From c554ae6e9c7d8e0aa5c377cb96a9e0b4237da066 Mon Sep 17 00:00:00 2001 From: daniel Date: Fri, 5 Mar 2021 18:18:03 +0100 Subject: [PATCH] renamed package (naming conflict with bioconductor) --- .gitattributes | 1 + {CVE => CVarE}/DESCRIPTION | 0 {CVE => CVarE}/NAMESPACE | 0 {CVE => CVarE}/R/CVE.R | 0 {CVE => CVarE}/R/coef.R | 0 {CVE => CVarE}/R/datasets.R | 0 {CVE => CVarE}/R/directions.R | 0 {CVE => CVarE}/R/estimateBandwidth.R | 0 {CVE => CVarE}/R/predict.R | 0 {CVE => CVarE}/R/predict_dim.R | 0 {CVE => CVarE}/R/summary.R | 0 {CVE => CVarE}/R/util.R | 0 {CVE => CVarE}/man/CVE-package.Rd | 0 {CVE => CVarE}/man/coef.cve.Rd | 0 {CVE => CVarE}/man/cve.Rd | 0 {CVE => CVarE}/man/cve.call.Rd | 0 {CVE => CVarE}/man/dataset.Rd | 0 {CVE => CVarE}/man/directions.cve.Rd | 0 {CVE => CVarE}/man/estimate.bandwidth.Rd | 0 {CVE => CVarE}/man/null.Rd | 0 {CVE => CVarE}/man/predict.cve.Rd | 0 {CVE => CVarE}/man/predict_dim.Rd | 0 {CVE => CVarE}/man/rStiefel.Rd | 0 {CVE => CVarE}/man/rgnorm.Rd | 0 {CVE => CVarE}/man/rlaplace.Rd | 0 {CVE => CVarE}/man/rmvnorm.Rd | 0 {CVE => CVarE}/man/rmvt.Rd | 0 {CVE => CVarE}/man/summary.cve.Rd | 0 {CVE => CVarE}/src/Makevars | 0 {CVE => CVarE}/src/Makevars.win | 0 {CVE => CVarE}/src/callLogger.c | 0 {CVE => CVarE}/src/cve.c | 0 {CVE => CVarE}/src/cve.h | 0 {CVE => CVarE}/src/cve_subroutines.c | 0 {CVE => CVarE}/src/export.c | 0 {CVE => CVarE}/src/init.c | 0 {CVE => CVarE}/src/matrix.c | 0 {CVE => CVarE}/src/rStiefel.c | 0 LaTeX/jss.bst | 1653 ---------------------- LaTeX/jss.cls | 490 ------- LaTeX/jsslogo.jpg | 3 - LaTeX/main.Rnw | 152 -- LaTeX/refs.bib | 35 - 43 files changed, 1 insertion(+), 2333 deletions(-) rename {CVE => CVarE}/DESCRIPTION (100%) rename {CVE => CVarE}/NAMESPACE (100%) rename {CVE => CVarE}/R/CVE.R (100%) rename {CVE => CVarE}/R/coef.R (100%) rename {CVE => CVarE}/R/datasets.R (100%) rename {CVE => CVarE}/R/directions.R (100%) rename {CVE => CVarE}/R/estimateBandwidth.R (100%) rename {CVE => CVarE}/R/predict.R (100%) rename {CVE => CVarE}/R/predict_dim.R (100%) rename {CVE => CVarE}/R/summary.R (100%) rename {CVE => CVarE}/R/util.R (100%) rename {CVE => CVarE}/man/CVE-package.Rd (100%) rename {CVE => CVarE}/man/coef.cve.Rd (100%) rename {CVE => CVarE}/man/cve.Rd (100%) rename {CVE => CVarE}/man/cve.call.Rd (100%) rename {CVE => CVarE}/man/dataset.Rd (100%) rename {CVE => CVarE}/man/directions.cve.Rd (100%) rename {CVE => CVarE}/man/estimate.bandwidth.Rd (100%) rename {CVE => CVarE}/man/null.Rd (100%) rename {CVE => CVarE}/man/predict.cve.Rd (100%) rename {CVE => CVarE}/man/predict_dim.Rd (100%) rename {CVE => CVarE}/man/rStiefel.Rd (100%) rename {CVE => CVarE}/man/rgnorm.Rd (100%) rename {CVE => CVarE}/man/rlaplace.Rd (100%) rename {CVE => CVarE}/man/rmvnorm.Rd (100%) rename {CVE => CVarE}/man/rmvt.Rd (100%) rename {CVE => CVarE}/man/summary.cve.Rd (100%) rename {CVE => CVarE}/src/Makevars (100%) rename {CVE => CVarE}/src/Makevars.win (100%) rename {CVE => CVarE}/src/callLogger.c (100%) rename {CVE => CVarE}/src/cve.c (100%) rename {CVE => CVarE}/src/cve.h (100%) rename {CVE => CVarE}/src/cve_subroutines.c (100%) rename {CVE => CVarE}/src/export.c (100%) rename {CVE => CVarE}/src/init.c (100%) rename {CVE => CVarE}/src/matrix.c (100%) rename {CVE => CVarE}/src/rStiefel.c (100%) delete mode 100644 LaTeX/jss.bst delete mode 100644 LaTeX/jss.cls delete mode 100644 LaTeX/jsslogo.jpg delete mode 100644 LaTeX/main.Rnw delete mode 100644 LaTeX/refs.bib diff --git a/.gitattributes b/.gitattributes index b634d85..33d976b 100644 --- a/.gitattributes +++ b/.gitattributes @@ -1 +1,2 @@ *.pdf filter=lfs diff=lfs merge=lfs -text +*.jpg filter=lfs diff=lfs merge=lfs -text diff --git a/CVE/DESCRIPTION b/CVarE/DESCRIPTION similarity index 100% rename from CVE/DESCRIPTION rename to CVarE/DESCRIPTION diff --git a/CVE/NAMESPACE b/CVarE/NAMESPACE similarity index 100% rename from CVE/NAMESPACE rename to CVarE/NAMESPACE diff --git a/CVE/R/CVE.R b/CVarE/R/CVE.R similarity index 100% rename from CVE/R/CVE.R rename to CVarE/R/CVE.R diff --git a/CVE/R/coef.R b/CVarE/R/coef.R similarity index 100% rename from CVE/R/coef.R rename to CVarE/R/coef.R diff --git a/CVE/R/datasets.R b/CVarE/R/datasets.R similarity index 100% rename from CVE/R/datasets.R rename to CVarE/R/datasets.R diff --git a/CVE/R/directions.R b/CVarE/R/directions.R similarity index 100% rename from CVE/R/directions.R rename to CVarE/R/directions.R diff --git a/CVE/R/estimateBandwidth.R b/CVarE/R/estimateBandwidth.R similarity index 100% rename from CVE/R/estimateBandwidth.R rename to CVarE/R/estimateBandwidth.R diff --git a/CVE/R/predict.R b/CVarE/R/predict.R similarity index 100% rename from CVE/R/predict.R rename to CVarE/R/predict.R diff --git a/CVE/R/predict_dim.R b/CVarE/R/predict_dim.R similarity index 100% rename from CVE/R/predict_dim.R rename to CVarE/R/predict_dim.R diff --git a/CVE/R/summary.R b/CVarE/R/summary.R similarity index 100% rename from CVE/R/summary.R rename to CVarE/R/summary.R diff --git a/CVE/R/util.R b/CVarE/R/util.R similarity index 100% rename from CVE/R/util.R rename to CVarE/R/util.R diff --git a/CVE/man/CVE-package.Rd b/CVarE/man/CVE-package.Rd similarity index 100% rename from CVE/man/CVE-package.Rd rename to CVarE/man/CVE-package.Rd diff --git a/CVE/man/coef.cve.Rd b/CVarE/man/coef.cve.Rd similarity index 100% rename from CVE/man/coef.cve.Rd rename to CVarE/man/coef.cve.Rd diff --git a/CVE/man/cve.Rd b/CVarE/man/cve.Rd similarity index 100% rename from CVE/man/cve.Rd rename to CVarE/man/cve.Rd diff --git a/CVE/man/cve.call.Rd b/CVarE/man/cve.call.Rd similarity index 100% rename from CVE/man/cve.call.Rd rename to CVarE/man/cve.call.Rd diff --git a/CVE/man/dataset.Rd b/CVarE/man/dataset.Rd similarity index 100% rename from CVE/man/dataset.Rd rename to CVarE/man/dataset.Rd diff --git a/CVE/man/directions.cve.Rd b/CVarE/man/directions.cve.Rd similarity index 100% rename from CVE/man/directions.cve.Rd rename to CVarE/man/directions.cve.Rd diff --git a/CVE/man/estimate.bandwidth.Rd b/CVarE/man/estimate.bandwidth.Rd similarity index 100% rename from CVE/man/estimate.bandwidth.Rd rename to CVarE/man/estimate.bandwidth.Rd diff --git a/CVE/man/null.Rd b/CVarE/man/null.Rd similarity index 100% rename from CVE/man/null.Rd rename to CVarE/man/null.Rd diff --git a/CVE/man/predict.cve.Rd b/CVarE/man/predict.cve.Rd similarity index 100% rename from CVE/man/predict.cve.Rd rename to CVarE/man/predict.cve.Rd diff --git a/CVE/man/predict_dim.Rd b/CVarE/man/predict_dim.Rd similarity index 100% rename from CVE/man/predict_dim.Rd rename to CVarE/man/predict_dim.Rd diff --git a/CVE/man/rStiefel.Rd b/CVarE/man/rStiefel.Rd similarity index 100% rename from CVE/man/rStiefel.Rd rename to CVarE/man/rStiefel.Rd diff --git a/CVE/man/rgnorm.Rd b/CVarE/man/rgnorm.Rd similarity index 100% rename from CVE/man/rgnorm.Rd rename to CVarE/man/rgnorm.Rd diff --git a/CVE/man/rlaplace.Rd b/CVarE/man/rlaplace.Rd similarity index 100% rename from CVE/man/rlaplace.Rd rename to CVarE/man/rlaplace.Rd diff --git a/CVE/man/rmvnorm.Rd b/CVarE/man/rmvnorm.Rd similarity index 100% rename from CVE/man/rmvnorm.Rd rename to CVarE/man/rmvnorm.Rd diff --git a/CVE/man/rmvt.Rd b/CVarE/man/rmvt.Rd similarity index 100% rename from CVE/man/rmvt.Rd rename to CVarE/man/rmvt.Rd diff --git a/CVE/man/summary.cve.Rd b/CVarE/man/summary.cve.Rd similarity index 100% rename from CVE/man/summary.cve.Rd rename to CVarE/man/summary.cve.Rd diff --git a/CVE/src/Makevars b/CVarE/src/Makevars similarity index 100% rename from CVE/src/Makevars rename to CVarE/src/Makevars diff --git a/CVE/src/Makevars.win b/CVarE/src/Makevars.win similarity index 100% rename from CVE/src/Makevars.win rename to CVarE/src/Makevars.win diff --git a/CVE/src/callLogger.c b/CVarE/src/callLogger.c similarity index 100% rename from CVE/src/callLogger.c rename to CVarE/src/callLogger.c diff --git a/CVE/src/cve.c b/CVarE/src/cve.c similarity index 100% rename from CVE/src/cve.c rename to CVarE/src/cve.c diff --git a/CVE/src/cve.h b/CVarE/src/cve.h similarity index 100% rename from CVE/src/cve.h rename to CVarE/src/cve.h diff --git a/CVE/src/cve_subroutines.c b/CVarE/src/cve_subroutines.c similarity index 100% rename from CVE/src/cve_subroutines.c rename to CVarE/src/cve_subroutines.c diff --git a/CVE/src/export.c b/CVarE/src/export.c similarity index 100% rename from CVE/src/export.c rename to CVarE/src/export.c diff --git a/CVE/src/init.c b/CVarE/src/init.c similarity index 100% rename from CVE/src/init.c rename to CVarE/src/init.c diff --git a/CVE/src/matrix.c b/CVarE/src/matrix.c similarity index 100% rename from CVE/src/matrix.c rename to CVarE/src/matrix.c diff --git a/CVE/src/rStiefel.c b/CVarE/src/rStiefel.c similarity index 100% rename from CVE/src/rStiefel.c rename to CVarE/src/rStiefel.c diff --git a/LaTeX/jss.bst b/LaTeX/jss.bst deleted file mode 100644 index ae75415..0000000 --- a/LaTeX/jss.bst +++ /dev/null @@ -1,1653 +0,0 @@ -%% -%% This is file `jss.bst', -%% generated with the docstrip utility. -%% -%% The original source files were: -%% -%% merlin.mbs (with options: `ay,nat,nm-rvx,keyxyr,dt-beg,yr-par,note-yr,tit-qq,atit-u,trnum-it,vol-bf,volp-com,num-xser,pre-edn,isbn,issn,edpar,pp,ed,xedn,xand,etal-it,revdata,eprint,url,url-blk,doi,nfss') -%% -%% ** BibTeX style file for JSS publications (http://www.jstatsoft.org/) -%% -%% License: GPL-2 | GPL-3 - % =============================================================== - % IMPORTANT NOTICE: - % This bibliographic style (bst) file has been generated from one or - % more master bibliographic style (mbs) files, listed above, provided - % with kind permission of Patrick W Daly. - % - % This generated file can be redistributed and/or modified under the terms - % of the General Public License (Version 2 or 3). - % =============================================================== - % Name and version information of the main mbs file: - % \ProvidesFile{merlin.mbs}[2011/11/18 4.33 (PWD, AO, DPC)] - % For use with BibTeX version 0.99a or later - %------------------------------------------------------------------- - % This bibliography style file is intended for texts in ENGLISH - % This is an author-year citation style bibliography. As such, it is - % non-standard LaTeX, and requires a special package file to function properly. - % Such a package is natbib.sty by Patrick W. Daly - % The form of the \bibitem entries is - % \bibitem[Jones et al.(1990)]{key}... - % \bibitem[Jones et al.(1990)Jones, Baker, and Smith]{key}... - % The essential feature is that the label (the part in brackets) consists - % of the author names, as they should appear in the citation, with the year - % in parentheses following. There must be no space before the opening - % parenthesis! - % With natbib v5.3, a full list of authors may also follow the year. - % In natbib.sty, it is possible to define the type of enclosures that is - % really wanted (brackets or parentheses), but in either case, there must - % be parentheses in the label. - % The \cite command functions as follows: - % \citet{key} ==>> Jones et al. (1990) - % \citet*{key} ==>> Jones, Baker, and Smith (1990) - % \citep{key} ==>> (Jones et al., 1990) - % \citep*{key} ==>> (Jones, Baker, and Smith, 1990) - % \citep[chap. 2]{key} ==>> (Jones et al., 1990, chap. 2) - % \citep[e.g.][]{key} ==>> (e.g. Jones et al., 1990) - % \citep[e.g.][p. 32]{key} ==>> (e.g. Jones et al., 1990, p. 32) - % \citeauthor{key} ==>> Jones et al. - % \citeauthor*{key} ==>> Jones, Baker, and Smith - % \citeyear{key} ==>> 1990 - %--------------------------------------------------------------------- - -ENTRY - { address - archive - author - booktitle - chapter - collaboration - doi - edition - editor - eid - eprint - howpublished - institution - isbn - issn - journal - key - month - note - number - numpages - organization - pages - publisher - school - series - title - type - url - volume - year - } - {} - { label extra.label sort.label short.list } -INTEGERS { output.state before.all mid.sentence after.sentence after.block } -FUNCTION {init.state.consts} -{ #0 'before.all := - #1 'mid.sentence := - #2 'after.sentence := - #3 'after.block := -} -STRINGS { s t} -FUNCTION {output.nonnull} -{ 's := - output.state mid.sentence = - { ", " * write$ } - { output.state after.block = - { add.period$ write$ - newline$ - "\newblock " write$ - } - { output.state before.all = - 'write$ - { add.period$ " " * write$ } - if$ - } - if$ - mid.sentence 'output.state := - } - if$ - s -} -FUNCTION {output} -{ duplicate$ empty$ - 'pop$ - 'output.nonnull - if$ -} -FUNCTION {output.check} -{ 't := - duplicate$ empty$ - { pop$ "empty " t * " in " * cite$ * warning$ } - 'output.nonnull - if$ -} -FUNCTION {fin.entry} -{ add.period$ - write$ - newline$ -} - -FUNCTION {new.block} -{ output.state before.all = - 'skip$ - { after.block 'output.state := } - if$ -} -FUNCTION {new.sentence} -{ output.state after.block = - 'skip$ - { output.state before.all = - 'skip$ - { after.sentence 'output.state := } - if$ - } - if$ -} -FUNCTION {add.blank} -{ " " * before.all 'output.state := -} - -FUNCTION {date.block} -{ - new.block -} - -FUNCTION {not} -{ { #0 } - { #1 } - if$ -} -FUNCTION {and} -{ 'skip$ - { pop$ #0 } - if$ -} -FUNCTION {or} -{ { pop$ #1 } - 'skip$ - if$ -} -FUNCTION {non.stop} -{ duplicate$ - "}" * add.period$ - #-1 #1 substring$ "." = -} - -STRINGS {z} - -FUNCTION {remove.dots} -{ 'z := - "" - { z empty$ not } - { z #1 #2 substring$ - duplicate$ "\." = - { z #3 global.max$ substring$ 'z := * } - { pop$ - z #1 #1 substring$ - z #2 global.max$ substring$ 'z := - duplicate$ "." = 'pop$ - { * } - if$ - } - if$ - } - while$ -} -FUNCTION {new.block.checkb} -{ empty$ - swap$ empty$ - and - 'skip$ - 'new.block - if$ -} -FUNCTION {field.or.null} -{ duplicate$ empty$ - { pop$ "" } - 'skip$ - if$ -} -FUNCTION {emphasize} -{ duplicate$ empty$ - { pop$ "" } - { "\emph{" swap$ * "}" * } - if$ -} -FUNCTION {bolden} -{ duplicate$ empty$ - { pop$ "" } - { "\textbf{" swap$ * "}" * } - if$ -} -FUNCTION {tie.or.space.prefix} -{ duplicate$ text.length$ #3 < - { "~" } - { " " } - if$ - swap$ -} - -FUNCTION {capitalize} -{ "u" change.case$ "t" change.case$ } - -FUNCTION {space.word} -{ " " swap$ * " " * } - % Here are the language-specific definitions for explicit words. - % Each function has a name bbl.xxx where xxx is the English word. - % The language selected here is ENGLISH -FUNCTION {bbl.and} -{ "and"} - -FUNCTION {bbl.etal} -{ "et~al." } - -FUNCTION {bbl.editors} -{ "eds." } - -FUNCTION {bbl.editor} -{ "ed." } - -FUNCTION {bbl.edby} -{ "edited by" } - -FUNCTION {bbl.edition} -{ "edition" } - -FUNCTION {bbl.volume} -{ "volume" } - -FUNCTION {bbl.of} -{ "of" } - -FUNCTION {bbl.number} -{ "number" } - -FUNCTION {bbl.nr} -{ "no." } - -FUNCTION {bbl.in} -{ "in" } - -FUNCTION {bbl.pages} -{ "pp." } - -FUNCTION {bbl.page} -{ "p." } - -FUNCTION {bbl.eidpp} -{ "pages" } - -FUNCTION {bbl.chapter} -{ "chapter" } - -FUNCTION {bbl.techrep} -{ "Technical Report" } - -FUNCTION {bbl.mthesis} -{ "Master's thesis" } - -FUNCTION {bbl.phdthesis} -{ "Ph.D. thesis" } - -MACRO {jan} {"January"} - -MACRO {feb} {"February"} - -MACRO {mar} {"March"} - -MACRO {apr} {"April"} - -MACRO {may} {"May"} - -MACRO {jun} {"June"} - -MACRO {jul} {"July"} - -MACRO {aug} {"August"} - -MACRO {sep} {"September"} - -MACRO {oct} {"October"} - -MACRO {nov} {"November"} - -MACRO {dec} {"December"} - -MACRO {acmcs} {"ACM Computing Surveys"} - -MACRO {acta} {"Acta Informatica"} - -MACRO {cacm} {"Communications of the ACM"} - -MACRO {ibmjrd} {"IBM Journal of Research and Development"} - -MACRO {ibmsj} {"IBM Systems Journal"} - -MACRO {ieeese} {"IEEE Transactions on Software Engineering"} - -MACRO {ieeetc} {"IEEE Transactions on Computers"} - -MACRO {ieeetcad} - {"IEEE Transactions on Computer-Aided Design of Integrated Circuits"} - -MACRO {ipl} {"Information Processing Letters"} - -MACRO {jacm} {"Journal of the ACM"} - -MACRO {jcss} {"Journal of Computer and System Sciences"} - -MACRO {scp} {"Science of Computer Programming"} - -MACRO {sicomp} {"SIAM Journal on Computing"} - -MACRO {tocs} {"ACM Transactions on Computer Systems"} - -MACRO {tods} {"ACM Transactions on Database Systems"} - -MACRO {tog} {"ACM Transactions on Graphics"} - -MACRO {toms} {"ACM Transactions on Mathematical Software"} - -MACRO {toois} {"ACM Transactions on Office Information Systems"} - -MACRO {toplas} {"ACM Transactions on Programming Languages and Systems"} - -MACRO {tcs} {"Theoretical Computer Science"} -FUNCTION {bibinfo.check} -{ swap$ - duplicate$ missing$ - { - pop$ pop$ - "" - } - { duplicate$ empty$ - { - swap$ pop$ - } - { swap$ - pop$ - } - if$ - } - if$ -} -FUNCTION {bibinfo.warn} -{ swap$ - duplicate$ missing$ - { - swap$ "missing " swap$ * " in " * cite$ * warning$ pop$ - "" - } - { duplicate$ empty$ - { - swap$ "empty " swap$ * " in " * cite$ * warning$ - } - { swap$ - pop$ - } - if$ - } - if$ -} -FUNCTION {format.eprint} -{ eprint duplicate$ empty$ - 'skip$ - { "\eprint" - archive empty$ - 'skip$ - { "[" * archive * "]" * } - if$ - "{" * swap$ * "}" * - } - if$ -} -FUNCTION {format.url} -{ - url - duplicate$ empty$ - { pop$ "" } - { "\urlprefix\url{" swap$ * "}" * } - if$ -} - -INTEGERS { nameptr namesleft numnames } - - -STRINGS { bibinfo} - -FUNCTION {format.names} -{ 'bibinfo := - duplicate$ empty$ 'skip$ { - 's := - "" 't := - #1 'nameptr := - s num.names$ 'numnames := - numnames 'namesleft := - { namesleft #0 > } - { s nameptr - "{vv~}{ll}{ jj}{ f{}}" - format.name$ - remove.dots - bibinfo bibinfo.check - 't := - nameptr #1 > - { - namesleft #1 > - { ", " * t * } - { - s nameptr "{ll}" format.name$ duplicate$ "others" = - { 't := } - { pop$ } - if$ - "," * - t "others" = - { - " " * bbl.etal emphasize * - } - { " " * t * } - if$ - } - if$ - } - 't - if$ - nameptr #1 + 'nameptr := - namesleft #1 - 'namesleft := - } - while$ - } if$ -} -FUNCTION {format.names.ed} -{ - 'bibinfo := - duplicate$ empty$ 'skip$ { - 's := - "" 't := - #1 'nameptr := - s num.names$ 'numnames := - numnames 'namesleft := - { namesleft #0 > } - { s nameptr - "{f{}~}{vv~}{ll}{ jj}" - format.name$ - remove.dots - bibinfo bibinfo.check - 't := - nameptr #1 > - { - namesleft #1 > - { ", " * t * } - { - s nameptr "{ll}" format.name$ duplicate$ "others" = - { 't := } - { pop$ } - if$ - "," * - t "others" = - { - - " " * bbl.etal emphasize * - } - { " " * t * } - if$ - } - if$ - } - 't - if$ - nameptr #1 + 'nameptr := - namesleft #1 - 'namesleft := - } - while$ - } if$ -} -FUNCTION {format.key} -{ empty$ - { key field.or.null } - { "" } - if$ -} - -FUNCTION {format.authors} -{ author "author" format.names - duplicate$ empty$ 'skip$ - { collaboration "collaboration" bibinfo.check - duplicate$ empty$ 'skip$ - { " (" swap$ * ")" * } - if$ - * - } - if$ -} -FUNCTION {get.bbl.editor} -{ editor num.names$ #1 > 'bbl.editors 'bbl.editor if$ } - -FUNCTION {format.editors} -{ editor "editor" format.names duplicate$ empty$ 'skip$ - { - " " * - get.bbl.editor - "(" swap$ * ")" * - * - } - if$ -} -FUNCTION {format.isbn} -{ isbn "isbn" bibinfo.check - duplicate$ empty$ 'skip$ - { - new.block - "ISBN " swap$ * - } - if$ -} - -FUNCTION {format.issn} -{ issn "issn" bibinfo.check - duplicate$ empty$ 'skip$ - { - new.block - "ISSN " swap$ * - } - if$ -} - -FUNCTION {format.doi} -{ doi empty$ - { "" } - { - new.block - "\doi{" doi * "}" * - } - if$ -} -FUNCTION {format.note} -{ - note empty$ - { "" } - { note #1 #1 substring$ - duplicate$ "{" = - 'skip$ - { output.state mid.sentence = - { "l" } - { "u" } - if$ - change.case$ - } - if$ - note #2 global.max$ substring$ * "note" bibinfo.check - } - if$ -} - -FUNCTION {format.title} -{ title - "title" bibinfo.check - duplicate$ empty$ 'skip$ - { - "\enquote{" swap$ * - add.period$ "}" * - } - if$ -} -FUNCTION {format.full.names} -{'s := - "" 't := - #1 'nameptr := - s num.names$ 'numnames := - numnames 'namesleft := - { namesleft #0 > } - { s nameptr - "{vv~}{ll}" format.name$ - 't := - nameptr #1 > - { - namesleft #1 > - { ", " * t * } - { - s nameptr "{ll}" format.name$ duplicate$ "others" = - { 't := } - { pop$ } - if$ - t "others" = - { - " " * bbl.etal emphasize * - } - { - numnames #2 > - { "," * } - 'skip$ - if$ - bbl.and - space.word * t * - } - if$ - } - if$ - } - 't - if$ - nameptr #1 + 'nameptr := - namesleft #1 - 'namesleft := - } - while$ -} - -FUNCTION {author.editor.key.full} -{ author empty$ - { editor empty$ - { key empty$ - { cite$ #1 #3 substring$ } - 'key - if$ - } - { editor format.full.names } - if$ - } - { author format.full.names } - if$ -} - -FUNCTION {author.key.full} -{ author empty$ - { key empty$ - { cite$ #1 #3 substring$ } - 'key - if$ - } - { author format.full.names } - if$ -} - -FUNCTION {editor.key.full} -{ editor empty$ - { key empty$ - { cite$ #1 #3 substring$ } - 'key - if$ - } - { editor format.full.names } - if$ -} - -FUNCTION {make.full.names} -{ type$ "book" = - type$ "inbook" = - or - 'author.editor.key.full - { type$ "proceedings" = - 'editor.key.full - 'author.key.full - if$ - } - if$ -} - -FUNCTION {output.bibitem} -{ newline$ - "\bibitem[{" write$ - label write$ - ")" make.full.names duplicate$ short.list = - { pop$ } - { * } - if$ - "}]{" * write$ - cite$ write$ - "}" write$ - newline$ - "" - before.all 'output.state := -} - -FUNCTION {n.dashify} -{ - 't := - "" - { t empty$ not } - { t #1 #1 substring$ "-" = - { t #1 #2 substring$ "--" = not - { "--" * - t #2 global.max$ substring$ 't := - } - { { t #1 #1 substring$ "-" = } - { "-" * - t #2 global.max$ substring$ 't := - } - while$ - } - if$ - } - { t #1 #1 substring$ * - t #2 global.max$ substring$ 't := - } - if$ - } - while$ -} - -FUNCTION {word.in} -{ bbl.in capitalize - " " * } - -FUNCTION {format.date} -{ year "year" bibinfo.check duplicate$ empty$ - { - "empty year in " cite$ * "; set to ????" * warning$ - pop$ "????" - } - 'skip$ - if$ - extra.label * - before.all 'output.state := - " (" swap$ * ")" * -} -FUNCTION {format.btitle} -{ title "title" bibinfo.check - duplicate$ empty$ 'skip$ - { - emphasize - } - if$ -} -FUNCTION {either.or.check} -{ empty$ - 'pop$ - { "can't use both " swap$ * " fields in " * cite$ * warning$ } - if$ -} -FUNCTION {format.bvolume} -{ volume empty$ - { "" } - { bbl.volume volume tie.or.space.prefix - "volume" bibinfo.check * * - series "series" bibinfo.check - duplicate$ empty$ 'pop$ - { swap$ bbl.of space.word * swap$ - emphasize * } - if$ - "volume and number" number either.or.check - } - if$ -} -FUNCTION {format.number.series} -{ volume empty$ - { number empty$ - { series field.or.null } - { series empty$ - { number "number" bibinfo.check } - { output.state mid.sentence = - { bbl.number } - { bbl.number capitalize } - if$ - number tie.or.space.prefix "number" bibinfo.check * * - bbl.in space.word * - series "series" bibinfo.check * - } - if$ - } - if$ - } - { "" } - if$ -} - -FUNCTION {format.edition} -{ edition duplicate$ empty$ 'skip$ - { - output.state mid.sentence = - { "l" } - { "t" } - if$ change.case$ - "edition" bibinfo.check - " " * bbl.edition * - } - if$ -} -INTEGERS { multiresult } -FUNCTION {multi.page.check} -{ 't := - #0 'multiresult := - { multiresult not - t empty$ not - and - } - { t #1 #1 substring$ - duplicate$ "-" = - swap$ duplicate$ "," = - swap$ "+" = - or or - { #1 'multiresult := } - { t #2 global.max$ substring$ 't := } - if$ - } - while$ - multiresult -} -FUNCTION {format.pages} -{ pages duplicate$ empty$ 'skip$ - { duplicate$ multi.page.check - { - bbl.pages swap$ - n.dashify - } - { - bbl.page swap$ - } - if$ - tie.or.space.prefix - "pages" bibinfo.check - * * - } - if$ -} -FUNCTION {format.journal.pages} -{ pages duplicate$ empty$ 'pop$ - { swap$ duplicate$ empty$ - { pop$ pop$ format.pages } - { - ", " * - swap$ - n.dashify - "pages" bibinfo.check - * - } - if$ - } - if$ -} -FUNCTION {format.journal.eid} -{ eid "eid" bibinfo.check - duplicate$ empty$ 'pop$ - { swap$ duplicate$ empty$ 'skip$ - { - ", " * - } - if$ - swap$ * - numpages empty$ 'skip$ - { bbl.eidpp numpages tie.or.space.prefix - "numpages" bibinfo.check * * - " (" swap$ * ")" * * - } - if$ - } - if$ -} -FUNCTION {format.vol.num.pages} -{ volume field.or.null - duplicate$ empty$ 'skip$ - { - "volume" bibinfo.check - } - if$ - bolden - number "number" bibinfo.check duplicate$ empty$ 'skip$ - { - swap$ duplicate$ empty$ - { "there's a number but no volume in " cite$ * warning$ } - 'skip$ - if$ - swap$ - "(" swap$ * ")" * - } - if$ * - eid empty$ - { format.journal.pages } - { format.journal.eid } - if$ -} - -FUNCTION {format.chapter.pages} -{ chapter empty$ - 'format.pages - { type empty$ - { bbl.chapter } - { type "l" change.case$ - "type" bibinfo.check - } - if$ - chapter tie.or.space.prefix - "chapter" bibinfo.check - * * - pages empty$ - 'skip$ - { ", " * format.pages * } - if$ - } - if$ -} - -FUNCTION {format.booktitle} -{ - booktitle "booktitle" bibinfo.check - emphasize -} -FUNCTION {format.in.ed.booktitle} -{ format.booktitle duplicate$ empty$ 'skip$ - { - editor "editor" format.names.ed duplicate$ empty$ 'pop$ - { - " " * - get.bbl.editor - "(" swap$ * "), " * - * swap$ - * } - if$ - word.in swap$ * - } - if$ -} -FUNCTION {format.thesis.type} -{ type duplicate$ empty$ - 'pop$ - { swap$ pop$ - "t" change.case$ "type" bibinfo.check - } - if$ -} -FUNCTION {format.tr.number} -{ number "number" bibinfo.check - type duplicate$ empty$ - { pop$ bbl.techrep } - 'skip$ - if$ - "type" bibinfo.check - swap$ duplicate$ empty$ - { pop$ "t" change.case$ } - { tie.or.space.prefix * * } - if$ -} -FUNCTION {format.article.crossref} -{ - word.in - " \cite{" * crossref * "}" * -} -FUNCTION {format.book.crossref} -{ volume duplicate$ empty$ - { "empty volume in " cite$ * "'s crossref of " * crossref * warning$ - pop$ word.in - } - { bbl.volume - capitalize - swap$ tie.or.space.prefix "volume" bibinfo.check * * bbl.of space.word * - } - if$ - " \cite{" * crossref * "}" * -} -FUNCTION {format.incoll.inproc.crossref} -{ - word.in - " \cite{" * crossref * "}" * -} -FUNCTION {format.org.or.pub} -{ 't := - "" - address empty$ t empty$ and - 'skip$ - { - t empty$ - { address "address" bibinfo.check * - } - { t * - address empty$ - 'skip$ - { ", " * address "address" bibinfo.check * } - if$ - } - if$ - } - if$ -} -FUNCTION {format.publisher.address} -{ publisher "publisher" bibinfo.warn format.org.or.pub -} - -FUNCTION {format.organization.address} -{ organization "organization" bibinfo.check format.org.or.pub -} - -FUNCTION {article} -{ output.bibitem - format.authors "author" output.check - author format.key output - format.date "year" output.check - date.block - format.title "title" output.check - new.block - crossref missing$ - { - journal - "journal" bibinfo.check - emphasize - "journal" output.check - format.vol.num.pages output - } - { format.article.crossref output.nonnull - format.pages output - } - if$ - format.issn output - format.doi output - new.block - format.note output - format.eprint output - format.url output - fin.entry -} -FUNCTION {book} -{ output.bibitem - author empty$ - { format.editors "author and editor" output.check - editor format.key output - } - { format.authors output.nonnull - crossref missing$ - { "author and editor" editor either.or.check } - 'skip$ - if$ - } - if$ - format.date "year" output.check - date.block - format.btitle "title" output.check - crossref missing$ - { format.bvolume output - new.block - format.number.series output - format.edition output - new.sentence - format.publisher.address output - } - { - new.block - format.book.crossref output.nonnull - } - if$ - format.isbn output - format.doi output - new.block - format.note output - format.eprint output - format.url output - fin.entry -} -FUNCTION {booklet} -{ output.bibitem - format.authors output - author format.key output - format.date "year" output.check - date.block - format.title "title" output.check - new.block - howpublished "howpublished" bibinfo.check output - address "address" bibinfo.check output - format.isbn output - format.doi output - new.block - format.note output - format.eprint output - format.url output - fin.entry -} - -FUNCTION {inbook} -{ output.bibitem - author empty$ - { format.editors "author and editor" output.check - editor format.key output - } - { format.authors output.nonnull - crossref missing$ - { "author and editor" editor either.or.check } - 'skip$ - if$ - } - if$ - format.date "year" output.check - date.block - format.btitle "title" output.check - crossref missing$ - { - format.bvolume output - format.chapter.pages "chapter and pages" output.check - new.block - format.number.series output - format.edition output - new.sentence - format.publisher.address output - } - { - format.chapter.pages "chapter and pages" output.check - new.block - format.book.crossref output.nonnull - } - if$ - crossref missing$ - { format.isbn output } - 'skip$ - if$ - format.doi output - new.block - format.note output - format.eprint output - format.url output - fin.entry -} - -FUNCTION {incollection} -{ output.bibitem - format.authors "author" output.check - author format.key output - format.date "year" output.check - date.block - format.title "title" output.check - new.block - crossref missing$ - { format.in.ed.booktitle "booktitle" output.check - format.bvolume output - format.number.series output - format.edition output - format.chapter.pages output - new.sentence - format.publisher.address output - format.isbn output - } - { format.incoll.inproc.crossref output.nonnull - format.chapter.pages output - } - if$ - format.doi output - new.block - format.note output - format.eprint output - format.url output - fin.entry -} -FUNCTION {inproceedings} -{ output.bibitem - format.authors "author" output.check - author format.key output - format.date "year" output.check - date.block - format.title "title" output.check - new.block - crossref missing$ - { format.in.ed.booktitle "booktitle" output.check - format.bvolume output - format.number.series output - format.pages output - new.sentence - publisher empty$ - { format.organization.address output } - { organization "organization" bibinfo.check output - format.publisher.address output - } - if$ - format.isbn output - format.issn output - } - { format.incoll.inproc.crossref output.nonnull - format.pages output - } - if$ - format.doi output - new.block - format.note output - format.eprint output - format.url output - fin.entry -} -FUNCTION {conference} { inproceedings } -FUNCTION {manual} -{ output.bibitem - format.authors output - author format.key output - format.date "year" output.check - date.block - format.btitle "title" output.check - organization address new.block.checkb - organization "organization" bibinfo.check output - address "address" bibinfo.check output - format.edition output - format.doi output - new.block - format.note output - format.eprint output - format.url output - fin.entry -} - -FUNCTION {mastersthesis} -{ output.bibitem - format.authors "author" output.check - author format.key output - format.date "year" output.check - date.block - format.btitle - "title" output.check - new.block - bbl.mthesis format.thesis.type output.nonnull - school "school" bibinfo.warn output - address "address" bibinfo.check output - format.doi output - new.block - format.note output - format.eprint output - format.url output - fin.entry -} - -FUNCTION {misc} -{ output.bibitem - format.authors output - author format.key output - format.date "year" output.check - date.block - format.title output - new.block - howpublished "howpublished" bibinfo.check output - format.doi output - new.block - format.note output - format.eprint output - format.url output - fin.entry -} -FUNCTION {phdthesis} -{ output.bibitem - format.authors "author" output.check - author format.key output - format.date "year" output.check - date.block - format.btitle - "title" output.check - new.block - bbl.phdthesis format.thesis.type output.nonnull - school "school" bibinfo.warn output - address "address" bibinfo.check output - format.doi output - new.block - format.note output - format.eprint output - format.url output - fin.entry -} - -FUNCTION {proceedings} -{ output.bibitem - format.editors output - editor format.key output - format.date "year" output.check - date.block - format.btitle "title" output.check - format.bvolume output - format.number.series output - new.sentence - publisher empty$ - { format.organization.address output } - { organization "organization" bibinfo.check output - format.publisher.address output - } - if$ - format.isbn output - format.issn output - format.doi output - new.block - format.note output - format.eprint output - format.url output - fin.entry -} - -FUNCTION {techreport} -{ output.bibitem - format.authors "author" output.check - author format.key output - format.date "year" output.check - date.block - format.title - "title" output.check - new.block - format.tr.number emphasize output.nonnull - institution "institution" bibinfo.warn output - address "address" bibinfo.check output - format.doi output - new.block - format.note output - format.eprint output - format.url output - fin.entry -} - -FUNCTION {unpublished} -{ output.bibitem - format.authors "author" output.check - author format.key output - format.date "year" output.check - date.block - format.title "title" output.check - format.doi output - new.block - format.note "note" output.check - format.eprint output - format.url output - fin.entry -} - -FUNCTION {default.type} { misc } -READ -FUNCTION {sortify} -{ purify$ - "l" change.case$ -} -INTEGERS { len } -FUNCTION {chop.word} -{ 's := - 'len := - s #1 len substring$ = - { s len #1 + global.max$ substring$ } - 's - if$ -} -FUNCTION {format.lab.names} -{ 's := - "" 't := - s #1 "{vv~}{ll}" format.name$ - s num.names$ duplicate$ - #2 > - { pop$ - " " * bbl.etal emphasize * - } - { #2 < - 'skip$ - { s #2 "{ff }{vv }{ll}{ jj}" format.name$ "others" = - { - " " * bbl.etal emphasize * - } - { bbl.and space.word * s #2 "{vv~}{ll}" format.name$ - * } - if$ - } - if$ - } - if$ -} - -FUNCTION {author.key.label} -{ author empty$ - { key empty$ - { cite$ #1 #3 substring$ } - 'key - if$ - } - { author format.lab.names } - if$ -} - -FUNCTION {author.editor.key.label} -{ author empty$ - { editor empty$ - { key empty$ - { cite$ #1 #3 substring$ } - 'key - if$ - } - { editor format.lab.names } - if$ - } - { author format.lab.names } - if$ -} - -FUNCTION {editor.key.label} -{ editor empty$ - { key empty$ - { cite$ #1 #3 substring$ } - 'key - if$ - } - { editor format.lab.names } - if$ -} - -FUNCTION {calc.short.authors} -{ type$ "book" = - type$ "inbook" = - or - 'author.editor.key.label - { type$ "proceedings" = - 'editor.key.label - 'author.key.label - if$ - } - if$ - 'short.list := -} - -FUNCTION {calc.label} -{ calc.short.authors - short.list - "(" - * - year duplicate$ empty$ - short.list key field.or.null = or - { pop$ "" } - 'skip$ - if$ - * - 'label := -} - -FUNCTION {sort.format.names} -{ 's := - #1 'nameptr := - "" - s num.names$ 'numnames := - numnames 'namesleft := - { namesleft #0 > } - { s nameptr - "{vv{ } }{ll{ }}{ f{ }}{ jj{ }}" - format.name$ 't := - nameptr #1 > - { - " " * - namesleft #1 = t "others" = and - { "zzzzz" 't := } - 'skip$ - if$ - t sortify * - } - { t sortify * } - if$ - nameptr #1 + 'nameptr := - namesleft #1 - 'namesleft := - } - while$ -} - -FUNCTION {sort.format.title} -{ 't := - "A " #2 - "An " #3 - "The " #4 t chop.word - chop.word - chop.word - sortify - #1 global.max$ substring$ -} -FUNCTION {author.sort} -{ author empty$ - { key empty$ - { "to sort, need author or key in " cite$ * warning$ - "" - } - { key sortify } - if$ - } - { author sort.format.names } - if$ -} -FUNCTION {author.editor.sort} -{ author empty$ - { editor empty$ - { key empty$ - { "to sort, need author, editor, or key in " cite$ * warning$ - "" - } - { key sortify } - if$ - } - { editor sort.format.names } - if$ - } - { author sort.format.names } - if$ -} -FUNCTION {editor.sort} -{ editor empty$ - { key empty$ - { "to sort, need editor or key in " cite$ * warning$ - "" - } - { key sortify } - if$ - } - { editor sort.format.names } - if$ -} -FUNCTION {presort} -{ calc.label - label sortify - " " - * - type$ "book" = - type$ "inbook" = - or - 'author.editor.sort - { type$ "proceedings" = - 'editor.sort - 'author.sort - if$ - } - if$ - #1 entry.max$ substring$ - 'sort.label := - sort.label - * - " " - * - title field.or.null - sort.format.title - * - #1 entry.max$ substring$ - 'sort.key$ := -} - -ITERATE {presort} -SORT -STRINGS { last.label next.extra } -INTEGERS { last.extra.num last.extra.num.extended last.extra.num.blank number.label } -FUNCTION {initialize.extra.label.stuff} -{ #0 int.to.chr$ 'last.label := - "" 'next.extra := - #0 'last.extra.num := - "a" chr.to.int$ #1 - 'last.extra.num.blank := - last.extra.num.blank 'last.extra.num.extended := - #0 'number.label := -} -FUNCTION {forward.pass} -{ last.label label = - { last.extra.num #1 + 'last.extra.num := - last.extra.num "z" chr.to.int$ > - { "a" chr.to.int$ 'last.extra.num := - last.extra.num.extended #1 + 'last.extra.num.extended := - } - 'skip$ - if$ - last.extra.num.extended last.extra.num.blank > - { last.extra.num.extended int.to.chr$ - last.extra.num int.to.chr$ - * 'extra.label := } - { last.extra.num int.to.chr$ 'extra.label := } - if$ - } - { "a" chr.to.int$ 'last.extra.num := - "" 'extra.label := - label 'last.label := - } - if$ - number.label #1 + 'number.label := -} -FUNCTION {reverse.pass} -{ next.extra "b" = - { "a" 'extra.label := } - 'skip$ - if$ - extra.label 'next.extra := - extra.label - duplicate$ empty$ - 'skip$ - { "{\natexlab{" swap$ * "}}" * } - if$ - 'extra.label := - label extra.label * 'label := -} -EXECUTE {initialize.extra.label.stuff} -ITERATE {forward.pass} -REVERSE {reverse.pass} -FUNCTION {bib.sort.order} -{ sort.label - " " - * - year field.or.null sortify - * - " " - * - title field.or.null - sort.format.title - * - #1 entry.max$ substring$ - 'sort.key$ := -} -ITERATE {bib.sort.order} -SORT -FUNCTION {begin.bib} -{ preamble$ empty$ - 'skip$ - { preamble$ write$ newline$ } - if$ - "\begin{thebibliography}{" number.label int.to.str$ * "}" * - write$ newline$ - "\newcommand{\enquote}[1]{``#1''}" - write$ newline$ - "\providecommand{\natexlab}[1]{#1}" - write$ newline$ - "\providecommand{\url}[1]{\texttt{#1}}" - write$ newline$ - "\providecommand{\urlprefix}{URL }" - write$ newline$ - "\expandafter\ifx\csname urlstyle\endcsname\relax" - write$ newline$ - " \providecommand{\doi}[1]{doi:\discretionary{}{}{}#1}\else" - write$ newline$ - " \providecommand{\doi}{doi:\discretionary{}{}{}\begingroup \urlstyle{rm}\Url}\fi" - write$ newline$ - "\providecommand{\eprint}[2][]{\url{#2}}" - write$ newline$ -} -EXECUTE {begin.bib} -EXECUTE {init.state.consts} -ITERATE {call.type$} -FUNCTION {end.bib} -{ newline$ - "\end{thebibliography}" write$ newline$ -} -EXECUTE {end.bib} -%% End of customized bst file -%% -%% End of file `jss.bst'. diff --git a/LaTeX/jss.cls b/LaTeX/jss.cls deleted file mode 100644 index 2a5ba18..0000000 --- a/LaTeX/jss.cls +++ /dev/null @@ -1,490 +0,0 @@ -%% -%% This is file `jss.cls' -\def\fileversion{3.2} -\def\filename{jss} -\def\filedate{2020/12/09} -%% -%% Package `jss' to use with LaTeX2e for JSS publications (http://www.jstatsoft.org/) -%% License: GPL-2 | GPL-3 -%% Copyright: (C) Achim Zeileis -%% Please report errors to Achim.Zeileis@R-project.org -%% -\NeedsTeXFormat{LaTeX2e} -\ProvidesClass{jss}[\filedate\space\fileversion\space jss class by Achim Zeileis] -%% options -\newif\if@article -\newif\if@codesnippet -\newif\if@bookreview -\newif\if@softwarereview -\newif\if@review -\newif\if@shortnames -\newif\if@nojss -\newif\if@notitle -\newif\if@noheadings -\newif\if@nofooter - -\@articletrue -\@codesnippetfalse -\@bookreviewfalse -\@softwarereviewfalse -\@reviewfalse -\@shortnamesfalse -\@nojssfalse -\@notitlefalse -\@noheadingsfalse -\@nofooterfalse - -\DeclareOption{article}{\@articletrue% - \@codesnippetfalse \@bookreviewfalse \@softwarereviewfalse} -\DeclareOption{codesnippet}{\@articlefalse% - \@codesnippettrue \@bookreviewfalse \@softwarereviewfalse} -\DeclareOption{bookreview}{\@articlefalse% - \@codesnippetfalse \@bookreviewtrue \@softwarereviewfalse} -\DeclareOption{softwarereview}{\@articlefalse% - \@codesnippetfalse \@bookreviewfalse \@softwarereviewtrue} -\DeclareOption{shortnames}{\@shortnamestrue} -\DeclareOption{nojss}{\@nojsstrue} -\DeclareOption{notitle}{\@notitletrue} -\DeclareOption{noheadings}{\@noheadingstrue} -\DeclareOption{nofooter}{\@nofootertrue} - -\ProcessOptions -\LoadClass[11pt,a4paper,twoside]{article} -%% required packages -\RequirePackage{graphicx,color,ae,fancyvrb} -\RequirePackage[T1]{fontenc} -\IfFileExists{upquote.sty}{\RequirePackage{upquote}}{} -\IfFileExists{lmodern.sty}{\RequirePackage{lmodern}}{} -%% bibliography -\if@shortnames - \usepackage[authoryear,round]{natbib} -\else - \usepackage[authoryear,round,longnamesfirst]{natbib} -\fi -\bibpunct{(}{)}{;}{a}{}{,} -\bibliographystyle{jss} -%% page layout -\topmargin 0pt -\textheight 46\baselineskip -\advance\textheight by \topskip -\oddsidemargin 0.1in -\evensidemargin 0.15in -\marginparwidth 1in -\oddsidemargin 0.125in -\evensidemargin 0.125in -\marginparwidth 0.75in -\textwidth 6.125in -%% paragraphs -\setlength{\parskip}{0.7ex plus0.1ex minus0.1ex} -\setlength{\parindent}{0em} -%% for all publications -\newcommand{\Address}[1]{\def\@Address{#1}} -\newcommand{\Plaintitle}[1]{\def\@Plaintitle{#1}} -\newcommand{\Shorttitle}[1]{\def\@Shorttitle{#1}} -\newcommand{\Plainauthor}[1]{\def\@Plainauthor{#1}} -\newcommand{\Volume}[1]{\def\@Volume{#1}} -\newcommand{\Year}[1]{\def\@Year{#1}} -\newcommand{\Month}[1]{\def\@Month{#1}} -\newcommand{\Issue}[1]{\def\@Issue{#1}} -\newcommand{\Submitdate}[1]{\def\@Submitdate{#1}} -%% for articles and code snippets -\newcommand{\Acceptdate}[1]{\def\@Acceptdate{#1}} -\newcommand{\Abstract}[1]{\def\@Abstract{#1}} -\newcommand{\Keywords}[1]{\def\@Keywords{#1}} -\newcommand{\Plainkeywords}[1]{\def\@Plainkeywords{#1}} -%% for book and software reviews -\newcommand{\Reviewer}[1]{\def\@Reviewer{#1}} -\newcommand{\Booktitle}[1]{\def\@Booktitle{#1}} -\newcommand{\Bookauthor}[1]{\def\@Bookauthor{#1}} -\newcommand{\Publisher}[1]{\def\@Publisher{#1}} -\newcommand{\Pubaddress}[1]{\def\@Pubaddress{#1}} -\newcommand{\Pubyear}[1]{\def\@Pubyear{#1}} -\newcommand{\ISBN}[1]{\def\@ISBN{#1}} -\newcommand{\Pages}[1]{\def\@Pages{#1}} -\newcommand{\Price}[1]{\def\@Price{#1}} -\newcommand{\Plainreviewer}[1]{\def\@Plainreviewer{#1}} -\newcommand{\Softwaretitle}[1]{\def\@Softwaretitle{#1}} -\newcommand{\URL}[1]{\def\@URL{#1}} -\newcommand{\DOI}[1]{\def\@DOI{#1}} -%% for internal use -\newcommand{\Seriesname}[1]{\def\@Seriesname{#1}} -\newcommand{\Hypersubject}[1]{\def\@Hypersubject{#1}} -\newcommand{\Hyperauthor}[1]{\def\@Hyperauthor{#1}} -\newcommand{\Footername}[1]{\def\@Footername{#1}} -\newcommand{\Firstdate}[1]{\def\@Firstdate{#1}} -\newcommand{\Seconddate}[1]{\def\@Seconddate{#1}} -\newcommand{\Reviewauthor}[1]{\def\@Reviewauthor{#1}} -%% defaults -\author{Firstname Lastname\\Affiliation} -\title{Title} -\Abstract{---!!!---an abstract is required---!!!---} -\Plainauthor{\@author} -\Volume{VV} -\Year{YYYY} -\Month{MMMMMM} -\Issue{II} -\Submitdate{yyyy-mm-dd} -\Acceptdate{yyyy-mm-dd} -\Address{ - 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\newcommand\@doi[1]{doi:\discretionary{}{}{}#1}\else - \newcommand\@doi{doi:\discretionary{}{}{}\begingroup -\urlstyle{tt}\Url}\fi -\newcommand{\doi}[1]{\href{https://doi.org/#1}{\normalfont\texttt{\@doi{#1}}}} -\newcommand{\E}{\mathsf{E}} -\newcommand{\VAR}{\mathsf{VAR}} -\newcommand{\COV}{\mathsf{COV}} -\newcommand{\Prob}{\mathsf{P}} -\endinput -%% -%% End of file `jss.cls'. diff --git a/LaTeX/jsslogo.jpg b/LaTeX/jsslogo.jpg deleted file mode 100644 index dd099db..0000000 --- a/LaTeX/jsslogo.jpg +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:b9f97c51e25b2fe013c89751788aa71ea6958050b3993993cc2e4fcb0cbcf90c -size 22731 diff --git a/LaTeX/main.Rnw b/LaTeX/main.Rnw deleted file mode 100644 index a6566a4..0000000 --- a/LaTeX/main.Rnw +++ /dev/null @@ -1,152 +0,0 @@ -\documentclass[article]{jss} - -\usepackage{thumbpdf, lmodern} % recommended by `JSS` -\usepackage{amsmath, amssymb, amstext} -% Configure `Sweave` -% Prevent `Sweave` to include its styles (line as is, already in `JSS` styles) -%% need no \usepackage{Sweave.sty} -%\SweaveUTF8 -<>= -options(prompt = "R> ", continue = "+ ", width = 70, useFancyQuotes = FALSE) -set.seed(1729) # taxicab number -@ - -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Typesetting %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -% \newcommand{\class}[1]{`\code{#1}'} -% \newcommand{\fct}[1]{\code{#1()}} - -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Operators %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -\renewcommand{\t}[1]{{#1}^{T}} -\renewcommand{\epsilon}{\varepsilon} -\renewcommand{\E}{\operatorname{\mathbb{E}}} -\newcommand{\var}{\operatorname{Var}} -% \newcommand{\sd}{\operatorname{sd}} -% \newcommand{\independent}{\operatorname{\bot\!\!\!\bot}} -% \newcommand{\stiefel}[2]{\operatorname{St_{#2}}(\mathbb{R}^{#1})} -% \newcommand{\grassmann}[2]{\operatorname{Gr_{#2}}(\mathbb{R}^{#1})} -% \newcommand{\orthogonalGroup}[1]{\operatorname{O}(#1)} -% \newcommand{\argmin}{\operatorname*{arg\,min}} -% \newcommand{\argmax}{\operatorname*{arg\,max}} - -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Meta Information %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -\author{Daniel Kapla\\TU Wien - \And Lukas Fertl\\TU Wien - \And Efstathia Bura\\TU Wien} -\Plainauthor{Daniel Kapla, Lukas Fertl, Efstathia Bura} - -%% - \title{} in title case -%% - \Plaintitle{} without LaTeX markup (if any) -%% - \Shorttitle{} with LaTeX markup (if any), used as running title -\title{Conditional Variance Estimation With the \pkg{CVE} Package in \proglang{R}} -\Plaintitle{Conditional Variance Estimation With the CVE Package in R} -\Shorttitle{The \pkg{CVE} Package} - -\Abstract{ - Conditional variance estimation (CVE) is a novel sufficient dimension - reduction (SDR) method for regressions satisfying $\E(Y | X) = \E(Y | \t{B} X)$, - where $\t{B}X$ is a lower dimensional projection of the predictors. CVE, - similarly to its main competitor, the mean average variance estimation (MAVE), - is not based on inverse regression, and does not require the restrictive - linearity and constant variance conditions of moment based SDR methods. CVE - is data-driven and applies to additive error regressions with continuous - predictors and link function. Let $Y$ be a real univariate response and $X$ - a real $p$-dimensional covariate vector. We assume that the dependence of - $Y$ and $X$ is modelled by - \begin{displaymath} - Y = g(\t{B}X) + \epsilon - \end{displaymath} - where $X$ is independent of $\epsilon$ with positive definite variance-covariance - matrix $\var(X) = \Sigma_X$. $\epsilon$ is a mean zero random variable with - finite $\var(\epsilon) = \E(\epsilon^2)$, $g$ is an unknown, continuous - non-constant function, and $B = (b_1 , ..., b_k)$ is a real $p \times k$ - matrix of rank $k \leq p$. Without loss of generality $B$ is assumed to be - orthonormal. -} - -%% - \Keywords{} with LaTeX markup, at least one required -%% - \Plainkeywords{} without LaTeX markup (if necessary) -%% - Should be comma-separated and in sentence case. -\Keywords{Dimension reduction, \proglang{R}} -\Plainkeywords{Dimension reduction, R} - -%% - \Address{} of at least one author -%% - May contain multiple affiliations for each author -%% (in extra lines, separated by \emph{and}\\). -%% - May contain multiple authors for the same affiliation -%% (in the same first line, separated by comma). -\Address{ - Daniel Kapla\\ - Technische Universit\"at Wien\\ - Institute of Statistics and Mathematical Methods in Economics\\ - Faculty of Mathematics and Geoinformation\\ - TU Wien, Vienna, Austria\\ - E-mail: \email{daniel.kapla@tuwien.ac.at}\\ - URL: \url{https://kapla.at}\\ - \\ - Lukas Fertl\\ - Technische Universit\"at Wien\\ - Institute of Statistics and Mathematical Methods in Economics\\ - Faculty of Mathematics and Geoinformation\\ - TU Wien, Vienna, Austria\\ - E-mail: \email{lukas.fertl@tuwien.ac.at}\\ - \\ - Efstathia Bura\\ - Technische Universit\"at Wien\\ - Institute of Statistics and Mathematical Methods in Economics\\ - Faculty of Mathematics and Geoinformation\\ - TU Wien, Vienna, Austria -} - -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Document %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -\begin{document} - -\section[Introduction: Sufficient dimension reduction in R]{Introduction: Sufficient dimension reduction in \proglang{R}}\label{sec:intro} - -A bit of text -<<>>= -library(CVE) - -dataset <- function(n, p = 20, p.mix = 0.5, lambda = 1, sd = 0.5) { - B <- rep(1 / sqrt(p), p) - # B <- c(rep(1 / sqrt(p), p / 2), rep(-1 / sqrt(p), p / 2)) - X <- matrix(rnorm(n * p), n, p) - X <- X + lambda * (2 * rbinom(n, 1, p.mix) - 1) - Y <- abs(X %*% B) + rnorm(n, 0, sd) - list(B = B, X = X, Y = Y) -} - -ds <- dataset(100) -ds.test <- dataset(100) -@ -Then we apply both methods, the \code{CVE} and the \code{MAVE} methods -<<>>= -fit.cve <- with(ds, cve(Y ~ X, k = 1)) -fit.mave <- with(ds, MAVE::mave(Y ~ X, max.dim = 1, method = "meanMAVE")) -@ -Get the estimated reduction matrices -<<>>= -B.cve <- coef(fit.cve, 1) -B.mave <- coef(fit.mave, 1) -@ -and compute the prediction errors -<<>>= -Y.hat.cve <- with(ds.test, predict(fit.cve, X, 1)) -Y.hat.mave <- with(ds.test, predict(fit.mave, X, 1)) -# MSE - cve -mean((ds.test$Y - Y.hat.cve)^2) -# MSE - mave -mean((ds.test$Y - Y.hat.mave)^2) -@ -and another bit of text - - -\newpage % required! Fixes vertical spacing problems with code chunks (last page) -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Bibliography %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -%% - References need to be provided in a .bib BibTeX database. -%% - All references should be made with \cite, \citet, \citep, \citealp etc. -%% - `JSS` - specific markup (\proglang, \pkg, \code) should be used in the .bib. -%% - Titles in the .bib should be in title case. -%% - DOIs should be included where available. -\bibliography{refs} - -\end{document} diff --git a/LaTeX/refs.bib b/LaTeX/refs.bib deleted file mode 100644 index e4fe954..0000000 --- a/LaTeX/refs.bib +++ /dev/null @@ -1,35 +0,0 @@ -@Manual{R, - title = {\proglang{R}: {A} Language and Environment for Statistical Computing}, - author = {{\proglang{R} Core Team}}, - organization = {\proglang{R} Foundation for Statistical Computing}, - address = {Vienna, Austria}, - year = {2020}, - url = {https://www.R-project.org/}, -} - -@Manual{pkg:MAVE, - title = {\pkg{MAVE}: Methods for Dimension Reduction}, - author = {Hang Weiqiang and Xia Yingcun}, - year = {2019}, - note = {\proglang{R} package version 1.3.10}, - url = {https://CRAN.R-project.org/package=MAVE} -} - -@Book{pkg:MASS, - title = {Modern Applied Statistics with S}, - author = {W. N. Venables and B. D. Ripley}, - publisher = {Springer}, - edition = {Fourth}, - address = {New York}, - year = {2002}, - note = {ISBN 0-387-95457-0}, - url = {http://www.stats.ox.ac.uk/pub/MASS4/} -} - -@Manual{pkg:mda, - title = {\pkg{mda}: Mixture and Flexible Discriminant Analysis}, - author = {S original by Trevor Hastie & Robert Tibshirani. Original R port by Friedrich Leisch and Kurt Hornik and Brian D. Ripley.}, - year = {2017}, - note = {\proglang{R} package version 0.4-10}, - url = {https://CRAN.R-project.org/package=mda} -}