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Merge pull request #17 from mihaiconstantin/release/1.7.4
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mihaiconstantin authored Apr 30, 2022

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archive
^\.github$
^man-roxygen$
CNAME
temp.R
4 changes: 2 additions & 2 deletions DESCRIPTION
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Package: powerly
Title: Sample Size Analysis for Psychological Networks and More
Version: 1.7.3
Version: 1.7.4
Authors@R:
person(given = "Mihai",
family = "Constantin",
@@ -18,7 +18,7 @@ Description: An implementation of the sample size computation method for network
sample size range. The final step employs stratified bootstrapping to quantify
the uncertainty around the fitted curve.
License: MIT + file LICENSE
URL: https://github.com/mihaiconstantin/powerly
URL: https://powerly.dev
BugReports: https://github.com/mihaiconstantin/powerly/issues
Imports:
R6,
405 changes: 166 additions & 239 deletions NEWS.md
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# `powerly` (development)

## Bug fixes

* Add missing import for `mvnorm` package.

# `powerly` `1.7.3`

## Improvements

* Update badges order in `README.md` and removed open issues badge.

* Fix typos in `NEWS` file.

# `powerly` `1.7.2`

## Improvements

* Update GGM estimation test to check if the estimation fails when variables
# Changelog
All notable changes to this project will be documented in this file. The format
is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this
project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## [1.7.4] - 2022-04-30
### Added
- Add `duration` field to `StepTwo` class to record the execution time for the
spline fitting procedure
- Add `CNAME` for apex domain `https://powerly.dev` served via GitHub Pages.

### Fixed
- Fix missing import for `mvnorm` package (#11). Closes #5.
- Fix missing number of `cores` in `Backend` when more cores than available were
requested (#12). Closes #2.
- Fix legend overlapping spline confidence bands for `StepThree` plot (#13).
Closes #3.
- Fix recording and reporting of `Method` and step classes execution time (#15).
The duration is now recorded in seconds. Closes #9.

### Removed
- Remove `dev` branch from all `GitHub` workflows (#14). Switched to the
`GitHub` flow. Closes #4.

## [1.7.3]
#### Changed
- Update badges order in `README.md` and removed open issues badge.

#### Fixed
- Fix typos in `NEWS` file.

## [1.7.2]
### Added
- Add GitHub badges with latest release version and number of open issues.

### Changed
- Update GGM estimation test to check if the estimation fails when variables
with zero standard deviation are present in the generated data.

* Update GGM estimation to fail when the generated data contains at least one
- Update GGM estimation to fail when the generated data contains at least one
variable that has a standard deviation equal to zero (i.e., as a result of
generating data with a sample size value that is too low).

* Add GitHub badges with latest release version and number of open issues.

## Bug fixes

* Add tolerance (i.e., `0.0000001`) for test checking whether the spline
### Fixed
- Add tolerance (i.e., `0.0000001`) for test checking whether the spline
coefficients are estimated correctly.

* Fix test for the updating of the bounds of a `Range` instance to run only when
- Fix test for the updating of the bounds of a `Range` instance to run only when
the the 2.5th and 97.5th selected sample sizes are different quantities.

* Fix bug in GGM data generating test where the number of nodes to generate data
- Fix bug in GGM data generating test where the number of nodes to generate data
for were incorrectly sampled.

# `powerly` `1.7.1`

## Improvements

* Update moved URL https://codecov.io/gh/mihaiconstantin/powerly to
## [1.7.1]
### Changed
- Update moved URL https://codecov.io/gh/mihaiconstantin/powerly to
https://app.codecov.io/gh/mihaiconstantin/powerly based on comments of CRAN
maintainer Uwe Ligges.

# `powerly` `1.7.0`

## Features

* Add `summary` S3 method support for `Validation` class objects.

## Improvements

* Add new `R` version to the CI pipeline for the `R CMD check` job.

* Update `R CMD check` workflow to use `check` action from `r-lib/actions`.
## [1.7.0]
### Added
- Add `summary` S3 method support for `Validation` class objects.

* Add explicit `.data` and `.env` pronoun calls (i.e., from the `rlang` package)
### Changed
- Add new `R` version to the CI pipeline for the `R CMD check` job.
- Update `R CMD check` workflow to use `check` action from `r-lib/actions`.
- Add explicit `.data` and `.env` pronoun calls (i.e., from the `rlang` package)
to variables used inside data-masking function (e.g., `ggplot2::aes()`) to
avoid `CRAN` notes regarding missing bindings for global variables. See this
question for more information: https://stackoverflow.com/q/9439256/5252007.

* Update plot functions to respect the signature of the S3 plot generic.

* Improve documentation and positioning of figures in the help pages.

* Create `roxygen2` templates for documenting the public API and S3 methods.

* Extract `plot()` methods from `R6` classes into standalone S3 methods.

* Update package start-up logo with message to welcome and encourage users to
- Update plot functions to respect the signature of the S3 plot generic.
- Improve documentation and positioning of figures in the help pages.
- Create `roxygen2` templates for documenting the public API and S3 methods.
- Extract `plot()` methods from `R6` classes into standalone S3 methods.
- Update package start-up logo with message to welcome and encourage users to
submit ideas for improving the package.
- Extend CI workflow to include branch `dev`.

* Extend CI workflow to include branch `dev`.

* Fix preprint URL in package documentation.

* Fix heading typo in news file.

## Bug fixes

* Fix backend test where the cluster would contain an unexpected `.Random.seed`.
### Fixed
- Fix backend test where the cluster would contain an unexpected `.Random.seed`.
The `.Random.seed` is caused by loading the `bootnet` package which in turn
loads the `snow` package. The `snow` package uses the `RNG` within the
`.onLoad()` function to draw from the uniform distribution and set a port
number. The result of this operation is a `.Random.seed` in the `.GlobalEnv`.
For more information see: https://stackoverflow.com/q/69866215/5252007 and
https://github.com/SachaEpskamp/bootnet/issues/82.
- Fix preprint URL in package documentation.
- Fix heading typo in news file.

# `powerly` `1.6.1`

## Improvements

* Update line exclusions for `covr::codecov()`.

# `powerly` `1.6.0`

## Improvements

* Add new `Validation` class plot to `README.md` file.
## [1.6.1]
### Changed
- Update line exclusions for `covr::codecov()`.

* Update `GgmModel` tests to vary various model estimation and data generation
## [1.6.0]
### Changed
- Add new `Validation` class plot to `README.md` file.
- Update `GgmModel` tests to vary various model estimation and data generation
parameters.

* Update `testthat::expect_equal` to test with a tolerance of `1e-6` for `Basis`
- Update `testthat::expect_equal` to test with a tolerance of `1e-6` for `Basis`
and `Solver`.

* Replace own `GgmModel` estimation with `qgraph::EBICglasso()`.

* Add ECDF plot to `Validation` class.

* Import external functions to `NAMESPACE` via `Roxygen2`.

* Add more cool badges to `README.md` (e.g., CRAN version and check status).

* Fix missing missing period in package description in `DESCRIPTION` file.

## Bug fixes

* Fix issue where `GGM` estimation test would fail due to a precision level set
- Replace own `GgmModel` estimation with `qgraph::EBICglasso()`.
- Add ECDF plot to `Validation` class.
- Import external functions to `NAMESPACE` via `Roxygen2`.
- Add more cool badges to `README.md` (e.g., CRAN version and check status).
- Fix missing missing period in package description in `DESCRIPTION` file.

### Fixed
- Fix issue where `GGM` estimation test would fail due to a precision level set
too high.

# `powerly` `1.5.2`

## Bug fixes

* Update `Description` field in `DESCRIPTION` file to follow CRAN guidelines.

# `powerly` `1.5.1`
## [1.5.2]
### Fixed
- Update `Description` field in `DESCRIPTION` file to follow CRAN guidelines.

## Bug fixes

* Update preprint link in `powerly()` documentation to use the `\doi{}` syntax
## [1.5.1]
### Fixed
- Update preprint link in `powerly()` documentation to use the `\doi{}` syntax
as indicated by CRAN member Uwe Ligges.

* Update `DESCRIPTION` to start with capital letter as indicated by CRAN member
- Update `DESCRIPTION` to start with capital letter as indicated by CRAN member
Uwe Ligges.
- Fix typo in `DESCRIPTION`.

* Fix typo in `DESCRIPTION`.

# `powerly` `1.5.0`

## Features

* Add preliminary `summary()` support for `Method` and `Validation` objects.

* Update citation and references to the preprint available at
## [1.5.0]
### Added
- Add preliminary `summary()` support for `Method` and `Validation` objects.
- Update citation and references to the preprint available at
[psyarxiv.com/j5v7u](https://psyarxiv.com/j5v7u).

* Add `ggplot` plots and saving support for `StepOne`, `StepTwo`, `StepThree`
- Add `ggplot` plots and saving support for `StepOne`, `StepTwo`, `StepThree`
and `Validation` objects.

## Improvements

* Migrate from `R` base plots to `ggplot2` and `patchwork`.

* Add more detailed `Description` in `DESCRIPTION` file as per comment by CRAN
### Changed
- Migrate from `R` base plots to `ggplot2` and `patchwork`.
- Add more detailed `Description` in `DESCRIPTION` file as per comment by CRAN
member Julia Haider.

## Bug fixes

* Fix seed in `StepOne` unit test.

* Fix superfluous test fail for `GGM` model estimation. Restricted the unit test
### Fixed
- Fix seed in `StepOne` unit test.
- Fix superfluous test fail for `GGM` model estimation. Restricted the unit test
to compare the estimated edge weights up to 7 digits precision.

# `powerly` `1.4.0`

## Features

* Add code coverage workflow based on action provided by
## [1.4.0]
### Added
- Add code coverage workflow based on action provided by
`usethis::use_github_action("test-coverage")` and badge to `README.md`.

# `powerly` `1.3.0`

## Bug fixes

* Fix cluster creation bug in `Backend` when the machine had only 1 or 2 cores.
## [1.3.0]
### Fixed
- Fix cluster creation bug in `Backend` when the machine had only 1 or 2 cores.
The previous version would result in an error when the machine contained only
1 or 2 cores. Now, when the machine has only 1 core, the cluster creation will
fail, with a message that not enough cores are available. When the machine has
2 cores, all 2 cores are used. In all other cases, the number of cores used is
given by the number of cores on the machine minus one.

## Improvements

* Add names and comments to workflow file `R-CMD-check.yaml`.

* Update `README.md` and package startup logo to only show major version.

* Update existing tests and added new ones.

* Add type check for `method` argument of `validate()` to ensure that only
### Changed
- Add names and comments to workflow file `R-CMD-check.yaml`.
- Update `README.md` and package startup logo to only show major version.
- Update existing tests and added new ones.
- Add type check for `method` argument of `validate()` to ensure that only
instances of `Method` class (i.e., produced by `powerly()` are passed).

* Add `Backend` stopping to `on.exit()` in `powerly()` to ensure the cluster is
- Add `Backend` stopping to `on.exit()` in `powerly()` to ensure the cluster is
stopped no matter the execution status of the function.

* Improve logic around setting and resetting the number of cores when the
- Improve logic around setting and resetting the number of cores when the
cluster is created and stopped (i.e., also for adopted clusters).
- Correct version number and add changes in `NEWS.md` for `1.2.0`.

* Correct version number and add changes in `NEWS.md` for `1.2.0`.

# `powerly` `1.2.0`

## Features
## [1.2.0]
### Added
- Add *CI* workflow via `usethis::use_github_action_check_standard()`.

* Add *CI* workflow via `usethis::use_github_action_check_standard()`.
### Fixed
- Restrict tests to using a maximum of two cores to respect CRAN restriction.

## Bug fixes
### Changed
- Hide package logo at startup if the `R` session is not interactive.
- Add more informative changelogs to `NEWS.md` for previous releases.

* Restrict tests to using a maximum of two cores to respect CRAN restriction.

## Improvements

* Hide package logo at startup if the `R` session is not interactive.

* Add more informative changelogs to `NEWS.md` for previous releases.

# `powerly` `1.1.1`

## Bug fixes

* Add `.remove_missing()` to clear any `NA` values that may be present in
## [1.1.1]
### Fixed
- Add `.remove_missing()` to clear any `NA` values that may be present in
`.measures` in `StepOne` class after the *Monte Carlo* procedure.

# `powerly` `1.1.1`

## Bug fixes

* Fix broken URLs in documentation causing build warnings.

# `powerly` `1.1.0`

## Features

* Add `validate()` public *API* to validate method results.

* Add `Validation` class to perform validation on a `Method` object.

## Improvements

* Add example in `README.md` for `validation()` and fixed images.

* Decrease legend font size in `StepThree` class.

* Rename from quantile to percentile in `StepThree` class plots.

# `powerly` `1.0.0`

* Add `powerly()` public *API* to run the method.

* Add `generate_model()` public *API* to generate true models.

* Add package documentation for public *API*.

* Add plotting for all three method steps.

* Add option to save last two iterations in `Method` class.

* Add `Method` class to run the method steps iteratively.

* Add parallel support for *Step 1* and *Step 3* of the method.

* Add `Backend` class to manage parallel clusters.

* Add support for multiple solvers for estimating spline coefficients.

* Rewrite prototype using `R6` *OOP* style into first stable release.

# `powerly` `0.2.0`

* Remove text feedback from each method step function.

# `powerly` `0.1.1`

* Fix bug cased by initial candidate sample size ranges being too narrow.

# `powerly` `0.1.0`

## Features

* Add preliminary support for the *Gaussian Graphical Model* via `ggm` object.

* Add preliminary support for two statistics via `statistic.power()` and
## [1.1.1]
### Fixed
- Fix broken URLs in documentation causing build warnings.

## [1.1.0]
### Added
- Add `validate()` public *API* to validate method results.
- Add `Validation` class to perform validation on a `Method` object.

### Changed
- Add example in `README.md` for `validation()` and fixed images.
- Decrease legend font size in `StepThree` class.
- Rename from quantile to percentile in `StepThree` class plots.

## [1.0.0]
### Added
- Add `powerly()` public *API* to run the method.
- Add `generate_model()` public *API* to generate true models.
- Add package documentation for public *API*.
- Add plotting for all three method steps.
- Add option to save last two iterations in `Method` class.
- Add `Method` class to run the method steps iteratively.
- Add parallel support for *Step 1* and *Step 3* of the method.
- Add `Backend` class to manage parallel clusters.
- Add support for multiple solvers for estimating spline coefficients.
- Rewrite prototype using `R6` *OOP* style into first stable release.

## [0.2.0]
### Removed
- Remove text feedback from each method step function.

## [0.1.1]
### Fixed
- Fix bug cased by initial candidate sample size ranges being too narrow.

## [0.1.0]
### Added
- Add preliminary support for the *Gaussian Graphical Model* via `ggm` object.
- Add preliminary support for two statistics via `statistic.power()` and
`statistic.mean()`.

* Add `validate.recommendation()` prototype for validating a sample size
- Add `validate.recommendation()` prototype for validating a sample size
recommendation.

* Add `run.method()` prototype for running all method steps iteratively.

* Add `run.step.1()` prototype for *Step 1* of the method.

* Add `run.step.2()` prototype for *Step 2* of the method.

* Add `run.step.3()` prototype for *Step 3* of the method.
- Add `run.method()` prototype for running all method steps iteratively.
- Add `run.step.1()` prototype for *Step 1* of the method.
- Add `run.step.2()` prototype for *Step 2* of the method.
- Add `run.step.3()` prototype for *Step 3* of the method.

---

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