Fetches the PKNCA output for a specified analysis
Arguments
- state
NCA state from
NCA_fetch_state()- current_ana
Current value in the analysis
Examples
library(ruminate)
# Module IDs
id = "NCA"
# We need session and input variables to be define
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: f280116ab6b4488df6de76aff513a83f
#> → DM: State initialized
#> → DM: ds checksum updated: 641fcbc6616d24d05acded4317a3bb12
#> → DM: module checksum updated: 78099100dae67cc0fee50517ea72a920
#> → 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: 1f770fa2a631ddd1e582239c7468e7d6
#> → DM: module checksum updated: ec605cad36bca1397aac8e6263ca3d5c
#> → DM: added element idx: 1
#> → DM: loading element idx: 2
#> → DM: ds checksum updated: 3bf190e19bf8dca506f55cba251d2384
#> → DM: module checksum updated: 133b76a0fd8f446ad7348d6b25db49bb
#> → DM: added element idx: 2
#> → DM: loading element idx: 3
#> → DM: ds checksum updated: 7c8dcb77b613b7a338e1b8688d7a8b80
#> → DM: module checksum updated: 4a4bd43268f180f1d0c578b61255013d
#> → DM: added element idx: 3
#> → DM: loading element idx: 4
#> → DM: ds checksum updated: c91df0e5e39b32339dd2bb6853809bcf
#> → DM: module checksum updated: 2ed5f5ce7ddaf06a0fee7195121014fa
#> → 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: data view checksum updated:
#> → DW: old:
#> → DW: new: e19ddb59715ba77afdd1907053aa5d14
#> → DW: module checksum updated:a9496b622f92f683cc8c69f65ac1ece4
#> → DW: State initialized
#> → DW: data view checksum updated:
#> → DW: old:
#> → DW: new: e19ddb59715ba77afdd1907053aa5d14
#> → DW: module checksum updated:0955d1f9a1922b95277b4ad1df38e987
#> → DW: data view checksum updated:
#> → DW: old:
#> → DW: new: e19ddb59715ba77afdd1907053aa5d14
#> → DW: module checksum updated:3d3523604fcde20ce1792b16611bdba2
#> → DW: data view checksum updated:
#> → DW: old:
#> → DW: new: e19ddb59715ba77afdd1907053aa5d14
#> → DW: module checksum updated:dfec3d5aa14c2716ccf367706931693f
#> → DW: loading data view idx: 1
#> → DW: -> setting data source: myDS
#> → DW: setting name: Observations
#> → DW: module checksum updated:4d9fd3d913355669d14e0ac710b0b5dc
#> → DW: -> filter
#> → DW: data view checksum updated:
#> → DW: old: e19ddb59715ba77afdd1907053aa5d14
#> → DW: new: 0017bd7cdc15ff708408b2d60672ef88
#> → DW: module checksum updated:2aba88838dee694a3d2813ed9f2837d2
#> → DW: -> filter
#> → DW: data view checksum updated:
#> → DW: old: 0017bd7cdc15ff708408b2d60672ef88
#> → DW: new: 278da634fa74dc23eae6db31314e0324
#> → DW: module checksum updated:c181a352a2bd3592494d917b87057086
#> → DW: -> mutate
#> → DW: data view checksum updated:
#> → DW: old: 278da634fa74dc23eae6db31314e0324
#> → DW: new: a164ecd5a527b2b38058230c1daa0080
#> → DW: module checksum updated:048df4e8afa9494121e72808981c842c
#> → DW: loading data view idx: 2
#> → DW: -> setting data source: myDS
#> → DW: setting name: PK 3mg SD IV
#> → DW: module checksum updated:c54c6fc20ff13fd14fbb61c786f65078
#> → DW: -> filter
#> → DW: data view checksum updated:
#> → DW: old: e19ddb59715ba77afdd1907053aa5d14
#> → DW: new: 0017bd7cdc15ff708408b2d60672ef88
#> → DW: module checksum updated:496c1149f14ec1c48d4ddbc5aec72a72
#> → DW: -> filter
#> → DW: data view checksum updated:
#> → DW: old: 0017bd7cdc15ff708408b2d60672ef88
#> → DW: new: 278da634fa74dc23eae6db31314e0324
#> → DW: module checksum updated:d65a6b3c16bea4262f7fb15a1d961512
#> → DW: -> filter
#> → DW: data view checksum updated:
#> → DW: old: 278da634fa74dc23eae6db31314e0324
#> → DW: new: 00bd5f01d02d634acf134cf01970a1c3
#> → DW: module checksum updated:f90816b8f2ef9aeaad82e4a00880e536
#> → DW: -> filter
#> → DW: data view checksum updated:
#> → DW: old: 00bd5f01d02d634acf134cf01970a1c3
#> → DW: new: a01562e32a19fd4b10f88ace089346c6
#> → DW: module checksum updated:452fc9d9131592650a93b4b49de961d1
#> → DW: loading data view idx: 3
#> → DW: -> setting data source: myDS
#> → DW: setting name: PK 3mg SD IV (NCA)
#> → DW: module checksum updated:3b177ed09a80dfaf15c9f3dde8b9a8fb
#> → DW: -> filter
#> → DW: data view checksum updated:
#> → DW: old: e19ddb59715ba77afdd1907053aa5d14
#> → DW: new: 0017bd7cdc15ff708408b2d60672ef88
#> → DW: module checksum updated:ce7e35b3bc2e1f53088ae7edd5b4345e
#> → DW: -> filter
#> → DW: data view checksum updated:
#> → DW: old: 0017bd7cdc15ff708408b2d60672ef88
#> → DW: new: 198f7d878f23121868e677c0b86a5f3c
#> → DW: module checksum updated:64a5146d5e7070664557a7ff3d80f6f0
#> → DW: -> filter
#> → DW: data view checksum updated:
#> → DW: old: 198f7d878f23121868e677c0b86a5f3c
#> → DW: new: 4326a7b6b9040676b320b387ba5b8ad9
#> → DW: module checksum updated:2cf968d6e72262f9274ea0389f717e84
#> → DW: loading data view idx: 4
#> → DW: -> setting data source: myDS
#> → DW: setting name: PKPD 3mg SD IV (NCA)
#> → DW: module checksum updated:67e9d6e6b2e085808be155613f8efe20
#> → DW: -> filter
#> → DW: data view checksum updated:
#> → DW: old: e19ddb59715ba77afdd1907053aa5d14
#> → DW: new: 0017bd7cdc15ff708408b2d60672ef88
#> → DW: module checksum updated:a7a211de4eb91c91098a1f20e62bec73
#> → DW: -> filter
#> → DW: data view checksum updated:
#> → DW: old: 0017bd7cdc15ff708408b2d60672ef88
#> → DW: new: 198f7d878f23121868e677c0b86a5f3c
#> → DW: module checksum updated:306f66790aca305ff1b715f34802610e
#> → DW: -> filter
#> → 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: module checksum updated:87e9bf7cae52913d38f093b2a7e3698c
#> → NCA: NCA_add_int: append
#> → NCA: analysis fresh flag set to FALSE
#> → NCA: analysis checksum updated:61ef29d35c2ad127f4d8408129938dfd
#> → NCA: module checksum updated:6ba7b094c1b57d093f0d762c6c2ec855
#> ✖ NCA: failed to add element idx: 1
#> ✖ NCA: message: could not find function "as_PKNCAconc"
#> ✖ NCA: call: as_PKNCAconc
#> ✖ NCA: call: nca_res
#> ✖ NCA: Unable to create: fg_ind_obs see above for details.
#> ✖ NCA: Unable to create: fg_ind_obs_subset see above for details.
#> ✖ NCA: Unable to create: tb_ind_obs see above for details.
#> ✖ NCA: Unable to create: tb_ind_obs_flags see above for details.
#> ✖ NCA: Unable to create: tb_ind_params see above for details.
#> → NCA: module isgood: TRUE
#> → # preload_complete is good: TRUE ------------------------------------------
# Extracting the session and input variables
session = sess_res$session
input = sess_res$input
react_state = list()
# We also need configuration files
FM_yaml_file = system.file(package = "formods", "templates", "formods.yaml")
MOD_yaml_file = system.file(package = "ruminate", "templates", "NCA.yaml")
# Getting the current module state
state = NCA_fetch_state(id = id,
input = input,
session = session,
FM_yaml_file = FM_yaml_file,
MOD_yaml_file = MOD_yaml_file,
react_state = react_state)
# Pulls out the active analysis
current_ana = NCA_fetch_current_ana(state)
# This will get the dataset associated with this analysis
ds = NCA_fetch_ana_ds(state, current_ana)
# After making changes you can update those in the state
state = NCA_set_current_ana(state, current_ana)
# You can use this to check the current analysis
current_ana = NCA_process_current_ana(state)
# This will pull out the code for the module
fc_res = NCA_fetch_code(state)
# This will use patterns defined for the site to detect
# columns. In this example we are detecting the id column:
id_col = NCA_find_col(
patterns = state[["MC"]][["detect_col"]][["id"]],
dscols = names(ds))
# This creates a new analysis
state = NCA_new_ana(state)
# Switching back to the previous analysis
state = NCA_mkactive_ana(state, "NCA_1")
# Forcing a checksum update
state = NCA_update_checksum(state)
#> → NCA: module checksum updated:d6b574c8bdbc981ad0ce522e1f28fb60