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0.0.1.9000

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Øystein Olav Skaar
Øystein Olav Skaar committed Jun 15, 2018
1 parent 2aef3b2 commit 1714d0e5cb27c134b924e44012dcf9f6ac50dc91
Showing with 54 additions and 24 deletions.
  1. +19 −10 DESCRIPTION
  2. +21 −0 LICENSE.md
  3. +10 −10 NEWS.md
  4. +4 −4 README.md
@@ -1,27 +1,36 @@
Package: bfw
Version: 0.0.1
Date: 2018-06-09
Version: 0.0.1.9000
Date: 2018-06-15
Title: Bayesian Framework for Computational Modelling
Authors@R: person( "Øystein Olav","Skaar", email="bayesianfw@gmail.com", role=c("aut","cre"))
Maintainer: Øystein Olav Skaar <bayesianfw@gmail.com>
URL: https://github.com/oeysan/bfw/
BugReports: https://github.com/oeysan/bfw/issues/
Description: Derived from the work of Kruschke (2015, <ISBN:9780124058880>),
the present package aim to provide a framework for conducting Bayesian
analysis using Markov chain Monte Carlo (MCMC)'' sampling utilizing the
Just Another Gibbs Sampler ("JAGS", Plummer, 2003, <http://mcmc-jags.sourceforge.net/>).
analysis using Markov chain Monte Carlo (MCMC) sampling utilizing the
Just Another Gibbs Sampler ('JAGS', Plummer, 2003, <http://mcmc-jags.sourceforge.net/>).
The initial version include several modules for conducting Bayesian
equivalents of chi-squared tests, analysis of variance (ANOVA),
multiple (hierarchical) regression, softmax regression, and for fitting data
(e.g., structural equation modeling).
SystemRequirements: JAGS >=4.3.0 <http://mcmc-jags.sourceforge.net/>,
Java JDK >=1.4 <https://www.java.com/en/download/manual.jsp>
Java JDK >=1.4 <https://www.java.com/en/download/manual.jsp>
Depends: R (>= 3.4.0),
Imports: plyr (>= 1.8.4), methods (>= 3.5.0), MASS (>= 7.3-47), pbapply
(>= 1.3-4), ReporteRs (>= 0.8.9), coda (>= 0.19-1), psych (>=
1.7.8), rJava (>= 0.9-9), runjags (>= 2.0.4-2), ggplot2 (>=
2.2.1), scales (>= 0.5.0), truncnorm (>= 1.0-8), robust (>=
0.4-18), lavaan (>= 0.6-1)
Imports: plyr (>= 1.8.4),
methods (>= 3.5.0),
MASS (>= 7.3-47),
pbapply (>= 1.3-4),
ReporteRs (>= 0.8.9),
coda (>= 0.19-1),
psych (>= 1.7.8),
rJava (>= 0.9-9),
runjags (>= 2.0.4-2),
ggplot2 (>= 2.2.1),
scales (>= 0.5.0),
truncnorm (>= 1.0-8),
robust (>= 0.4-18),
lavaan (>= 0.6-1)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
@@ -0,0 +1,21 @@
# MIT License

Copyright (c) 2018 Øystein Olav Skaar

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
20 NEWS.md
@@ -1,15 +1,15 @@
# bfw 0.0.1

* Initial launch with the following modules:
** Bernoulli trials
** Covariate estimations (including correlation and Cronbach's alpha)
** Fit data (e.g., SEM, CFA, mediation models)
** Bayesian equivalent of Cohen's kappa
** Mean and standard deviation estimations
** Predict metric values (cf., ANOVA)
** Predict nominal values (c.f., chi-square test)
** Simple, multiple and hierarchical regression
** Softmax regression (i.e., multinomial logistic regression)
+ Bernoulli trials
+ Covariate estimations (including correlation and Cronbach's alpha)
+ Fit data (e.g., SEM, CFA, mediation models)
+ Bayesian equivalent of Cohen's kappa
+ Mean and standard deviation estimations
+ Predict metric values (cf., ANOVA)
+ Predict nominal values (c.f., chi-square test)
+ Simple, multiple and hierarchical regression
+ Softmax regression (i.e., multinomial logistic regression)
* Added a `NEWS.md` file to track changes to the package.
* Added a `TODO.md` file to track future work on the package.
* Added a `README.md` file as an introduction to the package.
* Added a `README.md` file as an introduction to the package.
@@ -52,7 +52,7 @@ You can install `bfw` from GitHub. If you already have a previous
version of `bfw` installed, using the command below will update to the
latest development version.

#### Development version (GitHub)
#### Development version ([GitHub](https://github.com/oeysan/bfw/))

``` r
devtools::install_github("oeysan/bfw")
@@ -61,7 +61,7 @@ devtools::install_github("oeysan/bfw")
Please note that stable versions are hosted at CRAN, whereas GitHub
versions are in active development.

#### Stable version (CRAN)
#### Stable version ([CRAN](https://CRAN.R-project.org/package=bfw))

``` r
utils::install.packages("bfw")
@@ -176,10 +176,10 @@ round(biased.mcmc.robust$summary.MCMC[,c(3:6,9:12)],3)
``` r
# Running time for normal distribution analyis
biased.mcmc$run.time[2] - biased.mcmc$run.time[1]
#> Time difference of 6.43 secs
#> Time difference of 6.72 secs
# Running time for t-distribution analysis
biased.mcmc.robust$run.time[2] - biased.mcmc.robust$run.time[1]
#> Time difference of 31.2 secs
#> Time difference of 35 secs
```

## Example 3: Using custom function and model

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