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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

12.17 score 51 stars 101 dependents 38 scripts 23k 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.

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ecotoxicologyenvspecies-sensitivity-distributioncpp

9.92 score 37 stars 7 dependents 126 scripts 940 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

7.96 score 11 stars 15 dependents 43 scripts 403 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

7.82 score 20 stars 11 dependents 168 scripts 415 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

7.16 score 39 stars 2 dependents 13 scripts 66 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 437 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 250 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.

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assertioncheckr

6.46 score 13 stars 278 scripts 35 downloads

ssdsims - 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

6.15 score 1 stars 50 scripts

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

5.94 score 4 stars 24 dependents 1 scripts 687 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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5.65 score 5 stars 8 dependents 19 scripts

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.

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5.47 score 1 stars 4 dependents 116 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

5.26 score 9 stars 1 dependents 90 scripts 36 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.

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hmstimer

5.26 score 2 stars 1 dependents 4 scripts 233 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

4.91 score 9 dependents 6 scripts 265 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.

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analysesmbr

4.86 score 3 stars 4 dependents 10 scripts

jmbr - Analyses Using JAGS

Facilitates analyses using 'Just Another Gibbs Sampler'.

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jagsmbrcpp

4.77 score 3 stars 7 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

4.50 score 7 stars 9 scripts 9 downloads

subfoldr2 - 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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4.18 score 2 stars 1 dependents 5 scripts

fwatlasbc - Freshwater Atlas British Columbia

What the package does (one paragraph).

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bcfwapgfwapgr

4.13 score 10 stars 6 scripts

evrfish - 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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4.08 score 1 stars 4 scripts

smbr - Facilitates Bayesian Analysis using STAN

Facilitates analyses using STAN.

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mbrstan

3.95 score 2 stars 1 dependents 5 scripts

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.

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3.90 score

ssdvignettes - Species Sensitivity Distribution Vignettes

What the package does (one paragraph).

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3.78 score 1 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.

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3.78 score 5 stars 1 dependents 5 scripts

kootlake - Kootenay Lake Data

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

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bcgovkootenay-lake

3.78 score 4 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.

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3.68 score 8 dependents 8 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 scripts

subreport - 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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3.43 score 1 stars 3 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

tmbr - Analyses Using TMB

Facilitates analyses using 'Template Model Builder'.

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mbrtmb

2.65 score 4 scripts

ssdtests - Tests for ssdtools

Slow and unstable tests for ssdtools package.

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2.65 score 1 scripts

envirotox - Envirotox Datasets

The envirotox R data package provides Species Sensitivity Distribution (SSD) datasets from the Envirotox database 2.0.0 (Connors et al. 2019). The datasets are provided for assessing general patterns in SSD data and testing code. The datasets should not be used to draw any conclusions about the toxicity of the individual chemicals.

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2.48 score 1 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.

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2.48 score 7 scripts 42 downloads

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

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.

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2.00 score 2 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.

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1.70 score