Reads in the app state from yaml files.
Value
list with the following elements
isgood: Boolean indicating the exit status of the function.
msgs: Messages to be passed back to the user.
yaml_list: Lists with preload components.
Examples
# \donttest{
sess_res = CTS_test_mksession()
#> → ASM: including file
#> → ASM: source: file.path(system.file(package="onbrand"), "templates", "report.docx")
#> → ASM: dest: file.path("config","report.docx")
#> → ASM: including file
#> → ASM: source: file.path(system.file(package="onbrand"), "templates", "report.pptx")
#> → ASM: dest: file.path("config","report.pptx")
#> → ASM: including file
#> → ASM: source: file.path(system.file(package="onbrand"), "templates", "report.yaml")
#> → ASM: dest: file.path("config","report.yaml")
#> → ASM: State initialized
#> → ASM: setting word placeholders:
#> → ASM: -> setting docx ph: HEADERLEFT = left header
#> → ASM: -> setting docx ph: HEADERRIGHT = right header
#> → ASM: -> setting docx ph: FOOTERLEFT = left footer
#> → ASM: module isgood: TRUE
#> → MB: including file
#> → MB: source: file.path(system.file(package="onbrand"), "templates", "report.docx")
#> → MB: dest: file.path("config","report.docx")
#> → MB: including file
#> → MB: source: file.path(system.file(package="onbrand"), "templates", "report.pptx")
#> → MB: dest: file.path("config","report.pptx")
#> → MB: including file
#> → MB: source: file.path(system.file(package="onbrand"), "templates", "report.yaml")
#> → MB: dest: file.path("config","report.yaml")
#> ! MB: User-defined model: /private/var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T/RtmpajgEZL/preload_8ef86d9f0fb5/user_model.R not found (skipping)
#> ! MB: User-defined model: /private/var/folders/pq/7srbf_fx3rd3k706hgxkg61r0000gp/T/RtmpajgEZL/preload_8ef86d9f0fb5/user_model.ctl not found (skipping)
#> → MB: module checksum updated:f7de2055542d3ff1b085fafc2d30a1f8
#> → MB: State initialized
#> → MB: loading model idx: 1
#>
#>
#> ℹ parameter labels from comments are typically ignored in non-interactive mode
#> ℹ Need to run with the source intact to parse comments
#> → MB: model checksum updated: 9a803bdd28655e27db4877dfaa8c77fb
#> → MB: module checksum updated:8af01720bfa8712c5af8487fce805ef0
#>
#>
#> ℹ parameter labels from comments are typically ignored in non-interactive mode
#> ℹ Need to run with the source intact to parse comments
#> → MB: model checksum updated: 19ac346aeb18a000a0de4098ccaaa642
#> → MB: module checksum updated:d2097de5728854e14fbda55eb07e959b
#> → MB: -> setting name: One compartment model
#> → MB: -> setting time scale: hours
#> → MB: -> setting base from: user
#> → MB: -> setting catalog selection:
#> → MB: -> setting base model id: manual
#> → MB: -> setting base model name: manual
#> → MB: model checksum updated: 08bac287c9c275e050125c36cd9bab93
#> → MB: module checksum updated:a8b02547f67cb749004307a03e10db8f
#> → MB: added element idx: 1
#> → MB: loading model idx: 2
#>
#>
#> ℹ parameter labels from comments are typically ignored in non-interactive mode
#> ℹ Need to run with the source intact to parse comments
#> → MB: model checksum updated: 9c39b8923b0c5d0a217609967a43c209
#> → MB: module checksum updated:bbeaa1762f72e3043c2394e30f6d0f8c
#> → MB: -> setting name: PK Biomarker
#> → MB: -> setting time scale: days
#> → MB: -> setting base from: user
#> → MB: -> setting catalog selection:
#> → MB: -> setting base model id: manual
#> → MB: -> setting base model name: manual
#> → MB: model checksum updated: 5a7fab6f1b40ee72888862e945209212
#> → MB: module checksum updated:1da178e193d91e2063484800d129ff06
#> → MB: added element idx: 2
#> → MB: module isgood: TRUE
#> → CTS: including file
#> → CTS: source: file.path(system.file(package="onbrand"), "templates", "report.docx")
#> → CTS: dest: file.path("config","report.docx")
#> → CTS: including file
#> → CTS: source: file.path(system.file(package="onbrand"), "templates", "report.pptx")
#> → CTS: dest: file.path("config","report.pptx")
#> → CTS: including file
#> → CTS: source: file.path(system.file(package="onbrand"), "templates", "report.yaml")
#> → CTS: dest: file.path("config","report.yaml")
#> → CTS: source model change detected
#> → CTS: > covariates reset
#> → CTS: cohort checksum updated: abf8ce7252bb5071ded60606b94686e0
#> → CTS: module checksum updated: a0c47b2b08d74b93dc41d461c2ee4c2c
#> → CTS: State initialized
#> → CTS: loading element idx: 1
#> → CTS: setting cohort name: Single dose
#> → CTS: setting model source: MB_obj_1_rx
#> → CTS: setting trial options:
#> → CTS: - nsub: 3
#> → CTS: - visit_times: 0
#> → CTS: - trial_end: 100
#> → CTS: - fpage: 1
#> → CTS: - dvcols: Cc
#> → CTS: - time_scale:
#> → CTS: - tc_dim: d2x4
#> → CTS: - evplot: 1
#> → CTS: - cts_config_atol: 1e-8
#> → CTS: - cts_config_rtol: 1e-6
#> → CTS: - cts_config_sigdig: NULL
#> → CTS: - cts_config_seed: 5446
#> → CTS: - cts_config_nsteps: 5
#> → CTS: - cts_config_preamble:
#> → CTS: cohort checksum updated: 2f1d6fc47667e995cd5f4e04e613d322
#> → CTS: module checksum updated: cd8074cc498dccb8b5717b05cb9cfead
#> → CTS: adding rule: first_dose
#> → CTS: add rule success
#> → CTS: rule added
#> → CTS: cohort checksum updated: abe1ffdf5cd4bd2d379fe0bf572452e6
#> → CTS: module checksum updated: cad13b4e760021bda4611c2073ac6b4f
#>
#>
#> using C compiler: ‘Apple clang version 16.0.0 (clang-1600.0.26.6)’
#> using SDK: ‘’
#>
#>
#> using C compiler: ‘Apple clang version 16.0.0 (clang-1600.0.26.6)’
#> using SDK: ‘’
#> Warning: multi-subject simulation without without 'omega'
#> → CTS: CTS_simulate_element()
#> → CTS:
#> → CTS: # Setting the random seeds
#> → CTS: set.seed(5446)
#> → CTS: rxode2::rxSetSeed(5446)
#> → CTS:
#> → CTS: # Define the number of subjects to simulate for this cohort
#> → CTS: CTS_obj_1_nsub = 3
#> → CTS:
#> → CTS: # User defined functions used in the simulations
#> → CTS: CTS_obj_1_preamble = ""
#> → CTS:
#> → CTS: # Fetching the system information
#> → CTS: CTS_obj_1_rx_details = fetch_rxinfo(MB_obj_1_rx)
#> → CTS:
#> → CTS: # Defining covariates
#> → CTS: CTS_obj_1_cov = list()
#> → CTS:
#> → CTS: # Generating the subjects
#> → CTS: CTS_obj_1_subs = mk_subjects(object = MB_obj_1_rx,
#> → CTS: nsub = CTS_obj_1_nsub,
#> → CTS: covs = CTS_obj_1_cov)
#> → CTS:
#> → CTS: # Creating rules
#> → CTS: CTS_obj_1_rules = list()
#> → CTS:
#> → CTS: CTS_obj_1_rules[["first_dose"]] =
#> → CTS: list(condition = "time == 0", action = list(type = "dose", state = "central",
#> → CTS: values = "c(1)", times = "c(0)", durations = "c(0)"))
#> → CTS:
#> → CTS: # rxSolve options
#> → CTS: CTS_obj_1_rxopts = list(
#> → CTS: atol = 1e-8,
#> → CTS: rtol = 1e-6,
#> → CTS: sigdig = NULL)
#> → CTS:
#> → CTS: # Output times
#> → CTS: CTS_obj_1_output_times = formods::linspace(0,100,5)
#> → CTS:
#> → CTS: # Running simulation
#> → CTS: CTS_obj_1_simres =
#> → CTS: simulate_rules(object = MB_obj_1_rx,
#> → CTS: subjects = CTS_obj_1_subs[["subjects"]],
#> → CTS: eval_times = c(0),
#> → CTS: output_times = CTS_obj_1_output_times,
#> → CTS: time_scales = MB_obj_1_ts,
#> → CTS: preamble = CTS_obj_1_preamble,
#> → CTS: rules = CTS_obj_1_rules,
#> → CTS: rx_options = CTS_obj_1_rxopts)
#> → CTS:
#> → CTS: # Collecting the simulation and event history values
#> → CTS: CTS_obj_1_sim_tc = CTS_obj_1_simres[["simall"]]
#> → CTS: CTS_obj_1_sim_ev = CTS_obj_1_simres[["ev_history"]]
#> → CTS: message: could not find function "model"
#> → CTS: call: model
#> → CTS: call: object
#> → CTS: call: { depot(0) = 0 }
#> → CTS: simulate failed
#> → CTS: CTS_plot_element()
#> → CTS: # Plotting timecourse
#> → CTS: CTS_obj_1_fgtc =
#> → CTS: plot_sr_tc(sro = CTS_obj_1_simres,
#> → CTS: xcol = "time",
#> → CTS: xlab_str = "Time",
#> → CTS: fncol = 4,
#> → CTS: fnrow = 2,
#> → CTS: dvcols = "Cc",
#> → CTS: fpage = 1)
#> → CTS:
#> → CTS: # Plotting events
#> → CTS: CTS_obj_1_fgev =
#> → CTS: plot_sr_ev(sro = CTS_obj_1_simres,
#> → CTS: xcol = "time",
#> → CTS: xlab_str = "Time",
#> → CTS: fncol = 4,
#> → CTS: fnrow = 2,
#> → CTS: evplot = 1,
#> → CTS: fpage = 1)
#> → CTS: There was a problem with the simulation.
#> → CTS: simulate failed
#> → CTS: cohort checksum updated: 025db05f288afa8a6f141d9bb34f95e5
#> → CTS: module checksum updated: 20be2f2786b5adbe584130e93d8bb482
#> → CTS: module isgood: FALSE
#> ✖ Failure to preload module ID: CTS
#> ✖ failed to add element idx: 1
#> ✖ simulation failed
#> ✖ message: could not find function "model"
#> ✖ call: model
#> ✖ call: object
#> ✖ call: { depot(0) = 0 }
#> ✖ plot failed
#> ✖ There was a problem with the simulation.
#> → # preload_complete is good: FALSE -----------------------------------------
#> → # failed to add element idx: 1
#> → # simulation failed
#> → # message: could not find function "model"
#> → # call: model
#> → # call: object
#> → # call: { depot(0) = 0 }
#> → # plot failed
#> → # There was a problem with the simulation.
state = sess_res$state
res = CTS_mk_preload(state)
#> → CTS: saving element (1) Single dose
#> → CTS: -> rule dose
#> → CTS: mk_preload isgood: TRUE
# }