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dtrackr - Track your Data Pipelines

Track and document 'dplyr' data pipelines. As you filter, mutate, and join your way through a data set, 'dtrackr' seamlessly keeps track of your data flow and makes publication ready documentation of a data pipeline simple.

Last updated

8.57 score 72 stars 1 dependents 345 scripts 415 downloads

interfacer - Define and Enforce Contracts for Dataframes as Function Parameters

A dataframe validation framework for package builders who use dataframes as function parameters. It performs checks on column names, coerces data-types, and checks grouping to make sure user inputs conform to a specification provided by the package author. It provides a mechanism for package authors to automatically document supported dataframe inputs and selectively dispatch to functions depending on the format of a dataframe much like S3 does for classes. It also contains some developer tools to make working with and documenting dataframe specifications easier. It helps package developers to improve their documentation and simplifies parameter validation where dataframes are used as function parameters.

Last updated

6.37 score 2 stars 3 dependents 26 scripts 350 downloads

ggoutbreak - Estimate Incidence, Proportions and Exponential Growth Rates

Simple statistical models and visualisations for calculating the incidence, proportion, exponential growth rate, and reproduction number of infectious disease case time series. This toolkit was largely developed during the COVID-19 pandemic.

Last updated

5.00 score 4 stars 21 scripts

rsurvstat - Download Infectious Disease Data from 'SurvStat' (Robert Koch Institute)

Provides an interface to the 'SurvStat' web service from the Robert Koch Institute (<https://tools.rki.de/SurvStat/SurvStatWebService.svc>) allowing downloads of disease time series stratified by pathogen type and subtype, age, and geography from notifiable disease reports in Germany.

Last updated

4.54 score 7 scripts 361 downloads

tidyabc - Approximate Bayesian Computing with Tidy Data

A flexible framework for Approximate Bayesian Computation (ABC) that integrates with the tidyverse. Define simulation models and summary statistics as standard R functions, use 'dist_fns' to represent prior and posterior distributions, and perform inference via rejection sampling, Sequential Monte Carlo (SMC), or Adaptive ABC. The package provides tools for diagnostics, visualization, and convergence assessment, enabling reproducible Bayesian inference for complex models with intractable likelihoods.

Last updated

4.40 score 25 scripts

pkgutils - Functions for building functions

A suite of tools for helping in function and package development. This includes functions that check variables for consistency, or help parse out inputs to functions. This has a particular focus on inputs that use formula or `tidyselect` interfaces to define the parts of a dataframe that we might be interested in.

Last updated

3.86 score 2 stars 1 dependents 24 scripts 45 downloads

ukc19 - Datasets from the UK COVID-19 outbreak

Provides simple access to a small selection of pre-wrangled data sets relevant to the COVId-19 outbreak in the UK for teaching and demo purposes.

Last updated

3.48 score 1 stars 1 dependents 166 downloads

huxtableone - Descriptive Tables for Observational or Interventional Studies

Generating tabular summaries of data in a format suitable for reporting in journal articles is fiddly and slows down more detailed analysis. Comparing two populations with respect to an intervention, and reporting it is a task that can be largely automated.

Last updated

3.30 score

arear - Geospatial Convenience Functions and a Supply Demand Catchment Area Generator

Geospatial function collection from the COVID-19 pandemic. The main focus of this was integrating geospatial demographic, hospital capacity and COVID data from England, Scotland, Wales and Northern Ireland, all of which were available on different sites and methods. The UK has a wide range of administrative geographic boundaries for different purposes and moving from different scales and resolutions proved necessary. As the geospatial operations are quite time consuming but don't need to be repeated the ability to cache results of geospatial transformations is useful and embedded into these functions.

Last updated

3.30 score 4 stars 4 scripts

rmaven - Run Java Build Tool Maven from R

Distributing large files in packages is contrary to 'CRAN' policies. Java libraries frequently have large dependencies, and this makes them hard to submit to CRAN. Java has a sophisticated dependency management tool (Maven) which can calculate and cache dependencies. Running Maven from R allows for better integration of Java libraries into R. Maven provides various options for resolving complied Java code dependencies, configuring class path, or compiling Java source code, all of which are useful for efficient use of Java within R.

Last updated

2.70 score 2 scripts

pkgtools - Code generation and linting functions for R packages

Perform common tasks and fix common errors in project and package development. This is a developer tool rather than an end user package.

Last updated

2.18 score 1 stars 1 dependents 10 scripts

avoncap - AvonCap Study Analysis

A WIP set of functions allowing data load, wrangling of the AvonCap data set.

Last updated

2.04 score 11 scripts

modelfitter - Bootstrapping models and model fits

This is a very early work in progress.

Last updated

2.00 score 1 stars 2 scripts

testerror - Uncertainty in Multiplex Panel Testing

Provides methods to support the estimation of epidemiological parameters based on the results of multiplex panel tests.

Last updated

1.70 score 1 stars 6 scripts