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Merge pull request #129 from InsightRX/RXR-2907
RXR-2907: add new models for open access, fix misnamed fields
2 parents 8c109c0 + a172ddc commit 98131d2

10 files changed

Lines changed: 478 additions & 2 deletions

‎inst/models/pk_vanco_adane.json5‎

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{
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"id": "pk_vanco_adane",
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"ode_code": "\
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dAdt[0] = -(CLi/Vi)*A[0] \
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dAdt[1] = A[0]/Vi ",
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"pk_code": "\
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BSA = pow(WT,0.425) * pow(HT,0.725) * 0.007184 \
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CLi = CL * (CRCL/7.5) * (1.73/BSA) + CL_HEMO \
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Vi = V * WT \
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",
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"n_comp": 2,
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"obs": { "cmt": 1, "scale": "V * WT" },
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"dose": { "cmt": 1, "bioav": [1] },
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"covariates": [ "WT", "HT", "CRCL", "CL_HEMO" ],
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"variables": ["CLi", "Vi", "BSA"],
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"parameters" : {
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"V": 0.51,
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"CL": 6.54
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},
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"fixed": [],
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"omega_matrix": [
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0.057121,
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0, 0.071289
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],
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"ruv": {
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"prop": [0.189],
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"add": [0.0001]
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},
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"misc": {
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"model_type": "1cmt_iv",
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"linearity": "linear",
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"timevarying_parameter": false,
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"init_parameter": true
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},
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"references": [
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{
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"ref": "Adane, E.D. et al. Pharmacotherapy. 2015",
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"url": "https://www.ncbi.nlm.nih.gov/pubmed/25644478"
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}
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],
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"comments": [
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"A negligible additive error was added to stabilize MAP Bayesian estimation."
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],
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"version": "0.2.14"
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}

‎inst/models/pk_vanco_brooks.json5‎

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{
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"id": "pk_vanco_brooks",
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"description": "PK model for vancomycin in adults age 18-35 years",
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"ode_code": "\
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dAdt[0] = -(CLtot/Vi)*A[0] - (Qi/Vi)*A[0] + (Qi/V2i)*A[1] \
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dAdt[1] = +(Qi/Vi)*A[0] - (Qi/V2i)*A[1] \
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dAdt[2] = A[0]/Vi ",
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"pk_code": "\
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BMI = WT / pow((HT/100.0), 2.0) \
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if(SEX == 1) { \
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FFM = (9270.0 * WT) / (6680.0 + 216.0 * BMI) ;\
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} else { \
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FFM = (9270.0 * WT) / (8780.0 + 244.0 * BMI) ;\
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} \
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if(SEX == 0) { \
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A1 = -0.241 \
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K = 0.7 \
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FSEX = 1.012 \
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} else { \
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A1 = -0.302 \
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K = 0.9 \
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FSEX = 1.0 \
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} \
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if(CR >= K) { \
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A1 = -1.2 \
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} \
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CKDEPI = (142.0/16.66667) * pow(CR/K, A1) * pow(0.9938, AGE) * FSEX \
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BSA = pow(WT,0.425) * pow(HT,0.725) * 0.007184 \
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CRCL = CKDEPI * BSA / 1.73 \
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CLi = CL * pow(CRCL/6.0, 0.945165) * pow(FFM / 55.0, 0.27415) \
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CLtot = CLi + CL_HEMO \
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Vi = V * FFM / 55.0 \
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V2i = V2 * FFM / 55.0 \
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Qi = Q * pow(FFM / 55.0, 0.27415) \
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",
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"n_comp": 3,
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"obs": { "cmt": 1, "scale": "Vi" },
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"dose": { "cmt": 1, "bioav": [1] },
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"covariates": ["WT", "AGE", "SEX", "CR", "HT", "CL_HEMO"],
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"variables": [
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"CLi", "Vi", "V2i", "Qi", "CLtot", "CRCL", "BSA",
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"FFM", "CKDEPI", "BMI", "A1", "K", "FSEX"
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],
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"parameters" : {
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"CL": 4.2622,
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"V": 40.7349,
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"V2": 48.7348,
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"Q": 2.9295
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},
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"fixed": ["Q"],
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"omega_matrix": [
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0.10504,
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0.0550392, 0.0648416,
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0, 0.068372, 0.882951
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],
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"ruv": {
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"prop": [0.160962],
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"add": [0.92]
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},
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"misc": {
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"model_type": "2cmt_iv",
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"linearity": "linear",
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"timevarying_parameter": false,
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"init_parameter": true,
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"int_step_size": 0.01
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},
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"references": [
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{
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"ref": "Brooks et al., in review, 2025"
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}
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],
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"version": "0.1.7"
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}

‎inst/models/pk_vanco_buelga.json5‎

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{
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"id": "pk_vanco_buelga",
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"description": "PK model for vancomycin in adults with hematological malignancies",
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"ode_code": "\
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dAdt[0] = -(CLtot/Vi)*A[0];\n\
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dAdt[1] = A[0]/Vi;",
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"pk_code": "\n\
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CLi = CL*CRCL;\n\
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CLtot = CLi + TH_CVVH * CL_HEMO;\n\
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Vi = V * WT;\n\
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",
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"n_comp": 2,
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"obs": { "cmt": 1, "scale": "V * WT" },
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"dose": { "cmt": 1, "bioav": [1] },
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"parameters": {
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"CL": 1.08,
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"V": 0.98,
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"TH_CVVH": 1
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},
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"fixed": [
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"TH_CVVH"
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],
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"omega_matrix": [
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0.07929856,
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0.02418685, 0.1380123
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],
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"ruv": {
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"prop": [0],
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"add": [3.52]
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},
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"covariates": ["WT", "CRCL", "CL_HEMO"],
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"variables": ["CLi", "Vi", "CLtot"],
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"misc": {
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"model_type": "1cmt_iv",
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"linearity": "linear",
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"timevarying_parameter": false,
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"init_parameter": true
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},
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"references": [
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{
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"ref": "Buelga DS et al. Antimicrob Agents Chemother 2005",
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"url": "http://www.ncbi.nlm.nih.gov/pubmed/16304155"
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}
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],
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"comments": ["Assuming 25% correlation between CL and V."],
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"version": "0.2.16"
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}

‎inst/models/pk_vanco_carreno.json5‎

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{
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"id": "pk_vanco_carreno",
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"description": "PK model for vancomycin in obese adults (110-250 kg)",
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"ode_code": "\
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CLi = SCLInter + SCLSlope * (CRCL*16.667) + CL_HEMO \
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Vi = V \
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Qi = K12 * Vi \
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V2i = Qi / K21 \
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dAdt[0] = -(CLi/V)*A[0] - K12*A[0] + K21*A[1] \
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dAdt[1] = K12*A[0] - K21*A[1] \
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dAdt[2] = A[0]/V ",
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"pk_code": "",
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"n_comp": 3,
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"obs": { "cmt": 1, "scale": "V" },
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"dose": { "cmt": 1, "bioav": [1] },
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"covariates": [ "CRCL", "CL_HEMO" ],
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"variables": ["CLi", "Qi", "Vi", "V2i"],
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"parameters" : {
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"V": 25.76,
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"SCLSlope": 0.036,
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"K12": 2.29,
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"K21": 1.44,
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"SCLInter" : 0.18
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},
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"fixed": [],
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"omega_matrix": [
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0.20559,
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0, 0.30864,
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0, 0, 1.11676,
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0, 0, 0, 1.4433,
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0, 0, 0, 0, 0.057068
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],
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"ruv": {
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"prop": [0.1],
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"add": [0.1]
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},
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"misc": {
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"model_type": "2cmt_iv",
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"linearity": "linear",
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"timevarying_parameter": false,
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"init_parameter": true,
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"int_step_size": 0.01
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},
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"references": [
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{
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"ref": "Carreno JJ et al. Antimicrob. Agents Chemother. 2017",
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"url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5404576/"
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}
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],
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"comments": [
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"Described as Model 4 in this publication. BMI ranges and not weights should be considered for determining whether patient matches model development population."
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],
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"version": "0.2.18"
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}

‎inst/models/pk_vanco_goti.json5‎

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{
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"id": "pk_vanco_goti",
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"description": "PK model for vancomycin in adults with or without hemodialysis",
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"ode_code": "\
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dAdt[0] = -(CLtot/Vi)*A[0] - (Q/Vi)*A[0] + (Q/V2)*A[1];\
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dAdt[1] = +(Q/Vi)*A[0] - (Q/V2)*A[1];\
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dAdt[2] = A[0]/Vi;",
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"pk_code": "\
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CRcalc = CR;\
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if(AGE > 65.0 & CR < 1.0) { CRcalc = 1.0; }\
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CRCLi = min((140.0 - AGE) * WT * pow(0.85, (1-SEX)) / (72.0 * CRcalc), 150.0); \
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CLi = CL * pow((CRCLi/120.0), TH_CRCL) * pow(TH_DIAL_CL, DIAL);\
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CLtot = CLi + CL_HEMO;\
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Vi = V * (WT/70.0) * pow(TH_DIAL_V, DIAL);\
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V2i = V2;\
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Qi = Q \
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",
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"n_comp": 3,
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"obs": { "cmt": 1, "scale": "V * (WT/70.0) * pow(TH_DIAL_V, DIAL)" },
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"dose": { "cmt": 1, "bioav": [1] },
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"covariates": ["WT", "SEX", "AGE", "CR", "DIAL", "CL_HEMO"],
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"variables": ["CLi", "Qi", "Vi", "V2i", "CRCLi", "CLtot", "CRcalc"],
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"parameters" : {
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"CL": 4.5,
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"V": 58.4,
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"V2": 38.4,
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"Q": 6.5,
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"TH_CRCL": 0.8,
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"TH_DIAL_CL": 0.7,
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"TH_DIAL_V": 0.5
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},
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"fixed": [
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"Q",
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"TH_CRCL",
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"TH_DIAL_CL",
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"TH_DIAL_V"
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],
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"omega_matrix": [
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0.1584,
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0, 0.6659,
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0, 0, 0.326
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],
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"ruv": {
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"prop": [0.197],
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"add": [1.42]
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},
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"misc": {
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"model_type": "2cmt_iv",
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"linearity": "linear",
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"timevarying_parameter": false,
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"init_parameter": true
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},
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"references": [
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{
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"ref": "Goti V et al. TDM 2018",
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"url": "https://www.ncbi.nlm.nih.gov/pubmed/?term=29470227"
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},
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{
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"ref": "Goti V et al. TDM 2018, erratum",
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"url": "https://www.ncbi.nlm.nih.gov/pubmed/31306395"
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}
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],
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"comments": [
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"The residual error magnitude was reduced from 22.7% proportional + 3.4 mg/L additive to 19.7% proportional and 1.42 mg/L additive (the average of Thomson and Colin models) to be more realistic and in line with other models, and to improve MAP estimation stability.",
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"The original Goti publication mentions that the following rule was applied: when AGE>60 & CR<1 then CRcalc=1, erratum says when AGE>65 & CR<1 then CRcalc=1. The latter is applied here."
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],
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"version": "0.2.31"
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}

‎inst/models/pk_vanco_hughes.json5‎

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{
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"id": "pk_vanco_hughes",
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"description": "PK model for vancomycin in obese adults",
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"ode_code": "\
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dAdt[0] = -(CLtot/Vi)*A[0] - (Q/Vi)*A[0] + (Q/V2i)*A[1] \
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dAdt[1] = +(Q/Vi)*A[0] - (Q/V2i)*A[1] \
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dAdt[2] = A[0]/Vi ",
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"pk_code": "\
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BMI = WT / pow((HT/100.0), 2.0) \
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if(SEX == 1) { \
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FFM = (9270.0 * WT) / (6680.0 + 216.0 * BMI) ;\
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} else { \
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FFM = (9270.0 * WT) / (8780.0 + 244.0 * BMI) ;\
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} \
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CRCL = (140.0 - AGE) * FFM * pow(0.85, 1-SEX) / (72.0 * CR) \
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CLi = CL * pow(CRCL/100.0, 0.8509) \
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CLtot = CLi + CL_HEMO \
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Vi = V * FFM / 70.0 \
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V2i = V2 * FFM / 70.0 \
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",
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"n_comp": 3,
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"obs": { "cmt": 1, "scale": "Vi" },
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"dose": { "cmt": 1, "bioav": [1] },
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"covariates": ["WT", "AGE", "SEX", "CR", "HT", "CL_HEMO"],
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"variables": ["CLi", "Vi", "V2i", "CLtot", "FFM", "CRCL", "BMI"],
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"parameters" : {
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"CL": 5.0627,
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"V": 64.339,
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"V2": 59.019,
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"Q": 6.2402
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},
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"fixed": ["Q"],
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"omega_matrix": [
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0.0473154,
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0.00271032, 0.0322236,
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0.0132618, 0.138593, 0.634656
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],
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"ruv": {
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"prop": [0.1334],
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"add": [0.001]
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},
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"misc": {
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"model_type": "2cmt_iv",
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"linearity": "linear",
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"timevarying_parameter": false,
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"init_parameter": true,
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"int_step_size": 0.01
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},
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"references": [
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{
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"ref": "Hughes, M.S.A. et al., TDM (2024)",
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"url": "https://pubmed.ncbi.nlm.nih.gov/38758633/"
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}
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],
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"version": "0.1.8"
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}

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