epiverse-trace / bpmodels Goto Github PK

Methods for simulating and analysing the sizes and lengths of chains from branching process models

Home Page: https://epiverse-trace.github.io/bpmodels/

License: Other

R 100.00%

branching-process epidemic-dynamics epidemic-modelling epidemic-simulations outbreak-simulator r r-package transmission-chain transmission-chain-reconstruction epidemiology

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bpmodels's Issues

Version in description does not match news.md

Update R-CMD-check.yaml workflow to match {packagetemplate}

The "R-CMD-check.yaml" file here should be updated to match that in the Epiverse-TRACE template here.

Add copyright holder

Add the "cph" tag to the relevant copyright holder's DESCRIPTION author entry.

Create pkgdown site for bpmodels

Update README with aspirational install instructions

In preparation for the CRAN release, the README should provide instructions on how to install from CRAN.

Convert references database from .bibtex to CSL-JSON

See this issue in epiparameter for more details.

The following comment in the examples of chain_sim() says that specifying serial and setting tree=FALSE will throw an error but this has subsequently been relaxed to a warning (see #53), so the comment in the example here should be updated to reflect the change.

This will require a simple rewording of the comment and a rerun of devtools::check(), which will in turn run devtools::document() to regenerate the .Rd files.

Codecov badge pointing to master

This issue is to point out that the Codecov badge in the Readme points to the now renamed master branch. This could be fixed by pointing it to main. Should have caught this in #24 but slipped past me.

Explain why we set seed

It might be worth mentioning somewhere in the get started vignette that the simulation is stochastic and therefore setting the seed is required for consistent output. This could be in the text or a small comment above the set.seed()

Originally posted by @joshwlambert in #79 (comment)

Add use case vignettes

Adding use case vignettes would help the user identify ways to apply this package. Some use cases include:

Forecasting an epidemic given data (ideally a linelist) on the first few cases. (*Will update with more later)
Estimating R0 from epidemic data

Remove "lint_changed_files.yaml" and switch to TRACE org lint workflow

clarify documentation for @return in chain_sim / change behavior for `tree` + `serial` combinations

The documentation for return value in chain_sim suggests that all combinations of serial and tree are allowed, but function complains if tree=FALSE with a serial function defined.

This suggests either a documentation or behavior bug.

Relative to behavior option, I have a case where I don't need id, generation, ancestor information, but do need time and am memory constrained, so disregarding those would be useful.

Add citation file

Update .lintr to match {packagetemplate}

Check whether adding one in rbinom_size still makes sense

https://github.com/sbfnk/bpmodels/blob/09ef8cbec7aeeb81287a91c9a9e6efb9d2c82eb9/R/utils.r#L23

This seems wrong - should it be just x in the second argument?

Change package title in DESCRIPTION to title case

  The Title field should be in title case. Current version is:
  ‘Analysing transmission chain statistics using branching process models’
  In title case that is:
  ‘Analysing Transmission Chain Statistics using Branching Process Models’

Remove {epiparameter} from suggests and "Remotes" from DESCRIPTION for CRAN release

I didn't go for a full review just yet but I want to flag early that you cannot use Remotes on CRAN. There are alternatives but they have their own issues. Your best bet is to: - either wait that epiparameter is on CRAN - or drop epiparameter from Suggests

Originally posted by @Bisaloo in #79 (comment)

Add spell checking to package

Add spellchecking similar to the implementation in epichains and other epiverse-TRACE packages.

Update README to use explicit argument matching

I would use explicit argument matching in the README as it will likely be read by people new to the package and avoid position matching which can lead to issues for users.

Originally posted by @joshwlambert in #79 (comment)

Update website style

The website seems to be outdated and should be updated to use the latest version of bootstrap and Epiverse theme.

Revise package title in DESCRIPTION and README to include "Simulating"

Could add the word "simulating" somewhere in the package title in DESCRIPTION as currently only covers the inference part of the package

Originally posted by @joshwlambert in #79 (comment)

Citation file: change old-style `citEntry()` to `bibentry()`

> devtools::check(remote = TRUE, manual = TRUE)
 Package CITATION file contains call(s) to old-style citEntry().  Please
   use bibentry() instead.

Likelihoods as callable functions?

At present, it looks like the individual likelihood functions aren't in NAMESPACE so can't be called? Although maybe these are passed through chain_ll()?

Move quickstart in README to website

The current quickstart section in the README is probably best placed on the package website.

The quick start in the README should be simple and point out the current functionality without providing too many details on the inner workings of the functions.

Replace travis support with Github Actions

To conform with the Epiverse requirements/standards.

Update workflows to match {packagetemplate}

In general, the workflows in this package are out of date with those in packagetemplate and need updating. This is a larger PR to manage the following smaller and related issues:

Fix HTML validation problems

❯ checking HTML version of manual ... NOTE
  Found the following HTML validation problems:
  bpmodels-package.html:4:1 (bpmodels-package.Rd:7): Warning: <link> inserting "type" attribute
  bpmodels-package.html:12:1 (bpmodels-package.Rd:7): Warning: <script> proprietary attribute "onload"
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  chain_sim.html:4:1 (chain_sim.Rd:5): Warning: <link> inserting "type" attribute
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  chain_sim_susc.html:4:1 (chain_sim_susc.Rd:5): Warning: <link> inserting "type" attribute
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  chain_sim_susc.html:12:1 (chain_sim_susc.Rd:5): Warning: <script> inserting "type" attribute
  chain_sim_susc.html:17:1 (chain_sim_susc.Rd:5): Warning: <table> lacks "summary" attribute
  chain_sim_susc.html:46:1 (chain_sim_susc.Rd:20): Warning: <table> lacks "summary" attribute
  complementary_logprob.html:4:1 (complementary_logprob.Rd:5): Warning: <link> inserting "type" attribute
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  gborel_size_ll.html:4:1 (gborel_size_ll.Rd:5): Warning: <link> inserting "type" attribute
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  nbinom_size_ll.html:4:1 (nbinom_size_ll.Rd:5): Warning: <link> inserting "type" attribute
  nbinom_size_ll.html:12:1 (nbinom_size_ll.Rd:5): Warning: <script> proprietary attribute "onload"
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  nbinom_size_ll.html:37:1 (nbinom_size_ll.Rd:11): Warning: <table> lacks "summary" attribute
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  rnbinom_mean_disp.html:4:1 (rnbinom_mean_disp.Rd:5): Warning: <link> inserting "type" attribute
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  rnbinom_mean_disp.html:17:1 (rnbinom_mean_disp.Rd:5): Warning: <table> lacks "summary" attribute
  rnbinom_mean_disp.html:37:1 (rnbinom_mean_disp.Rd:11): Warning: <table> lacks "summary" attribute

add a condition to `offspring` in `chain_ll` function that checks for the current supported distributions

it would be good to check if the specified distribution is accounted for by your current release.

If not, it should bounce back with a message about the current supported distributions.

I have tried providing a normal distribution in chain_sim() but got an error

chain_sim(n = 5, offspring = "norm", stat = "size")

Allow user to specify tree=FALSE when serial is specified.

Currently, the user gets an error when they specify serial with tree = FALSE. I think this might be harsh on them. Maybe, we can make it more flexible by allowing that specification to happen, except that we'll set tree = TRUE internally and tell the user what happened.

Standardize all messages to sentence case

Standardize all messages to sentence case. Also note that the linebreak after "forget" will break your message up over two lines when printed - suggest using paste() or glue::glue() to concatenate small strings into one longer message without crossing 80 chars.

Originally posted by @pratikunterwegs in #27 (comment)

Also see #27 (comment)

Reset linguist to default behaviour

In a previous PR (#47), Github linguist was set to count .Rmd and .md files as R scripts and ignore the vignettes folder.

This was because linguist was counting .Rmd, .md, and .tex files separately and messing up the language statistics.

Currently, the workaround is to do #60. After closing the said issue, there will be no need to keep the reconfiguration and should be reset to the default.

Make clear whether `chain_ll()` function calculates a likelihood or loglikelihood

The current documentation of the chain_ll() function says it calculates the likelihood. But from what I can tell it is actually the loglikelihood. Indications of this also come from the function name (I assume _ll() stands for loglikelihood) and return value in the documentation of nbinom_size_ll() is "log-likelihood values".

I would recommend making it clear in the documentation of chain_ll() whether it is the likelihood or loglikelihood being returned.

Related to this could be a log argument in the function which accepts boolean values to turn the log transformation on or off.

Remove .gitattributes file

This file was previously used to customize Github Linguist (#62) but is no longer necessary and should be deleted.

Fix website deployment

pkgdown is not deploying the website as expected.

Collapse multiple `knitr::opts_chunk$set()` calls into single call

Currently there are two knitr::opts_chunk$set() calls in the README, these can probably be collapsed into a single call

Originally posted by @joshwlambert in #79 (comment)

Remove `context()` from tests

The context() function is now deprecated (see https://www.tidyverse.org/blog/2020/10/testthat-3-0-0/), consider removing.

Update "render-readme.yaml" workflow to match {packagetemplate}

Move package maintainer to first author

Rearrange the author names so that the package maintainer's name comes first.

Organize vignettes into topics

I propose to restructure the website vignettes into the following topics:
- [ ] Applications of branching processes (bibliography of modelling literature that uses branching processes)
- [ ] Modelling (including forecasting, etc.)

behavior near `infinite = ...`?

Using infinite = ... with a fixed value, I am routinely observing logistic style cumulative cases. While it's plausible to get that kind of result stochastically, this is a feature of every chain that doesn't go extinct. The expected behavior is the curve to generally be on an exponential growth trajectory, and then be censored to the value associated with infinite = ... (or all cases that occur <= the day when that value is surpassed.

I can manually censor to that value in the results, but fact the changing the infinite = ... value does not appear to change the fraction chains going to the limit, only where the curve begins to bend, suggests that something internally is not working the way I expect it to.

Update test-coverage.yaml workflow to match {packagetemplate}

Terminology: serial interval vs generation time

At the moment the package references the serial interval in describing the time between cases. Technically this should be the generation time, as time between infections. In practice, this distinction probably doesn't matter here as we don't have model of latent infections that lead to symptoms, i.e. implicitly assume that symptom onset is the same as infection/infectiousness onset.

We should either switch the terminology to use generation times, or mention the assumption somewhere explicitly (my preference being for the second option).

projection or forecast?

Great vignette for projecting incidence!

The vignette is consistent with the usage of the word "projection" in most of the document, except at the end of the second paragraph where it says "forecast an outbreak". In the referenced paper, after a quick skim, my initial impression is that the authors use both of them interchangeably, e.g. for the projection/forecast time intervals.

Could we use them interchangeably?

My last reference about this is the one below:

What do I mean by projections/forecasts/predictions?

Projections: short term not mechanistic – taking current trend and continuing

Forecasts: relies on somehow more mechanistic model but typically assumes conditions in future remain stable

Predictions: relies on understanding the system and making hypothesis about future conditions – closer scenario modelling

reference: https://www.reconlearn.org/post/projections.html

I would like to know if I can be flexible with the terminology given its usage in the field, or if they do refer to different things and then need to homogenize the terminology.

Literature vignette points to missing file

The literature vignette points to a missing file "vignettes/bp_applications_literature.json".

Release bpmodels 0.3.0

First release:

usethis::use_cran_comments()
Update (aspirational) install instructions in README
Proofread Title: and Description:
Check that all exported functions have @return and @examples
Check that Authors@R: includes a copyright holder (role 'cph')
Check licensing of included files
Review https://github.com/DavisVaughan/extrachecks

Prepare for release:

git pull
Check if any deprecation processes should be advanced, as described in Gradual deprecation
devtools::build_readme()
urlchecker::url_check()
devtools::check(remote = TRUE, manual = TRUE)
devtools::check_win_devel()
rhub::check_for_cran()
git push
Draft blog post

Submit to CRAN:

usethis::use_version('minor')
devtools::submit_cran()
Approve email

Wait for CRAN...

Fix urlchecker warning

> urlchecker::url_check()
! Warning: README.md:9:13 Moved
[![codecov](https://codecov.io/github/epiverse-trace/bpmodels/branch/main/graphs/badge.svg)](https://codecov.io/github/epiverse-trace/bpmodels)
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
            https://app.codecov.io/github/epiverse-trace/bpmodels
! Warning: README.md:13:60 Moved
MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
                                                           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                                           https://opensource.org/license/mit/

Add issue and pull request templates

See epiparameter and finalsize for examples of possible templates to use.

Fix reproduction number not rendering correctly in "Get Started" vignette

Reproduction number does not render correctly in get started vignette

Originally posted by @joshwlambert in #79 (comment)

epiverse-trace / bpmodels Goto Github PK

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