Merge pull request #152 from hneth/master

Getting ready for CRAN submission

DESCRIPTION

@@ -2,7 +2,7 @@ Package: FFTrees
 Type: Package
 Title: Generate, Visualise, and Evaluate Fast-and-Frugal Decision Trees
 Version: 1.9.0
-Date: 2023-02-07
+Date: 2023-02-08
 Authors@R: c(person("Nathaniel", "Phillips", role = c("aut"), email = "Nathaniel.D.Phillips.is@gmail.com", comment = c(ORCID = "0000-0002-8969-7013")),
              person("Hansjoerg", "Neth", role = c("aut", "cre"), email = "h.neth@uni.kn", comment = c(ORCID = "0000-0001-5427-3141")),
              person("Jan", "Woike", role = "aut", comment = c(ORCID = "0000-0002-6816-121X")),

NEWS.md

@@ -1,11 +1,11 @@
 
 # FFTrees 1.9
 
-This is the current development version of **FFTrees**, available at <https://github.com/ndphillips/FFTrees>. 
+<!-- This is the current development version of **FFTrees**, available at <https://github.com/ndphillips/FFTrees>. -->
 
 ## 1.9.0
 
-**FFTrees** version 1.9.0 is to be released [on CRAN](https://CRAN.R-project.org/package=FFTrees) [on 2023-02-08]. 
+**FFTrees** version 1.9.0 was released [on CRAN](https://CRAN.R-project.org/package=FFTrees) [on 2023-02-08]. 
 Apart from adding functionality and fixing minor bugs, this version improves consistency, robustness, and transparency. 
 
 <!-- Log of changes: --> 
@@ -409,6 +409,6 @@ Thus, the main tree building function is now `FFTrees()` and the new tree object
 
 ------ 
 
-[File `NEWS.md` last updated on 2023-02-06.]
+[File `NEWS.md` last updated on 2023-02-08.]
 
 <!-- eof. -->

README.Rmd

@@ -34,30 +34,28 @@ url_JDM_doi <- "https://doi.org/10.1017/S1930297500006239"
 # FFTrees `r packageVersion("FFTrees")` <img src = "./inst/FFTrees_Logo.jpg" align = "right" alt = "FFTrees" width = "225" />
 
 <!-- Devel badges start: --> 
-[![CRAN status](https://www.r-pkg.org/badges/version/FFTrees)](https://CRAN.R-project.org/package=FFTrees)
-[![Downloads/month](https://cranlogs.r-pkg.org/badges/FFTrees?color='00a9e0')](https://www.r-pkg.org/pkg/FFTrees)
-[![R-CMD-check](https://github.com/ndphillips/FFTrees/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ndphillips/FFTrees/actions/workflows/R-CMD-check.yaml)
+<!-- [![CRAN status](https://www.r-pkg.org/badges/version/FFTrees)](https://CRAN.R-project.org/package=FFTrees) -->
+<!-- [![Downloads/month](https://cranlogs.r-pkg.org/badges/FFTrees?color='00a9e0')](https://www.r-pkg.org/pkg/FFTrees) -->
+<!-- [![R-CMD-check](https://github.com/ndphillips/FFTrees/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ndphillips/FFTrees/actions/workflows/R-CMD-check.yaml) -->
 <!-- Devel badges end. -->
 
-
 <!-- Release badges start: -->
-<!-- [![CRAN status](https://www.r-pkg.org/badges/version/FFTrees)](https://CRAN.R-project.org/package=FFTrees) -->
-<!-- [![Total downloads](https://cranlogs.r-pkg.org/badges/grand-total/FFTrees?color='00a9e0')](https://www.r-pkg.org/pkg/FFTrees) -->
+[![CRAN status](https://www.r-pkg.org/badges/version/FFTrees)](https://CRAN.R-project.org/package=FFTrees)
+[![Total downloads](https://cranlogs.r-pkg.org/badges/grand-total/FFTrees?color='00a9e0')](https://www.r-pkg.org/pkg/FFTrees)
 <!-- Release badges end. -->
 
-
-<!-- ALL status badges start: --> 
+<!-- ALL badges start: --> 
 <!-- [![CRAN status](https://www.r-pkg.org/badges/version/FFTrees)](https://CRAN.R-project.org/package=FFTrees) -->
 <!-- [![Build Status](https://travis-ci.org/ndphillips/FFTrees.svg?branch=master)](https://travis-ci.org/ndphillips/FFTrees) -->
 <!-- [![R-CMD-check](https://github.com/ndphillips/FFTrees/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ndphillips/FFTrees/actions/workflows/R-CMD-check.yaml) -->
 <!-- [![Downloads/month](https://cranlogs.r-pkg.org/badges/FFTrees?color=brightgreen)](https://www.r-pkg.org/pkg/FFTrees) -->
 <!-- [![Total downloads](https://cranlogs.r-pkg.org/badges/grand-total/FFTrees?color='b22222')](https://www.r-pkg.org/pkg/FFTrees) -->
-<!-- ALL status badges end. --> 
+<!-- ALL badges end. --> 
 
 
 <!-- Pkg goal: -->
 
-The R package **FFTrees** creates, visualizes and evaluates _fast-and-frugal decision trees_ (FFTs) for solving binary classification tasks following the methods described in Phillips, Neth, Woike & Gaissmaier (2017, [doi](`r url_JDM_doi`) | [html](`r url_JDM_html`) | [PDF](`r url_JDM_pdf`)). 
+The R package **FFTrees** creates, visualizes and evaluates _fast-and-frugal decision trees_ (FFTs) for solving binary classification tasks, using the algorithms and methods described in Phillips, Neth, Woike & Gaissmaier (2017, doi\ [10.1017/S1930297500006239](`r url_JDM_doi`) | [html](`r url_JDM_html`) | [PDF](`r url_JDM_pdf`)). 
 
 
 ## What are fast-and-frugal trees (FFTs)?
@@ -269,24 +267,29 @@ When using **FFTrees** in your own work, please cite us and share your experienc
 By\ 2023, over 100\ scientific publications have used or cited **FFTrees** (see [Google Scholar](https://scholar.google.com/scholar?oi=bibs&hl=en&cites=205528310591558601) for the full list).  
 Examples include: 
 
-- [Lötsch, J., Haehner, A., & Hummel, T. (2020). Machine-learning-derived rules set excludes risk of Parkinson’s disease in patients with olfactory or gustatory symptoms with high accuracy. 
-_Journal of Neurology_, _267_(2), 469--478.](https://link.springer.com/article/10.1007/s00415-019-09604-6)
+- Lötsch, J., Haehner, A., & Hummel, T. (2020). Machine-learning-derived rules set excludes risk of Parkinson’s disease in patients with olfactory or gustatory symptoms with high accuracy. 
+_Journal of Neurology_, _267_(2), 469--478. 
+doi\ [10.1007/s00415-019-09604-6](https://doi.org/10.1007/s00415-019-09604-6)
 
-- [Kagan, R., Parlee, L., Beckett, B., Hayden, J. B., Gundle, K. R., & Doung, Y. C. (2020). 
+- Kagan, R., Parlee, L., Beckett, B., Hayden, J. B., Gundle, K. R., & Doung, Y. C. (2020). 
 Radiographic parameter-driven decision tree reliably predicts aseptic mechanical failure of compressive osseointegration fixation. 
-_Acta Orthopaedica_, _91_(2), 171--176.](https://www.tandfonline.com/doi/full/10.1080/17453674.2020.1716295)
+_Acta Orthopaedica_, _91_(2), 171--176. 
+doi\ [10.1080/17453674.2020.1716295](https://doi.org/10.1080/17453674.2020.1716295)
 
-- [Klement, R. J., Sonke, J. J., Allgäuer, M., Andratschke, N., Appold, S., Belderbos, J., ... & Mantel, F. (2020). 
+- Klement, R. J., Sonke, J. J., Allgäuer, M., Andratschke, N., Appold, S., Belderbos, J., ... & Mantel, F. (2020). 
 Correlating dose variables with local tumor control in stereotactic body radiotherapy for early stage non-small cell lung cancer: A modeling study on 1500 individual treatments. 
-_International Journal of Radiation Oncology * Biology * Physics_.](https://www.sciencedirect.com/science/article/pii/S036030162030897X)
+_International Journal of Radiation Oncology * Biology * Physics_. 
+doi\ [10.1016/j.ijrobp.2020.03.005](https://doi.org/10.1016/j.ijrobp.2020.03.005)
 
-- [Nobre, G. G., Hunink, J. E., Baruth, B., Aerts, J. C., & Ward, P. J. (2019). 
+- Nobre, G. G., Hunink, J. E., Baruth, B., Aerts, J. C., & Ward, P. J. (2019). 
 Translating large-scale climate variability into crop production forecast in Europe. 
-_Scientific Reports_, _9_(1), 1--13.](https://www.nature.com/articles/s41598-018-38091-4)
+_Scientific Reports_, _9_(1), 1--13. 
+doi\ [10.1038/s41598-018-38091-4](https://doi.org/10.1038/s41598-018-38091-4)
 
-- [Buchinsky, F. J., Valentino, W. L., Ruszkay, N., Powell, E., Derkay, C. S., Seedat, R. Y., ... & Mortelliti, A. J. (2019). 
+- Buchinsky, F. J., Valentino, W. L., Ruszkay, N., Powell, E., Derkay, C. S., Seedat, R. Y., ... & Mortelliti, A. J. (2019). 
 Age at diagnosis, but not HPV type, is strongly associated with clinical course in recurrent respiratory papillomatosis. 
-_PloS One_, _14_(6).](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6563955/)
+_PloS One_, _14_(6). 
+doi\ [10.1371/journal.pone.0216697](https://doi.org/10.1371/journal.pone.0216697)
 
 
 <!-- footer: -->

README.md

@@ -5,32 +5,33 @@
 # FFTrees 1.9.0 <img src = "./inst/FFTrees_Logo.jpg" align = "right" alt = "FFTrees" width = "225" />
 
 <!-- Devel badges start: -->
+<!-- [![CRAN status](https://www.r-pkg.org/badges/version/FFTrees)](https://CRAN.R-project.org/package=FFTrees) -->
+<!-- [![Downloads/month](https://cranlogs.r-pkg.org/badges/FFTrees?color='00a9e0')](https://www.r-pkg.org/pkg/FFTrees) -->
+<!-- [![R-CMD-check](https://github.com/ndphillips/FFTrees/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ndphillips/FFTrees/actions/workflows/R-CMD-check.yaml) -->
+<!-- Devel badges end. -->
+<!-- Release badges start: -->
 
 [![CRAN
 status](https://www.r-pkg.org/badges/version/FFTrees)](https://CRAN.R-project.org/package=FFTrees)
-[![Downloads/month](https://cranlogs.r-pkg.org/badges/FFTrees?color='00a9e0')](https://www.r-pkg.org/pkg/FFTrees)
-[![R-CMD-check](https://github.com/ndphillips/FFTrees/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ndphillips/FFTrees/actions/workflows/R-CMD-check.yaml)
-<!-- Devel badges end. -->
-
-<!-- Release badges start: -->
-<!-- [![CRAN status](https://www.r-pkg.org/badges/version/FFTrees)](https://CRAN.R-project.org/package=FFTrees) -->
-<!-- [![Total downloads](https://cranlogs.r-pkg.org/badges/grand-total/FFTrees?color='00a9e0')](https://www.r-pkg.org/pkg/FFTrees) -->
+[![Total
+downloads](https://cranlogs.r-pkg.org/badges/grand-total/FFTrees?color='00a9e0')](https://www.r-pkg.org/pkg/FFTrees)
 <!-- Release badges end. -->
-<!-- ALL status badges start: -->
+
+<!-- ALL badges start: -->
 <!-- [![CRAN status](https://www.r-pkg.org/badges/version/FFTrees)](https://CRAN.R-project.org/package=FFTrees) -->
 <!-- [![Build Status](https://travis-ci.org/ndphillips/FFTrees.svg?branch=master)](https://travis-ci.org/ndphillips/FFTrees) -->
 <!-- [![R-CMD-check](https://github.com/ndphillips/FFTrees/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ndphillips/FFTrees/actions/workflows/R-CMD-check.yaml) -->
 <!-- [![Downloads/month](https://cranlogs.r-pkg.org/badges/FFTrees?color=brightgreen)](https://www.r-pkg.org/pkg/FFTrees) -->
 <!-- [![Total downloads](https://cranlogs.r-pkg.org/badges/grand-total/FFTrees?color='b22222')](https://www.r-pkg.org/pkg/FFTrees) -->
-<!-- ALL status badges end. -->
+<!-- ALL badges end. -->
 <!-- Pkg goal: -->
 
 The R package **FFTrees** creates, visualizes and evaluates
 *fast-and-frugal decision trees* (FFTs) for solving binary
-classification tasks following the methods described in Phillips, Neth,
-Woike & Gaissmaier (2017,
-[doi](https://doi.org/10.1017/S1930297500006239) \|
-[html](https://journal.sjdm.org/17/17217/jdm17217.html) \|
+classification tasks, using the algorithms and methods described in
+Phillips, Neth, Woike & Gaissmaier (2017,
+doi [10.1017/S1930297500006239](https://doi.org/10.1017/S1930297500006239)
+\| [html](https://journal.sjdm.org/17/17217/jdm17217.html) \|
 [PDF](https://journal.sjdm.org/17/17217/jdm17217.pdf)).
 
 ## What are fast-and-frugal trees (FFTs)?
@@ -298,40 +299,41 @@ Scholar](https://scholar.google.com/scholar?oi=bibs&hl=en&cites=2055283105915586
 for the full list).  
 Examples include:
 
-- [Lötsch, J., Haehner, A., & Hummel, T. (2020).
-  Machine-learning-derived rules set excludes risk of Parkinson’s
-  disease in patients with olfactory or gustatory symptoms with high
-  accuracy. *Journal of Neurology*, *267*(2),
-  469–478.](https://link.springer.com/article/10.1007/s00415-019-09604-6)
+- Lötsch, J., Haehner, A., & Hummel, T. (2020). Machine-learning-derived
+  rules set excludes risk of Parkinson’s disease in patients with
+  olfactory or gustatory symptoms with high accuracy. *Journal of
+  Neurology*, *267*(2), 469–478.
+  doi [10.1007/s00415-019-09604-6](https://doi.org/10.1007/s00415-019-09604-6)
 
-- [Kagan, R., Parlee, L., Beckett, B., Hayden, J. B., Gundle, K. R., &
+- Kagan, R., Parlee, L., Beckett, B., Hayden, J. B., Gundle, K. R., &
   Doung, Y. C. (2020). Radiographic parameter-driven decision tree
   reliably predicts aseptic mechanical failure of compressive
-  osseointegration fixation. *Acta Orthopaedica*, *91*(2),
-  171–176.](https://www.tandfonline.com/doi/full/10.1080/17453674.2020.1716295)
+  osseointegration fixation. *Acta Orthopaedica*, *91*(2), 171–176.
+  doi [10.1080/17453674.2020.1716295](https://doi.org/10.1080/17453674.2020.1716295)
 
-- [Klement, R. J., Sonke, J. J., Allgäuer, M., Andratschke, N., Appold,
+- Klement, R. J., Sonke, J. J., Allgäuer, M., Andratschke, N., Appold,
   S., Belderbos, J., … & Mantel, F. (2020). Correlating dose variables
   with local tumor control in stereotactic body radiotherapy for early
   stage non-small cell lung cancer: A modeling study on 1500 individual
   treatments. *International Journal of Radiation Oncology \* Biology \*
-  Physics*.](https://www.sciencedirect.com/science/article/pii/S036030162030897X)
+  Physics*.
+  doi [10.1016/j.ijrobp.2020.03.005](https://doi.org/10.1016/j.ijrobp.2020.03.005)
 
-- [Nobre, G. G., Hunink, J. E., Baruth, B., Aerts, J. C., & Ward, P. J.
+- Nobre, G. G., Hunink, J. E., Baruth, B., Aerts, J. C., & Ward, P. J.
   (2019). Translating large-scale climate variability into crop
-  production forecast in Europe. *Scientific Reports*, *9*(1),
-  1–13.](https://www.nature.com/articles/s41598-018-38091-4)
+  production forecast in Europe. *Scientific Reports*, *9*(1), 1–13.
+  doi [10.1038/s41598-018-38091-4](https://doi.org/10.1038/s41598-018-38091-4)
 
-- [Buchinsky, F. J., Valentino, W. L., Ruszkay, N., Powell, E.,
+- Buchinsky, F. J., Valentino, W. L., Ruszkay, N., Powell, E.,
   Derkay, C. S., Seedat, R. Y., … & Mortelliti, A. J. (2019). Age at
   diagnosis, but not HPV type, is strongly associated with clinical
-  course in recurrent respiratory papillomatosis. *PloS One*,
-  *14*(6).](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6563955/)
+  course in recurrent respiratory papillomatosis. *PloS One*, *14*(6).
+  doi [10.1371/journal.pone.0216697](https://doi.org/10.1371/journal.pone.0216697)
 
 <!-- footer: -->
 
 ------------------------------------------------------------------------
 
-\[File `README.Rmd` last updated on 2023-02-06.\]
+\[File `README.Rmd` last updated on 2023-02-08.\]
 
 <!-- eof. -->

vignettes/fft.bib

@@ -1,5 +1,5 @@
 % fft.bib
-% Last update on 2023-02-07
+% Last update on 2023-02-08
 
 % FFTrees:  ----
 
@@ -16,11 +16,11 @@ @article{phillips2017FFTrees
 }
 
 @manual{FFTrees-pkg,
-  author = {Phillips, Nathaniel and Neth, Hansjörg and Gaissmaier, Wolfgang and Woike, Jan},
+  author = {Phillips, Nathaniel D and Neth, Hansjörg and Woike, Jan K and Gaissmaier, Wolfgang},
   title = {{FFTrees: Generate, visualize, and evaluate fast-and-frugal decision trees}},
   year = {2023},
-  url = {https://CRAN.R-project.org/package=FFTrees},
-  note = {FFTrees R package (version 1.9.0, February 8, 2023)}
+  number = {{FFTrees R package, version 1.9.0, February 8, 2023}},
+  url = {https://CRAN.R-project.org/package=FFTrees}
 }
 
 

vignettes/guide.Rmd

@@ -49,15 +49,18 @@ url_contact   <- "https://www.linkedin.com/in/nathanieldphillips/"
 
 <!-- Brief intro: -->
 
-The R package **FFTrees** [@phillips2017FFTrees] makes it easy to create, visualize, and evaluate fast-and-frugal decision trees\ (FFTs) for solving binary classification problems in an efficient, effective, and transparent fashion. 
+The R package **FFTrees** [@phillips2017FFTrees; @FFTrees-pkg] makes it easy to create, visualize, and evaluate fast-and-frugal decision trees\ (FFTs). 
+FFTs are simple and transparent decision algorithms for solving binary classification problems in an efficient and effective fashion. 
 
 
 ## Fast-and-Frugal Trees (FFTs) 
 
 <!-- Defining FFTs: -->
 
-A _fast-and-frugal tree_ (FFT) [@martignon2003naive] is a set of hierarchical rules for solving binary classification tasks based on very little pieces of information (usually\ 4 or fewer cues). 
-In contrast to more complex decision trees, each node of an FFT has exactly two branches, where at least one branch is an exit branch (and both branches of the final nodes are exits). 
+A _fast-and-frugal tree_ (FFT) [@martignon2003naive] is a set of hierarchical rules for solving binary classification tasks based on very little pieces of information (usually using\ 4 or fewer cues). 
+In contrast to more complex decision trees, each node of an\ FFT has exactly two branches. 
+A branch can either contain another cue (i.e., ask another question) or lead to an exit (i.e., yield a decision or prediction outcome).  
+Each non-final node of an\ FFT has one exit branch and the final node has two exit branches. 
 
 <!-- Characteristics and benefits of FFTs: -->
 
@@ -100,8 +103,9 @@ plot(heart.fft, data = "test")
 ## Getting started 
 
 To start using the **FFTrees** package, we recommend studying the [Tutorial: Creating FFTs for heart disease](FFTrees_heart.html). 
-This tutorial illustrates the basics steps of creating, visualizing, and evaluating fast-and-frugal trees (FFTs). The scientific background of FFTs and the development of **FFTrees** are described in @phillips2017FFTrees (in [html](`r url_JDM_html`) | [PDF](`r url_JDM_pdf`)). 
-The following vignettes provide details on additional topics and corresponding examples. 
+The tutorial illustrates the basics steps of creating, visualizing, and evaluating fast-and-frugal trees (FFTs). 
+The scientific background of FFTs and the development of **FFTrees** are described in @phillips2017FFTrees (doi\ [10.1017/S1930297500006239](`r url_JDM_doi`) | [html](`r url_JDM_html`) | [PDF](`r url_JDM_pdf`)). 
+The following vignettes provide details on related topics and corresponding examples. 
 
 ### Vignettes
 
@@ -137,7 +141,7 @@ The **FFTrees** package contains several datasets ---\ mostly from the [UCI Mach
 ## Citing **FFTrees** 
 
 We had a lot of fun creating **FFTrees** and hope you like it too! 
-For an accessible introduction to FFTs, we recommend reading our article in the journal _Judgment and Decision Making_ ([2017](`r url_JDM_doi`)), entitled _FFTrees: A toolbox to create, visualize,and evaluate fast-and-frugal decision trees_ (available in [html](`r url_JDM_html`) | [PDF](`r url_JDM_pdf`)\ ).  
+For an accessible introduction to FFTs, we recommend reading our article in the journal _Judgment and Decision Making_ ([2017](`r url_JDM_doi`)), entitled _FFTrees: A toolbox to create, visualize, and evaluate fast-and-frugal decision trees_ (available in [html](`r url_JDM_html`) | [PDF](`r url_JDM_pdf`)\ ).  
 
 **Citation** (in APA format):