ids - Generate Random Identifiers

Generate random or human readable and pronounceable identifiers.

Last updated 3 years ago

13.29 score 93 stars 163 packages 168 scripts 563k 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 4 years ago

10.00 score 116 stars 34 packages 57 scripts 2.9k 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 5 months ago

infrastructure

9.91 score 105 stars 2 packages 286 scripts 834 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 8 months ago

jsonjson-validationjsonvalidate

9.86 score 48 stars 42 packages 27 scripts 5.9k downloads

orderly - 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 1 years ago

9.63 score 117 stars 4 packages 94 scripts 235 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 11 months ago

9.16 score 91 stars 9 packages 41 scripts 1.8k 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 2 months ago

8.92 score 30 stars 3 packages 514 scripts 1.0k downloads

orderly2 - Orderly Next Generation

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 1 days ago

8.32 score 8 stars 2 packages 49 scripts

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 1 years ago

encryptionopensslpeer-reviewedsodium

8.18 score 93 stars 2 packages 34 scripts 315 downloads

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 2 months ago

7.84 score 18 stars 3 packages 60 scripts

rrq - Simple Redis Queue

Simple Redis queue in R.

Last updated 7 days ago

clusterinfrastructure

7.36 score 24 stars 3 packages 11 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 5 months ago

7.36 score 19 stars 84 scripts

thor - Interface to 'LMDB'

Key-value store, implemented as a wrapper around 'LMDB'; the "lightning memory-mapped database" <https://www.symas.com/lmdb>. '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 2 months ago

7.35 score 52 stars 13 packages 11 scripts 556 downloads

context - Contexts for evaluating R expressions

Contexts for evaluating R expressions.

Last updated 1 years ago

clusterinfrastructure

6.87 score 5 stars 2 packages 1.7k scripts

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 8 hours ago

6.83 score 2 stars 2 packages 24 scripts

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 1 years ago

6.75 score 23 stars 1 packages 2 scripts 1.6k downloads

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 1 years ago

6.68 score 134 stars 12 scripts 311 downloads

hipercow - High Performance Computing

Set up cluster environments and jobs. Moo.

Last updated 7 days ago

6.51 score 1 stars 1 packages 40 scripts

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 1 days ago

6.16 score 1 packages 23 scripts

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 2 months ago

6.01 score 15 stars 34 scripts 493 downloads

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 2 months ago

infrastructure

5.91 score 9 stars 3 packages 1 scripts 986 downloads

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 2 months ago

5.87 score 3 stars 119 scripts

odin2 - Next generation odin

Temporary package for rewriting odin.

Last updated 13 hours ago

5.78 score 3 stars 14 scripts

didehpc - DIDE HPC Support

DIDE HPC support.

Last updated 1 years ago

clusterinfrastructure

5.72 score 10 stars 58 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 3 years ago

4.72 score 23 scripts 1.1k 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 5 years ago

3.48 score 2 stars 3 scripts

hipercow.windows - DIDE HPC Support for Windows

Driver for using the DIDE windows cluster, via the hipercow package. Typically the user will install that package directly and this once they are requested to.

Last updated 7 days ago

3.43 score 1 stars 2 scripts

orderly.db - Database Support for 'orderly2'

Access databases from 'orderly2' 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 10 months ago

3.30 score 1 scripts

queuer - Queue Tasks

Queue tasks to number of backends.

Last updated 1 years ago

clusterinfrastructure

3.26 score 4 stars 1 packages 4 scripts

rrlite - R Bindings to rlite

R bindings to rlite. rlite is a "self-contained, serverless, zero-configuration, transactional redis-compatible database engine. rlite is to Redis what SQLite is to SQL.".

Last updated 16 days ago

peer-reviewed

3.23 score 17 stars 1 scripts

conan2 - Conan the Librarian

Create libraries. For us, there is no spring. Just the wind that smells fresh before the storm.

Last updated 8 months ago

3.22 score 1 packages 1 scripts

provisionr - Provision a Library

Provision a set of packages into a new library, possibly for use on a different architecture.

Last updated 4 years ago

clusterinfrastructure

3.13 score 27 stars 1 scripts

odin.js - 'odin' 'JavaScript' support

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

Last updated 2 years ago

2.88 score 5 stars 3 scripts

orderlyweb - Orderly Support for 'OrderlyWeb'

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

Last updated 2 years ago

2.78 score 1 packages 1 scripts

syncr - Synchronise Directories

Syncronise directories using rsync.

Last updated 7 years ago

clusterinfrastructure

2.65 score 9 stars 2 scripts

orderly.server - Serve Orderly

Run orderly reports as a server.

Last updated 1 years ago

2.40 score 1 scripts

heartbeatr - Heartbeat Support using 'Redis'

Simple heartbeat support for R using 'Redis'. A heartbeat is a background thread that acts as a dead-man's switch. It will create a key on Redis that will automatically expire after a number of seconds and then periodically refresh that key, even when the R process is busy. If the process dies for some reason, then the key will disappear. A heartbeat can be used to detect loss of worker processes on shared systems.

Last updated 4 years ago

2.30 score 2 stars 4 scripts

jenner - Internal Montagu Helpers

Helpers for Montagu.

Last updated 6 years ago

2.18 score 3 scripts

mode - Solve Multiple ODEs

Solve multiple ODEs in parallel.

Last updated 2 years ago

2.08 score 24 scripts

orderly.sharedfile - Package Title Here

Access files in shared locations from orderly.

Last updated 2 months ago

2.00 score 1 stars 2 scripts

orderly.sharepoint - Sharepoint Driver for Orderly

Store orderly reports on Sharepoint. Provides an orderly remote driver that can be used to share orderly reports using Sharepoint. You can use Sharepoint's access controls and use this to set up a lightweight way of using orderly within a team.

Last updated 1 years ago

2.00 score 2 scripts