vignettes/task_management.Rmd
task_management.Rmd
library(CoRC)
loadExamples(2)
#> [[1]]
#> # A COPASI model reference:
#> Model name: "Bacterial chemotaxis model"
#> Number of compartments: 1
#> Number of species: 21
#> Number of reactions: 14CoRC has implemented a variety of COPASI functions. Tasks generally
have an run execution function
(e.g. runTimeCourse), a settings set function
(e.g. setTimeCourseSettings) and a settings
get function (e.g. getTimeCourseSettings).
Get task settings:
Get functions return a list of settings in the same format as is
expected as input to set functions.
str(getTimeCourseSettings())
#> List of 11
#> $ duration : num 1000
#> $ dt : num 0.1
#> $ intervals : int 10000
#> $ automatic_intervals : logi FALSE
#> $ suppress_output_before: num 0
#> $ output_events : logi FALSE
#> $ save_result_in_memory : logi TRUE
#> $ start_in_steady_state : logi FALSE
#> $ update_model : logi FALSE
#> $ executable : logi FALSE
#> $ method :List of 6
#> ..$ method : chr "deterministic"
#> ..$ integrate_reduced_model: logi FALSE
#> ..$ relative_tolerance : num 1e-06
#> ..$ absolute_tolerance : num 1e-12
#> ..$ max_internal_steps : int 10000
#> ..$ max_internal_step_size : num 0Set task settings:
setTimeCourseSettings(duration = 100)
getTimeCourseSettings()$duration
#> [1] 100Run task:
Run functions return a list of results. Included in this list is an
entry settings with contains all tasks settings.
str(runTimeCourse())
#> List of 6
#> $ settings :List of 11
#> ..$ duration : num 100
#> ..$ dt : num 0.01
#> ..$ intervals : int 10000
#> ..$ automatic_intervals : logi FALSE
#> ..$ suppress_output_before: num 0
#> ..$ output_events : logi FALSE
#> ..$ save_result_in_memory : logi TRUE
#> ..$ start_in_steady_state : logi FALSE
#> ..$ update_model : logi FALSE
#> ..$ executable : logi FALSE
#> ..$ method :List of 6
#> .. ..$ method : chr "deterministic"
#> .. ..$ integrate_reduced_model: logi FALSE
#> .. ..$ relative_tolerance : num 1e-06
#> .. ..$ absolute_tolerance : num 1e-12
#> .. ..$ max_internal_steps : int 10000
#> .. ..$ max_internal_step_size : num 0
#> $ column_keys : chr [1:19] "Time" "T1{compartment}" "T3{compartment}" "CheY{compartment}" ...
#> $ units :List of 2
#> ..$ time : chr "s"
#> ..$ concentration: chr "µmol / l"
#> $ result : tibble [10,001 × 19] (S3: tbl_df/tbl/data.frame)
#> ..$ Time : num [1:10001] 0 0.01 0.02 0.03 0.04 0.05 0.06 0.07 0.08 0.09 ...
#> ..$ T1 : num [1:10001] 0 0.000612 0.001225 0.001837 0.002449 ...
#> ..$ T3 : num [1:10001] 0.00 1.36e-12 1.09e-11 3.68e-11 8.72e-11 ...
#> ..$ CheY : num [1:10001] 9.7 9.7 9.7 9.7 9.7 ...
#> ..$ CheA : num [1:10001] 5.3 5.3 5.3 5.3 5.3 ...
#> ..$ T2 : num [1:10001] 0.00 3.54e-08 1.42e-07 3.18e-07 5.66e-07 ...
#> ..$ CheBp : num [1:10001] 0.00 6.19e-08 2.73e-07 6.33e-07 1.14e-06 ...
#> ..$ T4 : num [1:10001] 0.00 3.94e-17 6.30e-16 3.19e-15 1.01e-14 ...
#> ..$ CheAp : num [1:10001] 0.00 1.63e-05 3.44e-05 5.25e-05 7.06e-05 ...
#> ..$ CheB : num [1:10001] 0.28 0.28 0.28 0.28 0.28 ...
#> ..$ T0 : num [1:10001] 5.3 5.3 5.3 5.3 5.3 ...
#> ..$ CheYp : num [1:10001] 0 0.000052 0.000173 0.000316 0.000467 ...
#> ..$ Tactive : num [1:10001] 0.00 6.64e-05 1.33e-04 1.99e-04 2.66e-04 ...
#> ..$ Tactive0: num [1:10001] 0 0 0 0 0 0 0 0 0 0 ...
#> ..$ Tactive1: num [1:10001] 0.00 6.64e-05 1.33e-04 1.99e-04 2.65e-04 ...
#> ..$ Tactive2: num [1:10001] 0.00 1.59e-08 6.34e-08 1.43e-07 2.54e-07 ...
#> ..$ Tactive3: num [1:10001] 0.00 1.02e-12 8.12e-12 2.74e-11 6.50e-11 ...
#> ..$ Tactive4: num [1:10001] 0.00 3.94e-17 6.30e-16 3.19e-15 1.01e-14 ...
#> ..$ Ttotal : num [1:10001] 5.3 5.3 5.3 5.3 5.3 ...
#> $ result_number: tibble [10,001 × 19] (S3: tbl_df/tbl/data.frame)
#> ..$ Time : num [1:10001] 0 0.01 0.02 0.03 0.04 0.05 0.06 0.07 0.08 0.09 ...
#> ..$ T1 : num [1:10001] 0 0.516 1.033 1.549 2.065 ...
#> ..$ T3 : num [1:10001] 0.00 1.15e-09 9.20e-09 3.10e-08 7.36e-08 ...
#> ..$ CheY : num [1:10001] 8178 8178 8178 8178 8178 ...
#> ..$ CheA : num [1:10001] 4468 4468 4468 4468 4468 ...
#> ..$ T2 : num [1:10001] 0.00 2.98e-05 1.19e-04 2.69e-04 4.77e-04 ...
#> ..$ CheBp : num [1:10001] 0.00 5.21e-05 2.30e-04 5.34e-04 9.63e-04 ...
#> ..$ T4 : num [1:10001] 0.00 3.32e-14 5.31e-13 2.69e-12 8.50e-12 ...
#> ..$ CheAp : num [1:10001] 0 0.0137 0.029 0.0443 0.0596 ...
#> ..$ CheB : num [1:10001] 236 236 236 236 236 ...
#> ..$ T0 : num [1:10001] 4468 4468 4467 4467 4466 ...
#> ..$ CheYp : num [1:10001] 0 0.0439 0.1457 0.2667 0.3938 ...
#> ..$ Tactive : num [1:10001] 0 0.056 0.112 0.168 0.224 ...
#> ..$ Tactive0: num [1:10001] 0 0 0 0 0 0 0 0 0 0 ...
#> ..$ Tactive1: num [1:10001] 0 0.056 0.112 0.168 0.224 ...
#> ..$ Tactive2: num [1:10001] 0.00 1.34e-05 5.35e-05 1.20e-04 2.14e-04 ...
#> ..$ Tactive3: num [1:10001] 0.00 8.56e-10 6.85e-09 2.31e-08 5.48e-08 ...
#> ..$ Tactive4: num [1:10001] 0.00 3.32e-14 5.31e-13 2.69e-12 8.50e-12 ...
#> ..$ Ttotal : num [1:10001] 4468 4468 4468 4468 4468 ...
#> $ task_error : NULL
#> - attr(*, "class")= chr "copasi_ts"Task settings can be set in two ways. The set familiy of
functions is the preferred way to set task settings.
getTimeCourseSettings()$duration
#> [1] 100
setTimeCourseSettings(duration = 10)
getTimeCourseSettings()$duration
#> [1] 10The run familiy of functions will generally take the
same arguments as the set familiy of functions but will
only set them temporarily.
getTimeCourseSettings()$duration
#> [1] 10
runTimeCourse(duration = 1)$settings$duration
#> [1] 1
getTimeCourseSettings()$duration
#> [1] 10The get familiy of functions will return a list that can
be used as a template for calling functions that expect settings as
input. A similar list is also given in every output of a
run function.
method_settings <- getTimeCourseSettings()$method
str(method_settings)
#> List of 6
#> $ method : chr "deterministic"
#> $ integrate_reduced_model: logi FALSE
#> $ relative_tolerance : num 1e-06
#> $ absolute_tolerance : num 1e-12
#> $ max_internal_steps : int 10000
#> $ max_internal_step_size : num 0
setTimeCourseSettings(method = method_settings)Executing a task will return a list containing all relevant task results.
str(runTimeCourse())
#> List of 6
#> $ settings :List of 11
#> ..$ duration : num 10
#> ..$ dt : num 0.001
#> ..$ intervals : int 10000
#> ..$ automatic_intervals : logi FALSE
#> ..$ suppress_output_before: num 0
#> ..$ output_events : logi FALSE
#> ..$ save_result_in_memory : logi TRUE
#> ..$ start_in_steady_state : logi FALSE
#> ..$ update_model : logi FALSE
#> ..$ executable : logi FALSE
#> ..$ method :List of 6
#> .. ..$ method : chr "deterministic"
#> .. ..$ integrate_reduced_model: logi FALSE
#> .. ..$ relative_tolerance : num 1e-06
#> .. ..$ absolute_tolerance : num 1e-12
#> .. ..$ max_internal_steps : int 10000
#> .. ..$ max_internal_step_size : num 0
#> $ column_keys : chr [1:19] "Time" "T1{compartment}" "T3{compartment}" "CheY{compartment}" ...
#> $ units :List of 2
#> ..$ time : chr "s"
#> ..$ concentration: chr "µmol / l"
#> $ result : tibble [10,001 × 19] (S3: tbl_df/tbl/data.frame)
#> ..$ Time : num [1:10001] 0 0.001 0.002 0.003 0.004 0.005 0.006 0.007 0.008 0.009 ...
#> ..$ T1 : num [1:10001] 0.00 6.13e-05 1.23e-04 1.84e-04 2.45e-04 ...
#> ..$ T3 : num [1:10001] 0.00 1.36e-15 1.09e-14 3.68e-14 8.73e-14 ...
#> ..$ CheY : num [1:10001] 9.7 9.7 9.7 9.7 9.7 ...
#> ..$ CheA : num [1:10001] 5.3 5.3 5.3 5.3 5.3 ...
#> ..$ T2 : num [1:10001] 0.00 3.54e-10 1.42e-09 3.19e-09 5.66e-09 ...
#> ..$ CheBp : num [1:10001] 0.00 1.96e-10 1.29e-09 3.67e-09 7.48e-09 ...
#> ..$ T4 : num [1:10001] 0.00 3.94e-21 6.30e-20 3.19e-19 1.01e-18 ...
#> ..$ CheAp : num [1:10001] 0.00 6.52e-07 2.03e-06 3.67e-06 5.42e-06 ...
#> ..$ CheB : num [1:10001] 0.28 0.28 0.28 0.28 0.28 ...
#> ..$ T0 : num [1:10001] 5.3 5.3 5.3 5.3 5.3 ...
#> ..$ CheYp : num [1:10001] 0.00 2.20e-07 1.40e-06 3.87e-06 7.63e-06 ...
#> ..$ Tactive : num [1:10001] 0.00 6.64e-06 1.33e-05 1.99e-05 2.66e-05 ...
#> ..$ Tactive0: num [1:10001] 0 0 0 0 0 0 0 0 0 0 ...
#> ..$ Tactive1: num [1:10001] 0.00 6.64e-06 1.33e-05 1.99e-05 2.66e-05 ...
#> ..$ Tactive2: num [1:10001] 0.00 1.59e-10 6.34e-10 1.43e-09 2.54e-09 ...
#> ..$ Tactive3: num [1:10001] 0.00 1.02e-15 8.12e-15 2.74e-14 6.50e-14 ...
#> ..$ Tactive4: num [1:10001] 0.00 3.94e-21 6.30e-20 3.19e-19 1.01e-18 ...
#> ..$ Ttotal : num [1:10001] 5.3 5.3 5.3 5.3 5.3 5.3 5.3 5.3 5.3 5.3 ...
#> $ result_number: tibble [10,001 × 19] (S3: tbl_df/tbl/data.frame)
#> ..$ Time : num [1:10001] 0 0.001 0.002 0.003 0.004 0.005 0.006 0.007 0.008 0.009 ...
#> ..$ T1 : num [1:10001] 0 0.0516 0.1033 0.1549 0.2066 ...
#> ..$ T3 : num [1:10001] 0.00 1.15e-12 9.20e-12 3.10e-11 7.36e-11 ...
#> ..$ CheY : num [1:10001] 8178 8178 8178 8178 8178 ...
#> ..$ CheA : num [1:10001] 4468 4468 4468 4468 4468 ...
#> ..$ T2 : num [1:10001] 0.00 2.98e-07 1.19e-06 2.69e-06 4.77e-06 ...
#> ..$ CheBp : num [1:10001] 0.00 1.66e-07 1.09e-06 3.09e-06 6.30e-06 ...
#> ..$ T4 : num [1:10001] 0.00 3.32e-18 5.32e-17 2.69e-16 8.50e-16 ...
#> ..$ CheAp : num [1:10001] 0 0.00055 0.00171 0.00309 0.00457 ...
#> ..$ CheB : num [1:10001] 236 236 236 236 236 ...
#> ..$ T0 : num [1:10001] 4468 4468 4468 4468 4468 ...
#> ..$ CheYp : num [1:10001] 0 0.000186 0.001184 0.003259 0.00643 ...
#> ..$ Tactive : num [1:10001] 0 0.0056 0.0112 0.0168 0.0224 ...
#> ..$ Tactive0: num [1:10001] 0 0 0 0 0 0 0 0 0 0 ...
#> ..$ Tactive1: num [1:10001] 0 0.0056 0.0112 0.0168 0.0224 ...
#> ..$ Tactive2: num [1:10001] 0.00 1.34e-07 5.35e-07 1.20e-06 2.14e-06 ...
#> ..$ Tactive3: num [1:10001] 0.00 8.56e-13 6.85e-12 2.31e-11 5.48e-11 ...
#> ..$ Tactive4: num [1:10001] 0.00 3.32e-18 5.31e-17 2.69e-16 8.50e-16 ...
#> ..$ Ttotal : num [1:10001] 4468 4468 4468 4468 4468 ...
#> $ task_error : NULL
#> - attr(*, "class")= chr "copasi_ts"
str(runSteadyState())
#> List of 9
#> $ settings :List of 5
#> ..$ calculate_jacobian : logi TRUE
#> ..$ perform_stability_analysis: logi TRUE
#> ..$ update_model : logi FALSE
#> ..$ executable : logi FALSE
#> ..$ method :List of 10
#> .. ..$ resolution : num 1e-09
#> .. ..$ derivation_factor : num 0.001
#> .. ..$ use_newton : logi TRUE
#> .. ..$ use_integration : logi TRUE
#> .. ..$ use_back_integration : logi TRUE
#> .. ..$ accept_negative_concentrations : logi FALSE
#> .. ..$ iteration_limit : int 50
#> .. ..$ maximum_duration_for_forward_integration : num 1e+09
#> .. ..$ maximum_duration_for_backward_integration: num 1e+06
#> .. ..$ target_criterion : chr "Distance and Rate"
#> $ result : chr "found"
#> $ species : tibble [11 × 8] (S3: tbl_df/tbl/data.frame)
#> ..$ key : chr [1:11] "CheA{compartment}" "CheAp{compartment}" "CheB{compartment}" "CheBp{compartment}" ...
#> ..$ name : chr [1:11] "CheA" "CheAp" "CheB" "CheBp" ...
#> ..$ type : chr [1:11] "reactions" "reactions" "reactions" "reactions" ...
#> ..$ concentration : num [1:11] 5.185 0.115 0.2082 0.0718 8.8118 ...
#> ..$ number : num [1:11] 4371.5 97 175.5 60.6 7429.2 ...
#> ..$ rate : num [1:11] 2.42e-13 -2.42e-13 -1.85e-16 1.85e-16 -1.90e-13 ...
#> ..$ number_rate : num [1:11] 2.04e-10 -2.04e-10 -1.56e-13 1.56e-13 -1.60e-10 ...
#> ..$ transition_time: num [1:11] 0.05112 0.00113 2.89824 1 0.08695 ...
#> $ compartments : tibble [0 × 5] (S3: tbl_df/tbl/data.frame)
#> ..$ key : chr(0)
#> ..$ name: chr(0)
#> ..$ type: chr(0)
#> ..$ size: num(0)
#> ..$ rate: num(0)
#> $ global_quantities: tibble [0 × 5] (S3: tbl_df/tbl/data.frame)
#> ..$ key : chr(0)
#> ..$ name : chr(0)
#> ..$ type : chr(0)
#> ..$ value: num(0)
#> ..$ rate : num(0)
#> $ reactions : tibble [14 × 4] (S3: tbl_df/tbl/data.frame)
#> ..$ key : chr [1:14] "(Che A phosph)" "(Che B phosph)" "(Che Y phosph)" "(Che Y autodephosph)" ...
#> ..$ name : chr [1:14] "Che A phosph" "Che B phosph" "Che Y phosph" "Che Y autodephosph" ...
#> ..$ flux : num [1:14] 1.42e-13 1.01e-16 1.42e-13 1.24e-16 4.75e-17 ...
#> ..$ number_flux: num [1:14] 85505.5 60.6 85445 74.9 28.6 ...
#> $ jacobian_complete: num [1:11, 1:11] -3.01e-02 -5.07e-04 0.00 -2.81e+01 8.71e-03 ...
#> ..- attr(*, "dimnames")=List of 2
#> .. ..$ : chr [1:11] "T1" "T3" "CheY" "CheA" ...
#> .. ..$ : chr [1:11] "T1" "T3" "CheY" "CheA" ...
#> $ jacobian_reduced : num [1:7, 1:7] -3.97e-02 1.29e-04 0.00 -2.81e+01 1.23e-02 ...
#> ..- attr(*, "dimnames")=List of 2
#> .. ..$ : chr [1:7] "T1" "T3" "CheY" "CheA" ...
#> .. ..$ : chr [1:7] "T1" "T3" "CheY" "CheA" ...
#> $ protocol : chr "Try Newton's method. \n Starting Newton Iterations...\n Newton step failed. Negative volume or concentrati"| __truncated__