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 parametric bootstrapping.

Last updated 2 months ago

ecotoxicologyenvspecies-sensitivity-distribution

29 stars 3.35 score 53 dependencies

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 5 months ago

chk

45 stars 5.90 score 4 dependencies 66 dependents

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 6 months ago

codamcmc

17 stars 2.60 score 21 dependencies 4 dependents

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 7 months ago

2 stars 1.16 score 23 dependencies

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 Superseded by the 'chk' package.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 9 months ago

assertioncheckr

13 stars 1.64 score 5 dependencies

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 9 months ago

derived-parametersmcmcmcmcr

1.18 score 22 dependencies

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 10 months ago

pdo

1 stars 1.02 score 5 dependencies

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 1 years ago

9 stars 1.81 score 22 dependencies 1 dependents

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 1 years ago

data-framenatomicnlistnlists

6 stars 2.09 score 20 dependencies 4 dependents

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 1 years ago

yield-per-recruit

6 stars 1.40 score 39 dependencies

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 1 years ago

datafishkootenay-lake

0.92 score 13 dependencies

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 years ago

dbilogmetadataposixctreadsfcsqliteunitswrite

37 stars 2.80 score 35 dependencies

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 years ago

genericsmodel-fittings3

4 stars 2.36 score 0 dependencies 7 dependents

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 years ago

coefficientsmcmcterm

9 stars 2.40 score 10 dependencies 5 dependents

hmstimer - 'hms' Based Timer

Tracks elapsed clock time using a `hms::hms()` scalar, which if running has an attribute named start that specifies the system time when the timer was started. The elapsed time is the value of the scalar plus the difference between the current system time and the system time when the timer was started.

Last updated 2 years ago

1 stars 0.09 score 7 dependencies

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/master/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 2 years ago

rtidetidal

14 stars 1.90 score 15 dependencies

yesno - Ask Yes-No Questions

Asks Yes-No questions with variable or custom responses.

Last updated 3 years ago

yesno

8 stars 3.74 score 0 dependencies 23 dependents

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 3 years ago

errorsmessageswarnings

7 stars 1.58 score 0 dependencies 1 dependents

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 3 years ago

0.00 score 29 dependencies