From db880fc0f260f99db5c5e1a914557db01d996ec7 Mon Sep 17 00:00:00 2001 From: Jean-Baptiste Camps Date: Tue, 24 Oct 2017 19:04:46 +0200 Subject: [PATCH 1/6] some doc correction --- R/incrementTable.R | 13 --- man/Import.TEIApparatus.Rd | 15 ++-- man/PCC.Exploratory.Rd | 4 +- man/PCC.Rd | 4 +- man/PCC.conflicts.Rd | 2 +- man/VL.pValues.Rd | 2 +- man/incrementTable.Rd | 74 ------------------ man/stemmatology-package.Rd | 18 ++--- .../stemmatology-concordance.tex | 0 {vignettes => vignettes_old}/stemmatology.Rnw | 0 {vignettes => vignettes_old}/stemmatology.log | 0 {vignettes => vignettes_old}/stemmatology.pdf | Bin .../stemmatology.synctex.gz | Bin {vignettes => vignettes_old}/stemmatology.tex | 0 14 files changed, 18 insertions(+), 114 deletions(-) delete mode 100644 R/incrementTable.R delete mode 100644 man/incrementTable.Rd rename {vignettes => vignettes_old}/stemmatology-concordance.tex (100%) rename {vignettes => vignettes_old}/stemmatology.Rnw (100%) rename {vignettes => vignettes_old}/stemmatology.log (100%) rename {vignettes => vignettes_old}/stemmatology.pdf (100%) rename {vignettes => vignettes_old}/stemmatology.synctex.gz (100%) rename {vignettes => vignettes_old}/stemmatology.tex (100%) diff --git a/R/incrementTable.R b/R/incrementTable.R deleted file mode 100644 index f743f27..0000000 --- a/R/incrementTable.R +++ /dev/null @@ -1,13 +0,0 @@ -incrementTable <- -function(tableToIncrement, tableVariantes, x, y) { - ### An «internal» function used to increment tables according to manuscript - ### sigla Soit la valeur est NA et on la crée, soit elle existe déjà et on - ### l'incrémente - if (is.na(tableToIncrement[colnames(tableVariantes)[x], colnames(tableVariantes)[y]])) { - tableToIncrement[colnames(tableVariantes)[x], colnames(tableVariantes)[y]] = 1 - } else { - tableToIncrement[colnames(tableVariantes)[x], colnames(tableVariantes)[y]] = tableToIncrement[colnames(tableVariantes)[x], - colnames(tableVariantes)[y]] + 1 - } - return(tableToIncrement) -} diff --git a/man/Import.TEIApparatus.Rd b/man/Import.TEIApparatus.Rd index 97a11c5..7b043e6 100644 --- a/man/Import.TEIApparatus.Rd +++ b/man/Import.TEIApparatus.Rd @@ -1,16 +1,12 @@ \name{Import.TEIApparatus} \alias{Import.TEIApparatus} %- Also NEED an '\alias' for EACH other topic documented here. -\title{ -Import TEI apparatus -} -\description{ -Allows the user to import a TEI document. -} +\title{Import TEI apparatus} +\description{Allows the user to import a TEI encoded parallel-segmentation apparatus.} \usage{ Import.TEIApparatus(file = x, fromCollatex = False) } -%- maybe also 'usage' for other objects documented here. + \arguments{ \item{file}{ Adress of valid TEI file. @@ -29,11 +25,12 @@ Default: \code{false} %% \item{comp2 }{Description of 'comp2'} %% ... } -\references{ +%\references{ +%} \author{ Jean-Baptiste Camps (\email{jbcamps@hotmail.com}) & Florian Cafiero(\email{florian.cafiero@polytechnique.edu}) } -\keyword{TEI } +\keyword{TEI} diff --git a/man/PCC.Exploratory.Rd b/man/PCC.Exploratory.Rd index 1685616..6a7f14b 100644 --- a/man/PCC.Exploratory.Rd +++ b/man/PCC.Exploratory.Rd @@ -56,8 +56,8 @@ Jean-Baptiste Camps (\email{jbcamps@hotmail.com}) & Florian Cafiero %% ~~objects to See Also as \code{\link{help}}, ~~~ } \examples{ -load(fournival) -PCC.Exploratory(fournival) +data(fournival) +%PCC.Exploratory(fournival) } % Add one or more standard keywords, see file 'KEYWORDS' in the % R documentation directory. diff --git a/man/PCC.Rd b/man/PCC.Rd index 5a8e393..06761c2 100644 --- a/man/PCC.Rd +++ b/man/PCC.Rd @@ -71,8 +71,8 @@ Jean-Baptiste Camps (\email{jbcamps@hotmail.com}) & Florian Cafiero(\email{flori \code{\link{PCC.Exploratory}}, \code{\link{PCC.Stemma}}. } \examples{ -load(fournival) -PCC(fournival) +%data(fournival) +%PCC(fournival) } % Add one or more standard keywords, see file 'KEYWORDS' in the % R documentation directory. diff --git a/man/PCC.conflicts.Rd b/man/PCC.conflicts.Rd index 7bef469..bba138a 100644 --- a/man/PCC.conflicts.Rd +++ b/man/PCC.conflicts.Rd @@ -55,7 +55,7 @@ Jean-Baptiste Camps (\email{jbcamps@hotmail.com}) & Florian Cafiero } \examples{ %TODO: fignoler globalement les exemples et les reprendre, voire les affiner. -load(fournival) +data(fournival) myConflicts = PCC.conflicts(fournival) myOverconflicting = PCC.overconflicting(myConflicts) myNewVariantsTable = PCC.elimination(myOverconflicting) diff --git a/man/VL.pValues.Rd b/man/VL.pValues.Rd index c97a212..a274bbb 100644 --- a/man/VL.pValues.Rd +++ b/man/VL.pValues.Rd @@ -36,7 +36,7 @@ Jean-Baptiste Camps %% ~~further notes~~ %} -\warning{This function is still in active development.} +\note{This function is still in active development.} %% ~Make other sections like Warning with \section{Warning }{....} ~ diff --git a/man/incrementTable.Rd b/man/incrementTable.Rd deleted file mode 100644 index 8bd8322..0000000 --- a/man/incrementTable.Rd +++ /dev/null @@ -1,74 +0,0 @@ -\name{incrementTable} -\alias{incrementTable} -%- Also NEED an '\alias' for EACH other topic documented here. -\title{ -%% ~~function to do ... ~~ -} -\description{ -%% ~~ A concise (1-5 lines) description of what the function does. ~~ -} -\usage{ -incrementTable(tableToIncrement, tableVariantes, x, y) -} -%- maybe also 'usage' for other objects documented here. -\arguments{ - \item{tableToIncrement}{ -%% ~~Describe \code{tableToIncrement} here~~ -} - \item{tableVariantes}{ -%% ~~Describe \code{tableVariantes} here~~ -} - \item{x}{ -%% ~~Describe \code{x} here~~ -} - \item{y}{ -%% ~~Describe \code{y} here~~ -} -} -\details{ -%% ~~ If necessary, more details than the description above ~~ -} -\value{ -%% ~Describe the value returned -%% If it is a LIST, use -%% \item{comp1 }{Description of 'comp1'} -%% \item{comp2 }{Description of 'comp2'} -%% ... -} -\references{ -%% ~put references to the literature/web site here ~ -} -\author{ -%% ~~who you are~~ -} -\note{ -%% ~~further notes~~ -} - -%% ~Make other sections like Warning with \section{Warning }{....} ~ - -\seealso{ -%% ~~objects to See Also as \code{\link{help}}, ~~~ -} -\examples{ -##---- Should be DIRECTLY executable !! ---- -##-- ==> Define data, use random, -##-- or do help(data=index) for the standard data sets. - -## The function is currently defined as -function (tableToIncrement, tableVariantes, x, y) -{ - if (is.na(tableToIncrement[colnames(tableVariantes)[x], colnames(tableVariantes)[y]])) { - tableToIncrement[colnames(tableVariantes)[x], colnames(tableVariantes)[y]] = 1 - } - else { - tableToIncrement[colnames(tableVariantes)[x], colnames(tableVariantes)[y]] = tableToIncrement[colnames(tableVariantes)[x], - colnames(tableVariantes)[y]] + 1 - } - return(tableToIncrement) - } -} -% Add one or more standard keywords, see file 'KEYWORDS' in the -% R documentation directory. -\keyword{ ~kwd1 } -\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line diff --git a/man/stemmatology-package.Rd b/man/stemmatology-package.Rd index ba8baa2..f33217f 100644 --- a/man/stemmatology-package.Rd +++ b/man/stemmatology-package.Rd @@ -16,7 +16,7 @@ License: \tab CC BY-NC-SA 2.0\cr This package includes various functions for stemmatological analysis. -\subsection{Input} +\subsection{Input}{ Most of the functions take, as input a \emph{numeric matrix}, with witnesses in columns, variant locations in rows, and readings coded by a number, e.g. @@ -41,6 +41,7 @@ Alternatively , if \code{alternateReadings = TRUE}, the input can be a \emph{cha 4 \tab 1,3 \tab 1,2 \tab 1 \tab 2 \tab 3 \cr } Notice how a witness can bear several readings (e.g., P1 at VL 1). +} % Import functions \subsection{Import functions}{ @@ -56,22 +57,13 @@ Notice how a witness can bear several readings (e.g., P1 at VL 1). \code{\link{PCC.Exploratory}}: global function for exploratory methods of the PCC family - \code{\link{PCC.Stemma}}: + \code{\link{PCC.Stemma}}: Building the Stemma Codicum. } \subsection{Other functions}{ The package contains also various other functions, particularly aimed at detecting contamination. It contains for instance the function \code{\link{VL.pValues}} (presented in Camps 2013 unpublished) -%TODO: reprendre doc de cette commande quand on l'aura écrite -} - -} - -% Exploratory methods -Methods to explore the possible proofs of contamination inside a textual tradition -\code{\link{VL.pValues}} - % Other methods The package aims at making available various other stemmatological methods, including further functions for contamination detection, or for theoretical stemmatology. @@ -79,8 +71,10 @@ or for theoretical stemmatology. %The package should include a function to generate arbitrary stemmata based on a set of parameters (fecundity, decimation rate at each level, number of generations, ...). %It should also have a function for the analysis of stemmata shapes, and making hypotheses on the parameters of the original tradition - +} + } + \author{ Jean-Baptiste Camps (École nationale des chartes, PSL Research University). diff --git a/vignettes/stemmatology-concordance.tex b/vignettes_old/stemmatology-concordance.tex similarity index 100% rename from vignettes/stemmatology-concordance.tex rename to vignettes_old/stemmatology-concordance.tex diff --git a/vignettes/stemmatology.Rnw b/vignettes_old/stemmatology.Rnw similarity index 100% rename from vignettes/stemmatology.Rnw rename to vignettes_old/stemmatology.Rnw diff --git a/vignettes/stemmatology.log b/vignettes_old/stemmatology.log similarity index 100% rename from vignettes/stemmatology.log rename to vignettes_old/stemmatology.log diff --git a/vignettes/stemmatology.pdf b/vignettes_old/stemmatology.pdf similarity index 100% rename from vignettes/stemmatology.pdf rename to vignettes_old/stemmatology.pdf diff --git a/vignettes/stemmatology.synctex.gz b/vignettes_old/stemmatology.synctex.gz similarity index 100% rename from vignettes/stemmatology.synctex.gz rename to vignettes_old/stemmatology.synctex.gz diff --git a/vignettes/stemmatology.tex b/vignettes_old/stemmatology.tex similarity index 100% rename from vignettes/stemmatology.tex rename to vignettes_old/stemmatology.tex From e58961a1a8241c234926dc5d71ed75b69e84a04e Mon Sep 17 00:00:00 2001 From: Jean-Baptiste Camps Date: Wed, 25 Oct 2017 13:20:15 +0200 Subject: [PATCH 2/6] More doc and tests --- .Rbuildignore | 7 +++++++ .gitignore | 1 + .travis.yml | 9 +++++++++ DESCRIPTION | 9 ++++++++- README.md | 15 +++++++++++++++ codecov.yml | 1 + man/heinrichi.Rd | 3 --- tests/testthat.R | 4 ++++ tests/testthat/test-PCC.R | 5 +++++ 9 files changed, 50 insertions(+), 4 deletions(-) create mode 100644 .Rbuildignore create mode 100644 .travis.yml create mode 100644 codecov.yml create mode 100644 tests/testthat.R create mode 100644 tests/testthat/test-PCC.R diff --git a/.Rbuildignore b/.Rbuildignore new file mode 100644 index 0000000..48bacd6 --- /dev/null +++ b/.Rbuildignore @@ -0,0 +1,7 @@ +^README\.Rmd$ +^README-.*\.png$ +^\.travis\.yml$ +^codecov\.yml$ +^\.Rhistory$ +^\.gitignore$ +^\.git$ diff --git a/.gitignore b/.gitignore index dc528e5..4946f79 100644 --- a/.gitignore +++ b/.gitignore @@ -1 +1,2 @@ .Rhistory +inst/doc diff --git a/.travis.yml b/.travis.yml new file mode 100644 index 0000000..d6c665f --- /dev/null +++ b/.travis.yml @@ -0,0 +1,9 @@ +# R for travis: see documentation at https://docs.travis-ci.com/user/languages/r + +language: R +sudo: false +cache: packages + + +after_success: + - Rscript -e 'covr::codecov()' diff --git a/DESCRIPTION b/DESCRIPTION index aafba72..5a066c7 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -6,7 +6,14 @@ Date: 2014-07-16 Author: Jean-Baptiste Camps ; Florian Cafiero Maintainer: Jean-Baptiste Camps Description: This package helps building and analysing the genealogy of textual or musical traditions. +BugReports: https://github.com/Jean-Baptiste-Camps/stemmatology/issues Imports: network, sna, cluster -Suggests: +Suggests: + testthat, + knitr, + rmarkdown, + covr License: CC BY-NC-SA 2.0 NeedsCompilation: no +URL: https://github.com/Jean-Baptiste-Camps/stemmatology +VignetteBuilder: knitr diff --git a/README.md b/README.md index fb63c4a..d592fb4 100644 --- a/README.md +++ b/README.md @@ -9,3 +9,18 @@ This repository contains the source file of the development version for the project of a stemmatology package for R. This package will contain functions for the PCC method as described in Jean-Baptiste Camps And Florian Cafiero, « Genealogical Variant Locations And Simplified Stemma: A Test Case », 2014, as well as other stemmatological methods (see roadmap at https://graal.hypotheses.org/925). +[![Travis-CI Build Status](https://travis-ci.org/Jean-Baptiste-Camps/stemmatology.svg?branch=master)](https://travis-ci.org/Jean-Baptiste-Camps/stemmatology) + +[![Coverage Status](https://img.shields.io/codecov/c/github/Jean-Baptiste-Camps/stemmatology/master.svg)](https://codecov.io/github/Jean-Baptiste-Camps/stemmatology?branch=master) + +[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/stemmatology)](https://cran.r-project.org/package=stemmatology) + +## Installation + +You can install stemmatology from Github with: + +```r +# install.packages("devtools") +devtools::install_github("Jean-Baptiste-Camps/stemmatology") +``` + diff --git a/codecov.yml b/codecov.yml new file mode 100644 index 0000000..69cb760 --- /dev/null +++ b/codecov.yml @@ -0,0 +1 @@ +comment: false diff --git a/man/heinrichi.Rd b/man/heinrichi.Rd index 77348ca..aba88de 100644 --- a/man/heinrichi.Rd +++ b/man/heinrichi.Rd @@ -59,9 +59,6 @@ Roos, Teemu, Heikkilä, Tuomas, and Myllymäki, Petri, « Computer-Assisted Ste \references{ Camps (Jean-Baptiste) & Cafiero (Florian), « Genealogical variant locations and simplified stemma: a test case », in Analysis of Ancient and Medieval Texts and Manuscripts: Digital Approaches, ed. Tara Andrews & Caroline Macé, Turnhout: Brepols, 2015, p. 69‑93 (Lectio, 1), \url{http://dx.doi.org/10.1484/M.LECTIO-EB.5.102565}. } -\references{ -Camps (Jean-Baptiste) & Cafiero (Florian), « Genealogical variant locations and simplified stemma: a test case », in Analysis of Ancient and Medieval Texts and Manuscripts: Digital Approaches, ed. Tara Andrews & Caroline Macé, Turnhout: Brepols, 2015, p. 69‑93 (Lectio, 1), \url{http://dx.doi.org/10.1484/M.LECTIO-EB.5.102565}. -} \examples{ data(heinrichi) } diff --git a/tests/testthat.R b/tests/testthat.R new file mode 100644 index 0000000..f1e4d0c --- /dev/null +++ b/tests/testthat.R @@ -0,0 +1,4 @@ +library(testthat) +library(stemmatology) + +test_check("stemmatology") diff --git a/tests/testthat/test-PCC.R b/tests/testthat/test-PCC.R new file mode 100644 index 0000000..56330ca --- /dev/null +++ b/tests/testthat/test-PCC.R @@ -0,0 +1,5 @@ +context("PCC") + +test_that("multiplication works", { + expect_equal(2 * 2, 4) +}) From 56fc2972334c4b782c33a0711f945428691d1acc Mon Sep 17 00:00:00 2001 From: Jean-Baptiste Camps Date: Wed, 25 Oct 2017 17:22:59 +0200 Subject: [PATCH 3/6] more doc and packaging --- .Rbuildignore | 6 +++--- .travis.yml | 1 - DESCRIPTION | 3 ++- NAMESPACE | 6 ++++++ R/PCC.conflicts.R | 2 +- README.md | 10 ++++------ man/Import.TEIApparatus.Rd | 3 ++- man/PCC.Exploratory.Rd | 1 + man/PCC.Rd | 1 + man/PCC.Stemma.Rd | 3 ++- man/PCC.buildGroup.Rd | 1 + man/PCC.conflicts.Rd | 7 ++++--- man/PCC.contam.Rd | 1 + man/PCC.disagreement.Rd | 1 + man/PCC.distribute.Rd | 5 +++-- man/PCC.elimination.Rd | 1 + man/PCC.equipollent.Rd | 1 + man/PCC.overconflicting.Rd | 1 + man/PCC.reconstructModel.Rd | 14 ++++++++------ man/VL.pValues.Rd | 1 + man/fournival.Rd | 1 + man/heinrichi.Rd | 1 + man/notreBesoin.Rd | 1 + man/otinel.Rd | 1 + man/parzival.Rd | 1 + man/stemmatology-package.Rd | 3 ++- 26 files changed, 51 insertions(+), 26 deletions(-) diff --git a/.Rbuildignore b/.Rbuildignore index 48bacd6..f524e6e 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -2,6 +2,6 @@ ^README-.*\.png$ ^\.travis\.yml$ ^codecov\.yml$ -^\.Rhistory$ -^\.gitignore$ -^\.git$ +\.Rhistory +\.gitignore +\.git diff --git a/.travis.yml b/.travis.yml index d6c665f..756ad0f 100644 --- a/.travis.yml +++ b/.travis.yml @@ -4,6 +4,5 @@ language: R sudo: false cache: packages - after_success: - Rscript -e 'covr::codecov()' diff --git a/DESCRIPTION b/DESCRIPTION index 5a066c7..56b35c6 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -7,7 +7,7 @@ Author: Jean-Baptiste Camps ; Florian Cafiero Maintainer: Jean-Baptiste Camps Description: This package helps building and analysing the genealogy of textual or musical traditions. BugReports: https://github.com/Jean-Baptiste-Camps/stemmatology/issues -Imports: network, sna, cluster +Imports: graphics, stats, utils, network, sna, cluster Suggests: testthat, knitr, @@ -17,3 +17,4 @@ License: CC BY-NC-SA 2.0 NeedsCompilation: no URL: https://github.com/Jean-Baptiste-Camps/stemmatology VignetteBuilder: knitr +RoxygenNote: 6.0.1 diff --git a/NAMESPACE b/NAMESPACE index d75f824..72cfc4d 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -1 +1,7 @@ exportPattern("^[[:alpha:]]+") +importFrom("graphics", "axis", "barplot", "legend", "par", "plot") +importFrom("stats", "fisher.test", "na.omit") +importFrom("utils", "read.csv") +importFrom("sna", "gplot", "gplot.layout.fruchtermanreingold") +importFrom("network", "as.network", "network.vertex.names", "as.matrix.network", "set.vertex.attribute", "get.vertex.attribute") +importFrom("cluster", "pam") diff --git a/R/PCC.conflicts.R b/R/PCC.conflicts.R index 0fe922c..f3234d5 100644 --- a/R/PCC.conflicts.R +++ b/R/PCC.conflicts.R @@ -65,11 +65,11 @@ PCC.conflicts <- # ".C" 0.46 0.89 0.46 0.89 # options(stringsAsFactors = FALSE) # Option to avoid using factor and gaining efficiency - #tableVariantes = as.matrix(x) # Perhaps better to do: if (!is.matrix(x)) { stop("Please input a matrix") } + tableVariantes = x #TODO(JBC): # Initial test to verify if the input is what it is supposed to be if (!is.numeric(tableVariantes) & alternateReadings == FALSE) { diff --git a/README.md b/README.md index d592fb4..caff56e 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,9 @@ # stemmatology : an R stemmatology package +[![Travis-CI Build Status](https://travis-ci.org/Jean-Baptiste-Camps/stemmatology.svg?branch=master)](https://travis-ci.org/Jean-Baptiste-Camps/stemmatology) +[![Coverage Status](https://img.shields.io/codecov/c/github/Jean-Baptiste-Camps/stemmatology/master.svg)](https://codecov.io/github/Jean-Baptiste-Camps/stemmatology?branch=master) +[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/stemmatology)](https://cran.r-project.org/package=stemmatology) + Version: 0.2.2 (pre-alpha) Date: 2014-07-16 Author: Jean-Baptiste Camps ; Florian Cafiero @@ -9,12 +13,6 @@ This repository contains the source file of the development version for the project of a stemmatology package for R. This package will contain functions for the PCC method as described in Jean-Baptiste Camps And Florian Cafiero, « Genealogical Variant Locations And Simplified Stemma: A Test Case », 2014, as well as other stemmatological methods (see roadmap at https://graal.hypotheses.org/925). -[![Travis-CI Build Status](https://travis-ci.org/Jean-Baptiste-Camps/stemmatology.svg?branch=master)](https://travis-ci.org/Jean-Baptiste-Camps/stemmatology) - -[![Coverage Status](https://img.shields.io/codecov/c/github/Jean-Baptiste-Camps/stemmatology/master.svg)](https://codecov.io/github/Jean-Baptiste-Camps/stemmatology?branch=master) - -[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/stemmatology)](https://cran.r-project.org/package=stemmatology) - ## Installation You can install stemmatology from Github with: diff --git a/man/Import.TEIApparatus.Rd b/man/Import.TEIApparatus.Rd index 7b043e6..edad470 100644 --- a/man/Import.TEIApparatus.Rd +++ b/man/Import.TEIApparatus.Rd @@ -1,10 +1,11 @@ +\encoding{utf8} \name{Import.TEIApparatus} \alias{Import.TEIApparatus} %- Also NEED an '\alias' for EACH other topic documented here. \title{Import TEI apparatus} \description{Allows the user to import a TEI encoded parallel-segmentation apparatus.} \usage{ -Import.TEIApparatus(file = x, fromCollatex = False) +Import.TEIApparatus(file = x, fromCollatex = FALSE) } \arguments{ diff --git a/man/PCC.Exploratory.Rd b/man/PCC.Exploratory.Rd index 6a7f14b..4a81995 100644 --- a/man/PCC.Exploratory.Rd +++ b/man/PCC.Exploratory.Rd @@ -1,3 +1,4 @@ +\encoding{utf8} \name{PCC.Exploratory} \alias{PCC.Exploratory} \title{PCC Exploratory methods} diff --git a/man/PCC.Rd b/man/PCC.Rd index 06761c2..05c5727 100644 --- a/man/PCC.Rd +++ b/man/PCC.Rd @@ -1,3 +1,4 @@ +\encoding{utf8} \name{PCC} \alias{PCC} %- Also NEED an '\alias' for EACH other topic documented here. diff --git a/man/PCC.Stemma.Rd b/man/PCC.Stemma.Rd index 4eacff8..7b96fa3 100644 --- a/man/PCC.Stemma.Rd +++ b/man/PCC.Stemma.Rd @@ -1,3 +1,4 @@ +\encoding{utf8} \name{PCC.Stemma} \alias{PCC.Stemma} %- Also NEED an '\alias' for EACH other topic documented here. @@ -53,7 +54,7 @@ Jean-Baptiste Camps (\email{jbcamps@hotmail.com}) & Florian Cafiero (\email{flor %% ~Make other sections like Warning with \section{Warning }{....} ~ \seealso{ -\code{\link{PCC.disagreement}}, \code{\link{PCC.buildgroup}}, \code{\link{PCC.reconstructModel}}. +\code{\link{PCC.disagreement}}, \code{\link{PCC.buildGroup}}, \code{\link{PCC.reconstructModel}}. } \examples{ diff --git a/man/PCC.buildGroup.Rd b/man/PCC.buildGroup.Rd index 0b8b2c3..e675c2a 100644 --- a/man/PCC.buildGroup.Rd +++ b/man/PCC.buildGroup.Rd @@ -1,3 +1,4 @@ +\encoding{utf8} \name{PCC.buildGroup} \alias{PCC.buildGroup} %- Also NEED an '\alias' for EACH other topic documented here. diff --git a/man/PCC.conflicts.Rd b/man/PCC.conflicts.Rd index bba138a..c01a0bc 100644 --- a/man/PCC.conflicts.Rd +++ b/man/PCC.conflicts.Rd @@ -1,3 +1,4 @@ +\encoding{utf8} \name{PCC.conflicts} \alias{PCC.conflicts} \title{PCC Exploratory Methods: Conflicts between Variant Locations} @@ -56,9 +57,9 @@ Jean-Baptiste Camps (\email{jbcamps@hotmail.com}) & Florian Cafiero \examples{ %TODO: fignoler globalement les exemples et les reprendre, voire les affiner. data(fournival) -myConflicts = PCC.conflicts(fournival) -myOverconflicting = PCC.overconflicting(myConflicts) -myNewVariantsTable = PCC.elimination(myOverconflicting) +%myConflicts = PCC.conflicts(fournival) +%myOverconflicting = PCC.overconflicting(myConflicts) +%myNewVariantsTable = PCC.elimination(myOverconflicting) } % Add one or more standard keywords, see file 'KEYWORDS' in the % R documentation directory. diff --git a/man/PCC.contam.Rd b/man/PCC.contam.Rd index af7a899..b8e945e 100644 --- a/man/PCC.contam.Rd +++ b/man/PCC.contam.Rd @@ -1,3 +1,4 @@ +\encoding{utf8} \name{PCC.contam} \alias{PCC.contam} %- Also NEED an '\alias' for EACH other topic documented here. diff --git a/man/PCC.disagreement.Rd b/man/PCC.disagreement.Rd index 744647c..5a09d3c 100644 --- a/man/PCC.disagreement.Rd +++ b/man/PCC.disagreement.Rd @@ -1,3 +1,4 @@ +\encoding{utf8} \name{PCC.disagreement} \alias{PCC.disagreement} %- Also NEED an '\alias' for EACH other topic documented here. diff --git a/man/PCC.distribute.Rd b/man/PCC.distribute.Rd index 9a6224a..9435b06 100644 --- a/man/PCC.distribute.Rd +++ b/man/PCC.distribute.Rd @@ -1,3 +1,4 @@ +\encoding{utf8} \name{PCC.distribute} \alias{PCC.distribute} %- Also NEED an '\alias' for EACH other topic documented here. @@ -50,5 +51,5 @@ Jean-Baptiste Camps & Florian Cafiero } % Add one or more standard keywords, see file 'KEYWORDS' in the % R documentation directory. -\keyword{ ~kwd1 } -\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line +\keyword{stemmatology} +\keyword{data-manipulation}%vérif keywords diff --git a/man/PCC.elimination.Rd b/man/PCC.elimination.Rd index c987bf7..e17f105 100644 --- a/man/PCC.elimination.Rd +++ b/man/PCC.elimination.Rd @@ -1,3 +1,4 @@ +\encoding{utf8} \name{PCC.elimination} \alias{PCC.elimination} %- Also NEED an '\alias' for EACH other topic documented here. diff --git a/man/PCC.equipollent.Rd b/man/PCC.equipollent.Rd index 13932aa..4a50526 100644 --- a/man/PCC.equipollent.Rd +++ b/man/PCC.equipollent.Rd @@ -1,3 +1,4 @@ +\encoding{utf8} \name{PCC.equipollent} \alias{PCC.equipollent} %- Also NEED an '\alias' for EACH other topic documented here. diff --git a/man/PCC.overconflicting.Rd b/man/PCC.overconflicting.Rd index 1f5ba4c..e77d8d3 100644 --- a/man/PCC.overconflicting.Rd +++ b/man/PCC.overconflicting.Rd @@ -1,3 +1,4 @@ +\encoding{utf8} \name{PCC.overconflicting} \alias{PCC.overconflicting} %- Also NEED an '\alias' for EACH other topic documented here. diff --git a/man/PCC.reconstructModel.Rd b/man/PCC.reconstructModel.Rd index f5017fa..089d95d 100644 --- a/man/PCC.reconstructModel.Rd +++ b/man/PCC.reconstructModel.Rd @@ -1,3 +1,4 @@ +\encoding{utf8} \name{PCC.reconstructModel} \alias{PCC.reconstructModel} %- Also NEED an '\alias' for EACH other topic documented here. @@ -19,11 +20,12 @@ A PCCbuildGroup object. Default: \code{FALSE}. } - \item{limit}{ -The maximum number of severe disagreements expected for witnesses to be in the same group. - - Default: \code{0}. -} +% \item{limit}{ +%The maximum number of severe disagreements expected for witnesses to be in the same group. +% +% Default: \code{0}. +%} +%TODO: faut-il implementer qqchose de ce genre pour cette fonction? \item{recoverNAs}{ logical; if \code{TRUE}, when an actual witness or reconstructed subarchetype is identified to the reconstructed model of a group, every NA it has is recovered by taking the value of the reconstructed model; if \code{FALSE}, their NAs values are kept. @@ -57,6 +59,6 @@ Jean-Baptiste Camps (\email{jbcamps@hotmail.com}) & Florian Cafiero %% ~Make other sections like Warning with \section{Warning }{....} ~ \seealso{ -More about the next step: \code{\link{PCC.stemma}}. +More about the next step: \code{\link{PCC.Stemma}}. More about the input: \code{\link{PCC.buildGroup}} } diff --git a/man/VL.pValues.Rd b/man/VL.pValues.Rd index a274bbb..cae534b 100644 --- a/man/VL.pValues.Rd +++ b/man/VL.pValues.Rd @@ -1,3 +1,4 @@ +\encoding{utf8} \name{VL.pValues} \alias{VL.pValues} %- Also NEED an '\alias' for EACH other topic documented here. diff --git a/man/fournival.Rd b/man/fournival.Rd index 7cf3b25..d649d6d 100644 --- a/man/fournival.Rd +++ b/man/fournival.Rd @@ -1,3 +1,4 @@ +\encoding{utf8} \name{fournival} \alias{fournival} \docType{data} diff --git a/man/heinrichi.Rd b/man/heinrichi.Rd index aba88de..8a6ea98 100644 --- a/man/heinrichi.Rd +++ b/man/heinrichi.Rd @@ -1,3 +1,4 @@ +\encoding{utf8} \name{heinrichi} \alias{heinrichi} \docType{data} diff --git a/man/notreBesoin.Rd b/man/notreBesoin.Rd index 6d01130..1721956 100644 --- a/man/notreBesoin.Rd +++ b/man/notreBesoin.Rd @@ -1,3 +1,4 @@ +\encoding{utf8} \name{notreBesoin} \alias{notreBesoin} \docType{data} diff --git a/man/otinel.Rd b/man/otinel.Rd index 1b30086..e98c96a 100644 --- a/man/otinel.Rd +++ b/man/otinel.Rd @@ -1,3 +1,4 @@ +\encoding{utf8} \name{otinel} \alias{otinel} \docType{data} diff --git a/man/parzival.Rd b/man/parzival.Rd index 8575376..1513a88 100644 --- a/man/parzival.Rd +++ b/man/parzival.Rd @@ -1,3 +1,4 @@ +\encoding{utf8} \name{parzival} \alias{parzival} \docType{data} diff --git a/man/stemmatology-package.Rd b/man/stemmatology-package.Rd index f33217f..5528648 100644 --- a/man/stemmatology-package.Rd +++ b/man/stemmatology-package.Rd @@ -1,9 +1,10 @@ +\encoding{utf8} \name{stemmatology} \alias{stemmatology-package} \docType{package} \title{An R stemmatology package} \description{ -This packages implements various methods from the stemmatological analysis of textual traditions. It contains both exploratory methods and algorithms aimed at building stemmata from a table of variant locations. +This packages implements various methods for the stemmatological analysis of textual traditions. It contains both exploratory methods and algorithms aimed at building stemmata from a table of variant locations. } \details{ \tabular{ll}{ From 182b8003f15beba489171057e6d6b33dc40a1695 Mon Sep 17 00:00:00 2001 From: Jean-Baptiste Camps Date: Wed, 25 Oct 2017 18:14:15 +0200 Subject: [PATCH 4/6] more packaging now building and checking --- man/PCC.conflicts.Rd | 4 +- man/PCC.elimination.Rd | 5 +- man/PCC.overconflicting.Rd | 4 +- man/PCC.reconstructModel.Rd | 4 + man/VL.pValues.Rd | 2 +- man/stemmatology-package.Rd | 2 +- .../stemmatology-concordance.tex | 0 {vignettes_old => vignettes}/stemmatology.Rnw | 0 vignettes/stemmatology.aux | 19 + {vignettes_old => vignettes}/stemmatology.log | 689 ++++++++++-------- vignettes/stemmatology.out | 6 + {vignettes_old => vignettes}/stemmatology.pdf | Bin 110188 -> 110203 bytes vignettes/stemmatology.synctex.gz | Bin 0 -> 3513 bytes {vignettes_old => vignettes}/stemmatology.tex | 0 vignettes_old/stemmatology.synctex.gz | Bin 3551 -> 0 bytes 15 files changed, 427 insertions(+), 308 deletions(-) rename {vignettes_old => vignettes}/stemmatology-concordance.tex (100%) rename {vignettes_old => vignettes}/stemmatology.Rnw (100%) create mode 100644 vignettes/stemmatology.aux rename {vignettes_old => vignettes}/stemmatology.log (59%) create mode 100644 vignettes/stemmatology.out rename {vignettes_old => vignettes}/stemmatology.pdf (99%) create mode 100644 vignettes/stemmatology.synctex.gz rename {vignettes_old => vignettes}/stemmatology.tex (100%) delete mode 100644 vignettes_old/stemmatology.synctex.gz diff --git a/man/PCC.conflicts.Rd b/man/PCC.conflicts.Rd index c01a0bc..3d7646f 100644 --- a/man/PCC.conflicts.Rd +++ b/man/PCC.conflicts.Rd @@ -57,11 +57,11 @@ Jean-Baptiste Camps (\email{jbcamps@hotmail.com}) & Florian Cafiero \examples{ %TODO: fignoler globalement les exemples et les reprendre, voire les affiner. data(fournival) -%myConflicts = PCC.conflicts(fournival) +myConflicts = PCC.conflicts(fournival) %myOverconflicting = PCC.overconflicting(myConflicts) %myNewVariantsTable = PCC.elimination(myOverconflicting) } % Add one or more standard keywords, see file 'KEYWORDS' in the % R documentation directory. \keyword{stemmatology} -\keyword{philology} \ No newline at end of file +%\keyword{philology} \ No newline at end of file diff --git a/man/PCC.elimination.Rd b/man/PCC.elimination.Rd index e17f105..dcc05c3 100644 --- a/man/PCC.elimination.Rd +++ b/man/PCC.elimination.Rd @@ -44,7 +44,4 @@ To spot the conflicts between variants: \code{\link{PCC.conflicts}} } % Add one or more standard keywords, see file 'KEYWORDS' in the % R documentation directory. -\keyword{over-conflicting} -\keyword{variants}% __ONLY ONE__ keyword per line -\keyword{selection} -\keyword{deletion} \ No newline at end of file +\keyword{stemmatology} \ No newline at end of file diff --git a/man/PCC.overconflicting.Rd b/man/PCC.overconflicting.Rd index e77d8d3..e86fcdf 100644 --- a/man/PCC.overconflicting.Rd +++ b/man/PCC.overconflicting.Rd @@ -41,11 +41,11 @@ Jean-Baptiste Camps (\email{jbcamps@hotmail.com}) & Florian Cafiero %% ~Make other sections like Warning with \section{Warning }{....} ~ \seealso{ -\code{\link{PCC.Exploratory}, +\code{\link{PCC.Exploratory}}, %About the input for this fonction : \code{\link{PCC.conflicts}}, %To remove the variants labeled as problematic: -\code{\link{PCC.elimination}}.} +\code{\link{PCC.elimination}}. } \examples{ } diff --git a/man/PCC.reconstructModel.Rd b/man/PCC.reconstructModel.Rd index 089d95d..fcdeca9 100644 --- a/man/PCC.reconstructModel.Rd +++ b/man/PCC.reconstructModel.Rd @@ -58,6 +58,10 @@ Jean-Baptiste Camps (\email{jbcamps@hotmail.com}) & Florian Cafiero %% ~Make other sections like Warning with \section{Warning }{....} ~ +\examples{ + +} + \seealso{ More about the next step: \code{\link{PCC.Stemma}}. More about the input: \code{\link{PCC.buildGroup}} diff --git a/man/VL.pValues.Rd b/man/VL.pValues.Rd index cae534b..cef4a52 100644 --- a/man/VL.pValues.Rd +++ b/man/VL.pValues.Rd @@ -16,7 +16,7 @@ VL.pValues(x) } } \details{ -In order to assess the significance of each variant location, and distinguish +In order to assess the significance of each variant location, and distinguish random polygenesis from contamination (i.e. copying based on several exemplars), this function crosses two by two every possible pair of variant locations, and applies a Fisher exact test. It then counts the number of configurations in which a VL has passed the significance threshold (i.e. p < 0.05). } \value{ diff --git a/man/stemmatology-package.Rd b/man/stemmatology-package.Rd index 5528648..2860f88 100644 --- a/man/stemmatology-package.Rd +++ b/man/stemmatology-package.Rd @@ -103,5 +103,5 @@ Please report issues with this package to \url{https://github.com/Jean-Baptiste- \examples{ data(fournival) -PCC.Exploratory(fournival) +%PCC.Exploratory(fournival) } diff --git a/vignettes_old/stemmatology-concordance.tex b/vignettes/stemmatology-concordance.tex similarity index 100% rename from vignettes_old/stemmatology-concordance.tex rename to vignettes/stemmatology-concordance.tex diff --git a/vignettes_old/stemmatology.Rnw b/vignettes/stemmatology.Rnw similarity index 100% rename from vignettes_old/stemmatology.Rnw rename to vignettes/stemmatology.Rnw diff --git a/vignettes/stemmatology.aux b/vignettes/stemmatology.aux new file mode 100644 index 0000000..b9c8980 --- /dev/null +++ b/vignettes/stemmatology.aux @@ -0,0 +1,19 @@ +\relax +\providecommand\hyper@newdestlabel[2]{} +\bibstyle{jss} +\providecommand\HyperFirstAtBeginDocument{\AtBeginDocument} +\HyperFirstAtBeginDocument{\ifx\hyper@anchor\@undefined +\global\let\oldcontentsline\contentsline +\gdef\contentsline#1#2#3#4{\oldcontentsline{#1}{#2}{#3}} +\global\let\oldnewlabel\newlabel +\gdef\newlabel#1#2{\newlabelxx{#1}#2} +\gdef\newlabelxx#1#2#3#4#5#6{\oldnewlabel{#1}{{#2}{#3}}} +\AtEndDocument{\ifx\hyper@anchor\@undefined +\let\contentsline\oldcontentsline +\let\newlabel\oldnewlabel +\fi} +\fi} +\global\let\hyper@last\relax +\gdef\HyperFirstAtBeginDocument#1{#1} +\providecommand\HyField@AuxAddToFields[1]{} +\providecommand\HyField@AuxAddToCoFields[2]{} diff --git a/vignettes_old/stemmatology.log b/vignettes/stemmatology.log similarity index 59% rename from vignettes_old/stemmatology.log rename to vignettes/stemmatology.log index c40183e..2c715e6 100644 --- a/vignettes_old/stemmatology.log +++ 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(decimal 304) defining Unicode char U+0131 (decimal 305) defining Unicode char U+0132 (decimal 306) defining Unicode char U+0133 (decimal 307) + defining Unicode char U+0134 (decimal 308) + defining Unicode char U+0135 (decimal 309) + defining Unicode char U+0136 (decimal 310) + defining Unicode char U+0137 (decimal 311) defining Unicode char U+0139 (decimal 313) defining Unicode char U+013A (decimal 314) + defining Unicode char U+013B (decimal 315) + defining Unicode char U+013C (decimal 316) defining Unicode char U+013D (decimal 317) defining Unicode char U+013E (decimal 318) defining Unicode char U+0141 (decimal 321) defining Unicode char U+0142 (decimal 322) defining Unicode char U+0143 (decimal 323) defining Unicode char U+0144 (decimal 324) + defining Unicode char U+0145 (decimal 325) + defining Unicode char U+0146 (decimal 326) defining Unicode char U+0147 (decimal 327) defining Unicode char U+0148 (decimal 328) defining Unicode char U+014A (decimal 330) defining Unicode char U+014B (decimal 331) + defining Unicode char U+014C (decimal 332) + defining Unicode char U+014D (decimal 333) + defining Unicode char U+014E (decimal 334) + defining Unicode char U+014F (decimal 335) defining Unicode char U+0150 (decimal 336) defining Unicode char U+0151 (decimal 337) defining Unicode char U+0152 (decimal 338) defining Unicode char U+0153 (decimal 339) defining Unicode char U+0154 (decimal 340) defining Unicode char U+0155 (decimal 341) + defining Unicode char U+0156 (decimal 342) + defining Unicode char U+0157 (decimal 343) defining Unicode char U+0158 (decimal 344) defining Unicode char U+0159 (decimal 345) defining Unicode char U+015A (decimal 346) defining Unicode char U+015B (decimal 347) + defining Unicode char U+015C (decimal 348) + defining Unicode char U+015D (decimal 349) defining Unicode char U+015E (decimal 350) defining Unicode char U+015F (decimal 351) defining Unicode char U+0160 (decimal 352) @@ -455,10 +492,22 @@ File: t1enc.dfu 2008/04/05 v1.1m UTF-8 support for inputenc defining Unicode char U+0163 (decimal 355) defining Unicode char U+0164 (decimal 356) defining Unicode char U+0165 (decimal 357) + defining Unicode char U+0168 (decimal 360) + defining Unicode char U+0169 (decimal 361) + defining Unicode char U+016A (decimal 362) + defining Unicode char U+016B (decimal 363) + defining Unicode char U+016C (decimal 364) + defining Unicode char U+016D (decimal 365) defining Unicode char U+016E (decimal 366) defining Unicode char U+016F (decimal 367) defining Unicode char U+0170 (decimal 368) defining Unicode char U+0171 (decimal 369) + defining Unicode char U+0172 (decimal 370) + defining Unicode char U+0173 (decimal 371) + defining Unicode char U+0174 (decimal 372) + defining Unicode char U+0175 (decimal 373) + defining Unicode char U+0176 (decimal 374) + defining Unicode char U+0177 (decimal 375) defining Unicode char U+0178 (decimal 376) defining Unicode char U+0179 (decimal 377) defining Unicode char U+017A (decimal 378) @@ -466,9 +515,40 @@ File: t1enc.dfu 2008/04/05 v1.1m UTF-8 support for inputenc defining Unicode char U+017C (decimal 380) defining Unicode char U+017D (decimal 381) defining Unicode char U+017E (decimal 382) + defining Unicode char U+01CD (decimal 461) + defining Unicode char U+01CE (decimal 462) + defining Unicode char U+01CF (decimal 463) + defining Unicode char U+01D0 (decimal 464) + defining Unicode char U+01D1 (decimal 465) + defining Unicode char U+01D2 (decimal 466) + defining Unicode char U+01D3 (decimal 467) + defining Unicode char U+01D4 (decimal 468) + defining Unicode char U+01E2 (decimal 482) + defining Unicode char U+01E3 (decimal 483) + defining Unicode char U+01E6 (decimal 486) + defining Unicode char U+01E7 (decimal 487) + defining Unicode char U+01E8 (decimal 488) + defining Unicode char U+01E9 (decimal 489) + defining Unicode char U+01EA (decimal 490) + defining Unicode char U+01EB (decimal 491) + defining Unicode char U+01F0 (decimal 496) + defining Unicode char U+01F4 (decimal 500) + defining Unicode char U+01F5 (decimal 501) + defining Unicode char U+0218 (decimal 536) + defining Unicode char U+0219 (decimal 537) + defining Unicode char U+021A (decimal 538) + defining Unicode char U+021B (decimal 539) + defining Unicode char U+0232 (decimal 562) + defining Unicode char U+0233 (decimal 563) + defining Unicode char U+1E02 (decimal 7682) + defining Unicode char U+1E03 (decimal 7683) defining Unicode char U+200C (decimal 8204) + defining Unicode char U+2010 (decimal 8208) + defining Unicode char U+2011 (decimal 8209) + defining Unicode char U+2012 (decimal 8210) defining Unicode char U+2013 (decimal 8211) defining Unicode char U+2014 (decimal 8212) + defining Unicode char U+2015 (decimal 8213) defining Unicode char U+2018 (decimal 8216) defining Unicode char U+2019 (decimal 8217) defining Unicode char U+201A (decimal 8218) @@ -480,14 +560,18 @@ File: t1enc.dfu 2008/04/05 v1.1m UTF-8 support for inputenc defining Unicode char U+2039 (decimal 8249) defining Unicode char U+203A (decimal 8250) defining Unicode char U+2423 (decimal 9251) + defining Unicode char U+1E20 (decimal 7712) + defining Unicode char U+1E21 (decimal 7713) ) Now handling font encoding OT1 ... ... processing UTF-8 mapping file for font encoding OT1 -(/usr/local/texlive/2014/texmf-dist/tex/latex/base/ot1enc.dfu -File: ot1enc.dfu 2008/04/05 v1.1m UTF-8 support for inputenc +(/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu +File: ot1enc.dfu 2017/01/28 v1.1t UTF-8 support for inputenc + defining Unicode char U+00A0 (decimal 160) defining Unicode char U+00A1 (decimal 161) defining Unicode char U+00A3 (decimal 163) + defining Unicode char U+00AD (decimal 173) defining Unicode char U+00B8 (decimal 184) defining Unicode char U+00BF (decimal 191) defining Unicode char U+00C5 (decimal 197) @@ -505,6 +589,14 @@ File: ot1enc.dfu 2008/04/05 v1.1m UTF-8 support for inputenc defining Unicode char U+0142 (decimal 322) defining Unicode char U+0152 (decimal 338) defining Unicode char U+0153 (decimal 339) + defining Unicode char U+0174 (decimal 372) + defining Unicode char U+0175 (decimal 373) + defining Unicode char U+0176 (decimal 374) + defining Unicode char U+0177 (decimal 375) + defining Unicode char U+0218 (decimal 536) + defining Unicode char U+0219 (decimal 537) + defining Unicode char U+021A (decimal 538) + defining Unicode char U+021B (decimal 539) defining Unicode char U+2013 (decimal 8211) defining Unicode char U+2014 (decimal 8212) defining Unicode char U+2018 (decimal 8216) @@ -515,8 +607,8 @@ File: ot1enc.dfu 2008/04/05 v1.1m UTF-8 support for inputenc Now handling font encoding OMS ... ... processing UTF-8 mapping file for font encoding OMS -(/usr/local/texlive/2014/texmf-dist/tex/latex/base/omsenc.dfu -File: omsenc.dfu 2008/04/05 v1.1m UTF-8 support for inputenc +(/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu +File: omsenc.dfu 2017/01/28 v1.1t UTF-8 support for inputenc defining Unicode char U+00A7 (decimal 167) defining Unicode char U+00B6 (decimal 182) defining Unicode char U+00B7 (decimal 183) @@ -531,8 +623,8 @@ Now handling font encoding U ... 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+\classnum@=\count104 +\DOTSCASE@=\count105 +LaTeX Info: Redefining \ldots on input line 472. +LaTeX Info: Redefining \dots on input line 475. +LaTeX Info: Redefining \cdots on input line 596. \Mathstrutbox@=\box27 \strutbox@=\box28 \big@size=\dimen111 -LaTeX Font Info: Redeclaring font encoding OML on input line 566. -LaTeX Font Info: Redeclaring font encoding OMS on input line 567. -\macc@depth=\count107 -\c@MaxMatrixCols=\count108 +LaTeX Font Info: Redeclaring font encoding OML on input line 712. +LaTeX Font Info: Redeclaring font encoding OMS on input line 713. +\macc@depth=\count106 +\c@MaxMatrixCols=\count107 \dotsspace@=\muskip11 -\c@parentequation=\count109 -\dspbrk@lvl=\count110 +\c@parentequation=\count108 +\dspbrk@lvl=\count109 \tag@help=\toks18 -\row@=\count111 -\column@=\count112 -\maxfields@=\count113 +\row@=\count110 +\column@=\count111 +\maxfields@=\count112 \andhelp@=\toks19 \eqnshift@=\dimen112 \alignsep@=\dimen113 @@ -678,39 +770,39 @@ LaTeX Font Info: Redeclaring 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Redeclaring font encoding T1 on input line 43. +(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def +File: t1enc.def 2017/04/05 v2.0i Standard LaTeX file +LaTeX Font Info: Redeclaring font encoding T1 on input line 48. )) Environment Schunk is already defined, stay with former definition) (./stemmatology.aux) @@ -730,52 +822,53 @@ LaTeX Font Info: Checking defaults for U/cmr/m/n on input line 44. LaTeX Font Info: ... okay on input line 44. LaTeX Font Info: Checking defaults for TS1/cmr/m/n on input line 44. LaTeX Font Info: Try loading font information for TS1+cmr on input line 44. - -(/usr/local/texlive/2014/texmf-dist/tex/latex/base/ts1cmr.fd -File: ts1cmr.fd 1999/05/25 v2.5h Standard LaTeX font definitions + (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd +File: ts1cmr.fd 2014/09/29 v2.5h Standard LaTeX font definitions ) LaTeX Font Info: ... okay on input line 44. LaTeX Font Info: Checking defaults for PD1/pdf/m/n on input line 44. LaTeX Font Info: ... okay on input line 44. -(/usr/local/texlive/2014/texmf-dist/tex/context/base/supp-pdf.mkii +(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] -\scratchcounter=\count114 +\scratchcounter=\count113 \scratchdimen=\dimen120 \scratchbox=\box29 -\nofMPsegments=\count115 -\nofMParguments=\count116 +\nofMPsegments=\count114 +\nofMParguments=\count115 \everyMPshowfont=\toks23 -\MPscratchCnt=\count117 +\MPscratchCnt=\count116 \MPscratchDim=\dimen121 -\MPnumerator=\count118 -\makeMPintoPDFobject=\count119 +\MPnumerator=\count117 +\makeMPintoPDFobject=\count118 \everyMPtoPDFconversion=\toks24 -) (/usr/local/texlive/2014/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty -Package: epstopdf-base 2010/02/09 v2.5 Base part for package epstopdf +) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty +Package: epstopdf-base 2016/05/15 v2.6 Base part for package epstopdf -(/usr/local/texlive/2014/texmf-dist/tex/latex/oberdiek/grfext.sty -Package: grfext 2010/08/19 v1.1 Manage graphics extensions (HO) +(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty +Package: grfext 2016/05/16 v1.2 Manage graphics extensions (HO) ) +Package epstopdf-base Info: Redefining graphics rule for `.eps' on input line 4 +38. 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LaTeX Info: Redefining \pageref on input line 44. @@ -787,29 +880,29 @@ LaTeX Info: Redefining \nameref on input line 44. LaTeX Font Info: Try loading font information for T1+aess on input line 44. -(/usr/local/texlive/2014/texmf-dist/tex/latex/ae/t1aess.fd +(/usr/share/texlive/texmf-dist/tex/latex/ae/t1aess.fd File: t1aess.fd 1997/11/16 Font definitions for T1/aess. ) LaTeX Font Info: Try loading font information for U+msa on input line 44. -(/usr/local/texlive/2014/texmf-dist/tex/latex/amsfonts/umsa.fd +(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd File: umsa.fd 2013/01/14 v3.01 AMS symbols A ) LaTeX Font Info: Try loading font information for U+msb on input line 44. -(/usr/local/texlive/2014/texmf-dist/tex/latex/amsfonts/umsb.fd +(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd File: umsb.fd 2013/01/14 v3.01 AMS symbols B ) (./stemmatology-concordance.tex) LaTeX Font Info: Try loading font information for T1+aett on input line 70. -(/usr/local/texlive/2014/texmf-dist/tex/latex/ae/t1aett.fd +(/usr/share/texlive/texmf-dist/tex/latex/ae/t1aett.fd File: t1aett.fd 1997/11/16 Font definitions for T1/aett. ) Package atveryend Info: Empty hook `BeforeClearDocument' on input line 92. 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