Creates Figures of Individual Observations from PKNCA Result

Takes the output of PKNCA and creates ggplot figures faceted by subject id highlighting of certain NCA aspects (e.g. points used for half-life)

Usage

mk_figure_ind_obs(
  nca_res,
  OBS_LAB = "Concentration ===CONCUNITS===",
  TIME_LAB = "Time ===TIMEUNITS===",
  OBS_STRING = "Observation",
  BLQ_STRING = "BLQ",
  NA_STRING = "Missing",
  log_scale = TRUE,
  scales = "fixed",
  nfrows = 4,
  nfcols = 3
)

Arguments

nca_res: Output of PKNCA.
OBS_LAB: Label of the observation axis with optional ===CONCUNITS=== placeholder for units.
TIME_LAB: Label of the time axis with optional ===TIMEUNITS=== placeholder for units.
OBS_STRING: Label for observation data.
BLQ_STRING: Label for BLQ data.
NA_STRING: Label for missing data.
log_scale: Boolean variable to control y-scale (TRUE: Log 10, FALSE: linear).
scales: String to determine the scales used when faceting. Can be either "fixed", "free", "free_x", or "free_y".
nfrows: Number of facet rows per page.
nfcols: Number of facet cols per page.

Value

List containing the element figures which is a list of figure pages ("Figure 1", "Figure 2", etc.). Each of these is a also a list containing two elements:

gg: A ggplot object for that page.
notes: Placeholder for future notes, but NULL now.

Examples

# We need a state variable 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: 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
#> → 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:5b0f0b05ee3ac7336a74c564bb6efdad
#> → DW: loading data view idx: 1
#> → DW: setting name: Observations
#> → DW: module checksum updated:1ac3e0afcc601f848943f92b854b3830
#> → DW:   -> filter
#> → DW: module checksum updated:67aff6e926eba73b3ecb361d26624844
#> → DW:   -> filter
#> → DW: module checksum updated:0234f6d458ef7487a3b2e991b2d0957b
#> → DW:   -> mutate
#> → DW: module checksum updated:37d0958f042076b974fdd3f894157822
#> → DW: loading data view idx: 2
#> → DW: setting name: PK 3mg SD IV
#> → DW: module checksum updated:4e7ca05728d66df3adfcf87387f9543a
#> → DW:   -> filter
#> → DW: module checksum updated:2d95bc56262f46b7f135dd33fc4722b3
#> → DW:   -> filter
#> → DW: module checksum updated:b8a30837145926d2d9cc6f788c10b7ed
#> → DW:   -> filter
#> → DW: module checksum updated:24b554ee8736ebc84979c896ac2e93c3
#> → DW:   -> filter
#> → DW: module checksum updated:daad88263faf7cbf90871ed00a0dd275
#> → DW: loading data view idx: 3
#> → DW: setting name: PK 3mg SD IV (NCA)
#> → DW: module checksum updated:a7b3ea35cdba272682716aa4619d3983
#> → DW:   -> filter
#> → DW: module checksum updated:e8d2f77c0bd731995d845ee8be623e22
#> → DW:   -> filter
#> → DW: module checksum updated:24cc7b591ca756a0abf560fb5295e04d
#> → DW:   -> filter
#> → DW: module checksum updated:f79ef26bdb4dac420c24650b9e96f721
#> → DW: loading data view idx: 4
#> → DW: setting name: PKPD 3mg SD IV (NCA)
#> → DW: module checksum updated:c737e8b3a28ba600a83ddf58a969c90a
#> → DW:   -> filter
#> → DW: module checksum updated:4c0d054f8ec47ae97fd1c650d8ddad55
#> → DW:   -> filter
#> → DW: module checksum updated:1e3d65ec1bd6ee5850d67bd2250e3223
#> → DW:   -> filter
#> → DW: module checksum updated:1e3d65ec1bd6ee5850d67bd2250e3223
#> → 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: Parameter specified in YAML is not a valid PKNCA parameter: sparse_se
#> ✖ NCA: Parameter specified in YAML is not a valid PKNCA parameter: sparse_df
#> → 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: NCA_add_int: append
#> → NCA: added element idx: 1
#> → NCA: loading element idx: 2
#> → NCA:   -> setting name: PK/PD Example
#> → NCA:   -> notes found and set
#> → NCA:   -> setting data source: DW_myDS_4
#> → NCA: NCA_add_int: append
#> → NCA: NCA_add_int: append
#> → NCA: added element idx: 2
#> → NCA: module isgood: TRUE

state = sess_res$state

# Pulls out the active analysis
current_ana = NCA_fetch_current_ana(state)

# This is the raw PKNCA output
pknca_res = NCA_fetch_ana_pknca(state, current_ana)

# Building the figure
mk_res = mk_figure_ind_obs(nca_res = pknca_res)
mk_res$figures$Figure_1$gg