Help for package Open.Visualization.Academy

Title:

Content to Support Classes Taught Through the Open Visualization Academy

Version:

1.0.0

Description:

This contains functions and data used by the Open Visualization Academy classes on data processing and visualization. The tutorial included with this package requires the 'gradethis' package which can be installed using "remotes::install_github('rstudio/gradethis')".

License:

AGPL (≥ 3)

Encoding:

UTF-8

RoxygenNote:

7.3.3

Suggests:

dplyr, gradethis, gtsummary (≥ 2.0.3), htmltools, kableExtra, learnr, quarto, rmarkdown, roxygen2, sortable, testthat (≥ 3.0.0), tibble

VignetteBuilder:

quarto

SystemRequirements:

quarto

Imports:

cli, clipr, hms, knitr, rlang (≥ 1.1.0)

Config/testthat/edition:

Depends:

R (≥ 4.1.0)

LazyData:

true

NeedsCompilation:

Packaged:

2026-01-15 13:51:03 UTC; raymondbalise

Author:

Raymond Balise

[aut, cre], Kyle Grealis

[aut], Ricky Lei

[ctb], Gabriel Odom

[ctb]

Maintainer:

Raymond Balise <balise@miami.edu>

Repository:

CRAN

Date/Publication:

2026-01-21 19:00:09 UTC

analysis dataset

Description

This dataset, which is ready for analysis, was created by setting the variable types, specifying factor levels instead of code numbers, and applying labels to the laryngectomy dataset. It includes demographics, surgery details, and outcomes for 123 individuals who underwent a laryngectomy at an unspecified medical center between 2000 and 2012.

Usage

analysis

Format

A labelled tibble with 123 rows and 33 variables:

age

Type:	integer

Description:	Age in years

sex

Type:	factor (First/Reference level = `Male`)

Description:	Sex assigned at Birth

Levels:	`⁠Male, Female⁠`

recur_site

Type:	factor (First/Reference level = `Supra`)

Description:	Recurrent Site

Levels:	`⁠Supra, Glottic, Transglottic, Unknown⁠`

trt_mod

Type:	factor (First/Reference level = `XRT`)

Description:	Treatment Modality

Levels:	`⁠XRT, Chemo+XRT, Unspecified⁠`

int_stg

Type:	ordered (First/Reference level = `Unknown`)

Description:	Initial Stage

Levels:	`⁠Unknown, T1, T2, T3, T4⁠`

recur_stg

Type:	ordered (First/Reference level = `Unknown`)

Description:	Recurrent staging

Levels:	`⁠Unknown, T1, T2, T3, T4⁠`

preop_img_mod

Type:	factor (First/Reference level = `CT`)

Description:	Imaging

Levels:	`⁠CT, PET, CT+PET, MRI⁠`

nk_dissection

Type:	factor (First/Reference level = `Yes`)

Description:	Neck Dissection

Levels:	`⁠Yes, No⁠`

laterality

Type:	factor (First/Reference level = `Bilateral`)

Description:	Laterality

Levels:	`⁠Bilateral, Unilateral⁠`

mic_vas_flap

Type:	factor (First/Reference level = `Yes`)

Description:	Microvascular Flap

Levels:	`⁠Yes, No⁠`

pec_flap

Type:	factor (First/Reference level = `Yes`)

Description:	Pectoralis major myocutaneous flap

Levels:	`⁠Yes, No⁠`

pathology

Type:	factor (First/Reference level = `Positive`)

Description:	Nodal Pathology evaluation of specimen

Levels:	`⁠Positive, Negative⁠`

path_stg

Type:	ordered (First/Reference level = `Unknown`)

Description:	Pathologic staging

Levels:	`⁠Unknown, T1, T2, T3, T4⁠`

complications

Type:	factor (First/Reference level = `Yes`)

Description:	Complications

Levels:	`⁠Yes, No⁠`

fistula

Type:	factor (First/Reference level = `Yes`)

Description:	Salivary fistula or leak

Levels:	`⁠Yes, No⁠`

wound_inf

Type:	factor (First/Reference level = `Yes`)

Description:	Wound Infection

Levels:	`⁠Yes, No⁠`

dehiscence

Type:	factor (First/Reference level = `Yes`)

Description:	Wound dehiscence

Levels:	`⁠Yes, No⁠`

wound_comp

Type:	factor (First/Reference level = `Yes`)

Description:	Wound Complications

Levels:	`⁠Yes, No⁠`

chyle_leak

Type:	factor (First/Reference level = `Yes`)

Description:	Chyle leak

Levels:	`⁠Yes, No⁠`

hematoma

Type:	factor (First/Reference level = `Yes`)

Description:	Hematoma

Levels:	`⁠Yes, No⁠`

revision_proc

Type:	factor (First/Reference level = `Yes`)

Description:	Revision procedure

Levels:	`⁠Yes, No⁠`

flap_fail

Type:	factor (First/Reference level = `Yes`)

Description:	Flap Failure

Levels:	`⁠Yes, No⁠`

periop_death

Type:	factor (First/Reference level = `Yes`)

Description:	Perioperative Death

Levels:	`⁠Yes, No⁠`

med_comp

Type:	factor (First/Reference level = `Yes`)

Description:	Medical Complications

Levels:	`⁠Yes, No⁠`

comp_2plus

Type:	factor (First/Reference level = `Yes`)

Description:	2 or more complications

Levels:	`⁠Yes, No⁠`

hosp_stay_days

Type:	integer

Description:	Hospital Stay

death

Type:	factor (First/Reference level = `Yes`)

Description:	Death status

Levels:	`⁠Yes, No⁠`

recur

Type:	factor (First/Reference level = `Yes`)

Description:	Recurrence status

Levels:	`⁠Yes, No⁠`

sor

Type:	factor (First/Reference level = `⁠No recurrence⁠`)

Description:	Site of Recurrence after salvage laryngectomy

Levels:	`⁠No recurrence, Local/regional, Distant⁠`

length_fu

Type:	integer

Description:	Days of follow-up

death_fu

Type:	integer

Description:	Days until death

recur_fu

Type:	integer

Description:	Days until recurrence

complications_count

Type:	integer

Description:	Number of complications

Predictors and outcomes for people underwent laryngectomy

Description

A dataset containing demographics and surgery details and outcomes on 123 people who underwent laryngectomy at an unspecified medical center between 2000 and 2012.

Usage

laryngectomy

Format

A tibble with 123 rows and 32 variables:

age: Age in years with 90+ removed
gender: sex (M=1, F=2)
recur_site: Recurrent Site (Supra=1, Glottic=2, Transglottic=3, Unknown=4)
trt_mod: Treatment Modality (XRT=1 Chemo+XRT=2 Unspecified=3)
int_stg: Initial Stage (T1=1, T2=2, T3=3, T4=4 Unknown=5)
recur_stg: Recurrent staging (T1=1, T2=2, T3=3, T4=4, unknown=5)
preop_Img_mod: Imaging (CT=1 PET=2 CT+PET=3 MRI=4)
nk_dissection: Neck Dissection (Yes=1, No=2)
Laterality: Laterality (Bilateral Neck Dissection=1, Unilateral Neck Dissection=2)
mic_vas_flap: Microvascular Flap (Yes=1, No=2)
pec_flap: Pectoralis major myocutaneous flap (Yes=1, No=2)
pathology: Nodal Pathology evaluation of specimen (Positive=1, Negative=2)
path_stg: Pathologic staging (T1=1, T2=2, T3=3, T4=4, unknown=5)
complications: Complications (Yes=1, No=2)
fistula: Salivary fistula or leak (Yes=1, No=2)
wound_inf: Wound Infection (Yes=1, No=2)
dehiscence: Wound dehiscence (Yes=1, No=2)
wound_comp: Wound Complications (Yes=1, No=2)
chyle_leak: Chyle leak (Yes=1, No=2)
hematoma: Hematoma (Yes=1, No=2)
revision_proc: Revision procedure (Yes=1, No=2)
flap_fail: Flap Failure (Yes=1, No=2)
periop_death: Perioperative Death (Yes=1, No=2)
med_comp: Medical Complications (Yes=1, No=2)
comp_2plus: 2 or more complications (Yes=1, No=2)
hosp_stay: Hospital Stay (<7 days=1, 7-14 days=2, >14 days)
death: Death status (Dead=1 Alive=2)
recur: Recurrence status (Recurred=1, No recurrence=2)
sor: Site of Recurrence after salvage laryngectomy (Locoregional=1, Distant=3, No recurrence=0)
length_fu: Days of follow-up
death_fu: Days until death
recur_fu: Days until recurrence

Print a description of the variables in a dataset

Description

This function prints the name of a dataset and then details on its variables. Run this, then check the output to make sure it does not show any sensitive information. If it does not, paste it into your favorite AI's chat box to help it understand the problem you are solving.

Usage

show_structure(data, display_redacted = FALSE, clipboard = TRUE)

Arguments

data

The name of an R dataset

display_redacted

Logical. Option to have empty table cells for character and date formats (the default) or to display "< redacted strings|dates >" for charater strings and dates, respectively.

clipboard

Copy results to clipboard (TRUE by default)

Value

A formatted markdown table (via knitr::kable) displaying the structure of the input dataset. The table contains three columns:

variable

Column names from the input data

type

Data type of each column (e.g., "numeric", "factor", "Date")

levels

For factors: comma-separated factor levels; for numeric/integer: value range; for other types: NA

Examples

show_structure(mtcars)