diff --git a/DESCRIPTION b/DESCRIPTION index 49654176..11a64f95 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: monty Title: Monte Carlo Models -Version: 0.2.39 +Version: 0.2.40 Authors@R: c(person("Rich", "FitzJohn", role = c("aut", "cre"), email = "rich.fitzjohn@gmail.com"), person("Wes", "Hinsley", role = "aut"), diff --git a/R/packer.R b/R/packer.R index eb0000f2..6c2a68cb 100644 --- a/R/packer.R +++ b/R/packer.R @@ -2,7 +2,7 @@ ##' unstructured vector of numbers (the vector being updated by an ##' MCMC for example) and a structured list of named values, which is ##' easier to program against. This is useful for the bridge between -##' model parameters and a models's implementation, but it is also +##' model parameters and a model's implementation, but it is also ##' useful for the state vector in a state-space model. We refer to ##' the process of taking a named list of scalars, vectors and arrays ##' and converting into a single vector "packing" and the inverse diff --git a/R/rng.R b/R/rng.R index 583e261b..f83074c3 100644 --- a/R/rng.R +++ b/R/rng.R @@ -297,7 +297,7 @@ monty_rng <- R6::R6Class( ##' ##' @param size The number of trials (zero or more, length 1 or n) ##' - ##' @param prob The mean probability of sucess on each trial + ##' @param prob The mean probability of success on each trial ##' (between 0 and 1, length 1 or n) ##' ##' @param rho The dispersion parameter (between 0 and 1, length 1 or n) diff --git a/R/runner-callr.R b/R/runner-callr.R index 67a5318e..dc2d282a 100644 --- a/R/runner-callr.R +++ b/R/runner-callr.R @@ -4,7 +4,7 @@ ##' this is the same as "worker" processes. Unless your chains take a ##' few seconds to run, this will be slower than running with the ##' default serial runner ([monty_runner_serial]), however for long -##' running chains, the speedup will typically scale with workers +##' running chains, the speed-up will typically scale with workers ##' added, so long as your chains divide neatly over workers. ##' ##' @title Run MCMC chains in parallel with `callr` diff --git a/R/runner.R b/R/runner.R index 6cc9f0d8..35788cc4 100644 --- a/R/runner.R +++ b/R/runner.R @@ -54,7 +54,7 @@ monty_runner_serial <- function(progress = NULL) { ##' Run MCMC chains in parallel (at the same time). This runner uses ##' the `parallel` package to distribute your chains over a number of ##' worker processes on the same machine. Compared with -##' [monty_runner_callr] (Whch is similar to the "worker" support in +##' [monty_runner_callr] (Which is similar to the "worker" support in ##' `mcstate` version 1), this is very simple. In particular we do ##' not report back any information about progress while a chain is ##' running on a worker or even across chains. There's also no diff --git a/README.md b/README.md index 4740e905..40632517 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ # monty -[![Project Status: Concept – Minimal or no implementation has been done yet, or the repository is only intended to be a limited example, demo, or proof-of-concept.](https://www.repostatus.org/badges/latest/concept.svg)](https://www.repostatus.org/#concept) +[![Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip) [![R-CMD-check](https://github.com/mrc-ide/monty/actions/workflows/R-CMD-check.yaml/badge.svg?branch=main)](https://github.com/mrc-ide/monty/actions/workflows/R-CMD-check.yaml) [![codecov.io](https://codecov.io/github/mrc-ide/monty/coverage.svg?branch=main)](https://codecov.io/github/mrc-ide/monty?branch=main) @@ -10,8 +10,6 @@ See the [package vignette](https://mrc-ide.github.io/monty/articles/monty.html) for a basic introduction. -The package is in an early, though rapid, stage of development and we cannot guarantee that interfaces will not change (in fact, we can guarantee that they **will** really). However the core concepts have now solidified. - The core of the package is built around some basic ideas: * you have some [statistical model](https://mrc-ide.github.io/monty/reference/monty_model.html) from which you would like to draw samples using MCMC ([`monty::monty_sample`](https://mrc-ide.github.io/monty/reference/monty_sample.html)) diff --git a/inst/WORDLIST b/inst/WORDLIST index 3a3e998b..7611b273 100644 --- a/inst/WORDLIST +++ b/inst/WORDLIST @@ -8,6 +8,8 @@ Poisson R's SEF VCV +WIP +burnin cli's codecov composable diff --git a/man/monty_packer.Rd b/man/monty_packer.Rd index cd192499..0b316665 100644 --- a/man/monty_packer.Rd +++ b/man/monty_packer.Rd @@ -67,7 +67,7 @@ Build a packer, which can be used to translate between an unstructured vector of numbers (the vector being updated by an MCMC for example) and a structured list of named values, which is easier to program against. This is useful for the bridge between -model parameters and a models's implementation, but it is also +model parameters and a model's implementation, but it is also useful for the state vector in a state-space model. We refer to the process of taking a named list of scalars, vectors and arrays and converting into a single vector "packing" and the inverse diff --git a/man/monty_rng.Rd b/man/monty_rng.Rd index 16a16425..20155de1 100644 --- a/man/monty_rng.Rd +++ b/man/monty_rng.Rd @@ -387,7 +387,7 @@ Generate \code{n} numbers from a beta-binomial distribution \item{\code{size}}{The number of trials (zero or more, length 1 or n)} -\item{\code{prob}}{The mean probability of sucess on each trial +\item{\code{prob}}{The mean probability of success on each trial (between 0 and 1, length 1 or n)} \item{\code{rho}}{The dispersion parameter (between 0 and 1, length 1 or n)} diff --git a/man/monty_runner_callr.Rd b/man/monty_runner_callr.Rd index c6e96f83..ebe5b470 100644 --- a/man/monty_runner_callr.Rd +++ b/man/monty_runner_callr.Rd @@ -36,6 +36,6 @@ worker processes on the same machine. If you have used \code{mcstate}, this is the same as "worker" processes. Unless your chains take a few seconds to run, this will be slower than running with the default serial runner (\link{monty_runner_serial}), however for long -running chains, the speedup will typically scale with workers +running chains, the speed-up will typically scale with workers added, so long as your chains divide neatly over workers. } diff --git a/man/monty_runner_parallel.Rd b/man/monty_runner_parallel.Rd index 209cf25e..f722c817 100644 --- a/man/monty_runner_parallel.Rd +++ b/man/monty_runner_parallel.Rd @@ -24,7 +24,7 @@ A runner of class \code{monty_runner} that can be passed to Run MCMC chains in parallel (at the same time). This runner uses the \code{parallel} package to distribute your chains over a number of worker processes on the same machine. Compared with -\link{monty_runner_callr} (Whch is similar to the "worker" support in +\link{monty_runner_callr} (Which is similar to the "worker" support in \code{mcstate} version 1), this is very simple. In particular we do not report back any information about progress while a chain is running on a worker or even across chains. There's also no diff --git a/vignettes/dsl.Rmd b/vignettes/dsl.Rmd index 4c77b693..11f99c10 100644 --- a/vignettes/dsl.Rmd +++ b/vignettes/dsl.Rmd @@ -52,14 +52,14 @@ We can draw samples from the model if we provide a `monty_rng` object ```{r} rng <- monty_rng$new() -theta <- prior$direct_sample(rng) +theta <- monty_model_direct_sample(prior, rng) theta ``` We can compute the (log) density at a point in parameter space ```{r} -prior$density(theta) +monty_model_density(prior, theta) ``` The computed properties for the model are: