ids - Generate Random Identifiers

Generate random or human readable and pronounceable identifiers.

Last updated

13.26 score 94 stars 170 dependents 230 scripts 367k 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

10.73 score 51 stars 51 dependents 52 scripts 17k 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.

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10.42 score 118 stars 27 dependents 62 scripts 7.4k 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.

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infrastructure

10.04 score 106 stars 6 dependents 292 scripts 1.1k 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

9.85 score 11 stars 3 dependents 135 scripts 652 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.

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hiredis

9.36 score 95 stars 6 dependents 55 scripts 6.0k 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

8.55 score 33 stars 4 dependents 600 scripts 585 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

8.39 score 97 stars 2 dependents 60 scripts 990 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.

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cpp

8.34 score 7 stars 7 dependents 81 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

7.83 score 116 stars 2 dependents 1 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>.

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cppopenmp

7.76 score 20 stars 4 dependents 59 scripts

odin2 - Next generation odin

Temporary package for rewriting odin.

Last updated

7.68 score 9 stars 1 dependents 99 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

7.51 score 137 stars 2 dependents 13 scripts 362 downloads

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

7.31 score 19 stars 1 dependents 100 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

cppopenmp

7.21 score 6 dependents 113 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

7.15 score 55 stars 2 dependents 11 scripts 3.9k 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 780 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

6.59 score 18 stars 2 dependents 36 scripts 439 downloads

rrq - Simple Redis Queue

Simple Redis queue in R.

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clusterinfrastructure

6.31 score 25 stars 2 dependents 15 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>.

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infrastructureopenblas

5.95 score 8 stars 7 dependents 2 scripts 1.1k downloads

orderly2 - Compatibility Wrapper for 'orderly'

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

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5.86 score 11 stars 126 scripts

hipercow - High Performance Computing

Set up cluster environments and jobs. Moo.

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5.83 score 1 stars 1 dependents 58 scripts

datastorr - Simple Data Versioning

Simple dataversioning using GitHub to store data.

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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

5.46 score 3 stars 137 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

5.31 score 23 scripts 4.5k 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.

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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.

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3.30 score 1 scripts

odin.js - 'odin' 'JavaScript' support

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

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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.

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2.78 score 1 dependents 1 scripts

syncr - Synchronise Directories

Syncronise directories using rsync.

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clusterinfrastructure

2.65 score 9 stars 2 scripts

hipercow.dide - HPC Support for the DIDE cluster

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

Last updated

2.48 score 1 stars 1 scripts

conan2 - Conan the Librarian

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

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2.48 score 1 dependents 1 scripts

mode - Solve Multiple ODEs

Solve multiple ODEs in parallel.

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2.32 score 42 scripts

conan - Conan the Librarian

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

Last updated

2.30 score 4 stars 8 scripts

orderly.sharedfile - Package Title Here

Access files in shared locations from orderly.

Last updated

2.18 score 1 stars 3 scripts