_l", "g_dl", or "micromol_l". Arguments supplied to 'value' and 'unit_in' units must be of the same length. "To" unit must be of length 1. #'

Usage

convert_albumin_unit(
  value,
  unit_in = valid_units("serum_albumin"),
  unit_out = valid_units("serum_albumin")
)

Arguments

Examples

## single values
convert_albumin_unit(0.6, "g_dl", "g_l")

## vectorized
convert_albumin_unit(
  c(0.4, 2, 0.3), 
  unit_in = c("g_dl", "g_l", "g_dl"),
  unit_out = c("g_l")
)
  

Convert bilirubin from / to units

Description

Accepted units are "mg_dl" and "micromol_l". Arguments supplied to 'value' and 'unit_in' units must be of the same length. "To" unit must be of length 1. #'

Usage

convert_bilirubin_unit(
  value,
  unit_in = valid_units("bilirubin"),
  unit_out = valid_units("bilirubin")
)

Arguments

Examples

## single values
convert_bilirubin_unit(1, "mg_dl", "micromol_l")

## vectorized
convert_bilirubin_unit(
  c(1, 1.1, 1.2),
  unit_in = "mg_dl",
  unit_out = "micromol_l"
)

Convert concentration units

Description

Lower-level function called by 'convert_creat_unit()', 'convert_albumin_unit()', and others.

Usage

convert_conc_unit(value, unit_in, unit_out, mol_weight = NULL)

Arguments

See Also

valid_units

Convert serum creatinine from various assays to Jaffe

Description

Based on equations as reported in Srivastava et al. 2009 (Pediatr Res. 2009 Jan;65(1):113-6. doi: 10.1203/PDR.0b013e318189a6e8)

Usage

convert_creat_assay(scr, from = "idms", to = "jaffe")

Arguments

Examples

convert_creat_assay(scr = c(1.1, 0.8, 0.7), from = "enzymatic", to = "jaffe")

Convert creatinine to different unit

Description

Convert creatinine to different unit

Usage

convert_creat_unit(
  value,
  unit_in = valid_units("scr"),
  unit_out = valid_units("scr")
)

Arguments

Examples

convert_creat_unit(1, "mg/dL", "micromol/l")
convert_creat_unit(88.42, "micromol/l", "mg/dL")

Convert flow (e.g. clearance) from / to units

Description

Flow units are expected to be specified as a combination of volume per time units, potentially specified per kg body weight, e.g. "mL/min", or "L/hr/kg".

Usage

convert_flow_unit(value = NULL, from = "l", to = "ml", weight = NULL)

Arguments

Details

Accepted volume units are "L", "dL", and "mL". Accepted time units are "min", "hr", and "day". The only accepted weight unit is "kg".

The function is not case-sensitive.

Examples

## single values
convert_flow_unit(60, "L/hr", "ml/min")
convert_flow_unit(1, "L/hr/kg", "ml/min", weight = 80)

## vectorized
convert_flow_unit(
  c(10, 20, 30), 
  from = c("L/hr", "mL/min", "L/hr"), 
  to = c("ml/min/kg", "L/hr", "L/hr/kg"), 
  weight = c(70, 80, 90))
  

Convert dose to expected AUCinf or AUCt for 1 compartment linear PK model

Description

Convert dose to expected AUCinf or AUCt for 1 compartment linear PK model

Usage

dose2auc(dose, CL, V, t_auc = NULL)

Arguments

Examples

dose2auc(dose = 1000, CL = 5, V = 50)
dose2auc(dose = 1000, CL = 5, V = 50, t_auc = c(12, 24, 48, 72))

Returns parameters needed to calculate eGFR according to the method specified.

Description

returns a named list, with the name being the eGFR method after being checked for certain typos or misspecifications, and the values being the required covariates.

Usage

egfr_cov_reqs(method, relative = NULL)

Arguments

Examples

egfr_cov_reqs('schwartz_revised')

Helper function to grab the conversion factor from an input unit and given list

Description

Helper function to grab the conversion factor from an input unit and given list

Usage

find_factor(full_unit, units = NULL, prefix = "^")

Arguments

Generic function to calculate the dose nearest to a specific dose unit increment

Description

Generic function to calculate the dose nearest to a specific dose unit increment

Usage

find_nearest_dose(dose = NULL, increment = 250, type = "round")

Arguments

Examples

find_nearest_dose(573)
find_nearest_dose(573, increment = 50)

Generic function to calculate the interval nearest to a possible dosing interval

Description

Generic function to calculate the interval nearest to a possible dosing interval

Usage

find_nearest_interval(
  interval = NULL,
  possible = c(4, 6, 8, 12, 24, 36, 48),
  type = "absolute"
)

Arguments

Examples

find_nearest_interval(19.7)
find_nearest_interval(19.7, c(6, 8, 12))

Calculate fraction of steady state at particular time after start of dosing

Description

Calculate fraction of steady state at particular time after start of dosing

Usage

fraction_of_ss(kel = NULL, halflife = NULL, t = NULL, n = NULL, tau = NULL)

Arguments

Examples

fraction_of_ss(halflife = 24, t = 72)
fraction_of_ss(halflife = 36, n = 3, tau = 24)

Convert inch to cm

Description

Convert inch to cm

Usage

inch2cm(inch)

Arguments

Examples

inch2cm(1)

Check if values in vector are empty

Description

Check if values in vector are empty

Usage

is.nil(x = NULL)

Arguments

Calculate AKI stage according to KDIGO criteria

Description

Calculate AKI stage according to KDIGO criteria

Usage

kdigo_stage(dat, baseline_scr, age)

Arguments

Convert kg to lbs

Description

Convert kg to lbs

Usage

kg2lbs(kg)

Arguments

Examples

kg2lbs(1)

Convert kg to oz

Description

Convert kg to oz

Usage

kg2oz(kg)

Arguments

Examples

kg2oz(1)

Convert lbs to kg

Description

Convert lbs to kg

Usage

lbs2kg(lbs)

Arguments

Examples

lbs2kg(2.20462)

Calculate mean between two values in a vector Used in NCA for calculation of mean between two or more timepoints.

Description

Calculate mean between two values in a vector Used in NCA for calculation of mean between two or more timepoints.

Usage

mean_step(x)

Arguments

Value

a vector of length(x)-1 with the mean timepoints

Convert molar to concentration

Description

Convert molar to concentration

Usage

mol2conc(mol = NULL, unit_mol = NULL, unit_conc = NULL, mol_weight = NULL)

Arguments

Examples

mol2conc(1, unit_mol = "mmol/l", mol_weight = 180)

Perform an NCA based on a NONMEM-style dataset

Description

Perform an NCA based on a NONMEM-style dataset

Usage

nca(
  data = NULL,
  dose = 100,
  tau = 24,
  method = c("log_linear", "log_log", "linear"),
  scale = list(auc = 1, conc = 1),
  dv_min = 0.001,
  t_inf = NULL,
  fit_samples = NULL,
  weights = NULL,
  extend = TRUE,
  has_baseline = TRUE,
  route = c("iv", "oral", "im", "sc")
)

Arguments

Value

Returns a list of three lists:

pk

Lists pk parameters.

• kel: elimination constant

• t_12: half-life

• v: distribution volume

• cl: clearance

descriptive

Lists exposure parameters.

• cav_t: the average concentration between the first observation and the last observation without extrapolating to tau

• cav_tau: the average concentration from 0 to tau

• cmin: the extrapolated concentration at time = tau

• c_max_true: only available if extend = TRUE, the extrapolated peak concentration

• c_max: only available if extend = FALSE, the observed maximum concentration

• auc_inf: the extrapolated AUC as time goes to infinity

• auc_24: the extrapolated AUC after 24 hours, provided no further doses are administered

• auc_tau: the extrapolated AUC at the end of the dosing interval

• auc_t: the AUC at the time of the last observation

settings

Lists dosing information.

• dose: dose quantity

• tau: dosing interval

Examples

data <- data.frame(time = c(0, 2, 4, 6, 8, 12, 16),
                   dv   = c(0, 10, 14, 11, 9, 5, 1.5))
nca(data, t_inf = 2)

NCA core function to perform linear trapezoid calculations for post-infusion

Description

NCA core function to perform linear trapezoid calculations for post-infusion

Usage

nca_linear(data)

Arguments

NCA core function to perform log-linear trapezoid calculations for post-infusion

Description

NCA core function to perform log-linear trapezoid calculations for post-infusion

Usage

nca_trapezoid(data)

Arguments

Convert oz to kg

Description

Convert oz to kg

Usage

oz2kg(oz)

Arguments

Examples

oz2kg(2.20462)

Percentile BMI for age for children

Description

Based on tables from WHO: http://www.who.int/growthref/who2007_bmi_for_age/en/

Usage

pct_bmi_for_age(
  age = NULL,
  bmi = NULL,
  sex = NULL,
  height = NULL,
  return_median = FALSE,
  ...
)

Arguments

Examples

pct_bmi_for_age(age = 8, sex = "male")
pct_bmi_for_age(age = 8, bmi = 15, sex = "male")

Percentile height or weight for age for children

Description

This is the underlying function, the exposed functions are pct_weight_for_age() and pct_height_for_age() Based on tables from WHO: http://www.who.int/childgrowth/standards/height_for_age/en/

Usage

pct_for_age_generic(
  age = NULL,
  value = NULL,
  sex = NULL,
  variable = "weight",
  ...
)

Arguments

Percentile height for age for children

Description

Based on tables from WHO: http://www.who.int/childgrowth/standards/height_for_age/en/

Usage

pct_height_for_age(
  age = NULL,
  height = NULL,
  sex = NULL,
  return_median = FALSE,
  ...
)

Arguments

Examples

pct_height_for_age(age = 5, sex = "female")
pct_height_for_age(age = 5, height = 112, sex = "female")

Percentile weight for age for children

Description

Based on tables from WHO: http://www.who.int/childgrowth/standards/weight_for_age/en/

Usage

pct_weight_for_age(
  age = NULL,
  weight = NULL,
  sex = NULL,
  return_median = FALSE,
  ...
)

Arguments

Examples

pct_weight_for_age(age = 5, sex = "female")
pct_weight_for_age(age = 5, weight = 20, sex = "female")

Concentration predictions for 1-compartmental PK model after single or multiple bolus doses

Description

Concentration predictions for 1-compartmental PK model after single or multiple bolus doses

Usage

pk_1cmt_bolus(t = c(0:24), dose = 100, tau = 12, CL = 3, V = 30, ruv = NULL)

Arguments

Examples

pk_1cmt_bolus(dose = 500, tau = 12, CL = 5, V = 50)
pk_1cmt_bolus(dose = 500, tau = 12, CL = 5, V = 50, t = 24)
pk_1cmt_bolus(
  dose = 500, tau = 12, CL = 5, V = 50,
  ruv = list(prop = 0.1, add = 0.1))

Cmax for linear 1-compartment PK model at steady state, bolus dosing

Description

Takes single values for dose or model parameters, or vector of either dose or parameters (but not both).

Usage

pk_1cmt_bolus_cmax_ss(dose = 100, tau = 12, CL = 3, V = 30, ruv = NULL)

Arguments

Examples

pk_1cmt_bolus_cmax_ss(
  dose = 500, tau = 12, CL = 5, V = 50)

Cmin (trough) for linear 1-compartment PK model at steady state, bolus dosing

Description

Takes single values for dose or model parameters, or vector of either dose or parameters (but not both).

Usage

pk_1cmt_bolus_cmin_ss(dose = 100, tau = 12, CL = 3, V = 30, ruv = NULL)

Arguments

Examples

pk_1cmt_bolus_cmin_ss(
  dose = 500, tau = 12, CL = 5, V = 50)

Calculate dose to achieve steady state Cmax for 1-compartmental PK model bolus dosing at steady state

Description

Calculate dose to achieve steady state Cmax for 1-compartmental PK model bolus dosing at steady state

Usage

pk_1cmt_bolus_dose_from_cmax(cmax = 1, tau = 12, CL = 3, V = 30)

Arguments

Examples

dos <- pk_1cmt_bolus_dose_from_cmax(
  cmax = 10, tau = 12, CL = 5, V = 50)
find_nearest_dose(dos, 100)

Calculate dose to achieve steady state trough for 1-compartmental PK model bolus dosing at steady state

Description

Calculate dose to achieve steady state trough for 1-compartmental PK model bolus dosing at steady state

Usage

pk_1cmt_bolus_dose_from_cmin(cmin = 1, tau = 12, CL = 3, V = 30)

Arguments

Examples

dos <- pk_1cmt_bolus_dose_from_cmin(
  cmin = 5, tau = 12, CL = 5, V = 50)
find_nearest_dose(dos, 100)

Concentration predictions for 1-compartmental PK model with bolus dosing at steady state

Description

Concentration predictions for 1-compartmental PK model with bolus dosing at steady state

Usage

pk_1cmt_bolus_ss(t = c(0:24), dose = 100, tau = 12, CL = 3, V = 30, ruv = NULL)

Arguments

Examples

pk_1cmt_bolus_ss(dose = 500, tau = 12, CL = 5, V = 50)
pk_1cmt_bolus_ss(
  dose = 500, tau = 12, CL = 5, V = 50,
  ruv = list(prop = 0.1, add = 0.1))

Concentration predictions for 1-compartmental PK model after single or multiple bolus doses

Description

Concentration predictions for 1-compartmental PK model after single or multiple bolus doses

Usage

pk_1cmt_inf(
  t = c(0:24),
  dose = 100,
  tau = 12,
  t_inf = 2,
  CL = 3,
  V = 30,
  ruv = NULL
)

Arguments

Examples

pk_1cmt_inf(dose = 500, tau = 12, t_inf = 2, CL = 5, V = 50)
pk_1cmt_inf(
  dose = 500, tau = 12, t_inf = 2, CL = 5, V = 50,
  ruv = list(prop = 0.1, add = 0.1))

Cmax for linear 1-compartment PK model at steady state

Description

Takes single values for dose or model parameters, or vector of either dose or parameters (but not both).

Usage

pk_1cmt_inf_cmax_ss(dose, tau, CL, V, t_inf, ruv = NULL)

Arguments

Examples

pk_1cmt_inf_cmax_ss(dose = 500, tau = 12, t_inf = 2, CL = 5, V = 50)

Cmin (trough) for linear 1-compartment PK model at steady state

Description

Takes single values for dose or model parameters, or vector of either dose or parameters (but not both).

Usage

pk_1cmt_inf_cmin_ss(
  dose = 100,
  tau = 12,
  CL = 3,
  V = 30,
  t_inf = 2,
  ruv = NULL
)

Arguments

Examples

pk_1cmt_inf_cmin_ss(dose = 500, tau = 12, t_inf = 2, CL = 5, V = 50)

Calculate dose based on a given AUC24, Cmax, and Cmin, assuming 1-compartment model

Description

Calculate dose based on a given AUC24, Cmax, and Cmin, assuming 1-compartment model

Usage

pk_1cmt_inf_dose_for_range(
  target = 500,
  type = "auc",
  conc_range = c(10, 40),
  parameters = list(),
  interval = 24,
  t_inf = 1,
  optimize_interval = TRUE,
  round_interval = TRUE
)

Arguments

Calculate dose to achieve steady state Cmax for 1-compartmental PK model with infusion dosing at steady state

Description

Calculate dose to achieve steady state Cmax for 1-compartmental PK model with infusion dosing at steady state

Usage

pk_1cmt_inf_dose_from_cmax(cmax = 1, tau = 12, t_inf = 1, CL = 3, V = 30)

Arguments

Examples

pk_1cmt_inf_dose_from_cmax(cmax = 20, tau = 12, t_inf = 2, CL = 5, V = 50)

Calculate dose to achieve steady state trough for 1-compartmental PK model with infusion dosing at steady state

Description

Calculate dose to achieve steady state trough for 1-compartmental PK model with infusion dosing at steady state

Usage

pk_1cmt_inf_dose_from_cmin(cmin = 1, tau = 12, t_inf = 1, CL = 3, V = 30)

Arguments

Examples

dos <- pk_1cmt_inf_dose_from_cmin(
  cmin = 20, tau = 12, t_inf = 2,
  CL = 5, V = 50)
find_nearest_dose(dos, 100)

Concentration predictions for 2-compartmental PK model with infusion dosing at steady state

Description

Concentration predictions for 2-compartmental PK model with infusion dosing at steady state

Usage

pk_1cmt_inf_ss(
  t = c(0:24),
  dose = 100,
  t_inf = 1,
  tau = 12,
  CL = 3,
  V = 30,
  ruv = NULL
)

Arguments

Examples

pk_1cmt_inf_ss(dose = 500, tau = 12, t_inf = 2, CL = 5, V = 50)
pk_1cmt_inf_ss(
  dose = 500, tau = 12, t_inf = 2, CL = 5, V = 50,
  ruv = list(prop = 0.1, add = 0.1))

Concentration predictions for 1-compartmental oral PK model after single or multiple bolus doses

Description

Concentration predictions for 1-compartmental oral PK model after single or multiple bolus doses

Usage

pk_1cmt_oral(
  t = c(0:24),
  dose = 100,
  tau = 12,
  KA = 1,
  CL = 3,
  V = 30,
  F = 1,
  ruv = NULL
)

Arguments

References

Garrett ER. The Bateman function revisited: a critical reevaluation of the quantitative expressions to characterize concentrations in the one compartment body model as a function of time with first-order invasion and first-order elimination. J Pharmacokinet Biopharm (1994) 22(2):103-128.

Bialer M. A simple method for determining whether absorption and elimination rate constants are equal in the one-compartment open model with first-order processes. J Pharmacokinet Biopharm (1980) 8(1):111-113

Nielsen JC, Hutmacher MM et al. J Pharmacokinet Pharmacodyn. 2012 Dec;39(6):619-34. doi: 10.1007/s10928-012-9274-0. Epub 2012 Sep 23.

https://static-content.springer.com/esm/art

Examples

pk_1cmt_oral(dose = 500, tau = 12, CL = 5, V = 50, KA = 1)

Calculate terminal half-life for 1-compartment model

Description

Calculate terminal half-life for 1-compartment model

Usage

pk_1cmt_t12(CL = 3, V = 30)

Arguments

Examples

pk_1cmt_t12(CL = 5, V = 50)

Concentration predictions for 2-compartmental PK model, single or multiple bolus doses

Description

Concentration predictions for 2-compartmental PK model, single or multiple bolus doses

Usage

pk_2cmt_bolus(
  t = c(0:24),
  dose = 100,
  tau = 12,
  CL = 3,
  V = 30,
  Q = 2,
  V2 = 20,
  ruv = NULL
)

Arguments

Examples

pk_2cmt_bolus(dose = 1000, tau = 24, CL = 5, V = 50, Q = 15, V2 = 200)

Cmax for 2-compartmental PK model, bolus dosing at steady state

Description

Cmax for 2-compartmental PK model, bolus dosing at steady state

Usage

pk_2cmt_bolus_cmax_ss(
  dose = 100,
  tau = 12,
  CL = 3,
  V = 30,
  Q = 2,
  V2 = 20,
  ruv = NULL
)

Arguments

Examples

pk_2cmt_bolus_cmax_ss(dose = 1000, tau = 12, CL = 5, V = 50, Q = 20, V2 = 200)

Cmin (trough) for 2-compartmental PK model, bolus dosing at steady state

Description

Cmin (trough) for 2-compartmental PK model, bolus dosing at steady state

Usage

pk_2cmt_bolus_cmin_ss(
  dose = 100,
  tau = 12,
  CL = 3,
  V = 30,
  Q = 2,
  V2 = 20,
  ruv = NULL
)

Arguments

Examples

pk_2cmt_bolus_cmin_ss(dose = 1000, tau = 12, CL = 5, V = 50, Q = 20, V2 = 200)

Calculate dose to achieve steady state Cmax for 2-compartmental PK model bolus dosing at steady state

Description

Calculate dose to achieve steady state Cmax for 2-compartmental PK model bolus dosing at steady state

Usage

pk_2cmt_bolus_dose_from_cmax(
  cmax = 1,
  tau = 12,
  CL = 3,
  V = 30,
  Q = 2,
  V2 = 20
)

Arguments

Examples

dos <- pk_2cmt_bolus_dose_from_cmax(
  cmax = 10, tau = 12,
  CL = 5, V = 50, Q = 20, V2 = 200)
find_nearest_dose(dos, 100)

Calculate dose to achieve steady state trough for 2-compartmental PK model bolus dosing at steady state

Description

Calculate dose to achieve steady state trough for 2-compartmental PK model bolus dosing at steady state

Usage

pk_2cmt_bolus_dose_from_cmin(
  cmin = 1,
  tau = 12,
  CL = 3,
  V = 30,
  Q = 2,
  V2 = 20
)

Arguments

Examples

dos <- pk_2cmt_bolus_dose_from_cmin(
  cmin = 5, tau = 12,
  CL = 5, V = 50, Q = 20, V2 = 200)
find_nearest_dose(dos, 100)

Concentration predictions for 2-compartmental PK model, bolus dosing at steady state

Description

Concentration predictions for 2-compartmental PK model, bolus dosing at steady state

Usage

pk_2cmt_bolus_ss(
  t = c(0:24),
  dose = 100,
  tau = 12,
  CL = 3,
  V = 30,
  Q = 2,
  V2 = 20,
  ruv = NULL
)

Arguments

Examples

pk_2cmt_bolus_ss(dose = 1000, tau = 12, CL = 5, V = 50, Q = 20, V2 = 200)

Concentration predictions for 2-compartmental PK model, single or multiple infusions

Description

Concentration predictions for 2-compartmental PK model, single or multiple infusions

Usage

pk_2cmt_inf(
  t = c(0:24),
  dose = 100,
  tau = 12,
  t_inf = 1,
  CL = 3,
  V = 30,
  Q = 2,
  V2 = 20,
  ruv = NULL
)

Arguments

Cmax (trough) for 2-compartmental PK model, bolus dosing at steady state

Description

Cmax (trough) for 2-compartmental PK model, bolus dosing at steady state

Usage

pk_2cmt_inf_cmax_ss(
  dose = 100,
  tau = 12,
  t_inf = 1,
  CL = 3,
  V = 30,
  Q = 2,
  V2 = 20,
  ruv = NULL
)

Arguments

Examples

pk_2cmt_inf_cmax_ss(
  dose = 1000, tau = 12, t_inf = 2,
  CL = 5, V = 50, Q = 20, V2 = 200)

Cmin (trough) for 2-compartmental PK model, bolus dosing at steady state

Description

Cmin (trough) for 2-compartmental PK model, bolus dosing at steady state

Usage

pk_2cmt_inf_cmin_ss(
  dose = 100,
  tau = 12,
  t_inf = 1,
  CL = 3,
  V = 30,
  Q = 2,
  V2 = 20,
  ruv = NULL
)

Arguments

Examples

pk_2cmt_inf_cmin_ss(
  dose = 1000, tau = 12, t_inf = 2,
  CL = 5, V = 50, Q = 20, V2 = 200)

Calculate dose to achieve steady state Cmax for 2-compartmental PK model with infusion dosing at steady state

Description

Calculate dose to achieve steady state Cmax for 2-compartmental PK model with infusion dosing at steady state

Usage

pk_2cmt_inf_dose_from_cmax(
  cmax = 1,
  tau = 12,
  t_inf = 1,
  CL = 3,
  V = 30,
  Q = 2,
  V2 = 20
)

Arguments

Examples

dos <- pk_2cmt_inf_dose_from_cmax(
  cmax = 25, tau = 12, t_inf = 2,
  CL = 5, V = 50, Q = 20, V2 = 200)
find_nearest_dose(dos, 100)

Calculate dose to achieve steady state trough for 2-compartmental PK model with infusion dosing at steady state

Description

Calculate dose to achieve steady state trough for 2-compartmental PK model with infusion dosing at steady state

Usage

pk_2cmt_inf_dose_from_cmin(
  cmin = 1,
  tau = 12,
  t_inf = 1,
  CL = 3,
  V = 30,
  Q = 2,
  V2 = 20
)

Arguments

Examples

dos <- pk_2cmt_inf_dose_from_cmin(
  cmin = 10, tau = 12, t_inf = 2,
  CL = 5, V = 50, Q = 20, V2 = 200)
find_nearest_dose(dos, 100)

Concentration predictions for 2-compartmental PK model with infusion dosing at steady state

Description

Concentration predictions for 2-compartmental PK model with infusion dosing at steady state

Usage

pk_2cmt_inf_ss(
  t = c(0:24),
  dose = 100,
  t_inf = 1,
  tau = 12,
  CL = 3,
  V = 30,
  Q = 2,
  V2 = 20,
  ruv = NULL
)

Arguments

Examples

pk_2cmt_inf_ss(
  dose = 1000, tau = 12, t_inf = 2,
  CL = 5, V = 50, Q = 20, V2 = 200)

Calculate half-life(s) for 2-compartment model

Description

Calculate half-life(s) for 2-compartment model

Usage

pk_2cmt_t12(CL = 3, V = 30, Q = 2, V2 = 20, phase = c("both", "alpha", "beta"))

Arguments

Examples

pk_2cmt_t12(CL = 5, V = 50, Q = 20, V2 = 200)

Calculate average half-life for 2-compartment model during a specific interval

Description

Calculate average half-life for 2-compartment model during a specific interval

Usage

pk_2cmt_t12_interval(CL = 3, V = 30, Q = 2, V2 = 20, tau = 12, t_inf = NULL)

Arguments

Examples

pk_2cmt_t12_interval(CL = 5, V = 50, Q = 20, V2 = 200, tau = 12, t_inf = 2)

Print function for output from nca()

Description

Print function for output from nca()

Usage

## S3 method for class 'nca_output'
print(x, ...)

Arguments

Read WHO growth tables

Description

Provides a data frame of the WHO growth table for a given age, sex, and type of measurement.

Usage

read_who_table(sex = NULL, age = NULL, type = "wfa")

Arguments

Details

This function uses files included in system.file(package = "clinPK"). Previously this function also gave the option to download the tables from WHO, but the original URL ("http://www.who.int/entity/childgrowth/standards") no longer exists as of 2021-05-19.

Convert quantity expressed relative to BSA to absolute units

Description

Often used for eGFR estimates

Usage

relative2absolute_bsa(quantity, bsa = NULL, ...)

Arguments

Value

quantity expressed in absolute units

Examples

relative2absolute_bsa(quantity = 60, bsa = 1.6)
relative2absolute_bsa(quantity = 60, weight = 14, height = 90, method = "dubois")

Remove less-than/greater-than symbols and convert to numeric

Description

The following characters will be removed from strings: <, >, =, space. If string contains other characters, the original string will be returned.

Usage

remove_lt_gt(x)

Arguments

Value

If non-numeric characters were successfully removed, returns a numeric vector. If some elements of 'x' contained other characters, their original value will be returned and the result will be a character vector.

Time to steady state In either time units or number of doses

Description

Time to steady state In either time units or number of doses

Usage

time_to_ss(kel = NULL, halflife = NULL, ss = 0.9, in_doses = FALSE, tau = NULL)

Arguments

Examples

time_to_ss(halflife = 12, ss = 0.9)
time_to_ss(halflife = 16, ss = 0.95, in_doses = TRUE, tau = 12)

Valid units

Description

Return recognized units for height, weight, age, scr, serum_albumin.

Usage

valid_units(
  covariate = c("height", "weight", "age", "scr", "serum_albumin", "bilirubin")
)

Arguments

Value

Vector of valid units for the given covariate

Examples

valid_units("height")
valid_units("weight")

Convert any weight unit to kg

Description

Convert any weight unit to kg

Usage

weight2kg(value = NULL, unit = NULL)

Arguments

Examples

weight2kg(250, unit = "oz")
weight2kg(250, unit = "pounds")
weight2kg(250, unit = "lbs")