README.md

In clinPK: Clinical Pharmacokinetics Toolkit

clinPK

Equations and tools for clinical pharmacokinetics

Miscellaneous functions

• nca(): Non-compartmental PK analysis, e.g. AUC, half-life, etc.
• calc_kel_single_tdm(): calculate elimination rate based on single TDM sample and provided volume of distribution (assuming linear 1-cmt model).
• calc_kel_double_tdm(): calculate elimination rate and other PK parameters based on two timed TDM samples (assuming on linear 1-cmt model).
• calc_t12(): calculate effective half-life based on two TDM points.
• calc_amts_for_conc(): Calculate the amounts in all compartments in a compartmental PK system based on a given concentration in the central compartment, and assuming steady state.
• find_nearest_dose(): Find nearest available dose based on smallest available dosing unit
• find_nearest_interval(): Find nearest (or nearest higher / nearest lower) dosing interval

Anthropomorphic equations

• calc_bsa(): BSA calculation using various equations
• calc_ffm(): Fat-free mass using various equations
• calc_bmi(): Body mass index
• calc_ibw(): Ideal body weight, using various equations for children and adults
• calc_lbw(): Lean body weight
• calc_abw(): Adjusted body weight (for obese patients)
• calc_dosing_weight(): Dosing weight
• pct_weight_for_age(): calculate percentile of weight given age (for kids <= 10 yrs)
• pct_height_for_age(): calculate percentile of height given age (for kids <= 19 yrs)
• pct_bmi_for_age(): calculate percentile of height given age (for kids <= 19 yrs)

Clinical chemistry

• calc_egfr(): eGFR calculation from serum creatinine using various equations (Cockcroft-Gault, MDRD, CKD-EPI, Jelliffe, Jelliffe for unstable patients, Wright, Lund-Malmo revised, Schwartz, Schwartz revised)
• calc_egfr_cystatin(): eGFR calculation from Cystatin C concentrations using various equations (Grubb, Larsson)
• calc_creat(): mean serum creatinine for children and adults (given age and sex)
• calc_creat_neo(): typical serum creatinine for neonates given post-natal age
• calc_aki_stage: detect and calculate stage of acute kidney injury based on serum creatinine history, based on various classification systems (RIFLE, pRIFLE, KDIGO)
• convert_creat_assay(): convert between various creatinine assays (Jaffe, IDMS, etc)
• convert_creat_unit(): convert between creatinine units (mmol/L, mg/dL)

Conversions

• kg2lbs(): kg to pounds
• lbs2kg(): pounds to kg
• kg2oz(): kg to ounces
• oz2kg(): ounces to kg
• weight2kg(): any weight unit to kg
• cm2inch(): cm to inches
• inch2cm(): inches to cm
• conc2mol(): concentration to molar
• mol2conc(): molar to concentration

PK compartmental equations

Functions to simulate concentrations for linear PK models.

| function | compartments | administration | type | output | | --- | --- | --- | --- | --- | | pk_1cmt_inf() | 1 | infusion | single/multi dose | concentration table | | pk_1cmt_inf_ss() | 1 | infusion | steady state | concentration table | | pk_1cmt_inf_cmin_ss() | 1 | infusion | steady state | Cmin | | pk_1cmt_inf_cmax_ss() | 1 | infusion | steady state | Cmax | | pk_2cmt_inf() | 2 | infusion | single/multi dose | concentration table | | pk_2cmt_inf_ss() | 2 | infusion | steady state | concentration table | | pk_2cmt_inf_cmin_ss() | 2 | infusion | steady state | Cmin | | pk_2cmt_inf_cmax_ss() | 2 | infusion | steady state | Cmax | | pk_1cmt_bolus() | 1 | bolus | single/multi dose | concentration table | | pk_1cmt_bolus_ss() | 1 | bolus | steady state | concentration table | | pk_1cmt_bolus_cmin_ss() | 1 | bolus | steady state | Cmin | | pk_1cmt_bolus_cmax_ss() | 1 | bolus | steady state | Cmax | | pk_1cmt_t12() | 1 | - | - | half-life | | pk_1cmt_oral() | 1 | oral | - | concentration | | pk_2cmt_bolus() | 2 | bolus | single/multi dose | concentration table | | pk_2cmt_bolus_ss() | 2 | bolus | steady state | concentration table | | pk_2cmt_bolus_cmin_ss() | 2 | bolus | steady state | Cmin | | pk_2cmt_bolus_cmax_ss() | 2 | bolus | steady state | Cmax | | pk_2cmt_t12() | 2 | - | - | terminal half-life | | pk_2cmt_t12_interval() | 2 | - | - | effective half-life in given interval |

PK steady state equations

• accumulation_ratio(): calculate the accumulation ratio for given halflife or elimination rate and dosing interval
• fraction_of_ss(): calculate fraction of steady state reached after certain time or number of doses
• time_to_ss(): calculate time to steady state in time units or number of doses

Dose / TDM calculations

Functions to calculate the dose expected to achieve a specific target exposure.

| function | compartments | administration | target | output | | --- | --- | --- | --- | --- | | pk_1cmt_inf_dose_for_cmin | 1 | infusion | cmin | dose | | pk_1cmt_bolus_dose_for_cmin | 1 | bolus | cmin | dose | | pk_2cmt_inf_dose_for_cmin() | 2 | infusion | cmin | dose | | pk_2cmt_bolus_dose_for_cmin() | 2 | bolus | cmin | dose | | pk_1cmt_inf_dose_for_cmax | 1 | infusion | cmax | dose | | pk_1cmt_bolus_dose_for_cmax | 1 | bolus | cmax | dose | | pk_2cmt_inf_dose_for_cmax() | 2 | infusion | cmax | dose | | pk_2cmt_bolus_dose_for_cmax() | 2 | bolus | cmax | dose | | pk_1cmt_inf_dose_for_range() | 1 | infusion | auc/cmin + conc range | dose | | dose2auc() | 1 | - | auc | auc | | auc2dose() | 1 | - | auc | dose |

clinPK documentation built on May 9, 2022, 9:06 a.m.