orderly2 - Orderly Next Generation

Reimplementation of orderly based on outpack.

Last updated 5 hours ago

3 stars 2.63 score 15 dependencies 2 dependents

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 2 days ago

1 stars 2.05 score 30 dependencies

hipercow - High Performance Computing

Set up cluster environments and jobs. Moo.

Last updated 2 days ago

1 stars 2.18 score 10 dependencies 1 dependents

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 4 days ago

infrastructure

101 stars 4.48 score 8 dependencies 2 dependents

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 4 days ago

19 stars 2.46 score 22 dependencies

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 10 days ago

3 stars 1.51 score 32 dependencies

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

18 stars 2.60 score 15 dependencies 3 dependents

rrq - Simple Redis Queue

Simple Redis queue in R.

Last updated 2 months ago

clusterinfrastructure

23 stars 2.76 score 24 dependencies 3 dependents

conan2 - Conan the Librarian

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

Last updated 3 months ago

1.45 score 5 dependencies 1 dependents

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 3 months ago

jsonjson-validationjsonvalidate

48 stars 5.11 score 5 dependencies 35 dependents

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 5 months ago

0.82 score 17 dependencies

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 months ago

15 stars 2.20 score 2 dependencies 2 dependents

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 6 months ago

87 stars 4.44 score 3 dependencies 9 dependents

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 7 months ago

52 stars 3.82 score 3 dependencies 10 dependents

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 7 months ago

infrastructure

9 stars 2.00 score 0 dependencies 3 dependents

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 8 months ago

22 stars 2.80 score 10 dependencies 3 dependents

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 9 months ago

30 stars 2.82 score 7 dependencies 2 dependents

orderly.sharedfile - Package Title Here

Access files in shared locations from orderly.

Last updated 10 months ago

1 stars 0.36 score 16 dependencies

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 11 months ago

encryptionopensslpeer-reviewedsodium

92 stars 4.17 score 6 dependencies 1 dependents

didehpc - DIDE HPC Support

DIDE HPC support.

Last updated 11 months ago

clusterinfrastructure

10 stars 1.38 score 30 dependencies

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 12 months ago

0.49 score 17 dependencies

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 12 months ago

134 stars 4.67 score 4 dependencies

orderly.server - Serve Orderly

Run orderly reports as a server.

Last updated 12 months ago

0.71 score 61 dependencies

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

116 stars 4.71 score 34 dependencies 4 dependents

queuer - Queue Tasks

Queue tasks to number of backends.

Last updated 1 years ago

clusterinfrastructure

4 stars 1.08 score 20 dependencies 1 dependents

context - Contexts for evaluating R expressions

Contexts for evaluating R expressions.

Last updated 1 years ago

clusterinfrastructure

5 stars 1.38 score 9 dependencies 2 dependents

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 1 years ago

0.82 score 40 dependencies 1 dependents

mode - Solve Multiple ODEs

Solve multiple ODEs in parallel.

Last updated 1 years ago

0.09 score 16 dependencies

odin.js - 'odin' 'JavaScript' support

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

Last updated 2 years ago

5 stars 0.91 score 12 dependencies

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 2 years ago

0.68 score 0 dependencies

ids - Generate Random Identifiers

Generate random or human readable and pronounceable identifiers.

Last updated 3 years ago

93 stars 8.88 score 0 dependencies 154 dependents

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 3 years ago

2 stars 0.49 score 4 dependencies

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

116 stars 5.65 score 2 dependencies 36 dependents

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

27 stars 2.09 score 20 dependencies

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

2 stars 0.61 score 22 dependencies

jenner - Internal Montagu Helpers

Helpers for Montagu.

Last updated 5 years ago

0.36 score 33 dependencies

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 6 years ago

peer-reviewed

16 stars 1.58 score 4 dependencies

syncr - Synchronise Directories

Syncronise directories using rsync.

Last updated 7 years ago

clusterinfrastructure

9 stars 1.00 score 0 dependencies