Takes the current state and runs the current analysis in that state.
Usage
run_nca_components(
state,
components = c("nca", "fg_ind_obs", "tb_ind_obs", "tb_ind_obs_flags", "tb_ind_params"),
verbose = TRUE
)Arguments
- state
NCA state from
NCA_fetch_state()- components
List of components to run. By default it will run all of the following to. If you just need to regenerate a figure based on the current nca results you can just specify that component. These are the valid
- verbose
Logical to enable or disable messaging components:
nca: Run NCA analysis
fg_ind_obs: Build the figure(s) with the indiviudal observations.
tb_ind_obs: Build the table(s) with the indiviudal observations.
tb_ind_params: Build the table(s) with the indiviudal parameters.
Value
List with the following components:
isgood: Return status of the function.
msgs: Error messages if any issues were encountered.
nca_res: PKNCA results if run was successful.
Examples
# We need a state object to use below
sess_res = NCA_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
#> → UD: including file
#> → UD: source: file.path(system.file(package="onbrand"), "templates", "report.docx")
#> → UD: dest: file.path("config","report.docx")
#> → UD: including file
#> → UD: source: file.path(system.file(package="onbrand"), "templates", "report.pptx")
#> → UD: dest: file.path("config","report.pptx")
#> → UD: including file
#> → UD: source: file.path(system.file(package="onbrand"), "templates", "report.yaml")
#> → UD: dest: file.path("config","report.yaml")
#> → UD: State initialized
#> → UD: module checksum updated:897d952fecbc804999396a96f9df4b20
#> → UD: module isgood: TRUE
#> → DM: including file
#> → DM: source: file.path(system.file(package="onbrand"), "templates", "report.docx")
#> → DM: dest: file.path("config","report.docx")
#> → DM: including file
#> → DM: source: file.path(system.file(package="onbrand"), "templates", "report.pptx")
#> → DM: dest: file.path("config","report.pptx")
#> → DM: including file
#> → DM: source: file.path(system.file(package="onbrand"), "templates", "report.yaml")
#> → DM: dest: file.path("config","report.yaml")
#> → DM: module checksum updated: 441abbd92e02d893eb5136ccdfcc717d
#> → DM: State initialized
#> → DM: ds checksum updated: 641fcbc6616d24d05acded4317a3bb12
#> → DM: module checksum updated: 5c077c5702479f330bf233040eb4a51b
#> → DM: adding preload sources
#> → DM: - file added: TEST_DATA.xlsx
#> → DM: added: TEST_DATA.xlsx
#> → DM: - url added: https://raw.githubusercontent.com/john-harrold/formods/refs/heads/master/inst/test_data/SDTM_PC.csv
#> → DM: url added: https://raw.githubusercontent.com/john-harrold/formods/refs/heads/master/inst/test_data/SDTM_PC.csv
#> → DM: - url added: https://raw.githubusercontent.com/john-harrold/formods/refs/heads/master/inst/test_data/SDTM_EX.csv
#> → DM: url added: https://raw.githubusercontent.com/john-harrold/formods/refs/heads/master/inst/test_data/SDTM_EX.csv
#> → DM: - url added: https://raw.githubusercontent.com/john-harrold/formods/refs/heads/master/inst/test_data/SDTM_DM.csv
#> → DM: url added: https://raw.githubusercontent.com/john-harrold/formods/refs/heads/master/inst/test_data/SDTM_DM.csv
#> → DM: loading element idx: 1
#> → DM: ds checksum updated: 195704908ee59dbb44872d92c6cb1f7e
#> → DM: module checksum updated: 8285902f9fed2bb4ca4525fe915fb3ac
#> → DM: added element idx: 1
#> → DM: loading element idx: 2
#> → DM: ds checksum updated: 47a377d21a7c073ef2ec742b73bb10fd
#> → DM: module checksum updated: 95fac5833992b680679e24f13ea00076
#> → DM: added element idx: 2
#> → DM: loading element idx: 3
#> → DM: ds checksum updated: 943f63f73280e39af69b852105b0ae59
#> → DM: module checksum updated: 11b0a96e888ca6bcace101986c54f200
#> → DM: added element idx: 3
#> → DM: loading element idx: 4
#> → DM: ds checksum updated: dcb7eba136af03abe31115e6eb4e99d3
#> → DM: module checksum updated: 0b4d38a5637d3310b7b461e39c127646
#> → DM: added element idx: 4
#> → DM: module isgood: TRUE
#> → DW: including file
#> → DW: source: file.path(system.file(package="onbrand"), "templates", "report.docx")
#> → DW: dest: file.path("config","report.docx")
#> → DW: including file
#> → DW: source: file.path(system.file(package="onbrand"), "templates", "report.pptx")
#> → DW: dest: file.path("config","report.pptx")
#> → DW: including file
#> → DW: source: file.path(system.file(package="onbrand"), "templates", "report.yaml")
#> → DW: dest: file.path("config","report.yaml")
#> → DW: State initialized
#> → DW: module checksum updated:a9496b622f92f683cc8c69f65ac1ece4
#> → DW: loading data view idx: 1
#> → DW: setting data source: myDS
#> → DW: module checksum updated:dfec3d5aa14c2716ccf367706931693f
#> → DW: setting name: Observations
#> → DW: module checksum updated:4d9fd3d913355669d14e0ac710b0b5dc
#> → DW: -> filter
#> → DW: module checksum updated:2aba88838dee694a3d2813ed9f2837d2
#> → DW: -> filter
#> → DW: module checksum updated:c181a352a2bd3592494d917b87057086
#> → DW: -> mutate
#> → DW: module checksum updated:048df4e8afa9494121e72808981c842c
#> → DW: loading data view idx: 2
#> → DW: setting data source: myDS
#> → DW: module checksum updated:048df4e8afa9494121e72808981c842c
#> → DW: setting name: PK 3mg SD IV
#> → DW: module checksum updated:c54c6fc20ff13fd14fbb61c786f65078
#> → DW: -> filter
#> → DW: module checksum updated:496c1149f14ec1c48d4ddbc5aec72a72
#> → DW: -> filter
#> → DW: module checksum updated:d65a6b3c16bea4262f7fb15a1d961512
#> → DW: -> filter
#> → DW: module checksum updated:f90816b8f2ef9aeaad82e4a00880e536
#> → DW: -> filter
#> → DW: module checksum updated:452fc9d9131592650a93b4b49de961d1
#> → DW: loading data view idx: 3
#> → DW: setting data source: myDS
#> → DW: module checksum updated:452fc9d9131592650a93b4b49de961d1
#> → DW: setting name: PK 3mg SD IV (NCA)
#> → DW: module checksum updated:3b177ed09a80dfaf15c9f3dde8b9a8fb
#> → DW: -> filter
#> → DW: module checksum updated:ce7e35b3bc2e1f53088ae7edd5b4345e
#> → DW: -> filter
#> → DW: module checksum updated:64a5146d5e7070664557a7ff3d80f6f0
#> → DW: -> filter
#> → DW: module checksum updated:2cf968d6e72262f9274ea0389f717e84
#> → DW: loading data view idx: 4
#> → DW: setting data source: myDS
#> → DW: module checksum updated:2cf968d6e72262f9274ea0389f717e84
#> → DW: setting name: PKPD 3mg SD IV (NCA)
#> → DW: module checksum updated:67e9d6e6b2e085808be155613f8efe20
#> → DW: -> filter
#> → DW: module checksum updated:a7a211de4eb91c91098a1f20e62bec73
#> → DW: -> filter
#> → DW: module checksum updated:306f66790aca305ff1b715f34802610e
#> → DW: -> filter
#> → DW: module checksum updated:306f66790aca305ff1b715f34802610e
#> → DW: module isgood: TRUE
#> → NCA: including file
#> → NCA: source: file.path(system.file(package="onbrand"), "templates", "report.docx")
#> → NCA: dest: file.path("config","report.docx")
#> → NCA: including file
#> → NCA: source: file.path(system.file(package="onbrand"), "templates", "report.pptx")
#> → NCA: dest: file.path("config","report.pptx")
#> → NCA: including file
#> → NCA: source: file.path(system.file(package="onbrand"), "templates", "report.yaml")
#> → NCA: dest: file.path("config","report.yaml")
#> → NCA: including file
#> → NCA: source: file.path(system.file(package="onbrand"), "templates", "report.docx")
#> → NCA: dest: file.path("config","report.docx")
#> → NCA: including file
#> → NCA: source: file.path(system.file(package="onbrand"), "templates", "report.pptx")
#> → NCA: dest: file.path("config","report.pptx")
#> → NCA: including file
#> → NCA: source: file.path(system.file(package="onbrand"), "templates", "report.yaml")
#> → NCA: dest: file.path("config","report.yaml")
#> → NCA: State initialized
#> → NCA: State initialized
#> → NCA: loading element idx: 1
#> → NCA: -> setting name: PK Example
#> → NCA: -> notes found and set
#> → NCA: -> setting data source: DW_myDS_3
#> → NCA: NCA_add_int: append
#> → NCA: added element idx: 1
#> → NCA: module isgood: TRUE
#> → # preload_complete is good: TRUE ------------------------------------------
state = sess_res$state
state = run_nca_components(state, components="tb_ind_params")
#> → NCA: module checksum updated:6d3176921bf145b747286b2eecabafe7