Create paginated tables from PKNCA to use in reports and Shiny apps.
Usage
mk_table_nca_params(
nca_res,
type = "individual",
grouping = "interval",
not_calc = "NC",
obnd = NULL,
nps = NULL,
mult_str = "*",
infinity = "inf",
digits = NULL,
text_format = "text",
notes_detect = NULL,
max_height = 7,
max_width = 6.5,
max_row = NULL,
max_col = NULL
)Arguments
- nca_res
Output of PKNCA.
- type
Type of table to generate. Can be either
"individual"or"summary"].- grouping
How to group columns in tables. Can be either
"interval"or"parameter"].- not_calc
Text string to replace NA values with to indicated values were not calculated.
- obnd
onbrand reporting object.
- nps
NCA parameter summary table with the following columns.
parameter: PKNCA Paramter name.
text: Name used in text output.
md: Name used markdown output.
latex: Name used in latex output.
description: Verbose textual description of the parameter.
- mult_str
Text string to replace * values in units.
- infinity
Text string to replace infinity in time intervals in column headers.
- digits
Number of significant figures to report (set to
NULLto disable rounding)- text_format
Either
"md"for markdown or"text"(default) for plain text.- notes_detect
Vector of strings to detect in output tables (example
c("NC", "BLQ")).- max_height
Maximum height of the final table in inches (A value of
NULLwill use 100 inches).- max_width
Maximum width of the final table in inches (A value of
NULLwill use 100 inches).- max_row
Maximum number of rows to have on a page. Spillover will hang over the side of the page..
- max_col
Maximum number of columns to have on a page. Spillover will be wrapped to multiple pages.
Value
list containing the following elements
raw_nca: Raw PKNCA output.
isgood: Boolean indicating the exit status of the function.
one_table: Dataframe of the entire table with the first lines containing the header.
one_body: Dataframe of the entire table (data only).
one_header: Dataframe of the entire header (row and body, no data).
tables: Named list of tables. Each list element is of the output
msgs: Vector of text messages describing any errors that were found. format from
build_span.
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$state
# Pulls out the active analysis
current_ana = NCA_fetch_current_ana(state)
# This is the raw PKNCA output
pknca_res = NCA_fetch_ana_pknca(state, current_ana)
# Parameter reporting details from the ruminate configuration
nps = state[["NCA"]][["nca_parameters"]][["summary"]]
# Building the figure
mk_res = mk_table_nca_params(nca_res = pknca_res, nps=nps, digits=3)
mk_res$tables[["Table 1"]]$ft
ID
CMT
AUClast
Cmax
AUCinf,obs
day*ng/mL
ng/mL
day*ng/mL
[0,21]
[0,inf]
1
BM_ng_ml
48,900
2,580
244,000
1
C_ng_ml
5,900
690
9,590
2
BM_ng_ml
29,500
1,500
271,000
2
C_ng_ml
8,240
750
17,000
3
BM_ng_ml
23,600
1,180
192,000
3
C_ng_ml
6,140
670
9,520
4
BM_ng_ml
34,300
1,690
282,000
4
C_ng_ml
6,030
638
10,900
5
BM_ng_ml
43,700
2,200
277,000
5
C_ng_ml
7,590
855
15,900
6
BM_ng_ml
26,100
1,310
215,000
6
C_ng_ml
6,440
611
12,600
7
BM_ng_ml
19,400
993
159,000
7
C_ng_ml
6,460
554
13,200
8
BM_ng_ml
29,900
1,550
325,000
8
C_ng_ml
6,730
501
16,300
9
BM_ng_ml
40,400
2,060
250,000
9
C_ng_ml
8,810
1,100
16,300
10
BM_ng_ml
26,700
1,350
159,000
10
C_ng_ml
8,760
828
16,000
11
BM_ng_ml
35,100
1,740
530,000
11
C_ng_ml
6,520
553
14,400
12
BM_ng_ml
34,000
1,720
278,000
12
C_ng_ml
5,160
580
8,700
13
BM_ng_ml
28,200
1,490
158,000