Read yaml spec file and split according to filter lists
Arguments
- spec_file
`character`. Path to a yaml spec file
- metadata
Study-level token values merged into every spec entry. Either a named `list` (or `NULL`), or a `character(1)` path to a yaml metadata file (see [read_metadata()] and the example at `system.file("metadata.yml", package = "autoslider.core")`), which is read into a list for you. Its elements can be referenced as `token` placeholders in the `titles` and `footnotes` fields of the spec and are substituted during decoration (see [apply_tokens()]). For example, with `metadata = list(study = "BP12345")` a spec title of `"Demographics - Study study"` becomes `"Demographics - Study BP12345"`.
Value
An object of class `spec` which is a `list` where each element corresponds to one output, e.g. `t_dm_IT`.
Examples
spec_file <- system.file("spec.yml", package = "autoslider.core")
## Take a look at the 'raw' content of the spec file
cat(readLines(spec_file)[1:24], sep = "\n")
#> # ---------------------------------------------------------------------------
#> # Metadata tokens
#> #
#> # Any {token} in a `titles` or `footnotes` field below is replaced during
#> # decoration with the matching value from the `metadata` list passed to
#> # read_spec(), e.g.:
#> #
#> # read_spec("spec.yml", metadata = list(study = "BP12345"))
#> #
#> # turns a title of "Demographics - Study {study}" into
#> # "Demographics - Study BP12345". Unknown tokens raise an error.
#> # See ?read_spec, ?apply_tokens and the generate_placeholder_slides vignette.
#> # ---------------------------------------------------------------------------
#> - program: l_dsl01_slide
#> titles: Analysis Sets ({filter_titles("adsl")})
#> footnotes: 'Analysis Sets footer'
#> paper: L6
#> suffix: SE
#> - program: t_pop_slide
#> titles: Analysis Sets ({filter_titles("adsl")})
#> footnotes: 'Analysis Sets footer'
#> paper: L6
#> suffix: FAS
#> - program: t_ds_slide
## This is how it looks once read into R
spec <- read_spec(spec_file)
spec[1:3]
#> $l_dsl01_slide_SE
#> $l_dsl01_slide_SE$program
#> [1] "l_dsl01_slide"
#>
#> $l_dsl01_slide_SE$titles
#> [1] "Analysis Sets ({filter_titles(\"adsl\")})"
#>
#> $l_dsl01_slide_SE$footnotes
#> [1] "Analysis Sets footer"
#>
#> $l_dsl01_slide_SE$paper
#> [1] "L6"
#>
#> $l_dsl01_slide_SE$suffix
#> [1] "SE"
#>
#> $l_dsl01_slide_SE$output
#> [1] "l_dsl01_slide_SE"
#>
#>
#> $t_pop_slide_FAS
#> $t_pop_slide_FAS$program
#> [1] "t_pop_slide"
#>
#> $t_pop_slide_FAS$titles
#> [1] "Analysis Sets ({filter_titles(\"adsl\")})"
#>
#> $t_pop_slide_FAS$footnotes
#> [1] "Analysis Sets footer"
#>
#> $t_pop_slide_FAS$paper
#> [1] "L6"
#>
#> $t_pop_slide_FAS$suffix
#> [1] "FAS"
#>
#> $t_pop_slide_FAS$output
#> [1] "t_pop_slide_FAS"
#>
#>
#> $t_ds_slide_FAS
#> $t_ds_slide_FAS$program
#> [1] "t_ds_slide"
#>
#> $t_ds_slide_FAS$titles
#> [1] "Patient Disposition"
#>
#> $t_ds_slide_FAS$footnotes
#> [1] "t_ds footnotes"
#>
#> $t_ds_slide_FAS$paper
#> [1] "L6"
#>
#> $t_ds_slide_FAS$suffix
#> [1] "FAS"
#>
#> $t_ds_slide_FAS$output
#> [1] "t_ds_slide_FAS"
#>
#>
## Supply study metadata so that `{token}` placeholders in titles/footnotes
## are filled in during decoration (e.g. a title of "... Study {study}").
spec <- read_spec(spec_file, metadata = list(study = "BP12345"))
## The same metadata can be kept in a yaml file and read via `read_spec()`
metadata_file <- system.file("metadata.yml", package = "autoslider.core")
spec <- read_spec(spec_file, metadata = metadata_file)