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++.

Last updated 8 months ago

devtoolsdocumentationcpp

18.50 score 607 stars 217 dependents 2.4k scripts 168k 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.

Last updated 21 days ago

githubsetup

17.54 score 869 stars 336 dependents 5.6k scripts 188k 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.

Last updated 2 months ago

chk

11.89 score 48 stars 95 dependents 22 scripts 20k downloads

fledge - Smoother Change Tracking and Versioning for R Packages

Streamlines the process of updating changelogs (NEWS.md) and versioning R packages developed in git repositories.

Last updated 3 months ago

changeloggitpackage-creation

8.73 score 188 stars 10 scripts 205 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.

Last updated 2 months ago

8.49 score 9 stars 16 dependents 15 scripts 691 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.

Last updated 2 months ago

yield-per-recruit

7.84 score 7 stars 1 dependents 55 scripts 201 downloads

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.

Last updated 1 months ago

bccpp

7.81 score 5 dependents 111 scripts 1.7k downloads

revdepcheck - Automated Reverse Dependency Checking

Automated, isolated reserve dependency checking, with automatic comparison of the results to the current CRAN checks.

Last updated 1 months ago

7.77 score 104 stars 148 scripts

yesno - Ask Yes-No Questions

Asks Yes-No questions with variable or custom responses.

Last updated 2 months ago

yesno

7.69 score 9 stars 27 dependents 14 scripts 1.2k 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>.

Last updated 2 months ago

codamcmc

7.66 score 17 stars 10 dependents 111 scripts 613 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.

Last updated 2 months ago

data-framenatomicnlistnlists

7.23 score 6 stars 12 dependents 13 scripts 890 downloads

checkr - 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.

Last updated 2 months ago

assertioncheckr

7.18 score 13 stars 1 dependents 258 scripts 114 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.

Last updated 2 months ago

coefficientsmcmcterm

7.15 score 10 stars 13 dependents 15 scripts 395 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.

Last updated 2 months ago

dbilogmetadataposixctreadsfcsqliteunitswrite

6.42 score 38 stars 1 dependents 11 scripts 165 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.

Last updated 2 months ago

genericsmodel-fittings3

6.37 score 4 stars 20 dependents 1 scripts 1.6k downloads

tidyplus - 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().

Last updated 2 months ago

6.33 score 9 stars 4 dependents 1 scripts 268 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).

Last updated 2 months ago

blobdatabasesflobsqlite

5.86 score 6 stars 5 scripts 252 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.

Last updated 2 months ago

5.65 score 10 stars 6 dependents 5 scripts 388 downloads

tinter - Generate a Monochromatic Palette

Generate a palette of tints, shades or both from a single colour.

Last updated 5 years ago

colorcolour

5.65 score 51 stars 1 dependents 29 scripts 163 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>.

Last updated 1 months ago

derived-parametersmcmcmcmcr

5.53 score 8 dependents 5 scripts 252 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.

Last updated 2 months ago

5.45 score 4 stars 7 dependents 12 scripts

sims - 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.

Last updated 2 months ago

5.38 score 6 scripts 155 downloads

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.

Last updated 2 months ago

hmstimer

5.35 score 2 stars 1 dependents 4 scripts 252 downloads

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.

Last updated 2 months ago

blobflob

5.33 score 10 stars 1 dependents 12 scripts 279 downloads

timer - R6 Timer

A simple timer as an R6 class. The timer has four functions: start(), stop(), reset() and elapsed(). The elapsed() function returns the elapsed wall clock time (as opposed to CPU time) as an object of class lubridate::Duration.

Last updated 2 months ago

5.32 score 3 dependents 97 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.

Last updated 5 years ago

clipboard-buttonsknitrrmarkdown

5.26 score 57 stars 64 scripts

bbouretro - Traditional Survival, Recruitment and Population Growth Methods

Estimates annual survival, recruitment and population growth using the traditional methods. This package is part of the bbou suite of tools.

Last updated 2 months ago

5.26 score 1 dependents 3 scripts

fwapgr - Client for BC Freshwater Atlas fwapg API

Client for fwapg, a PostgreSQL database and web API for BC Freshwater Atlas data.

Last updated 2 months ago

bcfreshwater-atlasfwapg

5.26 score 8 stars 1 dependents 6 scripts

bboutools - Boreal Caribou Survival, Recruitment and Population Growth

Estimates annual survival, recruitment and population growth for boreal caribou populations using Bayesian and Maximum Likelihood models with fixed and random effects.

Last updated 2 months ago

5.11 score 1 stars 2 dependents 13 scripts

jmbr - Analyses Using JAGS

Facilitates analyses using 'Just Another Gibbs Sampler'.

Last updated 1 months ago

jagsmbrcpp

4.98 score 3 stars 5 scripts

codegrip - Syntax-Based Editing and Navigation of R Code

Provides addins for reshaping R code and navigating across syntactic constructs.

Last updated 6 months ago

4.93 score 215 stars 2 scripts

wqbench - 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.

Last updated 2 months ago

4.86 score 1 dependents 5 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.

Last updated 2 months ago

errorsmessageswarnings

4.80 score 7 stars 2 dependents 50 scripts 52 downloads

bbousims - Simulate Boreal Caribou Survival, Recruitment and Population Growth

Simulates survival and recruitment data for boreal caribou populations using hierarchical Bayesian models.

Last updated 4 months ago

4.78 score 1 dependents 6 scripts

fishbc - 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.

Last updated 2 months ago

bcfish

4.65 score 5 stars 2 scripts 182 downloads

embr - Model Builder Utility Functions and Virtual Classes

Utility functions and virtual classes shared by model builder packages such as tmbr, jmbr and smbr.

Last updated 2 months ago

analysesmbr

4.61 score 3 stars 3 dependents 4 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.

Last updated 2 months ago

batch-processing

4.56 score 6 stars 8 scripts 40 downloads

poissontemplate - 'pkgdown' Templates for Poisson Consulting Packages

This is a private template for use by Poisson consulting packages. Please don't use for your own code.

Last updated 2 months ago

4.30 score

shinyypr - Run ypr Shiny App

A user interface to the 'ypr' R package. 'Ypr' implements equilibrium-based yield per recruit methods for estimating the optimal yield for a fish population.

Last updated 2 months ago

shiny

4.26 score 3 stars 3 scripts 32 downloads

wqbc - Tidy Water Quality Data and Calculate Thresholds for British Columbia

Tidies water quality data and calculates water quality thresholds for British Columbia.

Last updated 2 months ago

bc

4.23 score 34 scripts

rescale - Rescales Data Based on Other Data

Rescales columns in a data frame based on the columns in a second data frame. For example a column can be rescaled by subtracting the mean and dividing by the standard deviation. The user can pass the names of functions which calculate the value to subtract and/or the value to divide by. The package was developed for making predictions based on models with rescaled variables. For the predictions to be valid the new data frame must have its predictor variables rescaled based on the original data.

Last updated 2 months ago

3.98 score 7 dependents 6 scripts

bboudata - 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.

Last updated 2 months ago

3.73 score 3 dependents 8 scripts

fwatlasbc - Freshwater Atlas British Columbia

What the package does (one paragraph).

Last updated 2 months ago

bcfwapgfwapgr

3.73 score 9 stars 5 scripts

subfoldr2 - Save and Load R Objects

Facilitates saving and loading R objects, data frames, tables, plots, text blocks and numbers to subfolders.

Last updated 23 days ago

3.70 score 2 stars 5 scripts

ssdtests - Tests for ssdtools

Tests for ssdtools package.

Last updated 5 days ago

3.65 score 2 scripts

shinyssdtools - ssdtools Shiny App

Shiny application for fitting species sensitivity distributions using ssdtools.

Last updated 22 days ago

shiny

3.60 score 10 scripts

mcmcdata - Manipulate MCMC Samples and Data Frames

Manipulates Monte Carlo Markov Chain samples and associated data frames.

Last updated 2 months ago

3.56 score 1 stars 4 dependents 4 scripts

bbousuite - 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`).

Last updated 16 days ago

3.40 score 4 scripts

gsdd - 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.

Last updated 1 months ago

3.38 score 2 stars 5 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.

Last updated 2 months ago

3.32 score 1 dependents 3 scripts

kootlake - Kootenay Lake Data

Annual Rainbow Trout, Bull Trout and Kokanee datasets for Kootenay Lake.

Last updated 2 months ago

bcgovkootenay-lake

3.30 score 4 scripts

rtide - 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'.

Last updated 4 months ago

3.28 score 32 scripts 606 downloads

smbr - Facilitates Bayesian Analysis using STAN

Facilitates analyses using STAN.

Last updated 2 months ago

mbrstan

3.10 score 1 stars 4 scripts

pgfeatureserv - Client for pg_featureserv RESTful web service

Client for pg_featureserv, a RESTful geospatial feature server for PostGIS.

Last updated 5 months ago

3.08 score 1 stars 2 dependents 2 scripts

ssddata - 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.

Last updated 6 months ago

dataspecies-sensitivity-distributionssd

3.05 score 1 stars 5 dependents 11 scripts 1.4k downloads

shinywqg - Water Quality Guideline Shiny App

User interface to calculate water quality guidelines.

Last updated 2 months ago

shiny

3.00 score 1 scripts

shinywqbench - R Shiny App to Calculates Aquatic Life Benchmarks

This package is the user interface to the wqbench R package and allows users to easily access standardized ecotoxicology data for thousands of chemicals. Either a SSD or deterministic method is used to determine the critical toxicity value and assessment factors to compute the aquatic life water quality benchmark for a compound.

Last updated 2 months ago

2.95 score 2 scripts

poispalette - Poisson Palettes

An R package for Poisson Consulting colour palettes.

Last updated 2 months ago

2.78 score 3 scripts

tmbr - Analyses Using TMB

Facilitates analyses using 'Template Model Builder'.

Last updated 2 months ago

mbrtmb

2.78 score 4 scripts

bauw - Data from Bayesian Population Analysis using Winbugs

What the package does (one paragraph).

Last updated 2 months ago

2.48 score 2 scripts

wqindex - Water Quality Index Calculation for British Columbia

Calculates water quality thresholds and water quality indices and plots water quality indices spatially and temporally for British Columbia.

Last updated 1 years ago

bc

2.40 score 6 scripts

klexdatr - Kootenay Lake Exploitation Study Data

Six relational 'tibbles' from the Kootenay Lake Large Trout Exploitation study. The study which ran from 2008 to 2014 caught, tagged and released large Rainbow Trout and Bull Trout in Kootenay Lake by boat angling. The fish were tagged with internal acoustic tags and/or high reward external tags and subsequently detected by an acoustic receiver array as well as reported by anglers. The data are analysed by Thorley and Andrusak (1994) <doi:10.7717/peerj.2874> to estimate the natural and fishing mortality of both species.

Last updated 2 months ago

datafishkootenay-lake

2.30 score 7 scripts 64 downloads

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.

Last updated 2 months ago

pdo

2.29 score 1 stars 13 scripts 245 downloads

curtisquadata - Curtis and Qua Creeks Productivity Study Data

Fifteen relational tibbles from the Curtis and Qua Creeks Productivity study. The study which ran from 2015 to 2017 collected data on the water quality and temperature, periphyton, benthic invertebrates and fish populations of Curtis and Qua Creeks in the Salmo Watershed, British Columbia.

Last updated 2 months ago

2.18 score 2 scripts

wqbenchdata - Water Quality Benchmark Testing Data

Reference data from the ecotox database used for examples and testing in the wqbench package.

Last updated 2 months ago

2.00 score 3 scripts

sglekwy - Sage Grouse Lek Observations for Wyoming

Greater sage grouse lek observations for the State of Wyoming from 1948 to 2015. At the request of the State of Wyoming the geolocations of individual leks and the names of individuals conducting lek counts are not included although the official state individual lek identifiers are provided.

Last updated 8 years ago

1.70 score