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.
Readme
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.
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. | |
| No Results! | ||
Vignettes of pubh
| Name | ||
| introduction.Rmd | ||
| regression.Rmd | ||
| No Results! | ||
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Details
| License | GPL-2 |
| Encoding | UTF-8 |
| LazyData | true |
| RoxygenNote | 7.1.1 |
| VignetteBuilder | knitr |
| URL | https://github.com/josie-athens/pubh |
| BugReports | https://github.com/josie-athens/pubh/issues |
| NeedsCompilation | no |
| Packaged | 2020-07-06 22:06:45 UTC; josie |
| Repository | CRAN |
| Date/Publication | 2020-07-07 09:10:02 UTC |
| suggests | bookdown , broom , GGally , ggeffects , ggfortify , ggpubr , ggsci , haven , ISwR , jtools , knitr , latex2exp , lme4 , MASS , mosaic , nlme , nnet , ordinal , psych , reshape2 , rmarkdown , rms , scales , tidyverse |
| imports | car , dplyr , Epi , epiR , epitools , ggplot2 , Hmisc , huxtable , lmtest , moonBook , sandwich , sjlabelled , sjmisc , sjPlot , survival , tibble , tidyselect |
| depends | emmeans , ggformula , magrittr , R (>= 4.0.0) , stats |
| Contributors | Frank E Harrell Jr, John Fox, R-Core |
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