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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 NULL to 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 NULL will use 100 inches).

max_width

Maximum width of the final table in inches (A value of NULL will 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