Save a list of outputs
Usage
save_outputs(
outputs,
outfolder = file.path("output"),
generic_suffix = NULL,
save_rds = TRUE,
verbose_level = 1
)Arguments
- outputs
`list` of outputs as created by `generate_outputs`
- outfolder
Folder in which to store the `outputs“
- generic_suffix
generic suffix. must be length 1 character or NULL.
- save_rds
Should the input `outputs` be saved as `.rds` files in in addition to `.out` or `.pdf` files? Defaults to `FALSE`.
- verbose_level
Level of verbose information displayed. Default set to `1`.
Examples
## As `save_outputs` is the last step in the pipeline we have to run
## the 'whole machinery' in order to show its functionality.
library(dplyr, warn.conflicts = FALSE)
data <- list(
adsl = eg_adsl,
adae = eg_adae,
adtte = eg_adtte
)
filters::load_filters(
yaml_file = system.file("filters.yml", package = "autoslider.core"),
overwrite = TRUE
)
## For this example the outputs will be saved in a temporary directory. In a
## production run this should be the reporting event's 'output' folder instead.
output_dir <- tempdir()
spec_file <- system.file("spec.yml", package = "autoslider.core")
read_spec(spec_file) %>%
filter_spec(program == "t_dm_slide") %>%
generate_outputs(datasets = data) %>%
decorate_outputs() %>%
save_outputs(outfolder = output_dir)
#> ✔ 2/51 outputs matched the filter condition `program == "t_dm_slide"`.
#> ❯ Running program `t_dm_slide` with suffix 'FAS'.
#> Filter 'FAS' matched target ADSL.
#> 400/400 records matched the filter condition `FASFL == 'Y'`.
#> ❯ Running program `t_dm_slide` with suffix 'FAS'.
#> Filter 'FAS' matched target ADSL.
#> 400/400 records matched the filter condition `FASFL == 'Y'`.
#> ✔ Output saved in path /tmp/RtmpxkOG8D/t_dm_slide_FAS
#> ✔ Output saved in path /tmp/RtmpxkOG8D/t_dm_slide_FAS
#> ✔ Total number of success 2/2
#> $t_dm_slide_FAS
#> An object of class "dVTableTree"
#> Slot "tbl":
#> Patient Demographics and Baseline Characteristics, Full Analysis Set
#>
#> ———————————————————————————————————————————————————————————————————————————————————————————————————————
#> A: Drug X B: Placebo C: Combination All Patients
#> ———————————————————————————————————————————————————————————————————————————————————————————————————————
#> Sex
#> F 79 (59%) 82 (61.2%) 70 (53%) 231 (57.8%)
#> M 55 (41%) 52 (38.8%) 62 (47%) 169 (42.2%)
#> Age
#> Median 33.00 35.00 35.00 34.00
#> Min - Max 21.0 - 50.0 21.0 - 62.0 20.0 - 69.0 20.0 - 69.0
#> Race
#> ASIAN 68 (50.7%) 67 (50%) 73 (55.3%) 208 (52%)
#> BLACK OR AFRICAN AMERICAN 31 (23.1%) 28 (20.9%) 32 (24.2%) 91 (22.8%)
#> WHITE 27 (20.1%) 26 (19.4%) 21 (15.9%) 74 (18.5%)
#> AMERICAN INDIAN OR ALASKA NATIVE 8 (6%) 11 (8.2%) 6 (4.5%) 25 (6.2%)
#> MULTIPLE 0 1 (0.7%) 0 1 (0.2%)
#> NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER 0 1 (0.7%) 0 1 (0.2%)
#> OTHER 0 0 0 0
#> UNKNOWN 0 0 0 0
#> Ethnicity
#> NOT REPORTED 6 (4.5%) 10 (7.5%) 11 (8.3%) 27 (6.8%)
#> HISPANIC OR LATINO 15 (11.2%) 18 (13.4%) 15 (11.4%) 48 (12%)
#> NOT HISPANIC OR LATINO 104 (77.6%) 103 (76.9%) 101 (76.5%) 308 (77%)
#> UNKNOWN 9 (6.7%) 3 (2.2%) 5 (3.8%) 17 (4.2%)
#> ———————————————————————————————————————————————————————————————————————————————————————————————————————
#>
#> t_dm_slide footnote
#> Confidential and for internal use only
#> GitHub repository: NA
#> Git hash: 759265356b2ef63508c64624d41d358f83dd975d
#>
#> Slot "titles":
#> Patient Demographics and Baseline Characteristics, Full Analysis Set
#>
#> Slot "footnotes":
#> [1] "t_dm_slide footnote"
#> [2] "Confidential and for internal use only"
#>
#> Slot "paper":
#> [1] "L6"
#>
#> Slot "width":
#> [1] 41 11 11 14 12
#>
#>
#> $t_dm_slide_FAS
#> An object of class "dVTableTree"
#> Slot "tbl":
#> Patient Demographics and Baseline Characteristics, Full Analysis Set
#>
#> ———————————————————————————————————————————————————————————————————————————————————————————————————————
#> A: Drug X B: Placebo C: Combination All Patients
#> ———————————————————————————————————————————————————————————————————————————————————————————————————————
#> Sex
#> F 79 (59%) 82 (61.2%) 70 (53%) 231 (57.8%)
#> M 55 (41%) 52 (38.8%) 62 (47%) 169 (42.2%)
#> Age
#> Median 33.00 35.00 35.00 34.00
#> Min - Max 21.0 - 50.0 21.0 - 62.0 20.0 - 69.0 20.0 - 69.0
#> Race
#> ASIAN 68 (50.7%) 67 (50%) 73 (55.3%) 208 (52%)
#> BLACK OR AFRICAN AMERICAN 31 (23.1%) 28 (20.9%) 32 (24.2%) 91 (22.8%)
#> WHITE 27 (20.1%) 26 (19.4%) 21 (15.9%) 74 (18.5%)
#> AMERICAN INDIAN OR ALASKA NATIVE 8 (6%) 11 (8.2%) 6 (4.5%) 25 (6.2%)
#> MULTIPLE 0 1 (0.7%) 0 1 (0.2%)
#> NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER 0 1 (0.7%) 0 1 (0.2%)
#> OTHER 0 0 0 0
#> UNKNOWN 0 0 0 0
#> Ethnicity
#> NOT REPORTED 6 (4.5%) 10 (7.5%) 11 (8.3%) 27 (6.8%)
#> HISPANIC OR LATINO 15 (11.2%) 18 (13.4%) 15 (11.4%) 48 (12%)
#> NOT HISPANIC OR LATINO 104 (77.6%) 103 (76.9%) 101 (76.5%) 308 (77%)
#> UNKNOWN 9 (6.7%) 3 (2.2%) 5 (3.8%) 17 (4.2%)
#> ———————————————————————————————————————————————————————————————————————————————————————————————————————
#>
#> t_dm_slide footnote
#> Confidential and for internal use only
#> GitHub repository: NA
#> Git hash: 759265356b2ef63508c64624d41d358f83dd975d
#>
#> Slot "titles":
#> Patient Demographics and Baseline Characteristics, Full Analysis Set
#>
#> Slot "footnotes":
#> [1] "t_dm_slide footnote"
#> [2] "Confidential and for internal use only"
#>
#> Slot "paper":
#> [1] "L6"
#>
#> Slot "width":
#> [1] 41 11 11 14 12
#>
#>