Adjust to published version of paper

ppernot · Apr 29, 2020 · 4f62783 · 4f62783
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diff --git a/README.md b/README.md
@@ -3,6 +3,8 @@
 
 # SIP
 
-Codes and data to reproduce the results of the paper:
+Codes and data to reproduce the results of:
 
-* _Probabilistic performance estimators for computational chemistry methods: Systematic Improvement Probability and Ranking Probability Matrix_, by P. Pernot and A. Savin. WIP...
+* P. Pernot and A. Savin (2020) _Probabilistic performance estimators for computational chemistry methods: Systematic Improvement Probability and Ranking Probability Matrix. I. Theory_, [_J. Chem. Phys._ __152__:164108](http://dx.doi.org/10.1063/5.0006202).
+
+* P. Pernot and A. Savin (2020) _Probabilistic performance estimators for computational chemistry methods: Systematic Improvement Probability and Ranking Probability Matrix. II. Applications_, [_J. Chem. Phys._ __152__:164109](http://dx.doi.org/10.1063/5.0006204).
diff --git a/analysis/0-Setup.R b/analysis/0-Setup.R
@@ -15,7 +15,7 @@ for (lib in libs) {
   }
 }
 ## Load packages and generate biblio
-repmis::LoadandCite(libs,file='../article/packages.bib')
+repmis::LoadandCite(libs) #,file='../article/packages.bib')
 
 ## Github package
 lib = "ErrViewLib"

diff --git a/analysis/Appendix_B.R b/analysis/Appendix_B.R
@@ -2,7 +2,7 @@ source('0-Setup.R')
 
 caseName = 'AppB'
 
-# Fig. 30 ####
+# Fig. I-5 ####
 
 ## g-and-h Samples CC
 nMC = 1000

diff --git a/analysis/Appendix_C.R b/analysis/Appendix_C.R
@@ -167,7 +167,7 @@ stop()
 
 # Analysis ####
 
-## Fig. 31
+## Fig. I-6 ####
 
 source('0-Setup.R')
 

diff --git a/analysis/Appendix_D.R b/analysis/Appendix_D.R
@@ -62,7 +62,7 @@ b1l = boot(X, statistic = ErrViewLib::q95,R = nMC)
 b2l = boot(X, statistic = ErrViewLib::q95hd,R = nMC)
 
 
-# Fig. 32 ####
+# Fig. I-7 ####
 png(
   file = paste0(figRepo,caseName,'_Compare_Q95.png'),
   width = 1.75*gPars$reso,
@@ -332,7 +332,7 @@ for(score in scores) {
 
 # save(resp,file = 'scoresBS.Rda')
 
-# Fig. 33 ####
+# Fig. I-8 ####
 ifig=0
 png(
   file = paste0(figRepo,caseName,'_scoresBS.png'),

diff --git a/analysis/BOR2019.R b/analysis/BOR2019.R
@@ -100,7 +100,7 @@ sink()
 # Figures ####
 eps = 0.2 # eV : uncertainty level ("a few tenths of eV")
 
-# Fig. 3 ####
+# Fig. I-3 ####
 ifig =1
 png(file=paste0(figRepo,caseName,'_compareECDF.png'),
     width=gPars$reso,height=gPars$reso)
@@ -130,7 +130,7 @@ ErrViewLib::plotDeltaCDF(
 dev.off()
 ###
 
-# Fig. 8 ####
+# Fig. II-5 ####
 png(
   file = paste0(figRepo, caseName,'_Cormat_Errors_Spearman.png'),
   width = 13/12*gPars$reso,
@@ -141,7 +141,7 @@ ErrViewLib::plotCorMat(cErr, order = 'hclust', gPars=gPars)
 dev.off()
 ###
 
-# Fig. 9 ####
+# Fig. II-6 ####
 ifig =1
 png(file=paste0(figRepo,caseName,'_compareECDF2.png'),
     width=gPars$reso,height=gPars$reso)
@@ -171,7 +171,7 @@ ErrViewLib::plotDeltaCDF(
 dev.off()
 ####
 
-# Fig. 10 ####
+# Fig. II-7 ####
 png(
   file = paste0(figRepo, caseName,'_SIPHeatmap.png'),
   width = 13/12*gPars$reso,
@@ -181,7 +181,7 @@ ErrViewLib::plotSIPMat(statBS$sip, gPars = gPars)
 dev.off()
 ###
 
-# Fig. 11 ####
+# Fig. II-8 ####
 ifig = 0
 for (score in c('mue','q95hd','msip'))
   for (type in c('levels','ci')[1]) {

diff --git a/analysis/CAL2019.R b/analysis/CAL2019.R
@@ -60,7 +60,7 @@ sink()
 
 # Figures ####
 
-# Fig. 14 ####
+# Fig. II-11 ####
 # Selection of Delta CDF figs
 dfas = unique(sapply(methList,function(x) strsplit(x,'-D')[[1]][1]))
 
@@ -85,7 +85,7 @@ for(dfa in dfas[c(4,5,10)]) {
 }
 ###
 
-# Fig. 15 ####
+# Fig. II-12 ####
 # D4-ATM and D3
 sel1 = sort(c(seq(1,ncol(Errors),by=3),seq(3,ncol(Errors),by=3)))
 ifig = 0

diff --git a/analysis/DAS2019.R b/analysis/DAS2019.R
@@ -76,20 +76,9 @@ sink()
 
 # Figures ####
 
-# Fig. 19 ####
-png(filename = paste0(figRepo,caseName,'_ParPlot.png'),
-    width=reso,height=reso)
-ErrViewLib::plotParallel(
-  Errors,
-  rescale = TRUE,
-  labels = systems,
-  outliers = 'no',
-  lab.thresh = 1,
-  gPars=gPars)
-dev.off()
-###
 
-# Fig. 20 ####
+
+# Fig. II-16 ####
 ifig=1
 png(
   file = paste0(figRepo, caseName,'_CorrMat_Errors_Spearman.png'),
@@ -173,7 +162,21 @@ ErrViewLib::plotCorMat(
 dev.off()
 ###
 
-# Fig. 21 ####
+# Fig. II-17 ####
+png(filename = paste0(figRepo,caseName,'_ParPlot.png'),
+    width=reso,height=reso)
+ErrViewLib::plotParallel(
+  Errors,
+  rescale = TRUE,
+  labels = systems,
+  outliers = 'no',
+  outLabCex = 3,
+  lab.thresh = 1,
+  gPars=gPars)
+dev.off()
+###
+
+# Fig. II-18 ####
 ifig=1
 png(
   file = paste0(figRepo, caseName,'_SIPHeatmap_Pruned.png'),
@@ -209,7 +212,7 @@ ErrViewLib::plotDeltaCDF(
 dev.off()
 ###
 
-# Fig. 22 ####
+# Fig. II-19 ####
 ifig = 0
 for (score in c('mue','q95hd','msip'))
   for (type in c('levels','ci')[1]) {

diff --git a/analysis/JEN2018.R b/analysis/JEN2018.R
@@ -50,7 +50,7 @@ sink()
 
 # Figures ####
 
-# Fig. 16 ####
+# Fig. II-13 ####
 ifig=1
 png(
   file = paste0(figRepo, caseName,'_CorrMat_Errors_Spearman.png'),
@@ -94,7 +94,7 @@ ErrViewLib::plotCorMat(
 dev.off()
 ###
 
-# Fig. 17 ####
+# Fig. II-14 ####
 ifig=1
 png(file=paste0(figRepo,caseName,'_compareECDF.png'),
     width=gPars$reso,height=gPars$reso)
@@ -146,7 +146,7 @@ ErrViewLib::plotDeltaCDF(
 dev.off()
 ###
 
-# Fig. 18 ####
+# Fig. II-15 ####
 ifig = 0
 for (score in c('mue','q95hd','msip'))
   for (type in c('levels','ci')[1]) {

diff --git a/analysis/NAR2019.R b/analysis/NAR2019.R
@@ -54,7 +54,7 @@ sink()
 
 # Figures ####
 
-# Fig. 12 ####
+# Fig. II-9 ####
 cex.lab= 1.25
 ifig=1
 png(
@@ -102,7 +102,7 @@ ErrViewLib::plotCorMat(
 dev.off()
 ###
 
-# Fig. 13 ####
+# Fig. II-10 ####
 ifig=1
 png(file=paste0(figRepo,caseName,'_compareECDF.png'),
     width=gPars$reso,height=gPars$reso)

diff --git a/analysis/PER2018.R b/analysis/PER2018.R
@@ -33,7 +33,6 @@ gParsExt$cols     = colsExt
 gParsExt$cols_tr  = colsExt_tr
 gParsExt$cols_tr2 = colsExt_tr2
 
-
 # Generate stats ####
 
 statBS = ErrViewLib::estBS1(Errors,props = c("mue", "q95hd"))
@@ -55,7 +54,7 @@ sink()
 
 # Figures ####
 
-# Fig 2 ####
+# Fig. II-2 ####
 png(
   file = paste0(figRepo, caseName,'_SIPHeatmap.png'),
   width = 13/12*gPars$reso,
@@ -65,54 +64,8 @@ ErrViewLib::plotSIPMat(statBS$sip, gPars = gPars)
 dev.off()
 
 ###
-# Figs 4 and 7 ####
-ifig=0
-gParLoc = gPars
-for (score in c('mue'))
-  for (type in c('levels','ci')) {
-    png(
-      file = paste0(figRepo, caseName,'_figRanks_',score,'_',type,'.png'),
-      width = 1.5*gPars$reso,
-      height = 1.5*gPars$reso
-    )
-    ifig = ifig + 1
-    cex.lab = 1
-    if(type == 'ci'){
-      cex.lab = 1.1
-      gParLoc$cex = 1.2*gPars$cex
-    }
-    ErrViewLib::plotRankMat(
-      E = Errors,
-      score = score,
-      type = type,
-      label = ifig,
-      cex.lab = cex.lab,
-      gPars = gParLoc
-    )
-    dev.off()
-  }
-
-ifig=0
-for (score in c('q95hd','msip'))
-  for (type in c('levels')) {
-    png(
-      file = paste0(figRepo, caseName,'_figRanks_',score,'_',type,'.png'),
-      width = 1.5*gPars$reso,
-      height = 1.5*gPars$reso
-    )
-    ifig = ifig + 1
-    ErrViewLib::plotRankMat(
-      E = Errors,
-      score = score,
-      type = type,
-      label = ifig,
-      gPars = gPars
-    )
-    dev.off()
-  }
-###
 
-# Figs 4 SPLIT ####
+# Fig. II-4 ####
 ifig=0
 gParLoc = gPars
 for (score in c('mue','q95hd','msip'))
@@ -140,7 +93,7 @@ for (score in c('mue','q95hd','msip'))
   }
 ###
 
-# Fig. 5 ####
+# Fig. II-1 ####
 cex.lab = 1.25
 png(
   file = paste0(figRepo, caseName,'_CorrMat_Errors_Spearman.png'),
@@ -208,7 +161,7 @@ h = hist(X[lower.tri(X)],breaks = seq(-1.1,1.1,by=0.2),
 dev.off()
 ###
 
-# Fig. 6 ####
+# Fig. II-3 ####
 ifig =1
 png(file=paste0(figRepo,caseName,'_compareECDF.png'),
     width=gPars$reso,height=gPars$reso)

diff --git a/analysis/THA2015.R b/analysis/THA2015.R
@@ -93,7 +93,7 @@ sink()
 
 # Figures ####
 cex.lab = 1.0
-# Fig. 23 ####
+# Fig. II-20 ####
 ifig = 1
 png(file = paste0(figRepo, caseName,'_CorrMat_Errors.png'),
     width =  1.5*gPars$reso,
@@ -175,7 +175,7 @@ ErrViewLib::plotCorMat(
 dev.off()
 ###
 
-# Fig.25 ####
+# Fig. II-22 ####
 sel = c(1,2,4,7)
 ifig = 1
 png(file=paste0(figRepo,caseName,'_compareECDF_Pruned.png'),
@@ -207,7 +207,7 @@ ErrViewLib::plotUncEcdf(
 dev.off()
 ###
 
-# Fig. 26(a) ####
+# Fig. II-23(a) ####
 ifig = 1
 png(file = paste0(figRepo, caseName,'_SIPHeatmap_Pruned.png'),
     width =  13/12*gPars$reso,
@@ -217,7 +217,7 @@ dev.off()
 ###
 
 
-# Fig. 27 top-middle ####
+# Fig. II-24-(a-f) ####
 ifig = 0
 for (score in c('mue','q95hd','msip'))
   for (type in c('levels','ci')[1]) {

diff --git a/analysis/WU2015.R b/analysis/WU2015.R
@@ -60,7 +60,7 @@ sink()
 
 # Figures ####
 
-# Fig. 1 ####
+# Fig. I-1 ####
 cex.lab = 1.0
 ifig = 1
 png(file = paste0(figRepo, caseName,'_CorrMat_Data_Spearman.png'),
@@ -87,7 +87,7 @@ ErrViewLib::plotCorMat(
   gPars = gPars)
 dev.off()
 
-# Fig. 24 ####
+# Fig. II-21 ####
 cex.lab=1.0
 ifig = 1
 png(file = paste0(figRepo, caseName,'_CorrMat_Errors_Spearman.png'),
@@ -131,7 +131,7 @@ ErrViewLib::plotCorMat(
 dev.off()
 ###
 
-# Fig. 26(b) ####
+# Fig. II-23(b) ####
 png(
   file = paste0(figRepo, caseName,'_SIPHeatmap.png'),
   width =  13/12*gPars$reso,
@@ -143,7 +143,7 @@ ErrViewLib::plotSIPMat(statBS$sip,
 dev.off()
 ###
 
-# Fig. 27 bottom ####
+# Fig. II-24(g-i) ####
 cex.lab=1
 ifig = 6
 for (score in c('mue','q95hd','msip'))

diff --git a/analysis/ZAS2019.R b/analysis/ZAS2019.R
@@ -60,7 +60,7 @@ sink()
 
 # Figures ####
 
-# Fig. 28 ####
+# Fig. II-25 ####
 cex.lab = 1.0
 ifig=1
 png(
@@ -108,7 +108,7 @@ ErrViewLib::plotCorMat(
 dev.off()
 ###
 
-# Fig. 29 ####
+# Fig. II-26 ####
 ifig=1
 png(file=paste0(figRepo,caseName,'_compareECDF.png'),
     width= gPars$reso,height= gPars$reso)