pubh v1.1.16


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A Toolbox for Public Health and Epidemiology

A toolbox for making R functions and capabilities more accessible to students and professionals from Epidemiology and Public Health related disciplines. Includes a function to report coefficients and confidence intervals from models using robust standard errors (when available), functions that expand 'ggplot2' plots and functions relevant for introductory papers in Epidemiology or Public Health. Please note that use of the provided data sets is for educational purposes only.



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.

Functions in pubh

Name Description
Roberts Extracorporeal membrane oxygenation in neonates.
chisq.fisher Internal test for chi-squared assumption.Fisher (2 by 2). If results = T, it fails
cross_tab Cross-tabulation.
contingency Measures of association from two by two contingency tables (formula).
contingency2 Measures of association from two by two contingency tables (direct input).
coef_det Coefficient of determination.
bst Bootstrap Confidence Intervals.
estat Descriptive statistics for continuous variables.
Sharples Measured and self-reported weight in New Zealand.
expand_df Expand a data frame.
Thall RCT on the treatment of epilepsy.
hist_norm Histogram with Normal density curve.
axis_labs Apply labels from variables to axis-labels in plots.
bar_error Bar charts with error bars.
jack_knife Ranks leverage observations from Jackknife method.
gen_bst_df Generate a data frame with estimate and bootstrap CIs.
freq_cont Relative and Cumulative Frequency.
leverage Leverage.
knife_mean Jackknife for means.
bland_altman Bland-Altman agreement plots.
Tuzson Peak knee velocity in walking at flexion and extension.
inv_logit Inverse of the logit
predict_inv Given y solve for x in a simple linear model.
Vanderpump Smoking and mortality in Whickham, England.
box_plot Construct box plots.
gf_star Annotating a plot to display differences between groups.
diag_test Diagnostic tests from variables.
geo_mean Geometric mean.
diag_test2 Diagnostic tests from direct input.
prop_or Proportion, p1 from proportion p2 and OR.
rank_influence Ranks observations based upon influence measures on models.
rank_leverage Ranks observations by leverage.
multiple Multiple comparisons with plot.
glm_coef Table of coefficients from generalised linear models.
odds_trend Function to calculate OR using Wald CI, and plot trend.
ss_jk Sum of squares for Jackknife.
round_pval Rounding p-values.
harm_mean Harmonic mean.
mhor Mantel-Haenszel odds ratio.
model_labels Using labels as coefficient names in tables of coefficients.
logistic_gof Goodness of fit for Logistic Regression.
reference_range Reference range (reference interval).
rel_dis Relative Dispersion.
pseudo_r2 Pseudo R2 (logistic regression) pseudo_r2 Calculates R2 analogues (pseudo R2) of logistic regression.
stats_quotes Internal function to calculate descriptive statistics.
strip_error Strip plots with error bars.
qq_plot Quantile-quantile plots against the standard Normal distribution.
Macmahon Breast cancer and age of childbirth.
Sandler Passive smoking in adulthood and cancer risk.
Hodgkin T-cell counts from Hodgkin's disease patients.
Brenner Prevalence of Helicobacter pylori infection in preschool children.
Rothman Oral contraceptives and stroke.
Bernard Survival of patients with sepsis.
Fentress Migraine pain reduction.
Kirkwood Body weight and plasma volume.
Oncho Onchocerciasis in Sierra Leone.
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Vignettes of pubh

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