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Update master with new release v1.0.1 #220

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merged 30 commits into from
May 27, 2024
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60fee30
bump dev version for next cycle
venpopov Mar 26, 2024
40a4659
fix typo in use_model_template
venpopov Mar 26, 2024
fa5cd13
fix version argument for sdm
venpopov Mar 27, 2024
21706c5
fix sort_data global option
venpopov Mar 27, 2024
8df07b5
Update issue templates
GidonFrischkorn Mar 28, 2024
8bfd8dd
Merge pull request #193 from venpopov/GidonFrischkorn-patch-1
GidonFrischkorn Mar 28, 2024
d8fefbd
add file argument to bmm() (#195)
venpopov Mar 28, 2024
25cd618
temporarily disable windows cmd check
venpopov Mar 28, 2024
b356c56
quick bugfix for mc.cores defaults
venpopov Mar 28, 2024
142bbcd
Create CONTRIBUTING.md
GidonFrischkorn Mar 28, 2024
e09bc6d
Move Contributing.MD
GidonFrischkorn Mar 28, 2024
77e7664
Merge branch 'develop' into documentation/197-contributing-guidelines
GidonFrischkorn Mar 28, 2024
adbbeb2
Fix typo
venpopov Mar 28, 2024
6c7ca03
Add references to Contributor Guidelines in `ReadMe`
GidonFrischkorn Mar 29, 2024
02cba98
Merge pull request #198 from venpopov/documentation/197-contributing-…
GidonFrischkorn Mar 29, 2024
7b02117
add tests for default priors
venpopov Apr 7, 2024
18cae89
fix #201
venpopov Apr 7, 2024
aff7522
set constant(1e-8) prior on setsize1 random effects
venpopov Apr 7, 2024
174511f
Merge pull request #206 from venpopov/bugfix/default-prior-interactio…
GidonFrischkorn Apr 9, 2024
9267927
Bump Version
GidonFrischkorn Apr 9, 2024
db167d9
Merge pull request #207 from venpopov/bugfix/setsize1_ranef_constant_…
GidonFrischkorn Apr 9, 2024
90c961f
Update IMM specification & Fix random generation functions (#210)
GidonFrischkorn May 21, 2024
6c3eedd
improve package loading times (#211)
venpopov May 21, 2024
6e64234
update vignettes and delete internal datasets (#212)
venpopov May 22, 2024
81e4389
Remove links argument #214 (#215)
venpopov May 22, 2024
bda555a
change class `vwm` to `circular` (#216)
venpopov May 22, 2024
6e5b45a
website cleanup
venpopov May 22, 2024
995459d
Initial cran release (#217)
venpopov May 23, 2024
4bc2435
fix typos
venpopov May 23, 2024
8776592
Releases/v1.0.0 (#219)
venpopov May 27, 2024
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2 changes: 2 additions & 0 deletions .Rbuildignore
Original file line number Diff line number Diff line change
@@ -16,5 +16,7 @@
^index.md$
^tests/internal-.*$
^tests/internal$
^tests/testthat/assets$
^.dev$
^.Rprofile$
^CRAN-SUBMISSION$
66 changes: 66 additions & 0 deletions .github/CONTRIBUTING.md
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@@ -0,0 +1,66 @@
# Contributing to `bmm`

The `bmm` package is designed to be community driven and thus we appreciate your input! We attempt to make contributing to `bmm` as easy and transparent as possible. These contributor guidelines are designed to clarify different types of contributions and how they will be acknowledge in the package publication.

The following contributions will be acknowledge in the `NEWS` for each release of the package:

- Reporting a bug
- Submitting a bug fix
- Discussing and proposing improvements on the current state of the code, in particular:
- improving stability of model estimation
- speeding up model estimation
- generalizing functions across multiple already implemented `bmmodels`

More extensive contributions will be acknowledge by being listed as a contributor in the package documentation. These entail:

- adding a new model to `bmm`
- adding new function that ease the use of multiple models implemented in `bmm`
- adding functions that implement the communication of `bmm` with other R packages, such as `emmeans`, `tidybayes`, `bayesplot`, etc.

## Package Development on Github

We use Github to host all code, track issues and feature requests, as well as accept pull requests. Detailed info on the development process can be found in the `bmm` [Developer Notes](https://venpopov.github.io/bmm/dev/dev-notes/index.html)

All changes and additions to code have to be submitted via pull requests. We consider all pull requests as propositions for changes to the codebase. Thus, we reserve the right to not merge changes, if we feel that they are in conflict with general principles implemented in the `bmm` package. To avoid the rejection of pull requests, please consider contacting us before committing changes to `bmm`, especially if they involve changing a large number of files.

If you are interested in contributing to `bmm`, please follow the following steps.

1. Fork the repo and create your branch from `develop`.
2. If you've added code that should be tested, add tests.
3. Update the documentation for the changes you implemented.
4. Ensure that all unit tests passed.
5. Ensure the R CMD Checks passed.
6. Issue that pull request!

## Use a Consistent Coding Style

Please follow the general coding style used throughout `bmm`. This entails:

- labeling variables and functions using `snake_case`
- avoid upper case labels in variable and function names

The `bmm` [Developer Notes](https://venpopov.github.io/bmm/dev/dev-notes/index.html) provide an introduction into the file organization of the package. Please follow the guidelines where to put functions associated with the different steps in fitting `bmmodels`. If you have questions or an unsure about where to add code, feel free to ask us. There is a dedicated [Discussion](https://github.com/venpopov/bmm/discussions) page for informal chats and questions.

## Any contributions you make will be under the GPL-2 Software License

In short, when you submit code changes, your submissions are understood to be under the same [GPL-2](https://choosealicense.com/licenses/gpl-2.0/) that covers the project. Feel free to contact us if that's a concern.

## Report bugs using Github's [issues](https://github.com/venpopov/bmm/issues)

We use GitHub issues to track public bugs. Report a bug by [opening a new issue](https://github.com/venpopov/bmm/issues); it's that easy!

## Write bug reports with detail, background, and sample code

When reporting a bug, please use the provided template.

**Great Bug Reports** tend to have:

- A quick summary and/or background
- Steps to reproduce
- Be specific!
- Give sample code if you can.
- What you expected would happen
- What actually happens
- Notes (including why you think this might be happening, or stuff you tried that didn't work)

We appreciate thorough bug reports *a lot*.
25 changes: 25 additions & 0 deletions .github/ISSUE_TEMPLATE/bug_report.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,25 @@
---
name: Bug report
about: Create a report to help us improve
title: "[bug]"
labels: bug
assignees: ''

---

**Describe the bug**
A clear and concise description of what the bug is.

**To Reproduce**
Steps to reproduce the behavior (add code examples here)

**Expected behavior**
A clear and concise description of what you expected to happen.

**Desktop (please complete the following information):**
- OS: [e.g. Mac, Windows, Ubuntu (+ version]
- The R & RStudio version you have
- Copy of your R environment and used packages when the error occured

**Additional context**
Add any other context about the problem here.
20 changes: 20 additions & 0 deletions .github/ISSUE_TEMPLATE/feature_request.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,20 @@
---
name: Feature request
about: Suggest an idea for this project
title: "[feature-request]"
labels: ''
assignees: ''

---

**Is your feature request related to a problem? Please describe.**
A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]

**Describe the solution you'd like**
A clear and concise description of what you want to happen.

**Describe alternatives you've considered**
A clear and concise description of any alternative solutions or features you've considered.

**Additional context**
Add any other context or screenshots about the feature request here.
2 changes: 1 addition & 1 deletion .github/workflows/R-CMD-check.yaml
Original file line number Diff line number Diff line change
@@ -23,7 +23,7 @@ jobs:
matrix:
config:
- {os: macos-latest, r: 'release'}
- {os: windows-latest, r: 'release'}
# - {os: windows-latest, r: 'release'}
- {os: ubuntu-latest, r: 'release'}

env:
3 changes: 3 additions & 0 deletions CRAN-SUBMISSION
Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
Version: 1.0.1
Date: 2024-05-27 14:37:08 UTC
SHA: 8ada976031db6f46deea8e1f52e68046e8aae8a6
95 changes: 49 additions & 46 deletions DESCRIPTION
Original file line number Diff line number Diff line change
@@ -1,56 +1,59 @@
Package: bmm
Title: Easy and Accesible Bayesian Measurement Models using 'brms'
Version: 0.5.1
Title: Easy and Accessible Bayesian Measurement Models Using 'brms'
Version: 1.0.1
Authors@R: c(
person("Vencislav", "Popov", , "[email protected]", role = c("aut", "cre", "cph")),
person("Gidon", "Frischkorn", , "[email protected]", role = c("aut", "cph")),
person("Paul", "Bürkner", , "[email protected]", role = c("cph"),
comment = "Creator of brms, a package for Bayesian regression model that this package builds upon."))
Description: Implementations of computational measurement models using the 'brms' package.
Currently implemented models can be listed using supported_models(). The package also
provides functions to extract model informations such as priors, or the generated
STAN code. For all implemented models there are also density and random generation
functions to easily explore model predictions and evaluate parameter recovery.
Finally, helper functions aid in pre- and post-processing data for efficient communication
of results.
person("Vencislav", "Popov", , "[email protected]", role = c("aut", "cre", "cph"),
comment = c(ORCID = "0000-0002-8073-4199")),
person("Gidon T.", "Frischkorn", , "[email protected]", role = c("aut", "cph"),
comment = c(ORCID = "0000-0002-5055-9764")),
person("Paul-Christian", "Bürkner", , "[email protected]", role = "cph",
comment = "Creator of 'brms', code portions of which are used in 'bmm'.")
)
Description: Fit computational and measurement models using full Bayesian
inference. The package provides a simple and accessible interface by
translating complex domain-specific models into 'brms' syntax, a
powerful and flexible framework for fitting Bayesian regression models
using 'Stan'. The package is designed so that users can easily apply
state-of-the-art models in various research fields, and so that
researchers can use it as a new model development framework.
References: Frischkorn and Popov (2023) <doi:10.31234/osf.io/umt57>.
License: GPL-2
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1
URL: https://github.com/venpopov/bmm, https://venpopov.github.io/bmm/
BugReports: https://github.com/venpopov/bmm/issues
Depends:
R (>= 3.6.0)
Imports:
brms (>= 2.21.0),
crayon,
dplyr,
fs,
glue,
magrittr,
matrixStats,
methods,
parallel,
stats,
tidyr,
withr
Suggests:
testthat (>= 3.0.0),
usethis,
knitr,
rmarkdown,
bookdown,
tidybayes,
cmdstanr (>= 0.7.0),
cowplot,
fansi,
ggplot2,
mixtur,
ggthemes,
cowplot,
knitr,
mixtur,
remotes,
rmarkdown,
stringr,
remotes,
waldo,
fansi,
cmdstanr (>= 0.7.0)
testthat (>= 3.0.0),
tidybayes,
usethis,
waldo
Additional_repositories: https://mc-stan.org/r-packages/
Config/testthat/edition: 3
Imports:
magrittr,
glue,
parallel,
dplyr,
withr,
tidyr,
stats,
matrixStats,
crayon,
methods
URL: https://github.com/venpopov/bmm, https://venpopov.github.io/bmm/
BugReports: https://github.com/venpopov/bmm/issues
Additional_repositories:
https://mc-stan.org/r-packages/
VignetteBuilder: knitr
Depends:
R (>= 3.6.0),
brms (>= 2.21.0)
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1
6 changes: 5 additions & 1 deletion NAMESPACE
Original file line number Diff line number Diff line change
@@ -7,12 +7,12 @@ S3method(add_links,bmmfit)
S3method(add_links,bmmodel)
S3method(bmf2bf,bmmodel)
S3method(check_data,bmmodel)
S3method(check_data,circular)
S3method(check_data,default)
S3method(check_data,imm_bsc)
S3method(check_data,imm_full)
S3method(check_data,non_targets)
S3method(check_data,sdm)
S3method(check_data,vwm)
S3method(check_formula,bmmodel)
S3method(check_formula,default)
S3method(check_formula,non_targets)
@@ -79,6 +79,7 @@ export(calc_error_relative_to_nontargets)
export(check_data)
export(configure_model)
export(configure_prior)
export(default_prior)
export(deg2rad)
export(dimm)
export(dmixture2p)
@@ -101,6 +102,7 @@ export(qmixture2p)
export(qmixture3p)
export(qsdm)
export(rad2deg)
export(restructure)
export(revert_postprocess_brm)
export(rimm)
export(rmixture2p)
@@ -110,6 +112,8 @@ export(sdm)
export(sdmSimple)
export(softmax)
export(softmaxinv)
export(stancode)
export(standata)
export(supported_models)
export(use_model_template)
export(wrap)
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