roxygen2 - In-Line Documentation for R
Generate your Rd documentation, 'NAMESPACE' file, and collation field using specially formatted comments. Writing documentation in-line with code makes it easier to keep your documentation up-to-date as your requirements change. 'roxygen2' is inspired by the 'Doxygen' system for C++.
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devtoolsdocumentationcpp
19.58 score 649 stars 229 dependents 2.8k scripts 338k downloads
usethis - Automate Package and Project Setup
Automate package and project setup tasks that are otherwise performed manually. This includes setting up unit testing, test coverage, continuous integration, Git, 'GitHub', licenses, 'Rcpp', 'RStudio' projects, and more.
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githubsetup
17.91 score 918 stars 352 dependents 6.1k scripts 256k downloads
chk - Check User-Supplied Function Arguments
For developers to check user-supplied function arguments. It is designed to be simple, fast and customizable. Error messages follow the tidyverse style guide.
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chk
12.14 score 51 stars 98 dependents 38 scripts 20k downloadstibblify - Rectangle Nested Lists
A tool to rectangle a nested list, that is to convert it into a 'tibble'. This is done automatically or according to a given specification. A common use case is for nested lists coming from parsing 'JSON' files, or the 'JSON' responses of 'REST' 'APIs'. 'Rectangling' uses the 'vctrs' package, and therefore offers a wide support of vector types.
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cpp
9.53 score 74 stars 3 dependents 64 scripts 938 downloads
extras - Helper Functions for Bayesian Analyses
Functions to 'numericise' 'R' objects (coerce to numeric objects), summarise 'MCMC' (Monte Carlo Markov Chain) samples and calculate deviance residuals as well as 'R' translations of some 'BUGS' (Bayesian Using Gibbs Sampling), 'JAGS' (Just Another Gibbs Sampler), 'STAN' and 'TMB' (Template Model Builder) functions.
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8.86 score 10 stars 18 dependents 25 scripts 543 downloadsfledge - Smoother Change Tracking and Versioning for R Packages
Streamlines the process of updating changelogs (NEWS.md) and versioning R packages developed in git repositories.
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changeloggitpackage-creation
8.80 score 192 stars 14 scripts 308 downloads
term - Create, Manipulate and Query Parameter Terms
Creates, manipulates, queries and repairs vectors of parameter terms. Parameter terms are the labels used to reference values in vectors, matrices and arrays. They represent the names in coefficient tables and the column names in 'mcmc' and 'mcmc.list' objects.
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coefficientsmcmcterm
7.98 score 11 stars 15 dependents 43 scripts 450 downloads
yesno - Ask Yes-No Questions
Asks Yes-No questions with variable or custom responses.
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yesno
7.96 score 9 stars 26 dependents 15 scripts 2.6k downloads
mcmcr - Manipulate MCMC Samples
Functions and classes to store, manipulate and summarise Monte Carlo Markov Chain (MCMC) samples. For more information see Brooks et al. (2011) <isbn:978-1-4200-7941-8>.
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codamcmc
7.95 score 20 stars 11 dependents 168 scripts 437 downloadsrevdepcheck - Automated Reverse Dependency Checking
Automated, isolated reserve dependency checking, with automatic comparison of the results to the current CRAN checks.
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7.67 score 104 stars 157 scripts
ssdtools - Species Sensitivity Distributions
Species sensitivity distributions are cumulative probability distributions which are fitted to toxicity concentrations for different species as described by Posthuma et al.(2001) <isbn:9781566705783>. The ssdtools package uses Maximum Likelihood to fit distributions such as the gamma, log-logistic, log-normal and log-normal log-normal mixture. Multiple distributions can be averaged using Akaike Information Criteria. Confidence intervals on hazard concentrations and proportions are produced by bootstrapping.
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bccpp
7.57 score 1 stars 7 dependents 131 scripts 1.0k downloads
dttr2 - Manipulate Date, POSIXct and hms Vectors
Manipulates date ('Date'), date time ('POSIXct') and time ('hms') vectors. Date/times are considered discrete and are floored whenever encountered. Times are wrapped and time zones are maintained unless explicitly altered by the user.
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7.33 score 14 stars 7 dependents 6 scripts 479 downloads
readwritesqlite - Enhanced Reading and Writing for 'SQLite' Databases
Reads and writes data frames to 'SQLite' databases while preserving time zones (for POSIXct columns), projections (for 'sfc' columns), units (for 'units' columns), levels (for factors and ordered factors) and classes for logical, Date and 'hms' columns. It also logs changes to tables and provides more informative error messages.
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dbilogmetadataposixctreadsfcsqliteunitswrite
7.19 score 39 stars 2 dependents 13 scripts 71 downloads
nlist - Lists of Numeric Atomic Objects
Create and manipulate numeric list ('nlist') objects. An 'nlist' is an S3 list of uniquely named numeric objects. An numeric object is an integer or double vector, matrix or array. An 'nlists' object is a S3 class list of 'nlist' objects with the same names, dimensionalities and typeofs. Numeric list objects are of interest because they are the raw data inputs for analytic engines such as 'JAGS', 'STAN' and 'TMB'. Numeric lists objects, which are useful for storing multiple realizations of of simulated data sets, can be converted to coda::mcmc and coda::mcmc.list objects.
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data-framenatomicnlistnlists
7.10 score 6 stars 13 dependents 18 scripts 474 downloads
ypr - Yield Per Recruit
An implementation of equilibrium-based yield per recruit methods. Yield per recruit methods can used to estimate the optimal yield for a fish population as described by Walters and Martell (2004) <isbn:0-691-11544-3>. The yield can be based on the number of fish caught (or harvested) or biomass caught for all fish or just large (trophy) individuals.
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6.75 score 1 dependents 62 scripts 284 downloadscheckr - Check the Properties of Common R Objects
Expressive, assertive, pipe-friendly functions to check the properties of common R objects. In the case of failure the functions issue informative error messages. Superseded by the 'chk' package.
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assertioncheckr
6.46 score 13 stars 278 scripts 35 downloadstidyplus - Additional 'tidyverse' Functions
Provides functions such as str_crush(), add_missing_column(), coalesce_data() and drop_na_all() that complement 'tidyverse' functionality or functions that provide alternative behaviors such as if_else2() and str_detect2().
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6.27 score 10 stars 5 dependents 2 scripts 276 downloads
universals - S3 Generics for Bayesian Analyses
Provides S3 generic methods and some default implementations for Bayesian analyses that generate Markov Chain Monte Carlo (MCMC) samples. The purpose of 'universals' is to reduce package dependencies and conflicts. The 'nlist' package implements many of the methods for its 'nlist' class.
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genericsmodel-fittings3
6.11 score 4 stars 24 dependents 1 scripts 736 downloadsssdsims - Simulation Analyses for Species Sensitivity Distributions
Runs reproducible simulation studies for species sensitivity distribution (SSD) models built on the 'ssdtools' package. Expands a declarative scenario into per-step task tables, draws data, fits distributions, and estimates hazard concentrations, with a 'targets'-based, Hive-partitioned shard pipeline for running studies in parallel or on a cluster.
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quarto
6.09 score 1 stars 44 scripts
tinter - Generate a Monochromatic Palette
Generate a palette of tints, shades or both from a single colour.
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colorcolour
5.91 score 51 stars 1 dependents 53 scripts 233 downloadsssddata - Species Sensitivity Distribution Data
Reference data sets of species sensitivities to compare the results of fitting species sensitivity distributions using software such as 'ssdtools' and 'Burrlioz'. It consists of 17 primary data sets from four different Australian and Canadian organizations as well as five datasets from anonymous sources. It also includes a data set of the results of fitting various distributions using different software.
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dataspecies-sensitivity-distributionssdquarto
5.81 score 2 stars 8 dependents 17 scripts 506 downloadsfishbc - Fishes of British Columbia
Provides raw and curated data on the codes, classification and conservation status of freshwater fishes in British Columbia. Marine fishes will be added in a future release.
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bcfish
5.80 score 5 stars 1 dependents 1 scripts 147 downloads
newdata - Generate New Data Frames for Prediction
Generates new data frames for predictive purposes. By default, all specified variables vary across their range while all other variables are held constant at the default reference value. Types, classes, factor levels and time zones are always preserved. The user can specify the length of each sequence, require that only observed values and combinations are used and add new variables.
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5.68 score 5 stars 8 dependents 19 scripts
klippy - Copy to Clipboard Buttons for R Markdown HTML Documents
Insert copy to clipboard buttons in HTML documents generated with 'rmarkdown'. This package is suited for a call in a 'knitr' chunk. Buttons events are rendered using 'clipboard.js' library and 'Bootstrap.js' Tooltip plugin.
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clipboard-buttonsknitrrmarkdown
5.47 score 59 stars 99 scripts
err - Customizable Object Sensitive Messages
Messages should provide users with readable information about R objects without flooding their console. 'cc()' concatenates vector and data frame values into a grammatically correct string using commas, an ellipsis and conjunction. 'cn()' allows the user to define a string which varies based on a count. 'co()' combines the two to produce a customizable object aware string. The package further facilitates this process by providing five 'sprintf'-like types such as '%n' for the length of an object and '%o' for its name as well as wrappers for pasting objects and issuing errors, warnings and messages.
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errorsmessageswarnings
5.34 score 9 stars 1 dependents 90 scripts 41 downloads
fwapgr - Client for BC Freshwater Atlas fwapg API
Client for fwapg, a PostgreSQL database and web API for BC Freshwater Atlas data.
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bcfreshwater-atlasfwapg
5.33 score 9 stars 1 dependents 9 scripts
hmstimer - 'hms' Based Timer
Tracks elapsed clock time using a `hms::hms()` scalar. It was was originally developed to time Bayesian model runs. It should not be used to estimate how long extremely fast code takes to execute as the package code adds a small time cost.
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hmstimer
5.28 score 2 stars 1 dependents 4 scripts 267 downloads
mcmcderive - Derive MCMC Parameters
Generates derived parameter(s) from Monte Carlo Markov Chain (MCMC) samples using R code. This allows Bayesian models to be fitted without the inclusion of derived parameters which add unnecessary clutter and slow model fitting. For more information on MCMC samples see Brooks et al. (2011) <isbn:978-1-4200-7941-8>.
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derived-parametersmcmcmcmcr
5.08 score 9 dependents 6 scripts 310 downloadsembr - Model Builder Utility Functions and Virtual Classes
Utility functions and virtual classes shared by model builder packages such as tmbr, jmbr and smbr.
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analysesmbr
4.86 score 3 stars 4 dependents 10 scriptsjmbr - Analyses Using JAGS
Facilitates analyses using 'Just Another Gibbs Sampler'.
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jagsmbrcpp
4.80 score 3 stars 7 scriptscodegrip - Syntax-Based Editing and Navigation of R Code
Provides addins for reshaping R code and navigating across syntactic constructs.
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4.65 score 223 stars 3 scripts
batchr - Batch Process Files
Processes multiple files with a user-supplied function. The key design principle is that only files which were last modified before the directory was configured are processed. A hidden file stores the configuration time and function etc while successfully processed files are automatically touched to update their modification date. As a result batch processing can be stopped and restarted and any files created (or modified or deleted) during processing are ignored.
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batch-processing
4.62 score 7 stars 9 scripts 9 downloads
dbflobr - Read and Write Files to SQLite Databases
Reads and writes files to SQLite databases <https://www.sqlite.org/index.html> as flobs (a flob is a blob that preserves the file extension).
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blobdatabasesflobsqlite
4.57 score 5 stars 5 scripts 47 downloadssims - Simulate Data from R or 'JAGS' Code
Generates data from R or 'JAGS' code for use in simulation studies. The data are returned as an 'nlist::nlists' object and/or saved to file as individual '.rds' files. Parallelization is implemented using the 'future' package. Progress is reported using the 'progressr' package.
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4.48 score 9 scripts 235 downloadsbbousims - Simulate Boreal Caribou Survival, Recruitment and Population Growth
Simulates survival and recruitment data for boreal caribou populations using hierarchical Bayesian models.
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4.38 score 1 dependents 7 scriptssubfoldr2 - Save and Load R Objects
Facilitates saving and loading R objects, data frames, tables, plots, text blocks and numbers to subfolders.
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4.22 score 2 stars 1 dependents 5 scripts
flobr - Convert Files to and from Binary Objects (BLOBs)
Converts files to and from flobs. A flob is a file that was read into binary in integer-mode as little endian, saved as the single element of a named list (where the name is the name of the original file) and then serialized before being coerced into a blob. Flobs are useful for writing and reading files to and from databases.
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blobflob
4.21 score 10 stars 1 dependents 12 scripts 65 downloadsevrfish - R Tools for EVR Fish Projects
Provides functions linearly interpolate missing values and calculate growing season degree days and growing degree days from daily water temperature data. It also exports fish codes for British Columbia and Alberta from the `fishbc` package.
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4.15 score 1 stars 4 scripts
fwatlasbc - Freshwater Atlas British Columbia
What the package does (one paragraph).
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bcfwapgfwapgr
4.13 score 10 stars 6 scriptswqbench - Calculate Aquatic Life Benchmarks
Download recent versions of the US EPA ECOTOX database. Clean, standardize and classify data so values are comparable. Use a SSD or deterministic method to determine the critical toxicity value and assessment factors to compute the aquatic life water quality benchmark for a compound.
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4.08 score 1 dependents 5 scriptssmbr - Facilitates Bayesian Analysis using STAN
Facilitates analyses using STAN.
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mbrstan
4.02 score 2 stars 1 dependents 5 scriptsgsdd - Calculate Growing Season Degree Days from Water Temperature Data
Calculates Growing Season Degree Days (GSDD), Growing Degree Days (GDD) and the Growing Seasons (GSS) from water temperature data. GSSD is a water temperature metric that is a useful predictor of age-0 trout size at the beginning of winter. It is the accumulated thermal units (in C) during the growing season based on the mean daily water temperature values. GDD is the GSSD to a particular date.
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3.88 score 5 stars 1 dependents 5 scriptsssdvignettes - Species Sensitivity Distribution Vignettes
What the package does (one paragraph).
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3.78 score 1 scriptskootlake - Kootenay Lake Data
Annual Rainbow Trout, Bull Trout and Kokanee datasets for Kootenay Lake.
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bcgovkootenay-lake
3.78 score 4 scriptsbboudata - Data for bbou Project
This package contains boreal caribou demographic data which can be used as validation for the associated shiny-app and analysis. The overall goal of the bbou packages is to develop a more standardized and consistent method for the comparison of boreal caribou survival rates, recruitment and population dynamics across Canada.
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3.69 score 3 dependents 18 scripts
mcmcdata - Manipulate MCMC Samples and Data Frames
Manipulates Monte Carlo Markov Chain samples and associated data frames.
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3.65 score 1 stars 5 dependents 4 scriptspgfeatureserv - Client for pg_featureserv RESTful web service
Client for pg_featureserv, a RESTful geospatial feature server for PostGIS.
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3.56 score 2 stars 2 dependents 2 scripts
rpdo - Pacific Decadal Oscillation Index Data
Monthly Pacific Decadal Oscillation (PDO) index values from January 1900 to September 2018. Superseded by 'rsoi' package which includes the historical and most recent monthly PDO index values together with related climate indices.
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pdo
2.77 score 1 stars 13 scripts 67 downloads
shinyssdtools - ssdtools Shiny App
Shiny application for fitting species sensitivity distributions using ssdtools.
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shiny
3.56 score 7 scriptssubreport - Generate Reports from `subfoldr2` Objects
Facilitates generation of .Rmd and .html reports from tables, (code) blocks and figures (plots and windows) saved using the subfoldr2 package. To quickly view all the results use `sbr_knit_results()`. The `sbr_n()` and `sbr_s()` functions can be used to insert numbers or strings saved using subfoldr2.
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3.38 score 1 stars 3 scripts
bboushiny - Shiny App for Analysing Boreal Caribou Surival, Recruitment and Lambda
Use Bayesian methods to calculate survival, recruitment and lambda as well as confidence intervals.
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2.95 score 1 dependents 3 scriptsrtide - Tide Heights
Calculates tide heights based on tide station harmonics. It includes the harmonics data for 637 US stations. The harmonics data was converted from <https://github.com/poissonconsulting/rtide/blob/main/data-raw/harmonics-dwf-20151227-free.tar.bz2>, NOAA web site data processed by David Flater for 'XTide'. The code to calculate tide heights from the harmonics is based on 'XTide'.
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2.91 score 41 scripts 687 downloadspoispalette - Poisson Palettes
An R package for Poisson Consulting colour palettes.
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2.90 score 1 stars 3 scriptstmbr - Analyses Using TMB
Facilitates analyses using 'Template Model Builder'.
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mbrtmb
2.78 score 4 scriptsbbousuite - Easily Install and Load `bbou` (Boreal cariBOU) Packages
The `bbou` suite of packages are designed to allow analysis (`bbouretro` and `bboutools`) and simulation (`bbousims`) of Boreal Caribou survival and recruitment data ('bboudata') to estimate population growth rates. A shiny app is also available (`bboushiny`).
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2.78 score 1 stars 3 scripts
shinywqg - Water Quality Guideline Shiny App
User interface to calculate water quality guidelines.
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shiny
2.70 score 1 scriptsssdtests - Tests for ssdtools
Slow and unstable tests for ssdtools package.
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2.65 score 1 scripts
bauw - Data from Bayesian Population Analysis using Winbugs
What the package does (one paragraph).
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2.18 score 1 stars 4 scripts