Type:	Package
Title:	Slide Automation for Tables, Listings and Figures
Version:	0.2.5
Description:	The normal process of creating clinical study slides is that a statistician manually type in the numbers from outputs and a separate statistician to double check the typed in numbers. This process is time consuming, resource intensive, and error prone. Automatic slide generation is a solution to address these issues. It reduces the amount of work and the required time when creating slides, and reduces the risk of errors from manually typing or copying numbers from the output to slides. It also helps users to avoid unnecessary stress when creating large amounts of slide decks in a short time window.
License:	Apache License 2.0
URL:	https://github.com/insightsengineering/autoslider.core
BugReports:	https://github.com/insightsengineering/autoslider.core/issues
Depends:	R (≥ 4.1.0)
Imports:	assertthat (≥ 0.2.1), checkmate (≥ 2.2.0), cli (≥ 3.6.3), dplyr (≥ 1.1.3), flextable (≥ 0.9.4), forcats (≥ 1.0.0), ggplot2 (≥ 3.5.0), ggpubr (≥ 0.6.0), grid, gridExtra (≥ 2.3), gtsummary (≥ 2.0.3), methods, officer (≥ 0.3.18), rlang (≥ 1.1.1), rlistings (≥ 0.2.11), rtables (≥ 0.6.12), rvg (≥ 0.2.5), stringr (≥ 1.5.0), survival, tern (≥ 0.9.8), tidyr (≥ 1.3.0), yaml (≥ 2.3.7)
Suggests:	devtools (≥ 2.4.5), ellmer (≥ 0.2.0), filters (≥ 0.3.1), formatters (≥ 0.5.11), glue (≥ 1.8.0), htmltools (≥ 0.5.8.1), httr (≥ 1.4.7), knitr (≥ 1.49), lubridate (≥ 1.9.3), mime (≥ 0.12), nestcolor, purrr (≥ 1.0.2), R.utils (≥ 2.12.3), reticulate, rmarkdown (≥ 2.23), rsvg (≥ 0.3.4), styler (≥ 1.10.2), svglite (≥ 2.1.3), testthat (≥ 3.2.0), TMB (≥ 1.9.1), withr
VignetteBuilder:	knitr, rmarkdown
Config/Needs/verdepcheck:	insightsengineering/formatters, tidyverse/magrittr, mllg/checkmate, rstudio/htmltools, gagolews/stringi, tidymodels/broom, cran/car, tidyverse/dplyr, davidgohel/flextable, yihui/knitr, r-lib/lifecycle, davidgohel/officer, Merck/r2rtf, rstudio/rmarkdown, therneau/survival, r-lib/testthat, tidyverse/tibble, tidyverse/tidyr, r-lib/withr, r-lib/xml2
Config/testthat/edition:	3
Encoding:	UTF-8
Language:	en-US
LazyData:	true
LazyDataCompression:	xz
RoxygenNote:	7.3.2
NeedsCompilation:	no
Packaged:	2025-06-13 11:58:24 UTC; rstudio
Author:	Joe Zhu [cre, aut], Heng Wang [aut], Yinqi Zhao [aut], Bo Ci [aut], Liming Li [aut], Laura Wang [ctb], Xiaoli Duan [aut], Stefan Pascal Thoma [aut], Thomas Neitmann [ctb], Miles Almond [aut], Mahdi About [ctb], Kai Lim [ctb], Nolan Steed [ctb], Daoling Pang [ctb], Elisabeth Deutschmann [ctb], Chenkai Lv [aut], Nina Qi [ctb], Jasmina Uzunovic [aut]
Maintainer:	Joe Zhu <joe.zhu@roche.com>
Repository:	CRAN
Date/Publication:	2025-06-13 12:30:13 UTC

autoslider.core Package

Description

The normal process of creating clinical study slides is that a statistician manually type in the numbers from outputs and a separate statistician to double check the typed in numbers. This process is time consuming, resource intensive, and error prone. Automatic slide generation is a solution to address these issues. It reduces the amount of work and the required time when creating slides, and reduces the risk of errors from manually typing or copying numbers from the output to slides. It also helps users to avoid unnecessary stress when creating large amounts of slide decks in a short time window.

Author(s)

Maintainer: Joe Zhu joe.zhu@roche.com (ORCID)

Authors:

• Heng Wang

• Yinqi Zhao

• Bo Ci

• Liming Li

• Xiaoli Duan

• Stefan Pascal Thoma

• Miles Almond

• Chenkai Lv

• Jasmina Uzunovic

Other contributors:

• Laura Wang [contributor]

• Thomas Neitmann [contributor]

• Mahdi About [contributor]

• Kai Lim [contributor]

• Nolan Steed [contributor]

• Daoling Pang [contributor]

• Elisabeth Deutschmann [contributor]

• Nina Qi [contributor]

See Also

Useful links:

• https://github.com/insightsengineering/autoslider.core

• Report bugs at https://github.com/insightsengineering/autoslider.core/issues

Update footnote with AI response

Description

Update footnote with AI response

Usage

adding_ai_footnotes(outputs, prompt_list, platform, base_url, api_key, model)

Arguments

autoslider_error class

Description

autoslider_error class

Usage

autoslider_error(x, spec, step)

Arguments

Details

this function is used to create autoslider_error object. this function is for internal use only to create the autoslider_error object. It enable us for further functionalities, like providing help on easy debugging, e.g. if the error is inside the user function, provide the call and let the user run the code outside the pipeline.

Value

autoslider_error object

Table color and font

Description

Zebra themed color

Usage

autoslider_format(
  ft,
  odd_header = "#0EAED5",
  odd_body = "#EBF5FA",
  even_header = "#0EAED5",
  even_body = "#D0E4F2",
  font_name = "arial",
  body_font_size = 12,
  header_font_size = 14
)

blue_format(ft, ...)

orange_format(ft, ...)

red_format(ft, ...)

purple_format(ft, ...)

autoslider_dose_format(ft, header_vals = names(ft))

black_format_ae(ft, body_font_size = 8, header_font_size = 8, ...)

black_format_tb(ft, body_font_size = 8, header_font_size = 8, ...)

Arguments

Value

A flextable with applied theme.

Functions

• autoslider_format(): User defined color code and font size

• blue_format(): Blue color theme

• orange_format(): Orange color theme

• red_format(): Red color theme

• purple_format(): Purple color theme

• autoslider_dose_format(): 'AutoslideR' dose formats

• black_format_ae(): Black color theme for AE listing

• black_format_tb(): Black color theme

Author(s)

Nina Qi and Jasmina Uzunovic

Build table header, a utility function to help with construct structured header for table layout

Description

Build table header, a utility function to help with construct structured header for table layout

Usage

build_table_header(anl, arm, split_by_study, side_by_side)

Arguments

Value

A 'rtables' layout with desired header.

Create location container to center the figure, based on ppt size and user specified figure size

Description

Create location container to center the figure, based on ppt size and user specified figure size

Usage

center_figure_loc(fig_width, fig_height, ppt_width, ppt_height)

Arguments

Value

Location for a placeholder from scratch

create location container to center the table

Description

create location container to center the table

Usage

center_table_loc(ft, ppt_width, ppt_height)

Arguments

Value

Location for a placeholder

Assert function to check the cutoff

Description

Assert function to check the cutoff

Usage

check_and_set_cutoff(data, cutoff)

Arguments

Value

Set the cutoff value

Concatenate arguments into a string

Description

Concatenate arguments into a string

Usage

dec_paste(...)

Arguments

Value

No return value, called for side effects

generic function decorate

Description

generic function decorate

s3 method for decorate

Usage

decorate(x, ...)

decorate(x, ...)

Arguments

Value

No return value, called for side effects

Decorate TableTree

Description

Decorate TableTree

Usage

## S4 method for signature 'VTableTree'
decorate(x, titles = "", footnotes = "", paper = "P8", for_test = FALSE, ...)

Arguments

Value

No return value, called for side effects

decorate listing

Description

decorate listing

Usage

## S4 method for signature 'listing_df'
decorate(x, titles = "", footnotes = "", paper = "P8", for_test = FALSE, ...)

Arguments

Value

No return value, called for side effects

decorate method for autoslider_error class

Description

decorate method for autoslider_error class

Usage

decorate.autoslider_error(x, ...)

Arguments

Value

No return value, called for side effects

default method to decorate

Description

default method to decorate

Usage

decorate.default(x, ...)

Arguments

Value

No return value, called for side effects

Decorate ggplot object

Description

Decorate ggplot object

Usage

decorate.ggplot(
  x,
  titles = "",
  footnotes = "",
  paper = "L11",
  for_test = FALSE,
  ...
)

Arguments

Details

The paper default paper size, 'L11', indicate that the fontsize is 11. The fontsize of the footnotes, is the fontsize of the titles minus 2.

Value

No return value, called for side effects

decorate grob

Description

decorate grob

Usage

decorate.grob(
  x,
  titles = "",
  footnotes = "",
  paper = "L11",
  for_test = FALSE,
  ...
)

Arguments

Details

The paper default paper size, 'L11', indicate that the fontsize is 11. The fontsize of the footnotes, is the fontsize of the titles minus 2.

Value

No return value, called for side effects

decorate gtsummary

Description

decorate gtsummary

Usage

decorate.gtsummary(
  x,
  titles = "",
  footnotes = "",
  paper = "L11",
  for_test = FALSE,
  ...
)

Arguments

Details

The paper default paper size, 'L11', indicate that the fontsize is 11. The fontsize of the footnotes, is the fontsize of the titles minus 2.#'

Value

No return value, called for side effects

decorate list of grobs

Description

decorate list of grobs

Usage

decorate.list(x, titles, footnotes, paper = "L11", for_test = FALSE, ...)

Arguments

Details

The paper default paper size, 'L11', indicate that the fontsize is 11. The fontsize of the footnotes, is the fontsize of the titles minus 2.

Value

No return value, called for side effects

Decorate outputs

Description

Decorate outputs with titles and footnotes

Usage

decorate_outputs(
  outputs,
  generic_title = NULL,
  generic_footnote = "Confidential and for internal use only",
  version_label = get_version_label_output(),
  for_test = FALSE
)

Arguments

Details

'generic_title' and 'generic_footnote' will be added to *all* outputs. The use case is to add information such as protocol number and snapshot date defined in a central place (e.g. metadata.yml) to *every* output.

'version_label' must be either '"DRAFT"', '"APPROVED"' or 'NULL'. By default, when outputs are created on the master branch it is set to 'NULL', i.e. no version label will be displayed. Otherwise '"DRAFT"' will be added. To add '"APPROVED"' to the title you will need to explicitly set 'version_label = "APPROVED"'.

Value

No return value, called for side effects

Cached ADAE

Description

Cached ADAE data

Usage

data(eg_adae)

Format

An object of class tbl_df (inherits from tbl, data.frame) with 1934 rows and 93 columns.

Cached ADEG

Description

Cached ADEG data

Usage

data(eg_adeg)

Format

An object of class tbl_df (inherits from tbl, data.frame) with 13600 rows and 88 columns.

Cached ADEX

Description

Cached ADEX data

Usage

data(eg_adex)

Format

An object of class tbl_df (inherits from tbl, data.frame) with 6400 rows and 79 columns.

Cached ADLB

Description

Cached ADLB data

Usage

data(eg_adlb)

Format

An object of class tbl_df (inherits from tbl, data.frame) with 8400 rows and 102 columns.

Cached ADRS

Description

Cached ADRS data

Usage

data(eg_adrs)

Format

An object of class tbl_df (inherits from tbl, data.frame) with 3200 rows and 65 columns.

Cached ADSL

Description

Cached ADSL data

Usage

data(eg_adsl)

Format

An object of class tbl_df (inherits from tbl, data.frame) with 400 rows and 56 columns.

Cached ADTR

Description

Cached ADTR data

Usage

data(eg_adtr)

Format

An object of class data.frame with 2800 rows and 76 columns.

Cached ADTTE

Description

Cached ADTTE data

Usage

data(eg_adtte)

Format

An object of class tbl_df (inherits from tbl, data.frame) with 2000 rows and 67 columns.

Cached ADVS

Description

Cached ADVS data

Usage

data(eg_advs)

Format

An object of class tbl_df (inherits from tbl, data.frame) with 16800 rows and 87 columns.

Does do.call quicker, and avoids issues with debug mode within do.call

Description

copied from ms showcase app

Usage

fastDoCall(what, args, quote = FALSE, envir = parent.frame())

Arguments

Value

No return value, called for side effects

Add figure to slides

Description

Add figure to slides

Usage

figure_to_slide(
  ppt,
  content,
  decor = TRUE,
  fig_width,
  fig_height,
  figure_loc = ph_location_type("body"),
  ...
)

Arguments

Value

slide with the added content

Filter a spec object

Description

Filter a spec object

Usage

filter_spec(spec, filter_expr, verbose = TRUE)

Arguments

Value

A 'spec' object containing only the outputs matching 'filter_expr'

Author(s)

Thomas Neitmann ('neitmant')

Examples

library(dplyr)
spec_file <- system.file("spec.yml", package = "autoslider.core")
spec <- spec_file %>% read_spec()

## Keep only the t_dm_IT output
filter_spec(spec, output == "t_dm_IT")

## Same as above but more verbose
filter_spec(spec, program == "t_dm" && suffix == "IT")

## Keep all t_ae outputs
filter_spec(spec, program == "t_ae")

## Keep all output run on safety population
filter_spec(spec, "SE" %in% suffix)

## Keep t_dm_CHN_IT and t_dm_CHN_SE
filter_spec(spec, program == "t_dm" && suffix %in% c("CHN_IT", "CHN_SE"))

## Keep all tables
filter_spec(spec, grepl("^t_", program))

Format of xx.xx (xx.xx, xx.xx)

Description

Format of xx.xx (xx.xx, xx.xx)

Usage

format_3d(x, output)

Arguments

Value

formatted values

Convert dates from 'yyyy-mm-dd' format into 20APR2019 format 'Datetime' format removes the time and outputs date in the same way Able to handle truncated dates as well (e.g. just the year or year and month)

Description

'dplyr::case_when()' will check all RHS expressions on the input, this means if these expressions return warnings, they will happen even then the input doesn't doesn't satisfy the LHS. For this reason, I had to 'quiet' all 'lubridate' functions. This 'format_date()' function was tested with the inputs in the examples, all gave the expected returned value, so there should be no issues.

Usage

format_date(x)

Arguments

Value

A vector.

Examples

require(lubridate)

# expected to return "2019"
format_date("2019")

# expected to return "20APR2019"
format_date("2019-04-20")

# expected to return ""
format_date("")

# expected to return "18JUN2019"
format_date("2019-06-18T10:32")

# expected to return "APR2019"
format_date("2019-04")

function wrapper to pass filtered data

Description

function wrapper to pass filtered data

Usage

func_wrapper(func, datasets, spec, verbose = TRUE)

Arguments

Value

a wrapped function using filtered adam

Plot mean values of EG

Description

Wrapper for 'g_mean_general()'. Requires filtering of the datasets (e.g. using SUFFIX in spec.yml)

Usage

g_eg_slide(
  adsl,
  adeg,
  arm = "TRT01P",
  paramcd = "PARAM",
  subtitle = "Plot of Mean and 95% Confidence Limits by Visit.",
  ...
)

Arguments

Author(s)

Stefan Thoma ('thomas7')

Examples

library(dplyr)

adeg_filtered <- eg_adeg %>% filter(
  PARAMCD == "HR"
)
plot_eg <- g_eg_slide(
  adsl = eg_adsl,
  adeg = adeg_filtered,
  arm = "TRT01P",
  paramcd = "PARAM",
  subtitle_add_unit = FALSE
) +
  ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 45, hjust = 1))

generate_slides(plot_eg, paste0(tempdir(), "/g_eg.pptx"))

Plot mean values of LB

Description

Wrapper for 'g_mean_general()'. Requires filtering of the datasets (e.g. using SUFFIX in spec.yml)

Usage

g_lb_slide(
  adsl,
  adlb,
  arm = "TRT01P",
  paramcd = "PARAM",
  y = "AVAL",
  subtitle = "Plot of Mean and 95% Confidence Limits by Visit.",
  ...
)

Arguments

Author(s)

Stefan Thoma ('thomas7')

Examples

library(dplyr)

adlb_filtered <- eg_adlb %>% filter(
  PARAMCD == "CRP"
)
plot_lb <- g_lb_slide(
  adsl = eg_adsl,
  adlb = adlb_filtered,
  paramcd = "PARAM",
  subtitle_add_unit = FALSE
) +
  ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 45, hjust = 1))
generate_slides(plot_lb, paste0(tempdir(), "/g_lb.pptx"))

# Let's plot change values:
plot_lb_chg <- g_lb_slide(
  adsl = eg_adsl,
  adlb = adlb_filtered,
  paramcd = "PARAM",
  y = "CHG",
  subtitle = "Plot of change from baseline and 95% Confidence Limit by Visit."
)
generate_slides(plot_lb_chg, paste0(tempdir(), "/g_lb_chg.pptx"))

Plot mean values general function used by wrappers 'g_vs_slide','g_lb_slide', & 'g_eg_slide'

Description

adapted from https://insightsengineering.github.io/tlg-catalog/stable/graphs/other/mng01.html

Usage

g_mean_general(
  adsl,
  data,
  variables = control_lineplot_vars(group_var = "TRT01P"),
  by_vars = c("USUBJID", "STUDYID"),
  subtitle = "Plot of Mean and 95% Confidence Limits by Visit.",
  ...
)

Arguments

Author(s)

Stefan Thoma ('thomas7')

Examples

library(dplyr)
advs_filtered <- eg_advs %>% filter(
  PARAMCD == "SYSBP"
)
out1 <- g_mean_general(eg_adsl, advs_filtered)
generate_slides(out1, paste0(tempdir(), "/g_mean.pptx"))

Plot mean values of VS

Description

Wrapper for 'g_mean_general()'. Requires filtering of the datasets (e.g. using SUFFIX in spec.yml)

Usage

g_vs_slide(
  adsl,
  advs,
  arm = "TRT01P",
  paramcd = "PARAM",
  subtitle = "Plot of Mean and 95% Confidence Limits by Visit.",
  ...
)

Arguments

Author(s)

Stefan Thoma ('thomas7')

Examples

library(dplyr)
advs_filtered <- eg_advs %>% filter(
  PARAMCD == "SYSBP"
)

plot_vs <- g_vs_slide(
  adsl = eg_adsl,
  advs = advs_filtered,
  paramcd = "PARAM",
  subtitle_add_unit = FALSE
) +
  ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 45, hjust = 1))

generate_slides(plot_vs, paste0(tempdir(), "/g_vs.pptx"))

General notes

Description

General notes

Usage

gen_notes()

Note

* Default arm variables are set to '"TRT01A"' for safety output, and '"TRT01P"' for efficacy output

Generate output and apply filters, titles, and footnotes

Description

Generate output and apply filters, titles, and footnotes

Usage

generate_output(program, datasets, spec, verbose_level = 2, ...)

Arguments

Details

'verbose_level' is used to control how many messages are printed out. By default, '2' will show all filter messages and show output generation message. '1' will show output generation message only. '0' will display no message.

Value

No return value, called for side effects

Author(s)

Liming Li ('Lil128')

Examples

library(dplyr)
filters::load_filters(
  yaml_file = system.file("filters.yml", package = "autoslider.core"),
  overwrite = TRUE
)

spec_file <- system.file("spec.yml", package = "autoslider.core")
spec <- spec_file %>% read_spec()

data <- list(
  adsl = eg_adsl,
  adae = eg_adae
)
generate_output("t_ae_slide", data, spec$t_ae_slide_SE)

Generate all outputs from a spec

Description

Generate all outputs from a spec

Usage

generate_outputs(spec, datasets, verbose_level = 2)

Arguments

Details

'verbose_level' is used to control how many messages are printed out. By default, '2' will show all filter messages and show output generation message. '1' will show output generation message only. '0' will display no message.

Value

No return value, called for side effects

Author(s)

- Thomas Neitmann ('neitmant') - Liming Li ('Lil128')

Examples

library(dplyr, warn.conflicts = FALSE)
data <- list(
  adsl = eg_adsl,
  adae = eg_adae
)
filters::load_filters(
  yaml_file = system.file("filters.yml", package = "autoslider.core"),
  overwrite = TRUE
)

spec_file <- system.file("spec.yml", package = "autoslider.core")
spec_file %>%
  read_spec() %>%
  filter_spec(output %in% c("t_dm_slide_IT", "t_ae_slide_SE")) %>%
  generate_outputs(datasets = data)

generate slides based on output

Description

generate slides based on output

Usage

generate_slides(
  outputs,
  outfile = paste0(tempdir(), "/output.pptx"),
  template = file.path(system.file(package = "autoslider.core"), "theme/basic.pptx"),
  fig_width = 9,
  fig_height = 6,
  t_lpp = 20,
  t_cpp = 200,
  l_lpp = 20,
  l_cpp = 150,
  ...
)

Arguments

Value

No return value, called for side effects

Examples

# Example 1. When applying to the whole pipeline
library(dplyr)
data <- list(
  adsl = eg_adsl %>% dplyr::mutate(FASFL = SAFFL),
  adae = eg_adae
)


filters::load_filters(
  yaml_file = system.file("filters.yml", package = "autoslider.core"),
  overwrite = TRUE
)


spec_file <- system.file("spec.yml", package = "autoslider.core")
spec_file %>%
  read_spec() %>%
  filter_spec(program %in% c("t_dm_slide")) %>%
  generate_outputs(datasets = data) %>%
  decorate_outputs() %>%
  generate_slides()

# Example 2. When applying to an rtable object or an rlisting object
adsl <- eg_adsl
t_dm_slide(adsl, "TRT01P", c("SEX", "AGE")) %>%
  generate_slides()

Get an 'ellmer' chat API with given platform

Description

Get an 'ellmer' chat API with given platform

Usage

get_ellmer_chat(
  platform = "deepseek",
  base_url = "https://api.deepseek.com",
  api_key = get_deepseek_key(),
  model = "deepseek-chat"
)

Arguments

Read prompt list from yaml file

Description

Read prompt list from yaml file

Usage

get_prompt_list(filename)

Arguments

Adjust title line break and font size

Description

Adjust title line break and font size

Usage

get_proper_title(title, max_char = 60, title_color = "#1C2B39")

Arguments

Demographic table with gtsummary

Description

Demographic table with gtsummary

Usage

gt_t_dm_slide(adsl, arm = "TRT01P", vars = c("AGE", "SEX", "RACE"))

Arguments

Value

gtsummary object

Note

* Default arm variables are set to '"TRT01A"' for safety output, and '"TRT01P"' for efficacy output

Examples

library(dplyr)
adsl <- eg_adsl
out1 <- gt_t_dm_slide(adsl, "TRT01P", c("SEX", "AGE", "RACE", "ETHNIC", "COUNTRY"))
print(out1)
generate_slides(out1, paste0(tempdir(), "/dm.pptx"))

Adverse Events listing adapted from https://insightsengineering.github.io/tlg-catalog/stable/listings/adverse-events/ael02.html

Description

Adverse Events listing adapted from https://insightsengineering.github.io/tlg-catalog/stable/listings/adverse-events/ael02.html

Usage

l_ae_slide(adsl, adae)

Arguments

Examples

library(dplyr)
library(rlistings)
adsl <- eg_adsl
adae <- eg_adae

out <- l_ae_slide(adsl = adsl, adae = adae)
head(out)

Build side by side layout by cbind

Description

Build side by side layout by cbind

Usage

lyt_to_side_by_side(lyt, anl, side_by_side = NULL)

Arguments

Value

An 'rtables' layout

Build side by side layout by cbind

Description

Build side by side layout by cbind

Usage

lyt_to_side_by_side_two_data(lyt, anl, alt_counts_df, side_by_side = NULL)

Arguments

Value

An 'rtables' layout

Refactor active arm

Description

Refactor active arm

Usage

mutate_actarm(
  df,
  arm_var = "TRT01A",
  levels = c("PLACEBO + PACLITAXEL + CISPLATIN",
    "ATEZOLIZUMAB + TIRAGOLUMAB + PACLITAXEL + CISPLATIN"),
  labels = c("Pbo+Pbo+PC", "Tira+Atezo+PC")
)

Arguments

Value

Dataframe with re-level and re-labelled arm variable.

Replace NAs to NA

Description

Replace NAs to NA

Usage

na_replace(table_df)

Arguments

Value

Input dataframe with both column replaced to NA

Founding method

Description

Founding method

Usage

new_round(x, digits = 1)

Arguments

Value

rounded value

Null report

Description

Null report

Usage

null_report()

Details

This will create a null report similar as STREAM does. You can use it inside output functions as shown in the example below.

Value

An empty 'rtables' object

Author(s)

Thomas Neitmann ('neitmant')

Examples

library(dplyr)
library(filters)
data <- list(
  adsl = eg_adsl,
  adae = eg_adae %>% mutate(AREL = "")
)

null_report()

## An example how to use the `null_report()` inside an output function
t_ae <- function(datasets) {
  trt <- "ACTARM"
  anl <- semi_join(
    datasets$adae,
    datasets$adsl,
    by = c("STUDYID", "USUBJID")
  )

  return(null_report())
}

data %>%
  filters::apply_filter("SER_SE") %>%
  t_ae()

Format of (xx%, xx%)

Description

Format of (xx%, xx%)

Usage

perc_perc(x, output)

Arguments

Value

formatted values

Placeholder for ph_with_img

Description

Placeholder for ph_with_img

Usage

ph_with_img(ppt, figure, fig_width, fig_height, figure_loc)

Arguments

Value

Location for a placeholder

Preprocess t_dd function

Description

Preprocess t_dd function

Usage

preprocess_t_dd(
  df,
  levels = c("PROGRESSIVE DISEASE", "ADVERSE EVENT", "OTHER", "<Missing>"),
  labels = c("Progressive Disease", "Adverse Events", "Other", "<Missing>")
)

Arguments

Value

dataframe

Preprocess t_ds function

Description

Preprocess t_ds function

Usage

preprocess_t_ds(
  df,
  levels = c("Alive: On Treatment", "Alive: In Follow-up", "<Missing>"),
  labels = c("Alive: On Treatment", "Alive: In Follow-up", "<Missing>")
)

Arguments

Value

dataframe

Print decorated grob

Description

Print decorated grob

Usage

## S3 method for class 'decoratedGrob'
print(x, ...)

Arguments

Value

No return value, called for side effects

Print decorated grob set

Description

Print decorated grob set

Usage

## S3 method for class 'decoratedGrobSet'
print(x, ...)

Arguments

Value

No return value, called for side effects

Read yaml spec file

Description

Read yaml spec file and split according to filter lists

Usage

read_spec(spec_file = "spec.yml", metadata = NULL)

Arguments

Value

An object of class 'spec' which is a 'list' where each element corresponds to one output, e.g. 't_dm_IT'.

Author(s)

- Liming Li ('Lil128') - Thomas Neitmann ('neitmant') - Joe Zhu

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")

## This is how it looks once read into R
spec <- read_spec(spec_file)
spec[1:3]

survival time afun

Description

survival time afun

Usage

s_surv_time_1(df, .var, is_event, control = control_surv_time())

Arguments

Value

A function suitable for use in rtables::analyze() with element selection, reformatting, and relabeling performed automatically.

Save an Output

Description

Save an Output

Usage

save_output(output, file_name, save_rds = TRUE)

save_output(output, file_name, save_rds = TRUE)

save_output.autoslider_error(output, file_name, save_rds = TRUE)

## S4 method for signature 'dVTableTree'
save_output(output, file_name, save_rds = TRUE)

save_output.decoratedGrob(output, file_name, save_rds = TRUE)

save_output.decoratedGrobSet(output, file_name, save_rds = TRUE)

save_output.dgtsummary(output, file_name, save_rds = TRUE)

save_output.dlisting(output, file_name, save_rds = TRUE)

Arguments

Details

Tables are saved as RDS file

Value

The input 'object' invisibly

No return value, called for side effects

The input 'object' invisibly

The input 'object' invisibly

The input 'object' invisibly

The input 'object' invisibly

Examples

library(dplyr)
adsl <- eg_adsl %>%
  filter(SAFFL == "Y") %>%
  mutate(TRT01P = factor(TRT01P, levels = c("A: Drug X", "B: Placebo")))
output_dir <- tempdir()
t_dm_slide(adsl, "TRT01P", c("SEX", "AGE", "RACE", "ETHNIC", "COUNTRY")) %>%
  decorate(
    title = "Demographic table",
    footnote = ""
  ) %>%
  save_output(
    file_name = file.path(output_dir, "t_dm_SE"),
    save_rds = TRUE
  )

Save a list of outputs

Description

Save a list of outputs

Usage

save_outputs(
  outputs,
  outfolder = file.path("output"),
  generic_suffix = NULL,
  save_rds = TRUE,
  verbose_level = 1
)

Arguments

Value

The input 'object' invisibly

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)

Generate slides from rds files

Description

Generate slides from rds files

Usage

slides_from_rds(
  filenames,
  outfile = paste0(tempdir(), "/output.pptx"),
  template = file.path(system.file(package = "autoslider.core"), "theme/basic.pptx")
)

Arguments

Value

No return value, called for side effects

Examples

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)

slides_from_rds(list.files(file.path(output_dir, "t_dm_slide_FAS.rds")))

Generate flextable for preview first page

Description

Generate flextable for preview first page

Usage

slides_preview(x)

Arguments

Value

A flextable or a ggplot object depending to the input.

Examples

# Example 1. preview table
library(dplyr)
adsl <- eg_adsl
t_dm_slide(adsl, "TRT01P", c("SEX", "AGE")) %>% slides_preview()

Adverse event table

Description

Adverse event table

Usage

t_ae_pt_diff_slide(
  adsl,
  adae,
  arm = "TRT01A",
  cutoff = NA,
  split_by_study = FALSE,
  side_by_side = NULL
)

Arguments

Value

rtables object

Note

* Default arm variables are set to '"TRT01A"' for safety output, and '"TRT01P"' for efficacy output

Examples

library(dplyr)
adsl <- eg_adsl %>%
  dplyr::mutate(TRT01A = factor(TRT01A, levels = c("A: Drug X", "B: Placebo")))
adae <- eg_adae %>%
  dplyr::mutate(
    TRT01A = factor(TRT01A, levels = c("A: Drug X", "B: Placebo")),
    ATOXGR = AETOXGR
  )
out <- t_ae_pt_diff_slide(adsl, adae, "TRT01A", 2)
print(out)
generate_slides(out, paste0(tempdir(), "/ae_diff.pptx"))

Adverse event table

Description

Adverse event table

Usage

t_ae_pt_slide(
  adsl,
  adae,
  arm = "TRT01A",
  cutoff = NA,
  prune_by_total = FALSE,
  split_by_study = FALSE,
  side_by_side = NULL
)

Arguments

Value

rtables object

Note

* Default arm variables are set to '"TRT01A"' for safety output, and '"TRT01P"' for efficacy output

Examples

library(dplyr)
# Example 1
adsl <- eg_adsl %>%
  dplyr::mutate(TRT01A = factor(TRT01A, levels = c("A: Drug X", "B: Placebo")))
adae <- eg_adae %>%
  dplyr::mutate(
    TRT01A = factor(TRT01A, levels = c("A: Drug X", "B: Placebo")),
    ATOXGR = AETOXGR
  )
out <- t_ae_pt_slide(adsl, adae, "TRT01A", 2)
print(out)
generate_slides(out, paste0(tempdir(), "/ae.pptx"))

# Example 2, prune by total column
out2 <- t_ae_pt_slide(adsl, adae, "TRT01A", 25, prune_by_total = TRUE)
print(out2)
generate_slides(out, paste0(tempdir(), "/ae2.pptx"))

Adverse event table

Description

Adverse event table

Usage

t_ae_pt_soc_diff_slide(
  adsl,
  adae,
  arm = "TRT01A",
  cutoff = NA,
  split_by_study = FALSE,
  side_by_side = NULL
)

Arguments

Value

rtables object

Note

* Default arm variables are set to '"TRT01A"' for safety output, and '"TRT01P"' for efficacy output

Examples

library(dplyr)
adsl <- eg_adsl %>%
  dplyr::mutate(TRT01A = factor(TRT01A, levels = c("A: Drug X", "B: Placebo")))
adae <- eg_adae %>%
  dplyr::mutate(
    TRT01A = factor(TRT01A, levels = c("A: Drug X", "B: Placebo")),
    ATOXGR = AETOXGR
  )
out <- t_ae_pt_soc_diff_slide(adsl, adae, "TRT01A", 2)
print(out)
generate_slides(out, paste0(tempdir(), "/ae_diff.pptx"))

Adverse event table

Description

Adverse event table

Usage

t_ae_pt_soc_slide(
  adsl,
  adae,
  arm,
  cutoff = NA,
  prune_by_total = FALSE,
  split_by_study = FALSE,
  side_by_side = NULL
)

Arguments

Value

rtables object

Examples

library(dplyr)
# Example 1
adsl <- eg_adsl %>%
  dplyr::mutate(TRT01A = factor(TRT01A, levels = c("A: Drug X", "B: Placebo")))
adae <- eg_adae %>%
  dplyr::mutate(
    TRT01A = factor(TRT01A, levels = c("A: Drug X", "B: Placebo")),
    ATOXGR = AETOXGR
  )
out <- t_ae_pt_soc_slide(adsl, adae, "TRT01A", 2)
print(out)
generate_slides(out, paste0(tempdir(), "/ae.pptx"))


# Example 2, prune by total column
out2 <- t_ae_pt_soc_slide(adsl, adae, "TRT01A", 25, prune_by_total = TRUE)
print(out2)
generate_slides(out2, paste0(tempdir(), "/ae2.pptx"))

Adverse event table

Description

Adverse event table

Usage

t_ae_slide(
  adsl,
  adae,
  arm = "TRT01A",
  split_by_study = FALSE,
  side_by_side = NULL
)

Arguments

Value

rtables object

Note

* Default arm variables are set to '"TRT01A"' for safety output, and '"TRT01P"' for efficacy output

Examples

library(dplyr)
adsl <- eg_adsl %>%
  dplyr::mutate(TRT01A = factor(TRT01A, levels = c("A: Drug X", "B: Placebo")))
adae <- eg_adae %>%
  dplyr::mutate(
    TRT01A = factor(TRT01A, levels = c("A: Drug X", "B: Placebo")),
    ATOXGR = AETOXGR
  )
out <- t_ae_slide(adsl, adae, "TRT01A")
print(out)
generate_slides(out, paste0(tempdir(), "/ae.pptx"))

Adverse event summary table

Description

Adverse event summary table

Usage

t_ae_summ_slide(
  adsl,
  adae,
  arm = "TRT01A",
  dose_adjust_flags = NA,
  dose_adjust_labels = NA,
  gr34_highest_grade_only = TRUE
)

Arguments

Value

an rtables object

Examples

library(dplyr)
ADSL <- eg_adsl
ADAE <- eg_adae

ADAE <- ADAE %>%
  dplyr::mutate(ATOXGR = AETOXGR)
t_ae_summ_slide(adsl = ADSL, adae = ADAE)

# add flag for ae leading to dose reduction
ADAE$reduce_flg <- ifelse(ADAE$AEACN == "DOSE REDUCED", TRUE, FALSE)
t_ae_summ_slide(
  adsl = ADSL, adae = ADAE,
  dose_adjust_flags = c("reduce_flg"),
  dose_adjust_labels = c("AE leading to dose reduction of drug X")
)
# add flgs for ae leading to dose reduction, drug withdraw and drug interruption
ADAE$withdraw_flg <- ifelse(ADAE$AEACN == "DRUG WITHDRAWN", TRUE, FALSE)
ADAE$interrup_flg <- ifelse(ADAE$AEACN == "DRUG INTERRUPTED", TRUE, FALSE)
out <- t_ae_summ_slide(
  adsl = ADSL, adae = ADAE, arm = "TRT01A",
  dose_adjust_flags = c("withdraw_flg", "reduce_flg", "interrup_flg"),
  dose_adjust_labels = c(
    "AE leading to discontinuation from drug X",
    "AE leading to drug X reduction",
    "AE leading to drug X interruption"
  )
)
print(out)
generate_slides(out, paste0(tempdir(), "/ae_summary.pptx"))

Table of AEs of Special Interest adapted from https://insightsengineering.github.io/tlg-catalog/stable/tables/adverse-events/aet01_aesi.html

Description

Table of AEs of Special Interest adapted from https://insightsengineering.github.io/tlg-catalog/stable/tables/adverse-events/aet01_aesi.html

Usage

t_aesi_slide(adsl, adae, aesi, arm = "ACTARM", grad_var = "AETOXGR")

Arguments

Value

rtables object

Author(s)

Kai Xiang Lim ('limk43')

Examples

library(dplyr)
adsl <- eg_adsl
adae <- eg_adae
adae_atoxgr <- adae %>% dplyr::mutate(ATOXGR = AETOXGR)
t_aesi_slide(adsl, adae, aesi = "CQ01NAM")
t_aesi_slide(adsl, adae, aesi = "CQ01NAM", arm = "ARM", grad_var = "AESEV")
t_aesi_slide(adsl, adae_atoxgr, aesi = "CQ01NAM", grad_var = "ATOXGR")

Death table

Description

Death table

Usage

t_dd_slide(adsl, arm = "TRT01A", split_by_study = FALSE, side_by_side = NULL)

Arguments

Value

rtables object

Note

* Default arm variables are set to '"TRT01A"' for safety output, and '"TRT01P"' for efficacy output

Examples

library(dplyr)
adsl <- eg_adsl %>% preprocess_t_dd()
out1 <- t_dd_slide(adsl, "TRT01A")
print(out1)
generate_slides(out1, paste0(tempdir(), "/dd.pptx"))

out2 <- t_dd_slide(adsl, "TRT01A", split_by_study = TRUE)
print(out2)

Demographic table

Description

Demographic table

Usage

t_dm_slide(
  adsl,
  arm = "TRT01P",
  vars = c("AGE", "SEX", "RACE"),
  stats = c("median", "range", "count_fraction"),
  split_by_study = FALSE,
  side_by_side = NULL
)

Arguments

Value

rtables object

Note

* Default arm variables are set to '"TRT01A"' for safety output, and '"TRT01P"' for efficacy output

Examples

library(dplyr)
adsl <- eg_adsl
out1 <- t_dm_slide(adsl, "TRT01P", c("SEX", "AGE", "RACE", "ETHNIC", "COUNTRY"))
print(out1)
generate_slides(out1, paste0(tempdir(), "/dm.pptx"))

out2 <- t_dm_slide(adsl, "TRT01P", c("SEX", "AGE", "RACE", "ETHNIC", "COUNTRY"),
  split_by_study = TRUE
)
print(out2)

DOR table

Description

DOR table

Usage

t_dor_slide(adsl, adtte, arm = "TRT01P", refgroup = NULL)

Arguments

Value

An 'rtables' object

Note

* Default arm variables are set to '"TRT01A"' for safety output, and '"TRT01P"' for efficacy output

Examples

library(dplyr)
adsl <- eg_adsl %>%
  dplyr::mutate(TRT01P = factor(TRT01P, levels = c("A: Drug X", "B: Placebo", "C: Combination")))
adtte <- eg_adtte %>%
  dplyr::filter(PARAMCD == "OS") %>%
  dplyr::mutate(TRT01P = factor(TRT01P, levels = c("A: Drug X", "B: Placebo", "C: Combination")))
out <- t_dor_slide(adsl, adtte)
print(out)
generate_slides(out, paste0(tempdir(), "/dor.pptx"))

Discontinue table

Description

Discontinue table

Usage

t_ds_slide(adsl, arm = "TRT01P", split_by_study = FALSE, side_by_side = NULL)

Arguments

Note

* Default arm variables are set to '"TRT01A"' for safety output, and '"TRT01P"' for efficacy output

Examples

library(dplyr)
adsl <- eg_adsl %>%
  mutate(DISTRTFL = sample(c("Y", "N"), size = nrow(eg_adsl), replace = TRUE, prob = c(.1, .9))) %>%
  preprocess_t_ds()
out1 <- t_ds_slide(adsl, "TRT01P")
print(out1)
generate_slides(out1, paste0(tempdir(), "/ds.pptx"))

out2 <- t_ds_slide(adsl, "TRT01P", split_by_study = TRUE)
print(out2)

Add decorated flextable to slides

Description

Add decorated flextable to slides

Usage

table_to_slide(
  ppt,
  content,
  decor = TRUE,
  table_loc = ph_location_type("body"),
  ...
)

Arguments

Value

Slide with added content

Convert list of numbers to vectors

Description

Convert list of numbers to vectors

Usage

to_vector(num_list)

Arguments

Value

No return value, called for side effects

Cached trial

Description

Cached trial data

Usage

trial

Format

An object of class tbl_df (inherits from tbl, data.frame) with 200 rows and 8 columns.

Format of xx.xx (xx.x)

Description

Format of xx.xx (xx.x)

Usage

trim_perc(x, output)

Arguments

Value

formatted values

Format of xx.xx (xx.xx)

Description

Format of xx.xx (xx.xx)

Usage

trim_perc1(x, output)

Arguments

Value

formatted values