No packages match

ids - Generate Random Identifiers

Generate random or human readable and pronounceable identifiers.

Last updated

13.38 score 95 stars 163 dependents 341 scripts 337k downloads

jsonvalidate - Validate 'JSON' Schema

Uses the node library 'is-my-json-valid' or 'ajv' to validate 'JSON' against a 'JSON' schema. Drafts 04, 06 and 07 of 'JSON' schema are supported.

Last updated

jsonjson-validationjsonvalidate

10.99 score 52 stars 69 dependents 76 scripts 16k downloads

storr - Simple Key Value Stores

Creates and manages simple key-value stores. These can use a variety of approaches for storing the data. This package implements the base methods and support for file system, in-memory and DBI-based database stores.

Last updated

10.23 score 119 stars 30 dependents 70 scripts 3.8k downloads

odin - ODE Generation and Integration

Generate systems of ordinary differential equations (ODE) and integrate them, using a domain specific language (DSL). The DSL uses R's syntax, but compiles to C in order to efficiently solve the system. A solver is not provided, but instead interfaces to the packages 'deSolve' and 'dde' are generated. With these, while solving the differential equations, no allocations are done and the calculations remain entirely in compiled code. Alternatively, a model can be transpiled to R for use in contexts where a C compiler is not present. After compilation, models can be inspected to return information about parameters and outputs, or intermediate values after calculations. 'odin' is not targeted at any particular domain and is suitable for any system that can be expressed primarily as mathematical expressions. Additional support is provided for working with delays (delay differential equations, DDE), using interpolated functions during interpolation, and for integrating quantities that represent arrays.

Last updated

infrastructure

9.99 score 106 stars 6 dependents 292 scripts 835 downloads

orderly - Lightweight Reproducible Reporting

Distributed reproducible computing framework, adopting ideas from git, docker and other software. By defining a lightweight interface around the inputs and outputs of an analysis, a lot of the repetitive work for reproducible research can be automated. We define a simple format for organising and describing work that facilitates collaborative reproducible research and acknowledges that all analyses are run multiple times over their lifespans.

Last updated

9.48 score 11 stars 3 dependents 176 scripts 634 downloads

diversitree - Comparative 'Phylogenetic' Analyses of Diversification

Contains a number of comparative 'phylogenetic' methods, mostly focusing on analysing diversification and character evolution. Contains implementations of 'BiSSE' (Binary State 'Speciation' and Extinction) and its unresolved tree extensions, 'MuSSE' (Multiple State 'Speciation' and Extinction), 'QuaSSE', 'GeoSSE', and 'BiSSE-ness' Other included methods include Markov models of discrete and continuous trait evolution and constant rate 'speciation' and extinction.

Last updated

fftw3gslopenblascpp

9.35 score 33 stars 4 dependents 840 scripts 4.4k downloads

redux - R Bindings to 'hiredis'

A 'hiredis' wrapper that includes support for transactions, pipelining, blocking subscription, serialisation of all keys and values, 'Redis' error handling with R errors. Includes an automatically generated 'R6' interface to the full 'hiredis' API. Generated functions are faithful to the 'hiredis' documentation while attempting to match R's argument semantics. Serialisation must be explicitly done by the user, but both binary and text-mode serialisation is supported.

Last updated

hiredis

9.12 score 95 stars 7 dependents 56 scripts 3.0k downloads

cyphr - High Level Encryption Wrappers

Encryption wrappers, using low-level support from 'sodium' and 'openssl'. 'cyphr' tries to smooth over some pain points when using encryption within applications and data analysis by wrapping around differences in function names and arguments in different encryption providing packages. It also provides high-level wrappers for input/output functions for seamlessly adding encryption to existing analyses.

Last updated

encryptionopensslpeer-reviewedsodium

8.32 score 98 stars 2 dependents 51 scripts 612 downloads

monty - Monte Carlo Models

Experimental sources for the next generation of mcstate, now called 'monty', which will support much of the old mcstate functionality but new things like better parameter interfaces, Hamiltonian Monte Carlo, and other features.

Last updated

cpp

7.93 score 7 stars 7 dependents 82 scripts

dust - Iterate Multiple Realisations of Stochastic Models

An Engine for simulation of stochastic models. Includes support for running stochastic models in parallel, either with shared or varying parameters. Simulations are run efficiently in compiled code and can be run with a fraction of simulated states returned to R, allowing control over memory usage. Support is provided for building bootstrap particle filter for performing Sequential Monte Carlo (e.g., Gordon et al. 1993 <doi:10.1049/ip-f-2.1993.0015>). The core of the simulation engine is the 'xoshiro256**' algorithm (Blackman and Vigna <arXiv:1805.01407>), and the package is further described in FitzJohn et al 2021 <doi:10.12688/wellcomeopenres.16466.2>.

Last updated

cppopenmp

7.77 score 20 stars 4 dependents 61 scripts

mcstate - Monte Carlo Methods for State Space Models

Implements Monte Carlo methods for state-space models such as 'SIR' models in epidemiology. Particle MCMC (pmcmc) and SMC2 methods are planned. This package is particularly designed to work with odin/dust models, but we will see how general it becomes.

Last updated

7.51 score 19 stars 1 dependents 158 scripts

orderly1 - Lightweight Reproducible Reporting

Order, create and store reports from R. By defining a lightweight interface around the inputs and outputs of an analysis, a lot of the repetitive work for reproducible research can be automated. We define a simple format for organising and describing work that facilitates collaborative reproducible research and acknowledges that all analyses are run multiple times over their lifespans.

Last updated

7.35 score 116 stars 2 dependents 2 scripts

odin2 - Next generation odin

Temporary package for rewriting odin.

Last updated

7.33 score 11 stars 1 dependents 108 scripts

stevedore - Docker Client

Work with containers over the Docker API. Rather than using system calls to interact with a docker client, using the API directly means that we can receive richer information from docker. The interface in the package is automatically generated using the 'OpenAPI' (a.k.a., 'swagger') specification, and all return values are checked in order to make them type stable.

Last updated

7.23 score 136 stars 1 dependents 14 scripts 345 downloads

vaultr - Vault Client for Secrets and Sensitive Data

Provides an interface to a 'HashiCorp' vault server over its http API (typically these are self-hosted; see <https://www.vaultproject.io>). This allows for secure storage and retrieval of secrets over a network, such as tokens, passwords and certificates. Authentication with vault is supported through several backends including user name/password and authentication via 'GitHub'.

Last updated

6.89 score 26 stars 2 dependents 2 scripts 464 downloads

dde - Solve Delay Differential Equations

Solves ordinary and delay differential equations, where the objective function is written in either R or C. Suitable only for non-stiff equations, the solver uses a 'Dormand-Prince' method that allows interpolation of the solution at any point. This approach is as described by Hairer, Norsett and Wanner (1993) <ISBN:3540604529>. Support is also included for iterating difference equations.

Last updated

6.81 score 18 stars 2 dependents 60 scripts 494 downloads

dust2 - Next Generation dust

Experimental sources for the next generation of dust, which will properly adopt the particle filter, have support for partial parameter updates, support for multiple parameter sets and hopefully better GPU/MPI support.

Last updated

cppopenmp

6.63 score 6 dependents 118 scripts

thor - Interface to 'LMDB'

Key-value store, implemented as a wrapper around 'LMDB'; the "lightning memory-mapped database" <https://www.symas.com/mdb>. 'LMDB' is a transactional key value store that uses a memory map for efficient access. This package wraps the entire 'LMDB' interface (except duplicated keys), and provides objects for transactions and cursors.

Last updated

6.54 score 55 stars 2 dependents 13 scripts 1.6k downloads

rrq - Simple Redis Queue

Simple Redis queue in R.

Last updated

clusterinfrastructure

6.34 score 27 stars 2 dependents 15 scripts

hipercow - High Performance Computing

Set up cluster environments and jobs. Moo.

Last updated

5.93 score 1 stars 1 dependents 73 scripts

cinterpolate - Interpolation From C

Simple interpolation methods designed to be used from C code. Supports constant, linear and spline interpolation. An R wrapper is included but this package is primarily designed to be used from C code using 'LinkingTo'. The spline calculations are classical cubic interpolation, e.g., Forsythe, Malcolm and Moler (1977) <ISBN: 9780131653320>.

Last updated

infrastructureopenblas

5.92 score 8 stars 7 dependents 2 scripts 909 downloads

datastorr - Simple Data Versioning

Simple dataversioning using GitHub to store data.

Last updated

5.70 score 67 stars 5 dependents 3 scripts

odin.dust - Compile Odin to Dust

Less painful than it sounds, this package compiles an odin model to use dust, our new stochastic model system. Supports only a subset of odin models (discrete time stochastic models with no interpolation and no delays).

Last updated

5.61 score 3 stars 196 scripts

orderly2 - Compatibility Wrapper for 'orderly'

Acts as an installable package that can be used with repositories that reference 'orderly2', rather than orderly.

Last updated

5.39 score 11 stars 128 scripts

TRAMPR - 'TRFLP' Analysis and Matching Package for R

Matching terminal restriction fragment length polymorphism ('TRFLP') profiles between unknown samples and a database of known samples. 'TRAMPR' facilitates analysis of many unknown profiles at once, and provides tools for working directly with electrophoresis output through to generating summaries suitable for community analyses with R's rich set of statistical functions. 'TRAMPR' also resolves the issues of multiple 'TRFLP' profiles within a species, and shared 'TRFLP' profiles across species.

Last updated

4.83 score 22 scripts 1.5k downloads

montagu - Interface with 'montagu'

Client for interacting with the montagu API, and authentication with the montagu OrderlyWeb instance. This package is part of montagu.

Last updated

3.48 score 2 stars 3 scripts

orderly.db - Database Support for 'orderly'

Access databases from 'orderly' while running reports. Includes the basic 'SQL' support originally included in 'orderly' for establishing connections and setting up data for use within a report.

Last updated

3.00 score 1 scripts

mode - Solve Multiple ODEs

Solve multiple ODEs in parallel.

Last updated

2.88 score 153 scripts

odin.js - 'odin' 'JavaScript' support

Create 'JavaScript' differential equation models from an 'odin' model specification.

Last updated

2.88 score 5 stars 3 scripts

orderlyweb - Orderly Support for 'OrderlyWeb'

Client for 'OrderlyWeb' for use from the 'orderly1' package. Allows downloading of reports, running remote reports and other interaction with the remote report repository.

Last updated

2.78 score 1 dependents 1 scripts