Take a TOC in by the company's rules

toc_import_read() reads one TOC or several (a TFL workbook and a listing workbook of the same layout) by the company's rules: each source read once, its TOC sheet and header row found (toc_find_sheet()), the rule set picked (toc_pick_rules()), the columns mapped (toc_map_for()), the output ids made by the set's rule (or the one that gives unique ids for the most rows, toc_id_candidates()), one report a phase (toc_expand_phases()), the shell sheets linked (toc_link_shells()), the Topline batch (toc_batches()) and what is wrong (toc_problems()). Nothing is written.

Usage

toc_problems(x, lang = "en")

toc_import_read(
  sources,
  rules = toc_rules(),
  profile = NULL,
  choices = NULL,
  names = NULL
)

toc_import_spec(x)

Arguments

x

What toc_import_read() returned.

lang

The language of the messages ("en", "ja").

sources

The TOC files (paths) or toc_sources.

rules

What toc_rules() returned.

profile

The study's TOC profile (toc_profile()) or NULL.

choices

A list (see above) or NULL.

names

The sources' names as the user knows them (paths: their base names).

Value

toc_problems(): the problems as rows of the review's shape (#288: output_id, level – error, check, hand –, area "toc", sheet, row, field, message, hint, rule, draft), errors first.

A toc_import: sources, detection (a row a source: file, sheet, header_row, how – "name", "score", "rows", "chosen", "profile" –, rows, shells, topline_sheet, kind, note), sheets (each source's toc_find_sheet()), rule_set (the set in use), rule_sets (the scores), map (+ attr(, "missing")), id_rule, id_candidates, type_from, rows, reports, unread, batches, problems, profile, notes (what was not as the profile said: message).

toc_import_spec(): what tflspec::tfl_read_toc() returns for the reports (a table spec with the report sheets and their attributes); attr(, "guessed") the reports whose type no type column said (read from the id or the title: to check).

Details

toc_import_spec() gives the reports as tflspec::tfl_read_toc() gives a TOC, for toc_changes() and toc_apply().

What the user chose in the dialog (choices), else what the study's profile remembers (profile), wins over what is found: rule_set, sheet and header_row (named by the file's name), map, id_rule, type_from, overrides (the set's settings changed for the study).

Two example TOCs come with the package, made from the sample study (SAMPLE-01): system.file("extdata", "SAMPLE-01_TOC.xlsx", package = "tflplanner") – its reports as a company TOC (the header on row 2, section heading rows, Shell Number, Phase, Topline, Title1-3, Population, Footnote1-2, a shell sheet per report) – and SAMPLE-01_TOC_changed.xlsx, the same with two rows changed (a title, a footnote). Taken into the sample study, the first gives its reports their sections (and the Topline batch) and, taken in again, changes nothing; the second, taken in after it, shows those two.

Examples

f <- tempfile(fileext = ".csv")
writeLines(c("Output ID,Title 1,Title 2,Population",
             "T-14-1-1,Demographics,,Safety Population",
             "T-14-2-1,Adverse events,Overview,Safety Population"), f)
r <- toc_import_read(f, toc_rules(home = tempfile()))
r$reports[c("output_id", "label")]
#>   output_id label
#> 1  T-14-1-1  <NA>
#> 2  T-14-2-1  <NA>
toc_import_spec(r)$report
#>   output_id  type file program auto_section section_align auto_title
#> 1  T-14-1-1 table <NA>    <NA>         <NA>          <NA>       <NA>
#> 2  T-14-2-1 table <NA>    <NA>         <NA>          <NA>       <NA>
#>   title_align table_font_size_half_points title_font_size_half_points
#> 1        <NA>                        <NA>                        <NA>
#> 2        <NA>                        <NA>                        <NA>
#>   footnote_font_size_half_points page_header page_footer watermark
#> 1                           <NA>        <NA>        <NA>      <NA>
#> 2                           <NA>        <NA>        <NA>      <NA>
#>   figure_width_in figure_height_in ard_source pattern data_code content_code
#> 1            <NA>             <NA>       <NA>    <NA>      <NA>         <NA>
#> 2            <NA>             <NA>       <NA>    <NA>      <NA>         <NA>
#>   note
#> 1 <NA>
#> 2 <NA>

# the example TOC made from the sample study
f <- system.file("extdata", "SAMPLE-01_TOC.xlsx", package = "tflplanner")
r <- toc_import_read(f, toc_rules(home = tempfile()))
r$id_rule
#> [1] "column"
utils::head(r$reports[c("output_id", "label", "shell_sheet")])
#>   output_id         label shell_sheet
#> 1  T-14-0-1  Table 14.0.1    T-14-0-1
#> 2  T-14-1-1  Table 14.1.1    T-14-1-1
#> 3 T-14-1-1S Table 14.1.1S   T-14-1-1S
#> 4  T-14-1-2  Table 14.1.2    T-14-1-2
#> 5  T-14-1-3  Table 14.1.3    T-14-1-3
#> 6  T-14-1-4  Table 14.1.4    T-14-1-4