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pubh

A toolbox for Public Health and Epidemiology

"pubh" is an R pacakage for making R functions and capabilities more accessible to students and professionals from epidemiology and public health related disciplines.

Information on use with examples can be found in "vignettes".

To install, type in R console:

devtools::install_github("josie-athens/pubh", build_vignettes = TRUE)

Package "devtools" is required to install "pubh" from the GitHub repositories.

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Version

Install

install.packages('pubh')

Monthly Downloads

542

Version

1.1.3

License

GPL-2

Issues

4

Pull Requests

0

Stars

5

Forks

3

Maintainer

Josie Athens

Last Published

December 10th, 2019

Functions in pubh (1.1.3)

bst

Bootstrap Confidence Intervals.
reference_range

Reference range (reference interval).
logistic_gof

Goodness of fit for Logistic Regression.
gen_bst_df

Generate a data frame with estimate and bootstrap CIs.
axis_labs

Apply labels from variables to axis-labels in plots.
Roberts

Extracorporeal membrane oxygenation in neonates.
mhor

Mantel-Haenszel odds ratio.
bar_error

Bar charts with error bars.
geo_mean

Geometric mean.
rel_dis

Relative Dispersion.
Tuzson

Peak knee velocity in walking at flexion and extension.
bland_altman

Bland-Altman agreement plots.
contingency2

Measures of association from two by two contingency tables (direct input).
inv_logit

Inverse of the logit
box_plot

Construct box plots.
diag_test

Diagnostic tests from variables.
freq_cont

Relative and Cumulative Frequency.
expand_df

Expand a data frame.
jack_knife

Ranks leverage observations from Jackknife method.
knife_mean

Jackknife for means.
Vanderpump

Smoking and mortality in Whickham, England.
Sharples

Measured and self-reported weight in New Zealand.
prop_or

Proportion, p1 from proportion p2 and OR.
predict_inv

Given y solve for x in a simple linear model.
strip_error

Strip plots with error bars.
multiple

Multiple comparisons with plot.
leverage

Leverage.
stats_quotes

Internal function to calculate descriptive statistics.
odds_trend

Function to calculate OR using Wald CI, and plot trend.
Thall

RCT on the treatment of epilepsy.
diag_test2

Diagnostic tests from direct input.
chisq.fisher

Internal test for chi-squared assumption.Fisher (2 by 2). If results = T, it fails
coef_det

Coefficient of determination.
estat

Descriptive statistics for continuous variables.
contingency

Measures of association from two by two contingency tables (formula).
glm_coef

Table of coefficients from generalised linear models.
pseudo_r2

Pseudo R2 (logistic regression) pseudo_r2 Calculates R2 analogues (pseudo R2) of logistic regression.
gf_star

Annotating a plot to display differences between groups.
round_pval

Rounding p-values.
qq_plot

Quantile-quantile plots against the standard Normal distribution.
hist_norm

Histogram with Normal density curve.
rank_influence

Ranks observations based upon influence measures on models.
ss_jk

Sum of squares for Jackknife.
harm_mean

Harmonic mean.
rank_leverage

Ranks observations by leverage.
Macmahon

Breast cancer and age of childbirth.
Hodgkin

T-cell counts from Hodgkin's disease patients.
Fentress

Migraine pain reduction.
Rothman

Oral contraceptives and stroke.
Kirkwood

Body weight and plasma volume.
Sandler

Passive smoking in adulthood and cancer risk.
Bernard

Survival of patients with sepsis.
Brenner

Prevalence of Helicobacter pylori infection in preschool children.
Oncho

Onchocerciasis in Sierra Leone.