DigestiveDataSets: A Curated Collection of Digestive System and Gastrointestinal Disease Datasets

Description

This package provides a wide variety of datasets focused on the digestive system, stomach, intestines, liver, pancreas, and associated diseases, including clinical trials, observational studies, experimental datasets, cohort data, and case series involving gastrointestinal disorders such as gastritis, ulcers, pancreatitis, liver cirrhosis, colon cancer, colorectal conditions, Helicobacter pylori infection, irritable bowel syndrome, intestinal infections, and post-surgical outcomes.

Details

DigestiveDataSets: A Curated Collection of Digestive System and Gastrointestinal Disease Datasets

A Curated Collection of Digestive System and Gastrointestinal Disease Datasets.

Author(s)

Maintainer: Renzo Caceres Rossi arenzocaceresrossi@gmail.com

See Also

Useful links:

• https://github.com/lightbluetitan/digestivedatasets

Anorexia Weight Change

Description

This dataset, anorexia_weight_change_df, is a data frame containing weight change data for young female anorexia patients. It includes pre- and post-treatment weights, along with the type of treatment administered.

Usage

data(anorexia_weight_change_df)

Format

A data frame with 72 observations and 3 variables:

Treat

Factor indicating the treatment type (3 levels)

Prewt

Numeric vector indicating the patient's weight before treatment (in kilograms)

Postwt

Numeric vector indicating the patient's weight after treatment (in kilograms)

Details

The dataset name has been kept as 'anorexia_weight_change_df' to avoid confusion with other datasets in the R ecosystem. This naming convention helps distinguish this dataset as part of the DigestiveDataSets package and assists users in identifying its specific characteristics. The suffix 'df' indicates that the dataset is a data frame. The original content has not been modified in any way.

Source

Data taken from the MASS package version 7.3-65.

Recurrent Bleeding from Ulcers

Description

This dataset, bleeding_ulcers_df, is a data frame containing data from 40 experiments designed to compare a new surgery for stomach ulcer with an older surgery.

Usage

data(bleeding_ulcers_df)

Format

A data frame with 80 observations and 9 variables:

author

Factor indicating the author of the study (20 levels)

year

Integer indicating the year of the study

quality

Integer representing the quality score of the experiment

age

Integer indicating the age of the patients

r

Integer indicating the number of recurrent bleeds

m

Integer indicating the total number of patients

bleed

Integer indicating bleeding events

treat

Factor indicating treatment type (6 levels)

table

Factor representing the experiment table (40 levels)

Details

The dataset name has been kept as 'bleeding_ulcers_df' to avoid confusion with other datasets in the R ecosystem. This naming convention helps distinguish this dataset as part of the DigestiveDataSets package and assists users in identifying its specific characteristics. The suffix 'df' indicates that the dataset is a data frame. The original content has not been modified in any way.

Source

Data taken from the SMPracticals package version 1.4-3.1.

Campylobacter Infections Time Series

Description

This dataset, campylobacter_infections_ts, is a time series object containing the number of cases of campylobacter infections in northern Quebec (Canada), recorded in four-week intervals from January 1990 to October 2000. Campylobacterosis is an acute bacterial infectious disease attacking the digestive system.

Usage

data(campylobacter_infections_ts)

Format

A time series object ('ts') with 140 observations:

Start

c(1990, 1)

End

c(2000, 10)

Frequency

13 (observations per year)

Details

The dataset name has been kept as 'campylobacter_infections_ts' to avoid confusion with other datasets in the R ecosystem. This naming convention helps distinguish this dataset as part of the DigestiveDataSets package and assists users in identifying its specific characteristics. The suffix 'ts' indicates that the dataset is a time series object. The original content has not been modified in any way.

Source

Data taken from the tscount package version 1.4.3. Original source: Ferland, R., Latour, A. and Oraichi, D., "Integer-valued GARCH process". Journal of Time Series Analysis, 2006; 27(6): 923–942.

Cholera Daily Deaths in England, 1849

Description

This dataset, cholera_deaths_1849_tbl_df, is a tibble containing daily deaths from Cholera and Diarrhaea in England for each day of the 12 months of 1849. It includes the month, cause of death, day of month, number of deaths, date, and day of week for each observation.

Usage

data(cholera_deaths_1849_tbl_df)

Format

A tibble with 730 observations and 6 variables:

month

Character indicating the month of observation

cause_of_death

Factor with 2 levels indicating cause of death (Cholera or Diarrhaea)

day_of_month

Character indicating the day of the month

deaths

Numeric value indicating the number of deaths

date

Date object indicating the exact date

day_of_week

Ordered factor with 7 levels indicating the day of week

Details

The dataset name has been kept as 'cholera_deaths_1849_tbl_df' to avoid confusion with other datasets in the R ecosystem. This naming convention helps distinguish this dataset as part of the DigestiveDataSets package and assists users in identifying its specific characteristics. The suffix 'tbl_df' indicates that the dataset is a tibble. The original content has not been modified in any way.

Source

Data taken from the HistData package version 0.9-3. Original source: Bingham P., Verlander, N. Q., Cheal M. J. (2004). "John Snow, William Farr and the 1849 outbreak of cholera that affected London: a reworking of the data highlights the importance of the water supply". Public Health, 118(6), 387–394, Table 2.

Chemotherapy for Stage B/C Colon Cancer

Description

This dataset, colon_stageBC_chemo_df, is a data frame containing data from one of the first successful trials of adjuvant chemotherapy for stage B/C colon cancer. The dataset includes 1858 observations (with two records per patient: one for recurrence and one for death) and 16 clinical variables.

Usage

data(colon_stageBC_chemo_df)

Format

A data frame with 1858 observations and 16 variables:

id

Numeric patient identifier

study

Numeric study code

rx

Factor with 3 levels indicating treatment group

sex

Numeric gender code

age

Numeric age in years

obstruct

Numeric obstruction status

perfor

Numeric perforation status

adhere

Numeric adhesion status

nodes

Numeric count of lymph nodes

status

Numeric event status

differ

Numeric differentiation grade

extent

Numeric tumor extent

surg

Numeric surgery code

node4

Numeric node4 status

time

Numeric follow-up time

etype

Numeric event type

Details

The dataset name has been kept as 'colon_stageBC_chemo_df' to avoid confusion with other datasets in the R ecosystem. This naming convention helps distinguish this dataset as part of the DigestiveDataSets package and assists users in identifying its specific characteristics. The suffix 'df' indicates that the dataset is a data frame. The original content has not been modified in any way.

Source

Data taken from the OncoDataSets package version 0.1.0.

Features from Colonoscopic Video

Description

This dataset, colonoscopy_features_tbl_df, is a tibble containing features extracted from 76 colonoscopic videos. Each video was recorded using both White Light (WL) and Narrow Band Imaging (NBI). The dataset includes histology results (classification ground truth), the opinion of endoscopists (4 experts and 3 beginners), and 698 features derived from patients with gastrointestinal lesions.

Usage

data(colonoscopy_features_tbl_df)

Format

A tibble with 76 observations and 7 variables:

feature 294

Numeric feature extracted from colonoscopic videos

feature 441

Numeric feature extracted from colonoscopic videos

feature 472

Numeric feature extracted from colonoscopic videos

feature 486

Numeric feature extracted from colonoscopic videos

class_agreement

Numeric score representing agreement among endoscopists

missinglabel_indicator

Numeric indicator for missing labels

ground truth

Character string representing the histology-based classification

Details

The dataset name has been kept as 'colonoscopy_features_tbl_df' to avoid confusion with other datasets in the R ecosystem. This naming convention helps distinguish this dataset as part of the DigestiveDataSets package and assists users in identifying its specific characteristics. The suffix 'tbl_df' indicates that the dataset is a tibble. The original content has not been modified in any way.

Source

Data taken from the gmmsslm package version 1.1.6.

PubMed Data of miRNAs in Colorectal Cancer

Description

This dataset, crc_mirnas_pubmed_tbl_df, is a tibble containing information from PubMed abstracts related to microRNAs (miRNAs) in colorectal cancer. The data provides publication metadata, article abstracts, and associated miRNAs across 508 observations with 8 variables.

Usage

data(crc_mirnas_pubmed_tbl_df)

Format

A tibble with 508 observations and 8 variables:

PMID

Numeric PubMed identifier

Year

Numeric publication year

Title

Character article title

Abstract

Character full abstract text

Language

Character publication language

Type

Character article type

Topic

Character research topic

miRNA

Character microRNA identifiers

Details

The dataset name has been kept as 'crc_mirnas_pubmed_tbl_df' to avoid confusion with other datasets in the R ecosystem. This naming convention helps distinguish this dataset as part of the DigestiveDataSets package and assists users in identifying its specific characteristics. The suffix 'tbl_df' indicates that the dataset is a tibble. The original content has not been modified in any way.

Source

Data taken from the OncoDataSets package version 0.1.0.

Cystic Fibrosis SNP

Description

This dataset, cystic_fibrosis_snps_df, is a data frame containing genetic association data for cystic fibrosis, including a case-control indicator and 23 single nucleotide polymorphisms (SNPs) with specified inter-marker distances. The dataset contains 186 observations across 24 variables.

Usage

data(cystic_fibrosis_snps_df)

Format

A data frame with 186 observations and 24 variables:

y

Integer case-control indicator

loc1

Integer SNP genotype at location 1

loc2

Integer SNP genotype at location 2

loc3

Integer SNP genotype at location 3

loc4

Integer SNP genotype at location 4

loc5

Integer SNP genotype at location 5

loc6

Integer SNP genotype at location 6

loc7

Integer SNP genotype at location 7

loc8

Integer SNP genotype at location 8

loc9

Integer SNP genotype at location 9

loc10

Integer SNP genotype at location 10

loc11

Integer SNP genotype at location 11

loc12

Integer SNP genotype at location 12

loc13

Integer SNP genotype at location 13

loc14

Integer SNP genotype at location 14

loc15

Integer SNP genotype at location 15

loc16

Integer SNP genotype at location 16

loc17

Integer SNP genotype at location 17

loc18

Integer SNP genotype at location 18

loc19

Integer SNP genotype at location 19

loc20

Integer SNP genotype at location 20

loc21

Integer SNP genotype at location 21

loc22

Integer SNP genotype at location 22

loc23

Integer SNP genotype at location 23

Details

The dataset name has been kept as 'cystic_fibrosis_snps_df' to avoid confusion with other datasets in the R ecosystem. This naming convention helps distinguish this dataset as part of the DigestiveDataSets package and assists users in identifying its specific characteristics. The suffix 'df' indicates that the dataset is a data frame. The original content has not been modified in any way.

Source

Data taken from the gap.datasets package version 0.0.6. Original source: Liu JS, Sabatti C, Teng J, Keats BJB, Risch N (2001). "Bayesian Analysis of Haplotypes for Linkage Disequilibrium Mapping". Genome Research, 11:1716–1724.

Digestive Cancer Survival Times

Description

This dataset, digestive_cancer_survival_df, is a data frame containing survival times (in days) of cancer patients with advanced cancer of the stomach, bronchus, colon, ovary, or breast. All patients included in this dataset received treatment that involved supplemental ascorbate.

Usage

data(digestive_cancer_survival_df)

Format

A data frame with 17 observations and 5 variables:

stomach

Integer values indicating survival times (in days) for patients with stomach cancer

bronchus

Integer values indicating survival times (in days) for patients with bronchial cancer

colon

Integer values indicating survival times (in days) for patients with colon cancer

ovary

Integer values indicating survival times (in days) for patients with ovarian cancer

breast

Integer values indicating survival times (in days) for patients with breast cancer

Details

The dataset name has been kept as 'digestive_cancer_survival_df' to avoid confusion with other datasets in the R ecosystem. This naming convention helps distinguish this dataset as part of the DigestiveDataSets package and assists users in identifying its specific characteristics. The suffix 'df' indicates that the dataset is a data frame. The original content has not been modified in any way.

Source

Data taken from the RbyExample package version 0.0.100.

E. coli Infections Time Series

Description

This dataset, ecoli_infections_df, is a data frame containing the weekly number of reported disease cases caused by Escherichia coli in the state of North Rhine-Westphalia (Germany) from January 2001 to May 2013, excluding cases of EHEC and HUS.

Usage

data(ecoli_infections_df)

Format

A data frame with 646 observations and 3 variables:

year

Numeric value indicating the year of observation

week

Numeric value indicating the week of observation

cases

Numeric value indicating the number of reported E. coli cases

Details

The dataset name has been kept as 'ecoli_infections_df' to avoid confusion with other datasets in the R ecosystem. This naming convention helps distinguish this dataset as part of the DigestiveDataSets package and assists users in identifying its specific characteristics. The suffix 'df' indicates that the dataset is a data frame. The original content has not been modified in any way.

Source

Data taken from the tscount package version 1.4.3.

Gastric Cancer Clinical Trial

Description

This dataset, gastric_cancer_trial_df, is a data frame containing data from a randomized clinical trial conducted by the Gastrointestinal Tumor Study Group on patients with gastric cancer. It includes survival time, event occurrence, and group assignment.

Usage

data(gastric_cancer_trial_df)

Format

A data frame with 90 observations and 3 variables:

time

Numeric vector representing survival time

event

Numeric vector indicating event occurrence (e.g., death or relapse)

group

Factor with 2 levels representing treatment groups

Details

The dataset name has been kept as 'gastric_cancer_trial_df' to avoid confusion with other datasets in the R ecosystem. This naming convention helps distinguish this dataset as part of the DigestiveDataSets package and assists users in identifying its specific characteristics. The suffix 'df' indicates that the dataset is a data frame. The original content has not been modified in any way.

Source

Data taken from the package coin version 1.4-3.

Gastrointestinal Damage Prevention

Description

This dataset, gi_damage_prevention_df, is a data frame containing results from four randomised clinical trials on the prevention of gastrointestinal damages by Misoprostol, reported by Lanza et al. (1987–1989).

Usage

data(gi_damage_prevention_df)

Format

A data frame with 198 observations and 3 variables:

study

Factor indicating the clinical trial (4 levels)

treatment

Factor indicating the treatment group (2 levels: control or Misoprostol)

classification

Ordered factor indicating the degree of gastrointestinal damage (5 levels)

Details

The dataset name has been kept as 'gi_damage_prevention_df' to avoid confusion with other datasets in the R ecosystem. This naming convention helps distinguish this dataset as part of the DigestiveDataSets package and assists users in identifying its specific characteristics. The suffix 'df' indicates that the dataset is a data frame. The original content has not been modified in any way.

Source

Data taken from the HSAUR3 package version 1.0-15.

Helicobacter pylori Infection in Preschoolers

Description

This dataset, helicobacter_children_tbl_df, is a tibble containing the prevalence of Helicobacter pylori infection in preschool children according to parental history of duodenal or gastric ulcer.

Usage

data(helicobacter_children_tbl_df)

Format

A tibble with 863 observations and 2 variables:

ulcer

Factor with 2 levels indicating parental history of duodenal or gastric ulcer

infected

Factor with 2 levels indicating Helicobacter pylori infection status

Details

The dataset name has been kept as 'helicobacter_children_tbl_df' to avoid confusion with other datasets in the R ecosystem. This naming convention helps distinguish this dataset as part of the DigestiveDataSets package and assists users in identifying its specific characteristics. The suffix 'tbl_df' indicates that the dataset is a tibble. The original content has not been modified in any way.

Source

Data taken from the package pubh version 2.0.0.

Colic Horse Surgery

Description

This dataset, horse_colic_surgery_df, is a data frame containing clinical observations of horses with colic, where the primary task is to determine if the lesion requires surgery. The data consists of 300 cases with 31 clinical variables, modified from the original UCI repository version with adjusted factor levels.

Usage

data(horse_colic_surgery_df)

Format

A data frame with 300 observations and 31 variables:

surgery

Factor with 2 levels indicating surgical requirement

age

Factor with 1 level (age group)

hospitalID

Integer hospital identifier

temp_rectal

Numeric rectal temperature

pulse

Numeric pulse rate

respiratory_rate

Numeric respiratory rate

temp_extreme

Factor with 4 levels (temperature extremes)

pulse_peripheral

Factor with 4 levels (peripheral pulse)

capillayr_refill_time

Factor with 3 levels (capillary refill time)

pain

Numeric pain score

peristalsis

Numeric peristalsis measure

abdominal_distension

Numeric distension score

nasogastric_tube

Numeric tube measure

nasogastric_reflux

Numeric reflux quantity

nasogastric_reflux_PH

Numeric reflux pH

rectal_examination

Numeric exam result

abdomen

Numeric abdomen assessment

cell_volume

Numeric cell volume

protein

Numeric protein level

abdominocentesis_appearance

Numeric appearance score

abdomcentesis_protein

Numeric protein measure

outcome

Factor with 3 levels (outcome status)

surgical_lesion

Factor with 2 levels (lesion type)

lesion_type1

Factor with 60 levels (primary lesion type)

lesion_type2

Integer secondary lesion code

lesion_type3

Integer tertiary lesion code

cp_data

Factor with 2 levels (CP data)

temp_extreme_ordered

Ordered factor with 4 levels (temperature)

temp_extreme_num

Numeric temperature measure

mucous_membranes_col

Factor with 6 levels (membrane color)

mucous_membranes_group

Factor with 5 levels (membrane group)

Details

The dataset name has been kept as 'horse_colic_surgery_df' to avoid confusion with other datasets in the R ecosystem. This naming convention helps distinguish this dataset as part of the DigestiveDataSets package and assists users in identifying its specific characteristics. The suffix 'df' indicates that the dataset is a data frame. The original content has not been modified in any way beyond factor level adjustments.

Source

Data taken from the VIM package version 6.2.2 (originally from UCI repository).

Studies on CAM for Irritable Bowel Syndrome

Description

This dataset, ibs_cam_trials_df, is a data frame containing results from 19 clinical trials examining complementary and alternative medicine (CAM) interventions for irritable bowel syndrome (IBS). The dataset includes 12 variables characterizing each trial and its outcomes.

Usage

data(ibs_cam_trials_df)

Format

A data frame with 19 observations and 12 variables:

id

Integer trial identifier

study

Character study name/location

year

Integer publication year

country

Character country where study was conducted

ibs.crit

Character IBS diagnostic criteria used

days

Integer study duration in days

visits

Integer number of study visits

jadad

Integer Jadad score for study quality

x.a

Integer active treatment events

n.a

Integer active treatment sample size

x.p

Integer placebo group events

n.p

Integer placebo group sample size

Details

The dataset name has been kept as 'ibs_cam_trials_df' to avoid confusion with other datasets in the R ecosystem. This naming convention helps distinguish this dataset as part of the DigestiveDataSets package and assists users in identifying its specific characteristics. The suffix 'df' indicates that the dataset is a data frame. The original content has not been modified in any way.

Source

Data taken from the metadat package version 1.4-0.

SmartPill Intestinal Transit

Description

This dataset, intestinal_smartpill_df, is a data frame from a prospective cohort study evaluating gastric emptying, small bowel transit time, and total intestinal transit time using a SmartPill motility capsule. The study involved 8 critically ill trauma patients and 87 healthy volunteers. The capsule wirelessly transmitted pH, pressure, and temperature to a recorder attached to each subject's abdomen.

Usage

data(intestinal_smartpill_df)

Format

A data frame with 95 observations and 22 variables:

Group

Numeric indicator of group membership

Gender

Numeric indicator of gender

Race

Numeric code indicating racial background

Height

Height in centimeters

Weight

Weight in kilograms

Age

Age in years

GE.Time

Gastric emptying time (minutes)

SB.Time

Small bowel transit time (minutes)

C.Time

Colon transit time (minutes)

WG.Time

Whole gut transit time (minutes)

S.Contractions

Number of contractions in the stomach

S.Sum.of.Amplitudes

Sum of contraction amplitudes in the stomach

S.Mean.Peak.Amplitude

Mean peak amplitude in the stomach

S.Mean.pH

Mean pH level in the stomach

SB.Contractions

Number of contractions in the small bowel

SB.Sum.of.Amplitudes

Sum of contraction amplitudes in the small bowel

SB.Mean.Peak.Amplitude

Mean peak amplitude in the small bowel

SB.Mean.pH

Mean pH level in the small bowel

Colon.Contractions

Number of contractions in the colon

Colon.Sum.of.Amplitudes

Sum of contraction amplitudes in the colon

C.Mean.Peak.Amplitude

Mean peak amplitude in the colon

C.Mean.pH

Mean pH level in the colon

Details

The dataset name has been kept as 'intestinal_smartpill_df' to avoid confusion with other datasets in the R ecosystem. This naming convention helps distinguish this dataset as part of the DigestiveDataSets package and assists users in identifying its specific characteristics. The suffix 'df' indicates that the dataset is a data frame. The original content has not been modified in any way.

Source

Data taken from the medicaldata package version 0.2.0. Original source: Rauch et al., "Use of Wireless Utility Capsule to Determine Gastric Emptying and Small Intestinal Transit Times in Critically Ill Trauma Patients". Journal of Critical Care, 2012; 27(5): 534.e7–534.e12.

Satellite Tumors in GI Surgery

Description

This dataset, intestinal_surgery_df, is a data frame containing intestinal surgery data from 844 cancer patients. The data consists of pairs (n_i, s_i) where n_i is the number of satellites removed and s_i is the number of satellites found to be malignant.

Usage

data(intestinal_surgery_df)

Format

A data frame with 844 observations and 2 variables:

n

Numeric value representing the number of satellites removed

s

Numeric value representing the number of malignant satellites found

Details

The dataset name has been kept as 'intestinal_surgery_df' to avoid confusion with other datasets in the R ecosystem. This naming convention helps distinguish this dataset as part of the DigestiveDataSets package and assists users in identifying its specific characteristics. The suffix 'df' indicates that the dataset is a data frame. The original content has not been modified in any way.

Source

Data taken from the deconvolveR package version 1.2-1. Original source: Efron, B. (2016). "Empirical Bayes deconvolution estimates". Biometrika, 103(1), 1–20.

Prednisone vs Placebo in Liver Cirrhosis

Description

This dataset, liver_cirrhosis_prednisone_df, is a data frame containing data from a randomized control trial comparing prednisone (n=251) versus placebo (n=237) in 488 liver cirrhosis patients. The dataset includes both survival and longitudinal measurements of prothrombin index development over time, with 2968 total observations across 9 variables.

Usage

data(liver_cirrhosis_prednisone_df)

Format

A data frame with 2968 observations and 9 variables:

ID

Integer patient identifier

Time

Numeric time measurement

death

Integer death indicator

obstime

Numeric observation time

proth

Integer prothrombin index value

Trt

Factor with 2 levels indicating treatment group (prednisone/placebo)

start

Numeric start time

stop

Numeric stop time

event

Numeric event indicator

Details

The dataset name has been kept as 'liver_cirrhosis_prednisone_df' to avoid confusion with other datasets in the R ecosystem. This naming convention helps distinguish this dataset as part of the DigestiveDataSets package and assists users in identifying its specific characteristics. The suffix 'df' indicates that the dataset is a data frame. The original content has not been modified in any way.

Source

Data taken from the JSM package version 1.0.1.

Ontario Lynch Syndrome families

Description

This dataset, lynch_ontario_families_df, is a data frame containing data from 32 Lynch Syndrome families segregating mismatch repair mutations selected from the Ontario Familial Colorectal Cancer Registry. The dataset includes 765 individuals (both probands and relatives) with 11 variables per observation.

Usage

data(lynch_ontario_families_df)

Format

A data frame with 765 observations and 11 variables:

famID

Integer family identifier

indID

Integer individual identifier

fatherID

Integer father's identifier

motherID

Integer mother's identifier

gender

Integer gender code

status

Integer disease status

time

Integer time variable

currentage

Integer current age

mgene

Integer mutation gene status

proband

Integer proband indicator

relation

Integer relationship code

Details

The dataset name has been kept as 'lynch_ontario_families_df' to avoid confusion with other datasets in the R ecosystem. This naming convention helps distinguish this dataset as part of the DigestiveDataSets package and assists users in identifying its specific characteristics. The suffix 'df' indicates that the dataset is a data frame. The original content has not been modified in any way.

Source

Data taken from the FamEvent package version 3.2.

Norovirus Outbreak in Derbyshire

Description

This dataset, norovirus_derbyshire_df, is a data frame describing an outbreak of norovirus in the summer of 2001 in a primary school and nursery in Derbyshire, England. It contains 492 observations across 5 variables tracking illness patterns among students.

Usage

data(norovirus_derbyshire_df)

Format

A data frame with 492 observations and 5 variables:

class

Factor with 15 levels representing school classes

day_absent

Integer day of absence

start_illness

Integer day when illness started

end_illness

Integer day when illness ended

day_vomiting

Integer day when vomiting occurred

Details

The dataset name has been kept as 'norovirus_derbyshire_df' to avoid confusion with other datasets in the R ecosystem. This naming convention helps distinguish this dataset as part of the DigestiveDataSets package and assists users in identifying its specific characteristics. The suffix 'df' indicates that the dataset is a data frame. The original content has not been modified in any way.

Source

Data taken from the outbreaks package version 1.9.0. Original source: O'Neill and Marks (2005).

Pancreatic Cancer Clinical Trial

Description

This dataset, pancreatic_cancer_df, is a data frame containing data from a Phase II clinical trial of patients with locally advanced or metastatic pancreatic cancer. It includes time-to-event data for disease progression and death, as well as staging information.

Usage

data(pancreatic_cancer_df)

Format

A data frame with 41 observations and 4 variables:

stage

Factor indicating disease stage (locally advanced or metastatic)

onstudy

Factor indicating time (in days) from enrollment

progression

Factor indicating time (in days) to disease progression

death

Factor indicating time (in days) to death

Details

The dataset name has been kept as 'pancreatic_cancer_df' to avoid confusion with other datasets in the R ecosystem. This naming convention helps distinguish this dataset as part of the DigestiveDataSets package and assists users in identifying its specific characteristics. The suffix 'df' indicates that the dataset is a data frame. The original content has not been modified in any way.

Source

Data taken from the asaur package version 0.50.

Mayo Clinic Primary Biliary Cirrhosis

Description

This dataset, pbc_mayo_survival_df, is a data frame containing data from a randomized control trial conducted at Mayo Clinic from 1974 to 1984, studying the progression of primary biliary cirrhosis. The dataset includes both survival and longitudinal measurements with 1945 observations across 16 clinical variables.

Usage

data(pbc_mayo_survival_df)

Format

A data frame with 1945 observations and 16 variables:

ID

Integer patient identifier

Time

Numeric time measurement

death

Numeric death indicator

obstime

Numeric observation time

serBilir

Numeric serum bilirubin measurement

albumin

Numeric serum albumin measurement

alkaline

Integer alkaline phosphatase level

platelets

Integer platelet count

drug

Factor with 2 levels indicating treatment group

age

Numeric age in years

gender

Factor with 2 levels indicating patient sex

ascites

Factor with 2 levels indicating presence of ascites

hepatom

Factor with 2 levels indicating presence of hepatomegaly

start

Numeric start time for interval

stop

Numeric stop time for interval

event

Numeric event indicator

Details

The dataset name has been kept as 'pbc_mayo_survival_df' to avoid confusion with other datasets in the R ecosystem. This naming convention helps distinguish this dataset as part of the DigestiveDataSets package and assists users in identifying its specific characteristics. The suffix 'df' indicates that the dataset is a data frame. The original content has not been modified in any way.

Source

Data taken from the JSM package version 1.0.1.

Indomethacin for Post-ERCP Pancreatitis

Description

This dataset, post_ercp_pancreatitis_tbl_df, is a tibble containing results from a randomized, placebo-controlled, prospective 2-arm trial of rectal indomethacin (100 mg) versus placebo to prevent post-ERCP pancreatitis in 602 participants, as reported by Elmunzer, Higgins, et al. (2012) in the New England Journal of Medicine.

Usage

data(post_ercp_pancreatitis_tbl_df)

Format

A tibble with 602 observations and 33 variables:

id

Numeric subject identifier

site

Factor indicating study site (4 levels)

age

Numeric age of the participant

risk

Numeric risk score

gender

Factor indicating gender (2 levels)

outcome

Factor indicating study outcome (2 levels)

sod

Factor indicating presence of sphincter of Oddi dysfunction (2 levels)

pep

Factor indicating presence of post-ERCP pancreatitis (2 levels)

recpanc

Factor indicating recurrent pancreatitis (2 levels)

psphinc

Factor indicating pancreatic sphincterotomy (2 levels)

precut

Factor indicating precut sphincterotomy (2 levels)

difcan

Factor indicating difficult cannulation (2 levels)

pneudil

Factor indicating pneumatic dilation (2 levels)

amp

Factor indicating ampullary interventions (2 levels)

paninj

Factor indicating pancreatic injury (2 levels)

acinar

Factor indicating acinarization (2 levels)

brush

Factor indicating brushing procedures (2 levels)

asa81

Factor indicating ASA 81 mg use (3 levels)

asa325

Factor indicating ASA 325 mg use (3 levels)

asa

Factor indicating ASA status (3 levels)

prophystent

Factor indicating prophylactic stent placement (2 levels)

therastent

Factor indicating therapeutic stent use (2 levels)

pdstent

Factor indicating pancreatic duct stent (2 levels)

sodsom

Factor indicating somatostatin use for SOD (2 levels)

bsphinc

Factor indicating biliary sphincterotomy (2 levels)

bstent

Factor indicating biliary stent (2 levels)

chole

Factor indicating cholecystectomy (2 levels)

pbmal

Factor indicating presence of pancreaticobiliary malignancy (2 levels)

train

Factor indicating if performed by trainee (2 levels)

status

Factor indicating trial status (2 levels)

type

Factor indicating procedure type (4 levels)

rx

Factor indicating treatment group: placebo or indomethacin (2 levels)

bleed

Numeric bleeding indicator

Details

The dataset name has been kept as 'post_ercp_pancreatitis_tbl_df' to avoid confusion with other datasets in the R ecosystem. This naming convention helps distinguish this dataset as part of the DigestiveDataSets package and assists users in identifying its specific characteristics. The suffix 'tbl_df' indicates that the dataset is a tibble. The original content has not been modified in any way.

Source

Data taken from the medicaldata package version 0.2.0.

H2 Antagonists in UGIB

Description

This dataset, ugi_bleeding_df, is a data frame containing results from 27 studies examining the effectiveness of histamine H2 antagonists (cimetidine or ranitidine) in treating acute upper gastrointestinal hemorrhage, with 14 variables per study.

Usage

data(ugi_bleeding_df)

Format

A data frame with 27 observations and 14 variables:

id

Integer study identifier

trial

Character trial name/location

year

Integer publication year

ref

Integer reference number

trt

Character treatment description

ctrl

Character control description

nti

Integer treatment group sample size

b.xti

Integer treatment group bleeding events

o.xti

Integer treatment group other events

d.xti

Integer treatment group deaths

nci

Integer control group sample size

b.xci

Integer control group bleeding events

o.xci

Integer control group other events

d.xci

Integer control group deaths

Details

The dataset name has been kept as 'ugi_bleeding_df' to avoid confusion with other datasets in the R ecosystem. This naming convention helps distinguish this dataset as part of the DigestiveDataSets package and assists users in identifying its specific characteristics. The suffix 'df' indicates that the dataset is a data frame. The original content has not been modified in any way.

Source

Data taken from the metadat package version 1.4-0.

View Available Datasets in DigestiveDataSets

Description

This function lists all datasets available in the 'DigestiveDataSets' package. If the 'DigestiveDataSets' package is not loaded, it stops and shows an error message. If no datasets are available, it returns a message and an empty vector.

Usage

view_datasets_digestive()

Value

A character vector with the names of the available datasets. If no datasets are found, it returns an empty character vector.

Examples

if (requireNamespace("DigestiveDataSets", quietly = TRUE)) {
  library(DigestiveDataSets)
  view_datasets_digestive()
}

Obese Patient Weight Loss Data

Description

This dataset, weight_loss_df, is a data frame containing the weight, in kilograms, of an obese patient measured at 52 time points over an 8-month period as part of a weight rehabilitation programme.

Usage

data(weight_loss_df)

Format

A data frame with 52 observations and 2 variables:

Days

Integer vector indicating the number of days since the beginning of the programme

Weight

Numeric vector indicating the weight (in kilograms) of the patient at each time point

Details

The dataset name has been kept as 'weight_loss_df' to avoid confusion with other datasets in the R ecosystem. This naming convention helps distinguish this dataset as part of the DigestiveDataSets package and assists users in identifying its specific characteristics. The suffix 'df' indicates that the dataset is a data frame. The original content has not been modified in any way.

Source

Data taken from the MASS package version 7.3-65.