METHOD_OPTIONS¶
Type: dict_record
method options for msim_script
Example:-
METHOD_OPTIONS:
py_module: msim
rand_seed: 12345
float_format: default
py_module¶
Type: one_of(msim)
Python module required to process this script file
Example:-
py_module: msim
rand_seed¶
Option to set seed to make run result reproducible -e.g. when debugging.
Example:-
rand_seed: 12345
PARALLEL¶
Type: one_of_record
one of many possible servers
Example:-
PARALLEL:
SINGLE: {}
MPI_WORKERS¶
Type: dict_record
MPI local server spec.
Example:-
MPI_WORKERS:
n_workers: auto
cpu_load: 1.0
n_workers¶
Number of workers to use on this machine, defaults to number of processors, but could be more or fewer.
Example:-
n_workers: auto
DESCRIPTION¶
Type: dict_record
Description fields for script.
Example:-
DESCRIPTION:
name: my_pkpd_model
title: My PKPD model
author: My Name
abstract: |
Abstract describing the model
keywords: ['pkpd']
FILE_PATHS¶
Type: dict_record
file paths for pop_msim
Example:-
FILE_PATHS:
input_data_file: input_observations_soln.pyml
output_folder: auto
temp_folder: auto
log_folder: auto
output_file_ext: ['svg']
input_solution_file: solN\solution.pyml
input_data_file¶
Type: input_file
path to input comma separated value file in popy data format
Example:-
input_data_file: input_observations_soln.pyml
output_folder¶
Type: output_folder / auto
Output folder - results of computation stored here
Example:-
output_folder: auto
temp_folder¶
Type: output_folder / auto
Temp folder - temporary files stored here
Example:-
temp_folder: auto
log_folder¶
Type: output_folder / auto
Log folder - log files stored here
Example:-
log_folder: auto
output_file_ext¶
Type: list_of(pdf,png,svg)
Output file extension - determines graphical output file format.
Example:-
output_file_ext: ['svg']
input_solution_file¶
Type: input_file / none
Solution containing f[X] values from a previous run.
Example:-
input_solution_file: solN\solution.pyml
DATA_FIELDS¶
Type: dict_record
data fields for popy.dat.fields object
Example:-
DATA_FIELDS:
type_field: TYPE
id_field: ID
time_field: TIME
type_field¶
Type: str
Field name in data file that contains row type info, e.g. obs/dose etc
Example:-
type_field: TYPE
PREPROCESS¶
Type: verbatim
Code that preprocesses the input data. Use this to filter rows and create derived covariates.
Example:-
PREPROCESS: |
EFFECTS¶
Type: repeat_verb_record
EFFECT params to define hierarchical population model
Example:-
EFFECTS:
POP: |
f[KA] ~ P1.0
f[CL] ~ P1.0
f[V1] ~ P20
f[Q] ~ P0.5
f[V2] ~ P100
f[KA_isv,CL_isv,V1_isv,Q_isv,V2_isv] ~ spd_matrix() [
[0.05],
[0.01, 0.05],
[0.01, 0.01, 0.05],
[0.01, 0.01, 0.01, 0.05],
[0.01, 0.01, 0.01, 0.01, 0.05],
]
f[PNOISE] ~ P0.1
ID: |
r[KA, CL, V1, Q, V2] ~ mnorm([0,0,0,0,0], f[KA_isv,CL_isv,V1_isv,Q_isv,V2_isv])
MODEL_PARAMS¶
Type: verbatim
Defines the mapping from c[X], f[X] and r[X] variables to individual model m[X] parameters.
Example:-
MODEL_PARAMS: |
m[KA] = f[KA] * exp(r[KA])
m[CL] = f[CL] * exp(r[CL])
m[V1] = f[V1] * exp(r[V1])
m[Q] = f[Q] * exp(r[Q])
m[V2] = f[V2] * exp(r[V2])
m[ANOISE] = 0.001
m[PNOISE] = f[PNOISE]
STATES¶
Type: verbatim
Optional section for setting initial values of s[X] variables can also set slabel[X] text labels.
Example:-
STATES: |
DERIVATIVES¶
Type: verbatim
Define how the covariates and effects determine flows between compartments.
Example:-
DERIVATIVES: |
# s[DEPOT,CENTRAL,PERI] = @dep_two_cmp_cl{dose:@bolus{amt:c[AMT]}}
d[DEPOT] = @bolus{amt:c[AMT]} - m[KA]*s[DEPOT]
d[CENTRAL] = m[KA]*s[DEPOT] - s[CENTRAL]*m[CL]/m[V1] - s[CENTRAL]*m[Q]/m[V1] + s[PERI]*m[Q]/m[V2]
d[PERI] = s[CENTRAL]*m[Q]/m[V1] - s[PERI]*m[Q]/m[V2]
PREDICTIONS¶
Type: verbatim
Define the final predicted m[X] variables to be output by the compartment model system.
Example:-
PREDICTIONS: |
p[DV_CENTRAL] = s[CENTRAL]/m[V1]
plabel[DV_CENTRAL] = 'Drug conc. (units)'
var = m[ANOISE]**2 + m[PNOISE]**2 * p[DV_CENTRAL]**2
c[DV_CENTRAL] ~ norm(p[DV_CENTRAL], var)
ODE_SOLVER¶
Type: one_of_record
one of many possible solvers
Example:-
ODE_SOLVER:
CPPLSODA:
atol: 1e-06
rtol: 1e-06
max_nsteps: 10000000
use_supersections: True
use_sens: False
hmin: 0.0
ANALYTIC¶
Type: dict_record
Analytic method for solving ODE
Example:-
ANALYTIC:
use_supersections: auto
use_sens: True
use_supersections¶
Option to combine sections into supersections, which can make PoPy run faster, however with discontinuous ODE params you may need to turn this off (closer to nonmem approach).
Example:-
use_supersections: auto
SCIPY_ODEINT¶
Type: dict_record
odeint solver record
Example:-
SCIPY_ODEINT:
atol: 1e-06
rtol: 1e-06
max_nsteps: 10000000
use_supersections: auto
use_jacobian: False
use_sens: True
use_tcrit: False
use_supersections¶
Option to combine sections into supersections, which can make PoPy run faster, however with discontinuous ODE params you may need to turn this off (closer to nonmem approach).
Example:-
use_supersections: auto
CPPODE¶
Type: dict_record
C++ version of original cvode c library.
Example:-
CPPODE:
atol: 1e-06
rtol: 1e-06
max_nsteps: 10000000
use_supersections: auto
use_sens: True
use_supersections¶
Option to combine sections into supersections, which can make PoPy run faster, however with discontinuous ODE params you may need to turn this off (closer to nonmem approach).
Example:-
use_supersections: auto
CPPLSODA¶
Type: dict_record
C++ version of original cvode c library.
Example:-
CPPLSODA:
atol: 1e-06
rtol: 1e-06
max_nsteps: 10000000
use_supersections: auto
use_sens: True
hmin: 1e-12
use_supersections¶
Option to combine sections into supersections, which can make PoPy run faster, however with discontinuous ODE params you may need to turn this off (closer to nonmem approach).
Example:-
use_supersections: auto
OUTPUT_OPTIONS¶
Type: dict_record
Output options for msim_script
Example:-
OUTPUT_OPTIONS:
sim_time_step: -1.0
n_pop_samples: 100
OUTPUT_SCRIPTS¶
Type: dict_record
scripts to output for further processing
Example:-
OUTPUT_SCRIPTS:
VPC: {output_mode: run, vpc_list: ['OBS_vs_TIME_VPC']}
VPC¶
Type: dict_record
Options to pass to vpc_script.
Example:-
VPC:
output_mode: run
vpc_list: ['OBS_vs_TIME_VPC']