Package 'Open.Visualization.Academy'

Title: Content to Support Classes Taught Through the Open Visualization Academy
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')".
Authors: Raymond Balise [aut, cre] (ORCID: <https://orcid.org/0000-0002-9856-5901>), Kyle Grealis [aut] (ORCID: <https://orcid.org/0000-0002-9223-8854>), Ricky Lei [ctb] (ORCID: <https://orcid.org/0000-0003-1953-9236>), Gabriel Odom [ctb] (ORCID: <https://orcid.org/0000-0003-1341-4555>)
Maintainer: Raymond Balise <[email protected]>
License: AGPL (>= 3)
Version: 1.0.0
Built: 2026-05-22 06:00:17 UTC
Source: https://github.com/raymondbalise/open.visualization.academy

Help Index

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)