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pubh

A toolbox for Public Health and Epidemiology

pubh is an R package 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".

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Version

Install

install.packages('pubh')

Monthly Downloads

438

Version

1.2.7

License

GPL-2

Maintainer

Josie Athens

Last Published

April 4th, 2022

Functions in pubh (1.2.7)

Roberts

Extracorporeal membrane oxygenation in neonates.
Rothman

Oral contraceptives and stroke.
Oncho

Onchocerciasis in Sierra Leone.
Fentress

Migraine pain reduction.
Kirkwood

Body weight and plasma volume.
Bernard

Survival of patients with sepsis.
Hodgkin

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

Prevalence of Helicobacter pylori infection in preschool children.
Macmahon

Breast cancer and age of childbirth.
Sandler

Passive smoking in adulthood and cancer risk.
Sharples

Measured and self-reported weight in New Zealand.
bst

Bootstrap Confidence Intervals.
diag_test2

Diagnostic tests from direct input.
estat

Descriptive statistics for continuous variables.
Thall

RCT on the treatment of epilepsy.
expand_df

Expand a data frame.
chisq.fisher

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

Relative and Cumulative Frequency.
coef_det

Coefficient of determination.
gen_bst_df

Generate a data frame with estimate and bootstrap CIs.
contingency

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

Geometric mean.
get_r2

Estimate R2 or Pseudo-R2 from regression models
predict_inv

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

Proportion, p1 from proportion p2 and OR.
gf_star

Annotating a plot to display differences between groups.
Tuzson

Peak knee velocity in walking at flexion and extension.
leverage

Leverage.
logistic_gof

Goodness of fit for Logistic Regression.
axis_labs

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

Using labels as coefficient names in tables of coefficients.
pseudo_r2

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

Smoking and mortality in Whickham, England.
stats_quotes

Internal function to calculate descriptive statistics.
strip_error

Strip plots with error bars.
cross_tab

Cross-tabulation.
cosm_sum

Cosmetics for summary tables Adds some cosmetics to tables of descriptive statistics generated by tbl_summary.
hist_norm

Histogram with Normal density curve.
qq_plot

Quantile-quantile plots against the standard Normal distribution.
box_plot

Construct box plots.
cosm_reg

Cosmetics for tables of regression coefficients. Converts tables generated by tbl_regression to huxtable and adds some cosmetics.
contingency2

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

Bland-Altman agreement plots.
bar_error

Bar charts with error bars.
cross_tbl

Table of descriptive statistics by categorical variable.
diag_test

Diagnostic tests from variables.
rank_leverage

Ranks observations by leverage.
rank_influence

Ranks observations based upon influence measures on models.
odds_trend

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

Inverse of the logit
multiple

Multiple comparisons with plot.
round_pval

Rounding p-values.
ss_jk

Sum of squares for Jackknife.
theme_pubh

A theme for huxtables This function quickly set a default style for a huxtable.
harm_mean

Harmonic mean.
glm_coef

Table of coefficients from generalised linear models.
jack_knife

Ranks leverage observations from Jackknife method.
reference_range

Reference range (reference interval).
knife_mean

Jackknife for means.
rel_dis

Relative Dispersion.
mhor

Mantel-Haenszel odds ratio.