diff --git a/papers/JOSE/paper.Rmd b/papers/JOSE/paper.Rmd index 86dd99104..d2b4dbfe7 100644 --- a/papers/JOSE/paper.Rmd +++ b/papers/JOSE/paper.Rmd @@ -111,10 +111,11 @@ Beyond the challenge of keeping up-to-date with current best practices regarding Real-life data often contain observations that can be considered *abnormal* when compared to the main population. The cause of it---be it because they belong to a different distribution (originating from a different generative process) or simply being extreme cases, statistically rare but not impossible---can be hard to assess, and the boundaries of "abnormal" difficult to define. -Nonetheless, the improper handling of these outliers can substantially affect statistical model estimations, biasing effect estimations and weakening the models' predictive performance. -It is thus essential to address this problem in a thoughtful manner. Yet, despite the existence of established recommendations and guidelines, many researchers still do not treat outliers in a consistent manner, or do so using inappropriate strategies [@simmons2011false; @leys2013outliers]. +Nonetheless, the improper handling of these outliers can substantially affect statistical model estimations, biasing effect estimations and weakening the models' predictive performance. It is thus essential to address this problem in a thoughtful manner. Yet, despite the existence of established recommendations and guidelines, many researchers still do not treat outliers in a consistent manner, or do so using inappropriate strategies [@simmons2011false; @leys2013outliers]. -One possible reason is that researchers are not aware of the existing recommendations, or do not know how to implement them using their analysis software. In this paper, we show how to follow current best practices for automatic and reproducible statistical outlier detection (SOD) using R and the *{performance}* package [@ludecke2021performance], which is part of the *easystats* ecosystem of packages that build an R framework for easy statistical modeling, visualization, and reporting [@easystatspackage]. +One possible reason is that researchers are not aware of the existing recommendations, or do not know how to implement them using their analysis software. In this paper, we show how to follow current best practices for automatic and reproducible statistical outlier detection (SOD) using R and the *{performance}* package [@ludecke2021performance], which is part of the *easystats* ecosystem of packages that build an R framework for easy statistical modeling, visualization, and reporting [@easystatspackage]. Installation instructions can be found on [GitHub](https://github.com/easystats/performance) or its [website](https://easystats.github.io/performance/), and its list of dependencies on [CRAN](https://cran.r-project.org/package=performance). + +The instructional materials that follow is aimed at an audience of researchers who want to follow good practices, and is appropriate for advanced undergraduate students, graduate students, professors, or professionals having to deal with the nuances of outlier treatment. # Identifying Outliers diff --git a/papers/JOSE/paper.log b/papers/JOSE/paper.log index 30ce84931..046bb99c4 100644 --- a/papers/JOSE/paper.log +++ b/papers/JOSE/paper.log @@ -1,13 +1,14 @@ -This is XeTeX, Version 3.141592653-2.6-0.999995 (TeX Live 2023) (preloaded format=xelatex 2023.6.8) 16 JUN 2023 16:14 +This is XeTeX, Version 3.141592653-2.6-0.999995 (MiKTeX 23.5) (preloaded format=xelatex 2023.5.20) 27 SEP 2023 19:13 entering extended mode restricted \write18 enabled. %&-line parsing enabled. -**paper.tex -(./paper.tex +**./paper.tex +(paper.tex LaTeX2e <2022-11-01> patch level 1 -L3 programming layer <2023-06-05> (c:/Users/rempsyc/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/base/article.cls +L3 programming layer <2023-05-15> (C:\Users\there\AppData\Local\Programs\MiKTeX +\tex/latex/base\article.cls Document Class: article 2022/07/02 v1.4n Standard LaTeX document class -(c:/Users/rempsyc/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/base/size10.clo +(C:\Users\there\AppData\Local\Programs\MiKTeX\tex/latex/base\size10.clo File: size10.clo 2022/07/02 v1.4n Standard LaTeX file (size option) ) \c@part=\count181 @@ -21,34 +22,38 @@ File: size10.clo 2022/07/02 v1.4n Standard LaTeX file (size option) \abovecaptionskip=\skip48 \belowcaptionskip=\skip49 \bibindent=\dimen140 -) (c:/Users/rempsyc/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/marginnote/marginnote.sty +) +(C:\Users\there\AppData\Local\Programs\MiKTeX\tex/latex/marginnote\marginnote.s +ty Package: marginnote 2018/08/09 v1.4b non floating margin notes for LaTeX \c@mn@abspage=\count189 -) (c:/Users/rempsyc/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/graphics/graphicx.sty +) (C:\Users\there\AppData\Local\Programs\MiKTeX\tex/latex/graphics\graphicx.sty Package: graphicx 2021/09/16 v1.2d Enhanced LaTeX Graphics (DPC,SPQR) -(c:/Users/rempsyc/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/graphics/keyval.sty +(C:\Users\there\AppData\Local\Programs\MiKTeX\tex/latex/graphics\keyval.sty Package: keyval 2022/05/29 v1.15 key=value parser (DPC) \KV@toks@=\toks16 -) (c:/Users/rempsyc/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/graphics/graphics.sty +) (C:\Users\there\AppData\Local\Programs\MiKTeX\tex/latex/graphics\graphics.sty Package: graphics 2022/03/10 v1.4e Standard LaTeX Graphics (DPC,SPQR) -(c:/Users/rempsyc/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/graphics/trig.sty +(C:\Users\there\AppData\Local\Programs\MiKTeX\tex/latex/graphics\trig.sty Package: trig 2021/08/11 v1.11 sin cos tan (DPC) -) (c:/Users/rempsyc/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/graphics-cfg/graphics.cfg +) +(C:\Users\there\AppData\Local\Programs\MiKTeX\tex/latex/graphics-cfg\graphics.c +fg File: graphics.cfg 2016/06/04 v1.11 sample graphics configuration ) Package graphics Info: Driver file: xetex.def on input line 107. -(c:/Users/rempsyc/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/graphics-def/xetex.def +(C:\Users\there\AppData\Local\Programs\MiKTeX\tex/latex/graphics-def\xetex.def File: xetex.def 2022/09/22 v5.0n Graphics/color driver for xetex )) \Gin@req@height=\dimen141 \Gin@req@width=\dimen142 -) (c:/Users/rempsyc/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/xcolor/xcolor.sty +) (C:\Users\there\AppData\Local\Programs\MiKTeX\tex/latex/xcolor\xcolor.sty Package: xcolor 2022/06/12 v2.14 LaTeX color extensions (UK) -(c:/Users/rempsyc/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/graphics-cfg/color.cfg +(C:\Users\there\AppData\Local\Programs\MiKTeX\tex/latex/graphics-cfg\color.cfg File: color.cfg 2016/01/02 v1.6 sample color configuration ) Package xcolor Info: Driver file: xetex.def on input line 227. -(c:/Users/rempsyc/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/graphics/mathcolor.ltx) +(C:\Users\there\AppData\Local\Programs\MiKTeX\tex/latex/graphics\mathcolor.ltx) Package xcolor Info: Model `cmy' substituted by `cmy0' on input line 1353. 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Use iftex instead. -) (c:/Users/rempsyc/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/seqsplit/seqsplit.sty -Package: seqsplit 2006/08/07 v0.1 Splitting long sequences (DNA, RNA, proteins, etc.) -) (c:/Users/rempsyc/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/base/fixltx2e.sty +) (C:\Users\there\AppData\Local\Programs\MiKTeX\tex/latex/seqsplit\seqsplit.sty +Package: seqsplit 2006/08/07 v0.1 Splitting long sequences (DNA, RNA, proteins, + etc.) +) (C:\Users\there\AppData\Local\Programs\MiKTeX\tex/latex/base\fixltx2e.sty Package: fixltx2e 2016/12/29 v2.1a fixes to LaTeX (obsolete) Applying: [2015/01/01] Old fixltx2e package on input line 46. @@ -512,14 +676,14 @@ Package fixltx2e Warning: fixltx2e is not required with releases after 2015 (fixltx2e) See the latexrelease package for details. Already applied: [0000/00/00] Old fixltx2e package on input line 53. -) (c:/Users/rempsyc/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/biblatex/biblatex.sty +) (C:\Users\there\AppData\Local\Programs\MiKTeX\tex/latex/biblatex\biblatex.sty Package: biblatex 2023/03/05 v3.19 programmable bibliographies (PK/MW) -(c:/Users/rempsyc/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/logreq/logreq.sty +(C:\Users\there\AppData\Local\Programs\MiKTeX\tex/latex/logreq\logreq.sty Package: logreq 2010/08/04 v1.0 xml request logger \lrq@indent=\count315 -(c:/Users/rempsyc/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/logreq/logreq.def +(C:\Users\there\AppData\Local\Programs\MiKTeX\tex/latex/logreq\logreq.def File: logreq.def 2010/08/04 v1.0 logreq spec v1.0 -)) (c:/Users/rempsyc/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/base/ifthen.sty +)) (C:\Users\there\AppData\Local\Programs\MiKTeX\tex/latex/base\ifthen.sty Package: ifthen 2022/04/13 v1.1d Standard LaTeX ifthen package (DPC) ) \c@tabx@nest=\count316 @@ -575,13 +739,13 @@ Package: ifthen 2022/04/13 v1.1d Standard LaTeX ifthen package (DPC) \bibhang=\skip68 \blx@bcfin=\read4 \blx@bcfout=\write4 -\blx@langwohyphens=\language3 +\blx@langwohyphens=\language79 \c@mincomprange=\count359 \c@maxcomprange=\count360 \c@mincompwidth=\count361 Package biblatex Info: Trying to load biblatex default data model... Package biblatex Info: ... file 'blx-dm.def' found. -(c:/Users/rempsyc/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/biblatex/blx-dm.def +(C:\Users\there\AppData\Local\Programs\MiKTeX\tex/latex/biblatex\blx-dm.def File: blx-dm.def 2023/03/05 v3.19 biblatex localization (PK/MW) ) Package biblatex Info: Trying to load biblatex custom data model... @@ -670,15 +834,18 @@ Package biblatex Info: ... file 'biblatex-dm.cfg' not found. \localshorteditorwidth=\skip82 Package biblatex Info: Trying to load enhanced support for Unicode engines... Package biblatex Info: ... file 'blx-unicode.def' found. -(c:/Users/rempsyc/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/biblatex/blx-unicode.def) + +(C:\Users\there\AppData\Local\Programs\MiKTeX\tex/latex/biblatex\blx-unicode.de +f) Package biblatex Info: Trying to load compatibility code... Package biblatex Info: ... file 'blx-compat.def' found. -(c:/Users/rempsyc/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/biblatex/blx-compat.def + +(C:\Users\there\AppData\Local\Programs\MiKTeX\tex/latex/biblatex\blx-compat.def File: blx-compat.def 2023/03/05 v3.19 biblatex compatibility (PK/MW) ) Package biblatex Info: Trying to load generic definitions... Package biblatex Info: ... file 'biblatex.def' found. -(c:/Users/rempsyc/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/biblatex/biblatex.def +(C:\Users\there\AppData\Local\Programs\MiKTeX\tex/latex/biblatex\biblatex.def File: biblatex.def 2023/03/05 v3.19 biblatex compatibility (PK/MW) \c@textcitecount=\count430 \c@textcitetotal=\count431 @@ -696,18 +863,24 @@ File: biblatex.def 2023/03/05 v3.19 biblatex compatibility (PK/MW) ) Package biblatex Info: Trying to load bibliography style 'numeric'... Package biblatex Info: ... file 'numeric.bbx' found. -(c:/Users/rempsyc/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/biblatex/bbx/numeric.bbx + +(C:\Users\there\AppData\Local\Programs\MiKTeX\tex/latex/biblatex/bbx\numeric.bb +x File: numeric.bbx 2023/03/05 v3.19 biblatex bibliography style (PK/MW) Package biblatex Info: Trying to load bibliography style 'standard'... Package biblatex Info: ... file 'standard.bbx' found. -(c:/Users/rempsyc/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/biblatex/bbx/standard.bbx + +(C:\Users\there\AppData\Local\Programs\MiKTeX\tex/latex/biblatex/bbx\standard.b +bx File: standard.bbx 2023/03/05 v3.19 biblatex bibliography style (PK/MW) \c@bbx:relatedcount=\count439 \c@bbx:relatedtotal=\count440 )) Package biblatex Info: Trying to load citation style 'numeric'... Package biblatex Info: ... file 'numeric.cbx' found. -(c:/Users/rempsyc/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/biblatex/cbx/numeric.cbx + +(C:\Users\there\AppData\Local\Programs\MiKTeX\tex/latex/biblatex/cbx\numeric.cb +x File: numeric.cbx 2023/03/05 v3.19 biblatex citation style (PK/MW) Package biblatex Info: Redefining '\cite'. Package biblatex Info: Redefining '\parencite'. @@ -723,15 +896,17 @@ Package biblatex Info: Redefining '\smartcites'. ) Package biblatex Info: Trying to load configuration file... Package biblatex Info: ... file 'biblatex.cfg' found. -(c:/Users/rempsyc/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/biblatex/biblatex.cfg +(C:\Users\there\AppData\Local\Programs\MiKTeX\tex/latex/biblatex\biblatex.cfg File: biblatex.cfg ) Package biblatex Info: XeTeX detected. (biblatex) Assuming input encoding 'utf8'. Package biblatex Info: Document encoding is UTF8 .... -(c:/Users/rempsyc/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/l3kernel/expl3.sty -Package: expl3 2023-06-05 L3 programming layer (loader) -(c:/Users/rempsyc/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/l3backend/l3backend-xetex.def +(C:\Users\there\AppData\Local\Programs\MiKTeX\tex/latex/l3kernel\expl3.sty +Package: expl3 2023-05-15 L3 programming layer (loader) + +(C:\Users\there\AppData\Local\Programs\MiKTeX\tex/latex/l3backend\l3backend-xet +ex.def File: l3backend-xetex.def 2023-04-19 L3 backend support: XeTeX \g__graphics_track_int=\count441 \l__pdf_internal_box=\box74 @@ -740,16 +915,21 @@ File: l3backend-xetex.def 2023-04-19 L3 backend support: XeTeX \g__pdf_backend_link_int=\count444 )) Package biblatex Info: ... and expl3 -(biblatex) 2023-06-05 L3 programming layer (loader) +(biblatex) 2023-05-15 L3 programming layer (loader) (biblatex) is new enough (at least 2020/04/06), (biblatex) setting 'casechanger=expl3'. -(c:/Users/rempsyc/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/biblatex/blx-case-expl3.sty (c:/Users/rempsyc/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/l3packages/xparse/xparse.sty + +(C:\Users\there\AppData\Local\Programs\MiKTeX\tex/latex/biblatex\blx-case-expl3 +.sty +(C:\Users\there\AppData\Local\Programs\MiKTeX\tex/latex/l3packages/xparse\xpars +e.sty Package: xparse 2023-02-02 L3 Experimental document command parser ) Package: blx-case-expl3 2023/03/05 v3.19 expl3 case changing code for biblatex -)) (c:/Users/rempsyc/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/geometry/geometry.sty +)) (C:\Users\there\AppData\Local\Programs\MiKTeX\tex/latex/geometry\geometry.st +y Package: geometry 2020/01/02 v5.9 Page Geometry -(c:/Users/rempsyc/AppData/Roaming/TinyTeX/texmf-dist/tex/generic/iftex/ifvtex.sty +(C:\Users\there\AppData\Local\Programs\MiKTeX\tex/generic/iftex\ifvtex.sty Package: ifvtex 2019/10/25 v1.7 ifvtex legacy package. Use iftex instead. ) \Gm@cnth=\count445 @@ -764,8 +944,10 @@ Package: ifvtex 2019/10/25 v1.7 ifvtex legacy package. Use iftex instead. \Gm@layouthoffset=\dimen283 \Gm@layoutvoffset=\dimen284 \Gm@dimlist=\toks39 -) (c:/Users/rempsyc/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty +(C:\Users\there\AppData\Local\Programs\MiKTeX\tex/latex/geometry\geometry.cfg)) +(C:\Users\there\AppData\Local\Programs\MiKTeX\tex/latex/fancyhdr\fancyhdr.sty Package: fancyhdr 2022/11/09 v4.1 Extensive control of page headers and footers + \f@nch@headwidth=\skip83 \f@nch@O@elh=\skip84 \f@nch@O@erh=\skip85 @@ -775,12 +957,17 @@ Package: fancyhdr 2022/11/09 v4.1 Extensive control of page headers and footers \f@nch@O@erf=\skip89 \f@nch@O@olf=\skip90 \f@nch@O@orf=\skip91 -) (c:/Users/rempsyc/AppData/Roaming/TinyTeX/texmf-dist/tex/xelatex/mathspec/mathspec.sty -Package: mathspec 2016/12/22 v0.2b LaTeX Package (Mathematics font selection for XeLaTeX) -(c:/Users/rempsyc/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/fontspec/fontspec.sty +) +(C:\Users\there\AppData\Local\Programs\MiKTeX\tex/xelatex/mathspec\mathspec.sty +Package: mathspec 2016/12/22 v0.2b LaTeX Package (Mathematics font selection fo +r XeLaTeX) +(C:\Users\there\AppData\Local\Programs\MiKTeX\tex/latex/fontspec\fontspec.sty Package: fontspec 2022/01/15 v2.8a Font selection for XeLaTeX and LuaLaTeX -(c:/Users/rempsyc/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/fontspec/fontspec-xetex.sty -Package: fontspec-xetex 2022/01/15 v2.8a Font selection for XeLaTeX and LuaLaTeX + +(C:\Users\there\AppData\Local\Programs\MiKTeX\tex/latex/fontspec\fontspec-xetex +.sty +Package: fontspec-xetex 2022/01/15 v2.8a Font selection for XeLaTeX and LuaLaTe +X \l__fontspec_script_int=\count448 \l__fontspec_language_int=\count449 \l__fontspec_strnum_int=\count450 @@ -795,11 +982,13 @@ Package: fontspec-xetex 2022/01/15 v2.8a Font selection for XeLaTeX and LuaLaTeX \l__fontspec_tmpa_dim=\dimen285 \l__fontspec_tmpb_dim=\dimen286 \l__fontspec_tmpc_dim=\dimen287 -(c:/Users/rempsyc/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/base/fontenc.sty +(C:\Users\there\AppData\Local\Programs\MiKTeX\tex/latex/base\fontenc.sty Package: fontenc 2021/04/29 v2.0v Standard LaTeX package -) (c:/Users/rempsyc/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/fontspec/fontspec.cfg))) (c:/Users/rempsyc/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/xkeyval/xkeyval.sty +) (C:\Users\there\AppData\Local\Programs\MiKTeX\tex/latex/fontspec\fontspec.cfg +))) (C:\Users\there\AppData\Local\Programs\MiKTeX\tex/latex/xkeyval\xkeyval.sty Package: xkeyval 2022/06/16 v2.9 package option processing (HA) -(c:/Users/rempsyc/AppData/Roaming/TinyTeX/texmf-dist/tex/generic/xkeyval/xkeyval.tex (c:/Users/rempsyc/AppData/Roaming/TinyTeX/texmf-dist/tex/generic/xkeyval/xkvutils.tex +(C:\Users\there\AppData\Local\Programs\MiKTeX\tex/generic/xkeyval\xkeyval.tex ( +C:\Users\there\AppData\Local\Programs\MiKTeX\tex/generic/xkeyval\xkvutils.tex \XKV@toks=\toks40 \XKV@tempa@toks=\toks41 ) @@ -809,7 +998,13 @@ File: xkeyval.tex 2014/12/03 v2.7a key=value parser (HA) \c@eu@=\count460 \c@eu@i=\count461 \c@mkern=\count462 -) (c:/Users/rempsyc/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/microtype/microtype.sty +) (C:\Users\there\AppData\Local\Programs\MiKTeX\tex/latex/upquote\upquote.sty +Package: upquote 2012/04/19 v1.3 upright-quote and grave-accent glyphs in verba +tim +(C:\Users\there\AppData\Local\Programs\MiKTeX\tex/latex/base\textcomp.sty +Package: textcomp 2020/02/02 v2.0n Standard LaTeX package +)) +(C:\Users\there\AppData\Local\Programs\MiKTeX\tex/latex/microtype\microtype.sty Package: microtype 2023/03/13 v3.1a Micro-typographical refinements (RS) \MT@toks=\toks42 \MT@tempbox=\box75 @@ -822,22 +1017,27 @@ LaTeX Info: Redefining \textls on input line 1368. \MT@outer@kern=\dimen288 LaTeX Info: Redefining \textmicrotypecontext on input line 1988. \MT@listname@count=\count464 -(c:/Users/rempsyc/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/microtype/microtype-xetex.def + +(C:\Users\there\AppData\Local\Programs\MiKTeX\tex/latex/microtype\microtype-xet +ex.def File: microtype-xetex.def 2023/03/13 v3.1a Definitions specific to xetex (RS) LaTeX Info: Redefining \lsstyle on input line 238. ) Package microtype Info: Loading configuration file microtype.cfg. -(c:/Users/rempsyc/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/microtype/microtype.cfg + +(C:\Users\there\AppData\Local\Programs\MiKTeX\tex/latex/microtype\microtype.cfg File: microtype.cfg 2023/03/13 v3.1a microtype main configuration file (RS) )) Package hyperref Info: Option `unicode' set `true' on input line 154. Package hyperref Info: Option `breaklinks' set `true' on input line 154. -(c:/Users/rempsyc/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/grffile/grffile.sty -Package: grffile 2019/11/11 v2.1 Extended file name support for graphics (legacy) -Package grffile Info: This package is an empty stub for compatibility on input line 40. -) (c:/Users/rempsyc/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/parskip/parskip.sty +(C:\Users\there\AppData\Local\Programs\MiKTeX\tex/latex/grffile\grffile.sty +Package: grffile 2019/11/11 v2.1 Extended file name support for graphics (legac +y) +Package grffile Info: This package is an empty stub for compatibility on input +line 40. +) (C:\Users\there\AppData\Local\Programs\MiKTeX\tex/latex/parskip\parskip.sty Package: parskip 2021-03-14 v2.0h non-zero parskip adjustments -) (c:/Users/rempsyc/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty +) (C:\Users\there\AppData\Local\Programs\MiKTeX\tex/latex/fancyvrb\fancyvrb.sty Package: fancyvrb 2023/01/19 4.5a verbatim text (tvz,hv) \FV@CodeLineNo=\count465 \FV@InFile=\read5 @@ -845,14 +1045,14 @@ Package: fancyvrb 2023/01/19 4.5a verbatim text (tvz,hv) \c@FancyVerbLine=\count466 \FV@StepNumber=\count467 \FV@OutFile=\write5 -) (c:/Users/rempsyc/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/framed/framed.sty +) (C:\Users\there\AppData\Local\Programs\MiKTeX\tex/latex/framed\framed.sty Package: framed 2011/10/22 v 0.96: framed or shaded text with page breaks \OuterFrameSep=\skip92 \fb@frw=\dimen289 \fb@frh=\dimen290 \FrameRule=\dimen291 \FrameSep=\dimen292 -) (c:/Users/rempsyc/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/tools/longtable.sty +) (C:\Users\there\AppData\Local\Programs\MiKTeX\tex/latex/tools\longtable.sty Package: longtable 2021-09-01 v4.17 Multi-page Table package (DPC) \LTleft=\skip93 \LTright=\skip94 @@ -870,7 +1070,7 @@ Package: longtable 2021-09-01 v4.17 Multi-page Table package (DPC) \c@LT@tables=\count471 \c@LT@chunks=\count472 \LT@p@ftn=\toks44 -) (c:/Users/rempsyc/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/booktabs/booktabs.sty +) (C:\Users\there\AppData\Local\Programs\MiKTeX\tex/latex/booktabs\booktabs.sty Package: booktabs 2020/01/12 v1.61803398 Publication quality tables \heavyrulewidth=\dimen294 \lightrulewidth=\dimen295 @@ -889,7 +1089,7 @@ Package: booktabs 2020/01/12 v1.61803398 Publication quality tables \@thisruleclass=\count475 \@lastruleclass=\count476 \@thisrulewidth=\dimen306 -) (c:/Users/rempsyc/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/tools/array.sty +) (C:\Users\there\AppData\Local\Programs\MiKTeX\tex/latex/tools\array.sty Package: array 2022/09/04 v2.5g Tabular extension package (FMi) \col@sep=\dimen307 \ar@mcellbox=\box82 @@ -898,17 +1098,20 @@ Package: array 2022/09/04 v2.5g Tabular extension package (FMi) \extratabsurround=\skip97 \backup@length=\skip98 \ar@cellbox=\box83 -) (c:/Users/rempsyc/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/mdwtools/footnote.sty -Package: footnote 1997/01/28 1.13 Save footnotes around boxes -\fn@notes=\box84 -\fn@width=\dimen309 +) +(C:\Users\there\AppData\Local\Programs\MiKTeX\tex/latex/footnotehyper\footnoteh +yper.sty +Package: footnotehyper 2021/08/13 v1.1e hyperref aware footnote.sty (JFB) +\FNH@notes=\box84 +\FNH@width=\dimen309 +\FNH@toks=\toks46 ) \cslhangindent=\skip99 \csllabelwidth=\skip100 \cslentryspacingunit=\skip101 \@quotelevel=\count477 \@quotereset=\count478 -(./paper.aux) +(paper.aux) \openout1 = `paper.aux'. LaTeX Font Info: Checking defaults for OML/cmm/m/it on input line 295. @@ -920,8 +1123,9 @@ LaTeX Font Info: ... okay on input line 295. LaTeX Font Info: Checking defaults for T1/cmr/m/n on input line 295. LaTeX Font Info: ... okay on input line 295. LaTeX Font Info: Checking defaults for TS1/cmr/m/n on input line 295. -LaTeX Font Info: Trying to load font information for TS1+cmr on input line 295. -(c:/Users/rempsyc/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/base/ts1cmr.fd +LaTeX Font Info: Trying to load font information for TS1+cmr on input line 2 +95. +(C:\Users\there\AppData\Local\Programs\MiKTeX\tex/latex/base\ts1cmr.fd File: ts1cmr.fd 2022/07/10 v2.5l Standard LaTeX font definitions ) LaTeX Font Info: ... okay on input line 295. @@ -936,19 +1140,21 @@ LaTeX Font Info: ... okay on input line 295. LaTeX Font Info: Checking defaults for PU/pdf/m/n on input line 295. LaTeX Font Info: ... okay on input line 295. Package hyperref Info: Link coloring ON on input line 295. -(./paper.out) (./paper.out) +(paper.out) (paper.out) \@outlinefile=\write6 \openout6 = `paper.out'. Package caption Info: Begin \AtBeginDocument code. Package caption Info: longtable package is loaded. -(c:/Users/rempsyc/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/caption/ltcaption.sty +(C:\Users\there\AppData\Local\Programs\MiKTeX\tex/latex/caption\ltcaption.sty Package: ltcaption 2021/01/08 v1.4c longtable captions (AR) ) Package caption Info: End \AtBeginDocument code. Package biblatex Info: Trying to load language 'english'... Package biblatex Info: ... file 'english.lbx' found. -(c:/Users/rempsyc/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/biblatex/lbx/english.lbx + +(C:\Users\there\AppData\Local\Programs\MiKTeX\tex/latex/biblatex/lbx\english.lb +x File: english.lbx 2023/03/05 v3.19 biblatex localization (PK/MW) ) Package biblatex Info: XeTeX detected. @@ -1007,8 +1213,11 @@ Package microtype Info: Using protrusion set `basicmath'. Package microtype Info: No adjustment of tracking. Package microtype Info: No adjustment of spacing. 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[2] LaTeX Font Info: Font shape `TU/lmtt/bx/n' in size <10> not available -(Font) Font shape `TU/lmtt/b/n' tried instead on input line 449. +(Font) Font shape `TU/lmtt/b/n' tried instead on input line 458. -Overfull \hbox (32.66139pt too wide) in paragraph at lines 465--465 -[]\TU/lmtt/m/n/10 #> -----------------------------------------------------------------------------[] +Overfull \hbox (32.66139pt too wide) in paragraph at lines 474--474 +[]\TU/lmtt/m/n/10 #> ---------------------------------------------------------- +-------------------[] [] -Overfull \hbox (32.66139pt too wide) in paragraph at lines 474--474 -[]\TU/lmtt/m/n/10 #> -----------------------------------------------------------------------------[] +Overfull \hbox (32.66139pt too wide) in paragraph at lines 483--483 +[]\TU/lmtt/m/n/10 #> ---------------------------------------------------------- +-------------------[] [] -File: D:/Rpackages/rticles/rmarkdown/templates/joss/resources/JOSE-logo.png Graphic file (type bmp) - +File: C:/Users/there/AppData/Local/R/win-library/4.3/rticles/rmarkdown/template +s/joss/resources/JOSE-logo.png Graphic file (type bmp) + Package fancyhdr Warning: \headheight is too small (62.59596pt): (fancyhdr) Make it at least 64.31554pt, for example: (fancyhdr) \setlength{\headheight}{64.31554pt}. (fancyhdr) You might also make \topmargin smaller to compensate: + (fancyhdr) \addtolength{\topmargin}{-1.71957pt}. [3] -File: D:/Rpackages/rticles/rmarkdown/templates/joss/resources/JOSE-logo.png Graphic file (type bmp) - +File: C:/Users/there/AppData/Local/R/win-library/4.3/rticles/rmarkdown/template +s/joss/resources/JOSE-logo.png Graphic file (type bmp) + Package fancyhdr Warning: \headheight is too small (62.59596pt): (fancyhdr) Make it at least 64.31554pt, for example: (fancyhdr) \setlength{\headheight}{64.31554pt}. (fancyhdr) You might also make \topmargin smaller to compensate: + (fancyhdr) \addtolength{\topmargin}{-1.71957pt}. [4] File: paper_files/figure-latex/model-1.pdf Graphic file (type pdf) -File: D:/Rpackages/rticles/rmarkdown/templates/joss/resources/JOSE-logo.png Graphic file (type bmp) - +File: C:/Users/there/AppData/Local/R/win-library/4.3/rticles/rmarkdown/template +s/joss/resources/JOSE-logo.png Graphic file (type bmp) + Package fancyhdr Warning: \headheight is too small (62.59596pt): (fancyhdr) Make it at least 64.31554pt, for example: (fancyhdr) \setlength{\headheight}{64.31554pt}. (fancyhdr) You might also make \topmargin smaller to compensate: + (fancyhdr) \addtolength{\topmargin}{-1.71957pt}. [5] -File: D:/Rpackages/rticles/rmarkdown/templates/joss/resources/JOSE-logo.png Graphic file (type bmp) - +File: C:/Users/there/AppData/Local/R/win-library/4.3/rticles/rmarkdown/template +s/joss/resources/JOSE-logo.png Graphic file (type bmp) + Package fancyhdr Warning: \headheight is too small (62.59596pt): (fancyhdr) Make it at least 64.31554pt, for example: (fancyhdr) \setlength{\headheight}{64.31554pt}. (fancyhdr) You might also make \topmargin smaller to compensate: + (fancyhdr) \addtolength{\topmargin}{-1.71957pt}. [6] -File: D:/Rpackages/rticles/rmarkdown/templates/joss/resources/JOSE-logo.png Graphic file (type bmp) - +File: C:/Users/there/AppData/Local/R/win-library/4.3/rticles/rmarkdown/template +s/joss/resources/JOSE-logo.png Graphic file (type bmp) + Package fancyhdr Warning: \headheight is too small (62.59596pt): (fancyhdr) Make it at least 64.31554pt, for example: (fancyhdr) \setlength{\headheight}{64.31554pt}. (fancyhdr) You might also make \topmargin smaller to compensate: + (fancyhdr) \addtolength{\topmargin}{-1.71957pt}. [7] -Underfull \hbox (badness 1584) in paragraph at lines 910--916 -[]\TU/lmr/m/n/10 Simmons, J. P., Nelson, L. D., & Simonsohn, U. (2011). False-positive psy- +Underfull \hbox (badness 1584) in paragraph at lines 919--925 +[]\TU/lmr/m/n/10 Simmons, J. P., Nelson, L. D., & Simonsohn, U. (2011). False-p +ositive psy- [] -Underfull \hbox (badness 3049) in paragraph at lines 910--916 -\TU/lmr/m/n/10 chology: Undisclosed flexibility in data collection and analysis allows pre- +Underfull \hbox (badness 3049) in paragraph at lines 919--925 +\TU/lmr/m/n/10 chology: Undisclosed flexibility in data collection and analysis + allows pre- [] -Underfull \hbox (badness 3735) in paragraph at lines 910--916 -\TU/lmr/m/n/10 senting anything as significant. \TU/lmr/m/it/10 Psychological Science\TU/lmr/m/n/10 , \TU/lmr/m/it/10 22\TU/lmr/m/n/10 (11), 1359–1366. +Underfull \hbox (badness 3735) in paragraph at lines 919--925 +\TU/lmr/m/n/10 senting anything as significant. \TU/lmr/m/it/10 Psychological S +cience\TU/lmr/m/n/10 , \TU/lmr/m/it/10 22\TU/lmr/m/n/10 (11), 1359–1366. [] -File: D:/Rpackages/rticles/rmarkdown/templates/joss/resources/JOSE-logo.png Graphic file (type bmp) - +File: C:/Users/there/AppData/Local/R/win-library/4.3/rticles/rmarkdown/template +s/joss/resources/JOSE-logo.png Graphic file (type bmp) + Package fancyhdr Warning: \headheight is too small (62.59596pt): (fancyhdr) Make it at least 64.31554pt, for example: (fancyhdr) \setlength{\headheight}{64.31554pt}. (fancyhdr) You might also make \topmargin smaller to compensate: + (fancyhdr) \addtolength{\topmargin}{-1.71957pt}. -[8] (./paper.aux) +[8] (paper.aux) Package rerunfilecheck Info: File `paper.out' has not changed. (rerunfilecheck) Checksum: EEBE57815200557F8EDD73A1BF6F9118;2043. Package logreq Info: Writing requests to 'paper.run.xml'. @@ -1159,12 +1403,12 @@ Package logreq Info: Writing requests to 'paper.run.xml'. ) Here is how much of TeX's memory you used: - 37274 strings out of 478641 - 768952 string characters out of 5846292 - 1872382 words of memory out of 5000000 - 56849 multiletter control sequences out of 15000+600000 - 520299 words of font info for 87 fonts, out of 8000000 for 9000 - 14 hyphenation exceptions out of 8191 - 84i,12n,81p,1194b,848s stack positions out of 10000i,1000n,20000p,200000b,200000s + 37316 strings out of 411547 + 752904 string characters out of 5819451 + 1873476 words of memory out of 5000000 + 56952 multiletter control sequences out of 15000+600000 + 519199 words of font info for 85 fonts, out of 8000000 for 9000 + 1348 hyphenation exceptions out of 8191 + 84i,12n,81p,1196b,850s stack positions out of 10000i,1000n,20000p,200000b,200000s Output written on paper.pdf (8 pages). diff --git a/papers/JOSE/paper.md b/papers/JOSE/paper.md index b6c3946b9..983f9824d 100644 --- a/papers/JOSE/paper.md +++ b/papers/JOSE/paper.md @@ -99,10 +99,11 @@ Beyond the challenge of keeping up-to-date with current best practices regarding Real-life data often contain observations that can be considered *abnormal* when compared to the main population. The cause of it---be it because they belong to a different distribution (originating from a different generative process) or simply being extreme cases, statistically rare but not impossible---can be hard to assess, and the boundaries of "abnormal" difficult to define. -Nonetheless, the improper handling of these outliers can substantially affect statistical model estimations, biasing effect estimations and weakening the models' predictive performance. -It is thus essential to address this problem in a thoughtful manner. Yet, despite the existence of established recommendations and guidelines, many researchers still do not treat outliers in a consistent manner, or do so using inappropriate strategies [@simmons2011false; @leys2013outliers]. +Nonetheless, the improper handling of these outliers can substantially affect statistical model estimations, biasing effect estimations and weakening the models' predictive performance. It is thus essential to address this problem in a thoughtful manner. Yet, despite the existence of established recommendations and guidelines, many researchers still do not treat outliers in a consistent manner, or do so using inappropriate strategies [@simmons2011false; @leys2013outliers]. -One possible reason is that researchers are not aware of the existing recommendations, or do not know how to implement them using their analysis software. In this paper, we show how to follow current best practices for automatic and reproducible statistical outlier detection (SOD) using R and the *{performance}* package [@ludecke2021performance], which is part of the *easystats* ecosystem of packages that build an R framework for easy statistical modeling, visualization, and reporting [@easystatspackage]. +One possible reason is that researchers are not aware of the existing recommendations, or do not know how to implement them using their analysis software. In this paper, we show how to follow current best practices for automatic and reproducible statistical outlier detection (SOD) using R and the *{performance}* package [@ludecke2021performance], which is part of the *easystats* ecosystem of packages that build an R framework for easy statistical modeling, visualization, and reporting [@easystatspackage]. Installation instructions can be found on [GitHub](https://github.com/easystats/performance) or its [website](https://easystats.github.io/performance/), and its list of dependencies on [CRAN](https://cran.r-project.org/package=performance). + +The instructional materials that follow is aimed at an audience of researchers who want to follow good practices, and is appropriate for advanced undergraduate students, graduate students, professors, or professionals having to deal with the nuances of outlier treatment. # Identifying Outliers diff --git a/papers/JOSE/paper.pdf b/papers/JOSE/paper.pdf index f3c3372a6..76bf20f3b 100644 Binary files a/papers/JOSE/paper.pdf and b/papers/JOSE/paper.pdf differ diff --git a/papers/JOSE/paper_files/figure-latex/model-1.pdf b/papers/JOSE/paper_files/figure-latex/model-1.pdf index 27ea7d852..cc65121f5 100644 Binary files a/papers/JOSE/paper_files/figure-latex/model-1.pdf and b/papers/JOSE/paper_files/figure-latex/model-1.pdf differ