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Merge pull request #43 from Jean-Baptiste-Camps/dev
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| \.Rhistory | ||
| \.gitignore | ||
| \.git | ||
| version_history | ||
| deprec | ||
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| .Rhistory | ||
| inst/doc |
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| exportPattern("^[[:alpha:]]+") | ||
| importFrom("graphics", "axis", "barplot", "legend", "par", "plot","title") | ||
| exportPattern("^[^\\.]") # This exports everything from stemmatology | ||
| # namespace that does not start with a dot. If at some point we | ||
| # want a more explicit listing, we might use export(PCC, PCC.Exploratory…) | ||
| importFrom("graphics", "axis", "barplot", "plot","title") | ||
| # It would be possible to remove stats import with a few modifications (only 2 uses) | ||
| 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") | ||
| importFrom("igraph", "graph_from_edgelist", "layout_as_tree", "plot.igraph", "E", "union", "topo_sort","V","neighbors") | ||
| importFrom("igraph", "graph_from_edgelist", "layout_as_tree", "layout_with_fr", "plot.igraph", "E", "union", "topo_sort","V","neighbors", "as_adjacency_matrix") | ||
| importFrom("xml2", "read_xml", "xml_ns_strip", "xml_find_all", "xml_text") |
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| PCC.Exploratory <- | ||
| function(x, omissionsAsReadings = FALSE, alternateReadings = FALSE, pauseAtPlot = FALSE, | ||
| interactive = TRUE) { | ||
| # TODO(JBC): dans ce groupe de fonction, comme dans le précédent, il est | ||
| # impératif de tester que les options font bien leur job (y compris en | ||
| # étant passées aux sous-fonctions) This is the global function for | ||
| # exploratory methods of the PCC type. In entry, a matrix with a column | ||
| # per witness, and a row per variant location, with readings coded | ||
| # with numbers. TODO(JBC): une version prenant en compte interactive = | ||
| # FALSE, pour tout faire d'elle-même avec des valeurs moyennes (pas pour | ||
| function(x, | ||
| omissionsAsReadings = FALSE, | ||
| alternateReadings = FALSE, | ||
| pauseAtPlot = FALSE, | ||
| ask = TRUE, | ||
| threshold = NULL, | ||
| verbose = FALSE | ||
| ) { | ||
| # This is the global function for exploratory methods of the PCC type. | ||
| # In entry, a matrix with a column per witness, and a row per variant location, | ||
| # with readings coded with numbers. | ||
| # TODO(JBC): une version prenant en compte ask = FALSE, | ||
| # pour tout faire d'elle-même avec des valeurs moyennes (pas pour | ||
| # tout de suite) - ou demander à l'utilisateur de les choisir plutôt | ||
| # que de proposer des valeurs par défaut risquées | ||
| if (!is.matrix(x)) { | ||
| stop("Input must be a matrix.") | ||
| stop("Input must be a matrix.") | ||
| } | ||
| if (ask == FALSE & is.null(threshold)){ | ||
| stop("you must specify threshold with ask = FALSE") | ||
| } | ||
| tableVariantes = x | ||
| pccConflicts = PCC.conflicts(tableVariantes, omissionsAsReadings = omissionsAsReadings, alternateReadings = alternateReadings) # Simple interaction, which tests for value inputed by the user | ||
| answered = FALSE | ||
| while (answered == FALSE) { | ||
| pccConflicts = PCC.conflicts(tableVariantes, | ||
| omissionsAsReadings = omissionsAsReadings, | ||
| alternateReadings = alternateReadings) | ||
| # If there are no conflicts, output directly | ||
| if (sum(pccConflicts$conflictsTotal[, 1]) == 0) { | ||
| return(pccConflicts) | ||
| } | ||
| # Simple interaction, which tests for value inputed by the user | ||
| if(ask == TRUE){ | ||
| answered = FALSE | ||
| while (answered == FALSE) { | ||
| answerOne = readline("Do you want to proceed to the analysis of the network conflictuality ? Y/N \n ") | ||
| if (answerOne != "N" && answerOne != "Y") { | ||
| print("Please enter Y (yes) or N (no).") | ||
| print("Please enter Y (yes) or N (no).") | ||
| } | ||
| if (answerOne == "N") { | ||
| return(pccConflicts) | ||
| return(pccConflicts) | ||
| } | ||
| if (answerOne == "Y") { | ||
| answered = TRUE | ||
| answered = TRUE | ||
| } | ||
| } | ||
| } | ||
| answered = FALSE | ||
| while (answered == FALSE) { | ||
| pccOverconflicting = PCC.overconflicting(pccConflicts) | ||
| writeLines("Are you satisfied with this configuration and do you want to\n Proceed to actual elimination of over-conflicting variant locations [P],\n Try again with different value [T],\n or Quit [Q] ? \n ") | ||
| if(ask){ | ||
| answered = FALSE | ||
| while (answered == FALSE) { | ||
| pccOverconflicting = PCC.overconflicting(pccConflicts, ask = ask, threshold = threshold) | ||
| writeLines( | ||
| "Are you satisfied with this configuration and do you want to\n Proceed to actual elimination of over-conflicting variant locations [P],\n Try again with different value [T],\n or Quit [Q] ? \n " | ||
| ) | ||
| reiterateQuestion = TRUE | ||
| while (reiterateQuestion == TRUE) { | ||
| answerOne = readline("(P/T/Q)") | ||
| if (answerOne != "P" && answerOne != "T" && answerOne != "Q") { | ||
| print("Please enter P (Proceed), T (Try again) or Q (Quit).") | ||
| } | ||
| if (answerOne == "T") { | ||
| reiterateQuestion = FALSE | ||
| } | ||
| if (answerOne == "Q") { | ||
| return(pccOverconflicting) | ||
| } | ||
| if (answerOne == "P") { | ||
| reiterateQuestion = FALSE | ||
| answered = TRUE | ||
| } | ||
| answerOne = readline("(P/T/Q)") | ||
| if (answerOne != "P" && | ||
| answerOne != "T" && answerOne != "Q") { | ||
| print("Please enter P (Proceed), T (Try again) or Q (Quit).") | ||
| } | ||
| if (answerOne == "T") { | ||
| reiterateQuestion = FALSE | ||
| } | ||
| if (answerOne == "Q") { | ||
| return(pccOverconflicting) | ||
| } | ||
| if (answerOne == "P") { | ||
| reiterateQuestion = FALSE | ||
| answered = TRUE | ||
| } | ||
| } | ||
| } | ||
| } else{ | ||
| pccOverconflicting = PCC.overconflicting(pccConflicts, ask = ask, threshold = threshold) | ||
| } | ||
| pccElimination = PCC.elimination(pccOverconflicting) | ||
| pccConflicts = PCC.conflicts(pccElimination, omissionsAsReadings = omissionsAsReadings, alternateReadings = alternateReadings) | ||
| pccConflicts = PCC.conflicts(pccElimination, | ||
| omissionsAsReadings = omissionsAsReadings, | ||
| alternateReadings = alternateReadings) | ||
| if (sum(pccConflicts$conflictsTotal[, 1]) == 0) { | ||
| print("There is no longer any conflict in the database. Function will stop.") | ||
| return(pccConflicts) | ||
| if(verbose){ | ||
| cat("There is no longer any conflict in the database. Function will stop.") | ||
| } | ||
| return(pccConflicts) | ||
| } | ||
| message = paste("There is still ", nrow(pccConflicts$edgelist), "conflicts in the database. If this number is high it might indicate that : \n 1. The conflictuality index chosen was too low. \n 2. There are concurring structures in the tradition (due for instance to contamination).") | ||
| writeLines(message) | ||
| answered = FALSE | ||
| while (answered == FALSE) { | ||
| if(ask){ | ||
| cat( | ||
| "There is still ", | ||
| nrow(pccConflicts$edgelist), | ||
| "conflicts in the database.\n", | ||
| "If this number is high it might indicate that: \n", | ||
| "1. The conflictuality index chosen was too low.\n", | ||
| "2. There are concurring structures in the tradition (due for instance to contamination)." | ||
| ) | ||
| answered = FALSE | ||
| while (answered == FALSE) { | ||
| answerOne = readline("Do you want to proceed to contamination detection methods ? Y/N \n ") | ||
| if (answerOne != "N" && answerOne != "Y") { | ||
| print("Please enter Y (yes) or N (no).") | ||
| print("Please enter Y (yes) or N (no).") | ||
| } | ||
| if (answerOne == "N") { | ||
| return(pccConflicts) | ||
| return(pccConflicts) | ||
| } | ||
| if (answerOne == "Y") { | ||
| answered = TRUE | ||
| answered = TRUE | ||
| } | ||
| } | ||
| } | ||
| pccContam = PCC.contam(pccConflicts, pauseAtPlot = pauseAtPlot, omissionsAsReadings = omissionsAsReadings, alternateReadings = alternateReadings) | ||
| print(pccContam$conflictsDifferences) | ||
| answered = FALSE | ||
| while (answered == FALSE) { | ||
| pccContam = PCC.contam( | ||
| pccConflicts, | ||
| pauseAtPlot = pauseAtPlot, | ||
| omissionsAsReadings = omissionsAsReadings, | ||
| alternateReadings = alternateReadings | ||
| ) | ||
| if(ask){ | ||
| print(pccContam$conflictsDifferences) | ||
| answered = FALSE | ||
| while (answered == FALSE) { | ||
| answerOne = readline("Do you want to define alternate configurations for stemma building ? Y/N \n ") | ||
| if (answerOne != "N" && answerOne != "Y") { | ||
| print("Please enter Y (yes) or N (no).") | ||
| print("Please enter Y (yes) or N (no).") | ||
| } | ||
| if (answerOne == "N") { | ||
| return(pccContam) | ||
| return(pccContam) | ||
| } | ||
| if (answerOne == "Y") { | ||
| answered = TRUE | ||
| answered = TRUE | ||
| pccEquipollent = PCC.equipollent(pccConflicts, ask = ask, verbose = verbose) | ||
| return(pccEquipollent) | ||
| } | ||
| } | ||
| } | ||
| # and now, in the ask = FALSE mode, we will try to decide smartly for the user | ||
| # Either, there are one or several wits responsible for conficts, and | ||
| # we will equipollent for them, or, otherwise, we will try to do it | ||
| # on a global basis | ||
| myWits = rownames(pccContam$conflictsDifferences[ | ||
| pccContam$conflictsDifferences + (sum(pccContam$totalByMs[,1]) / 2) | ||
| == 0, , drop = FALSE | ||
| ]) | ||
| if(is.null(myWits)){ | ||
| pccEquipollent = PCC.equipollent(pccConflicts, ask = ask, scope = 'T', | ||
| verbose = verbose) | ||
| } else { | ||
| pccEquipollent = PCC.equipollent(pccConflicts, ask = ask, scope = 'W', | ||
| wits = myWits, verbose = verbose) | ||
| } | ||
| pccEquipollent = PCC.equipollent(pccConflicts) | ||
| return(pccEquipollent) | ||
| } | ||
| } |
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