Reformatting to comply with JSS requirements

inst/manuscript/manuscript.aux

@@ -58,7 +58,7 @@
     {1}{19.15776pt}\LT@entry 
     {1}{276.6107pt}}
 \newlabel{tab:metrics-summary}{{2}{5}{}{table.2}{}}
-\@writefile{lot}{\contentsline {table}{\numberline {2}{\ignorespaces Summary table of scores available in {\fontseries  {m}\fontseries  {b}\selectfont  scoringutils}. This table (including corresponding function names) can be accessed by calling \bgroup \catcode `\_12\relax \catcode `\~12\relax \catcode `\$12\relax {\normalfont  \ttfamily  \hyphenchar \font =-1 scoringutils::metrics}\egroup  in \textsf  {R}. Not all metrics are implemented for all types of forecasts and forecasting formats, as indicated by tickmarks, '-', or '$\sim $' (depends). D (discrete forecasts based on predictive samples), C (continuous, sample-based forecasts), B (binary), and Q (any forecasts in a quantile-based format) refer to different forecast formats. While the distinction is not clear-cut (e.g. binary is a special case of discrete), it is useful in the context of the package as available functions and functionality may differ. For a more detailed description of the terms used in this table see the corresponding paper sections (e.g. for 'global' and 'local' see section \ref  {localglobal}). For mathematical defintions of the metrics see Table \ref  {tab:score-table-detailed}.\relax }}{5}{table.2}\protected@file@percent }
+\@writefile{lot}{\contentsline {table}{\numberline {2}{\ignorespaces Summary table of scores available in {\fontseries  {m}\fontseries  {b}\selectfont  scoringutils}. This table (including corresponding function names) can be accessed by calling \bgroup \catcode `\_12\relax \catcode `\~12\relax \catcode `\$12\relax {\normalfont  \ttfamily  \hyphenchar \font =-1 scoringutils::metrics}\egroup  in \textsf  {R}. Not all metrics are implemented for all types of forecasts and forecasting formats, as indicated by tickmarks, '-', or '$\sim $' (depends). D (discrete forecasts based on predictive samples), C (continuous, sample-based forecasts), B (binary), and Q (any forecasts in a quantile-based format) refer to different forecast formats. While the distinction is not clear-cut (e.g., binary is a special case of discrete), it is useful in the context of the package as available functions and functionality may differ. For a more detailed description of the terms used in this table see the corresponding paper sections (e.g., for 'global' and 'local' see Section \ref  {localglobal}). For mathematical definitions of the metrics see Table \ref  {tab:score-table-detailed}.\relax }}{5}{table.2}\protected@file@percent }
 \citation{gneitingProbabilisticForecastsCalibration2007}
 \citation{dawidPresentPositionPotential1984}
 \citation{angusProbabilityIntegralTransform1994}
@@ -109,10 +109,13 @@
 \newlabel{pairwisetheory}{{2.4}{13}{Sensitivity to the order of magnitude of the forecast quantity}{subsection.2.4}{}}
 \newlabel{evaluation-example}{{3}{13}{Sensitivity to the order of magnitude of the forecast quantity}{section.3}{}}
 \citation{europeancovid-19forecasthubEuropeanCovid19Forecast2021}
+\citation{tibble}
+\citation{kableExtra}
 \newlabel{example-data}{{3.1}{14}{Sensitivity to the order of magnitude of the forecast quantity}{subsection.3.1}{}}
 \newlabel{expected-input-formats-and-data-checking}{{3.2}{14}{Sensitivity to the order of magnitude of the forecast quantity}{subsection.3.2}{}}
 \@writefile{lot}{\contentsline {table}{\numberline {3}{\ignorespaces Overview of the columns required for different input formats.\relax }}{15}{table.caption.11}\protected@file@percent }
 \newlabel{tab:column-requirements}{{3}{15}{Overview of the columns required for different input formats.\relax }{table.caption.11}{}}
+\citation{ggplot2}
 \newlabel{visualising-forecast-data}{{3.3}{17}{Sensitivity to the order of magnitude of the forecast quantity}{subsection.3.3}{}}
 \@writefile{lof}{\contentsline {figure}{\numberline {6}{\ignorespaces Overview of the number of available forecasts}}{18}{figure.caption.12}\protected@file@percent }
 \newlabel{fig:avail-forecasts-plot}{{6}{18}{Overview of the number of available forecasts}{figure.caption.12}{}}
@@ -143,8 +146,14 @@
     {1}{346.24875pt}}
 \newlabel{appendix-detailed-information-on-metrics}{{3.8}{29}{Sensitivity to the order of magnitude of the forecast quantity}{subsection.3.8}{}}
 \@writefile{toc}{\contentsline {section}{(APPENDIX) Detailed Information on Metrics}{29}{subsection.3.8}\protected@file@percent }
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-\@writefile{lot}{\contentsline {table}{\numberline {4}{\ignorespaces Detailed explanation of all the metrics,\relax }}{29}{table.4}\protected@file@percent }
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+\@writefile{lot}{\contentsline {table}{\numberline {4}{\ignorespaces Detailed explanation of all the metrics.\relax }}{35}{table.4}\protected@file@percent }
+\newlabel{tab:score-table-detailed}{{4}{36}{Sensitivity to the order of magnitude of the forecast quantity}{table.4}{}}
 \bibdata{references.bib,scoringutils-paper.bib}
 \bibcite{angusProbabilityIntegralTransform1994}{{1}{1994}{{Angus}}{{}}}
 \bibcite{bracherEvaluatingEpidemicForecasts2021}{{2}{2021{a}}{{Bracher \emph  {et~al.}}}{{Bracher, Ray, Gneiting, and Reich}}}
@@ -176,10 +185,13 @@
 \bibcite{mannTestWhetherOne1947}{{28}{1947}{{Mann and Whitney}}{{}}}
 \bibcite{mathesonScoringRulesContinuous1976}{{29}{1976}{{Matheson and Winkler}}{{}}}
 \bibcite{murphyNoteRankedProbability1971a}{{30}{1971}{{Murphy}}{{}}}
-\bibcite{R}{{31}{2021}{{R Core Team}}{{}}}
-\bibcite{reichCollaborativeMultiyearMultimodel2019}{{32}{2019}{{Reich \emph  {et~al.}}}{{Reich, Brooks, Fox, Kandula, McGowan, Moore, Osthus, Ray, Tushar, Yamana, Biggerstaff, Johansson, Rosenfeld, and Shaman}}}
-\bibcite{timmermannForecastingMethodsFinance2018}{{33}{2018}{{Timmermann}}{{}}}
-\bibcite{winklerScoringRulesEvaluation1996}{{34}{1996}{{Winkler \emph  {et~al.}}}{{Winkler, Mu{\~n}oz, Cervera, Bernardo, Blattenberger, Kadane, Lindley, Murphy, Oliver, and {R{\'i}os-Insua}}}}
-\bibcite{MLmetrics}{{35}{2016}{{Yan}}{{}}}
-\bibcite{topmodels}{{36}{2022}{{Zeileis and Lang}}{{}}}
+\bibcite{tibble}{{31}{2022}{{Müller and Wickham}}{{}}}
+\bibcite{R}{{32}{2021}{{R Core Team}}{{}}}
+\bibcite{reichCollaborativeMultiyearMultimodel2019}{{33}{2019}{{Reich \emph  {et~al.}}}{{Reich, Brooks, Fox, Kandula, McGowan, Moore, Osthus, Ray, Tushar, Yamana, Biggerstaff, Johansson, Rosenfeld, and Shaman}}}
+\bibcite{timmermannForecastingMethodsFinance2018}{{34}{2018}{{Timmermann}}{{}}}
+\bibcite{ggplot2}{{35}{2016}{{Wickham}}{{}}}
+\bibcite{winklerScoringRulesEvaluation1996}{{36}{1996}{{Winkler \emph  {et~al.}}}{{Winkler, Mu{\~n}oz, Cervera, Bernardo, Blattenberger, Kadane, Lindley, Murphy, Oliver, and {R{\'i}os-Insua}}}}
+\bibcite{MLmetrics}{{37}{2016}{{Yan}}{{}}}
+\bibcite{topmodels}{{38}{2022}{{Zeileis and Lang}}{{}}}
+\bibcite{kableExtra}{{39}{2021}{{Zhu}}{{}}}
 \gdef \@abspage@last{42}

inst/manuscript/manuscript.bbl

@@ -1,4 +1,4 @@
-\begin{thebibliography}{36}
+\begin{thebibliography}{39}
 \newcommand{\enquote}[1]{``#1''}
 \providecommand{\natexlab}[1]{#1}
 \providecommand{\url}[1]{\texttt{#1}}
@@ -62,8 +62,8 @@ Bracher J, Wolffram D, Deuschel J, G{\"o}rgen K, Ketterer JL, Ullrich A, Abbott
 
 \bibitem[{Brier(1950)}]{brierVERIFICATIONFORECASTSEXPRESSED1950}
 Brier GW (1950).
-\newblock \enquote{{{VERIFICATION OF FORECASTS EXPRESSED IN TERMS OF
-  PROBABILITY}}.}
+\newblock \enquote{{{Verification of Forecasts Expressed in Terms of
+  Probability}}.}
 \newblock \emph{Monthly Weather Review}, \textbf{78}(1), 1--3.
 \newblock ISSN 1520-0493, 0027-0644.
 \newblock \doi{10.1175/1520-0493(1950)078<0001:VOFEIT>2.0.CO;2}.
@@ -152,7 +152,7 @@ Cramer E, Reich NG, Wang SY, Niemi J, Hannan A, House K, Gu Y, Xie S, Horstman
 Dawid AP (1984).
 \newblock \enquote{Present {{Position}} and {{Potential Developments}}: {{Some
   Personal Views Statistical Theory}} the {{Prequential Approach}}.}
-\newblock \emph{Journal of the Royal Statistical Society: Series A (General)},
+\newblock \emph{Journal of the Royal Statistical Society A (General)},
   \textbf{147}(2), 278--290.
 \newblock ISSN 2397-2327.
 \newblock \doi{10.2307/2981683}.
@@ -229,7 +229,7 @@ Gelman A, Hwang J, Vehtari A (2014).
   Raftery}]{gneitingProbabilisticForecastsCalibration2007}
 Gneiting T, Balabdaoui F, Raftery AE (2007).
 \newblock \enquote{Probabilistic Forecasts, Calibration and Sharpness.}
-\newblock \emph{Journal of the Royal Statistical Society: Series B (Statistical
+\newblock \emph{Journal of the Royal Statistical Society B (Statistical
   Methodology)}, \textbf{69}(2), 243--268.
 \newblock ISSN 1467-9868.
 \newblock \doi{10.1111/j.1467-9868.2007.00587.x}.
@@ -347,6 +347,12 @@ Murphy AH (1971).
 \newblock ISSN 1520-0450.
 \newblock \doi{10.1175/1520-0450(1971)010<0155:ANOTRP>2.0.CO;2}.
 
+\bibitem[{Müller and Wickham(2022)}]{tibble}
+Müller K, Wickham H (2022).
+\newblock \emph{tibble: Simple Data Frames}.
+\newblock R package version 3.1.7,
+  \urlprefix\url{https://CRAN.R-project.org/package=tibble}.
+
 \bibitem[{{R Core Team}(2021)}]{R}
 {R Core Team} (2021).
 \newblock \emph{R: A Language and Environment for Statistical Computing}.
@@ -373,6 +379,13 @@ Timmermann A (2018).
   449--479.
 \newblock \doi{10.1146/annurev-financial-110217-022713}.
 
+\bibitem[{Wickham(2016)}]{ggplot2}
+Wickham H (2016).
+\newblock \emph{ggplot2: Elegant Graphics for Data Analysis}.
+\newblock Springer-Verlag New York.
+\newblock ISBN 978-3-319-24277-4.
+\newblock \urlprefix\url{https://ggplot2.tidyverse.org}.
+
 \bibitem[{Winkler \emph{et~al.}(1996)Winkler, Mu{\~n}oz, Cervera, Bernardo,
   Blattenberger, Kadane, Lindley, Murphy, Oliver, and
   {R{\'i}os-Insua}}]{winklerScoringRulesEvaluation1996}
@@ -396,4 +409,11 @@ Zeileis A, Lang MN (2022).
 \newblock R package version 0.1-0/r1498,
   \urlprefix\url{https://R-Forge.R-project.org/projects/topmodels/}.
 
+\bibitem[{Zhu(2021)}]{kableExtra}
+Zhu H (2021).
+\newblock \emph{kableExtra: Construct Complex Table with 'kable' and Pipe
+  Syntax}.
+\newblock R package version 1.3.4,
+  \urlprefix\url{https://CRAN.R-project.org/package=kableExtra}.
+
 \end{thebibliography}

inst/manuscript/manuscript.blg

@@ -5,44 +5,44 @@ The style file: jss.bst
 Database file #1: references.bib
 Database file #2: scoringutils-paper.bib
 Reallocated wiz_functions (elt_size=4) to 6000 items from 3000.
-You've used 36 entries,
+You've used 39 entries,
             3215 wiz_defined-function locations,
-            948 strings with 22335 characters,
-and the built_in function-call counts, 110905 in all, are:
-= -- 11669
-> -- 4189
-< -- 24
-+ -- 1584
-- -- 1534
-* -- 8714
-:= -- 12139
-add.period$ -- 190
-call.type$ -- 36
-change.case$ -- 658
-chr.to.int$ -- 37
-cite$ -- 36
-duplicate$ -- 11737
-empty$ -- 7294
-format.name$ -- 1631
-if$ -- 22415
+            965 strings with 22741 characters,
+and the built_in function-call counts, 112769 in all, are:
+= -- 11843
+> -- 4228
+< -- 27
++ -- 1599
+- -- 1546
+* -- 8828
+:= -- 12391
+add.period$ -- 201
+call.type$ -- 39
+change.case$ -- 676
+chr.to.int$ -- 40
+cite$ -- 39
+duplicate$ -- 11926
+empty$ -- 7454
+format.name$ -- 1650
+if$ -- 22793
 int.to.chr$ -- 4
 int.to.str$ -- 1
-missing$ -- 801
-newline$ -- 241
-num.names$ -- 144
-pop$ -- 6071
+missing$ -- 824
+newline$ -- 258
+num.names$ -- 156
+pop$ -- 6161
 preamble$ -- 1
-purify$ -- 655
+purify$ -- 671
 quote$ -- 0
-skip$ -- 1208
+skip$ -- 1260
 stack$ -- 0
-substring$ -- 14382
-swap$ -- 1941
+substring$ -- 14515
+swap$ -- 1990
 text.length$ -- 3
 text.prefix$ -- 0
 top$ -- 0
-type$ -- 324
+type$ -- 348
 warning$ -- 0
-while$ -- 668
+while$ -- 681
 width$ -- 0
-write$ -- 574
+write$ -- 616

inst/manuscript/manuscript.out

@@ -1,6 +1,6 @@
 \BOOKMARK [1][-]{Section.0.Introduction.1}{\376\377\000I\000n\000t\000r\000o\000d\000u\000c\000t\000i\000o\000n}{}% 1
 \BOOKMARK [2][-]{Subsection.1.0.Forecast types and forecast formats.2}{\376\377\000F\000o\000r\000e\000c\000a\000s\000t\000\040\000t\000y\000p\000e\000s\000\040\000a\000n\000d\000\040\000f\000o\000r\000e\000c\000a\000s\000t\000\040\000f\000o\000r\000m\000a\000t\000s}{Section.0.Introduction.1}% 2
-\BOOKMARK [2][-]{Subsection.1.1.The Forecasting paradigm.2}{\376\377\000T\000h\000e\000\040\000F\000o\000r\000e\000c\000a\000s\000t\000i\000n\000g\000\040\000p\000a\000r\000a\000d\000i\000g\000m}{Section.0.Introduction.1}% 3
+\BOOKMARK [2][-]{Subsection.1.1.The forecasting paradigm.2}{\376\377\000T\000h\000e\000\040\000f\000o\000r\000e\000c\000a\000s\000t\000i\000n\000g\000\040\000p\000a\000r\000a\000d\000i\000g\000m}{Section.0.Introduction.1}% 3
 \BOOKMARK [1][-]{Section.1.Scoring metrics implemented in scoringutils.1}{\376\377\000S\000c\000o\000r\000i\000n\000g\000\040\000m\000e\000t\000r\000i\000c\000s\000\040\000i\000m\000p\000l\000e\000m\000e\000n\000t\000e\000d\000\040\000i\000n\000\040\000s\000c\000o\000r\000i\000n\000g\000u\000t\000i\000l\000s}{}% 4
 \BOOKMARK [2][-]{Subsection.2.0.Assessing calibration.2}{\376\377\000A\000s\000s\000e\000s\000s\000i\000n\000g\000\040\000c\000a\000l\000i\000b\000r\000a\000t\000i\000o\000n}{Section.1.Scoring metrics implemented in scoringutils.1}% 5
 \BOOKMARK [3][-]{Subsubsection.2.1.0.Probabilistic calibration.3}{\376\377\000P\000r\000o\000b\000a\000b\000i\000l\000i\000s\000t\000i\000c\000\040\000c\000a\000l\000i\000b\000r\000a\000t\000i\000o\000n}{Subsection.2.0.Assessing calibration.2}% 6

inst/manuscript/references.bib

@@ -53,3 +53,28 @@ @Article{tscount
     pages = {1--51},
     doi = {10.18637/jss.v082.i05},
   }
+
+  @Book{ggplot2,
+    author = {Hadley Wickham},
+    title = {ggplot2: Elegant Graphics for Data Analysis},
+    publisher = {Springer-Verlag New York},
+    year = {2016},
+    isbn = {978-3-319-24277-4},
+    url = {https://ggplot2.tidyverse.org},
+  }
+
+  @Manual{tibble,
+    title = {tibble: Simple Data Frames},
+    author = {Kirill Müller and Hadley Wickham},
+    year = {2022},
+    note = {R package version 3.1.7},
+    url = {https://CRAN.R-project.org/package=tibble},
+  }
+
+  @Manual{kableExtra,
+    title = {kableExtra: Construct Complex Table with 'kable' and Pipe Syntax},
+    author = {Hao Zhu},
+    year = {2021},
+    note = {R package version 1.3.4},
+    url = {https://CRAN.R-project.org/package=kableExtra},
+  }

inst/manuscript/scoringutils-paper.bib

@@ -77,7 +77,7 @@ @article{bracherShorttermForecastingCOVID192021
 }
 
 @article{brierVERIFICATIONFORECASTSEXPRESSED1950,
-  title = {{{VERIFICATION OF FORECASTS EXPRESSED IN TERMS OF PROBABILITY}}},
+  title = {{{Verification of Forecasts Expressed in Terms of Probability}}},
   author = {Brier, Glenn W.},
   year = {1950},
   month = jan,
@@ -152,7 +152,7 @@ @article{dawidPresentPositionPotential1984
   shorttitle = {Present {{Position}} and {{Potential Developments}}},
   author = {Dawid, A. P.},
   year = {1984},
-  journal = {Journal of the Royal Statistical Society: Series A (General)},
+  journal = {Journal of the Royal Statistical Society A (General)},
   volume = {147},
   number = {2},
   pages = {278--290},
@@ -279,7 +279,7 @@ @article{gneitingProbabilisticForecastsCalibration2007
   title = {Probabilistic Forecasts, Calibration and Sharpness},
   author = {Gneiting, Tilmann and Balabdaoui, Fadoua and Raftery, Adrian E.},
   year = {2007},
-  journal = {Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
+  journal = {Journal of the Royal Statistical Society B (Statistical Methodology)},
   volume = {69},
   number = {2},
   pages = {243--268},