Package index

PheWAS

Get associations between a number of exposures and outcomes.

phewas() get_assoc()

PheWAS of exposure(s) on outcome(s) with tidy model output

Get summary statistics

‘Tidy’ model output with confidence intervals and other useful information.

tidy() tidy_ci()

Get tidy model output with fast CIs

Attributable fraction

Estimate attributable fraction in the exposed (AFE) and population attributable fraction (PAF) with 95% CIs.

paf()

Estimate attributable fraction in the exposed (AFE) and population attributable fraction (PAF)

Working with test statistics

Derived p-value, standard error (etc.) from other test statistics.

get_p()

Get p-value from Z-statistic

get_p_extreme()

Get extreme p-value

get_p_neglog10()

Get -log10 p-value (using Z only)

get_p_neglog10_n()

Get -log10 p-value (using Z & N)

get_se()

Get Standard Error from Confidence Intervals

get_z()

Get Z-statistic from p-value

Transform data

Manipulate variables.

carrec()

Recode a Variable

inv_norm()

Inverse normalize a variable

z_trans()

Z-transform a variable

Genetic epidemiology

Tools for genetics

estimate_ld()

Estimate haplotype frequencies and LD statistics from two biallelic variants

Plotting related

For working with plots.

annotate_textp()

Annotate a ggplot2 plot with text

theme_minimal_modified()

Modified theme_minimal for ggplots

Example data

Small dataset used in examples.

example_data

The Framingham Heart Study