Rich FitzJohn

Rich FitzJohn

20 packages on CRAN

4 packages on GitHub

cyphr

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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.

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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.

ids

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Generate random or human readable and pronounceable identifiers.

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Uses the node library 'is-my-json-valid' to validate 'JSON' against a 'JSON' schema.

redux

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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.

ring

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Circular / ring buffers in R and C. There are a couple of different buffers here with different implementations that represent different trade-offs.

storr

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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.

thor

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Key-value store, implemented as a wrapper around 'LMDB'; the "lightning memory-mapped database" <https://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.

TRAMPR

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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.

remake

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Make-like build management in R. The idea is to have some sort of declarative programming to build analysis pipelines, without having to use/install make.

rexcel

github
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rexcel now is part of a complete sentence.

cowsay

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Allows printing of character strings as messages/warnings/etc. with ASCII animals, including cats, cows, frogs, chickens, ghosts, and more.

distcrete

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Creates discretised versions of continuous distribution functions by mapping continuous values to an underlying discrete grid, based on a (uniform) frequency of discretisation, a valid discretisation point, and an integration range. For a review of discretisation methods, see Chakraborty (2015) <doi:10.1186/s40488-015-0028-6>.

geiger

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Methods for fitting macroevolutionary models to phylogenetic trees.

getPass

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A micro-package for reading "passwords", i.e. reading user input with masking, so that the input is not displayed as it is typed. Currently we have support for 'RStudio', the command line (every OS), and any platform where 'tcltk' is present.

incidence

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Provides functions and classes to compute, handle and visualise incidence from dated events for a defined time interval. Dates can be provided in various standard formats. The class 'incidence' is used to store computed incidence and can be easily manipulated, subsetted, and plotted. In addition, log-linear models can be fitted to 'incidence' objects using 'fit'. This package is part of the RECON (<http://www.repidemicsconsortium.org/>) toolkit for outbreak analysis.

jqr

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Client for 'jq', a 'JSON' processor (<https://stedolan.github.io/jq/>), written in C. 'jq' allows the following with 'JSON' data: index into, parse, do calculations, cut up and filter, change key names and values, perform conditionals and comparisons, and more.

jailbreakr

github
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Liberate data from really terrible excel spreadsheets. Provides functionality to turn any excel spreadsheet into data that can be manipulated in R, and tools to detect "logical" tables within such data. If you have well behaved data you will be better off with something like 'readxl' for quickly reading data in.

nodbi

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Simplified document database manipulation and analysis, including support for many 'NoSQL' databases, including document databases ('Elasticsearch', 'CouchDB', 'MongoDB'), 'key-value' databases ('Redis'), and other 'NoSQL' types ('etcd').

optparse

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A command line parser inspired by Python's 'optparse' library to be used with Rscript to write "#!" shebang scripts that accept short and long flag/options.

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Bayesian reconstruction of disease outbreaks using epidemiological and genetic information. Jombart T, Cori A, Didelot X, Cauchemez S, Fraser C and Ferguson N. 2014. <doi:10.1371/journal.pcbi.1003457>.

phyndr

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Use topological or taxonomic information to maximize the overlap of phylogenetic and comparative data.

progress

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Configurable Progress bars, they may include percentage, elapsed time, and/or the estimated completion time. They work in terminals, in 'Emacs' 'ESS', 'RStudio', 'Windows' 'Rgui' and the 'macOS' 'R.app'. The package also provides a 'C++' 'API', that works with or without 'Rcpp'.

notary

github
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Signing and verification of R packages.