Merge pull request #107 from IOHprofiler/EAF_Plots

[1.8.0] EAF-based plots

.github/workflows/R-CMD-check.yaml

@@ -22,8 +22,8 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: windows-latest, r: 'release'}
-          - {os: macOS-latest, r: 'release'}
+          - {os: windows-latest, r: '4.2'}
+          - {os: macOS-10.15, r: 'release'}
           - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
           - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
 

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: IOHanalyzer
 Type: Package
 Title: Data Analysis Part of 'IOHprofiler'
-Version: 0.1.7.4
+Version: 0.1.8.2
 Maintainer: Diederick Vermetten <d.l.vermetten@liacs.leidenuniv.nl>
 Authors@R: c(
     person("Hao", "Wang", email = "h.wang@liacs.leidenuniv.nl", role = "aut", comment = c(ORCID = "0000-0002-4933-5181")),
@@ -17,7 +17,7 @@ Description: The data analysis module for the Iterative Optimization Heuristics
 License: BSD_3_clause + file LICENSE
 Encoding: UTF-8
 LazyData: true
-URL: http://iohprofiler.liacs.nl, https://github.com/IOHprofiler/IOHAnalyzer
+URL: https://iohanalyzer.liacs.nl, https://github.com/IOHprofiler/IOHAnalyzer
 BugReports: https://github.com/IOHprofiler/IOHAnalyzer/issues
 Imports: 
   magrittr,
@@ -34,9 +34,11 @@ Imports:
   httr,
   knitr,
   methods,
-  rjson
+  rjson,
+  eaf,
+  viridis
 LinkingTo: Rcpp
-SystemRequirements: C++11
+SystemRequirements: C++
 RoxygenNote: 7.1.2
 Suggests: 
   Rcpp,

NAMESPACE

@@ -111,7 +111,11 @@ export(fast_RT_samples)
 export(generate_data.AUC)
 export(generate_data.Aggr)
 export(generate_data.CDP)
+export(generate_data.EAF)
+export(generate_data.EAF_Difference)
+export(generate_data.EAF_diff_Approximate)
 export(generate_data.ECDF)
+export(generate_data.ECDF_From_EAF)
 export(generate_data.ECDF_raw)
 export(generate_data.Heatmaps)
 export(generate_data.PMF)
@@ -161,6 +165,8 @@ export(glicko2_ranking)
 export(max_ERTs)
 export(mean_FVs)
 export(pairwise.test)
+export(plot_eaf_data)
+export(plot_eaf_differences)
 export(plot_general_data)
 export(read_IOH_v1plus)
 export(read_index_file)
@@ -183,15 +189,20 @@ importFrom(data.table,copy)
 importFrom(data.table,data.table)
 importFrom(data.table,frank)
 importFrom(data.table,fread)
+importFrom(data.table,getDTthreads)
 importFrom(data.table,is.data.table)
 importFrom(data.table,melt)
 importFrom(data.table,rbindlist)
 importFrom(data.table,setDT)
+importFrom(data.table,setDTthreads)
 importFrom(data.table,setnames)
+importFrom(data.table,setorder)
 importFrom(data.table,setorderv)
 importFrom(data.table,transpose)
 importFrom(dplyr,"%>%")
 importFrom(dplyr,mutate)
+importFrom(eaf,eafdiff)
+importFrom(eaf,eafs)
 importFrom(ggplot2,aes)
 importFrom(ggplot2,element_text)
 importFrom(ggplot2,facet_wrap)
@@ -226,8 +237,12 @@ importFrom(magrittr,set_names)
 importFrom(magrittr,set_rownames)
 importFrom(methods,hasArg)
 importFrom(plotly,add_annotations)
+importFrom(plotly,add_contour)
+importFrom(plotly,add_polygons)
 importFrom(plotly,add_trace)
 importFrom(plotly,animation_opts)
+importFrom(plotly,colorbar)
+importFrom(plotly,hide_colorbar)
 importFrom(plotly,layout)
 importFrom(plotly,orca)
 importFrom(plotly,plot_ly)
@@ -254,10 +269,12 @@ importFrom(stringi,stri_locate_all)
 importFrom(stringi,stri_rand_strings)
 importFrom(stringi,stri_replace)
 importFrom(stringi,stri_sub)
+importFrom(utils,compareVersion)
 importFrom(utils,data)
 importFrom(utils,head)
 importFrom(utils,read.csv)
 importFrom(utils,tail)
 importFrom(utils,type.convert)
 importFrom(utils,write.csv)
+importFrom(viridis,viridis)
 useDynLib(IOHanalyzer)

R/DataSet.R

@@ -72,24 +72,16 @@ DataSet <- function(info, verbose = F, maximization = NULL, format = IOHprofiler
     tdatFile <- file.path(path, paste0(datBaseName, '.tdat'))
     cdatFile <- file.path(path, paste0(datBaseName, '.cdat'))
 
-    # NOTE: preference on data file for the alignment by RT: cdat > tdat > dat
-    if (file.exists(cdatFile))
-      fvFile <- cdatFile
-    else if (file.exists(tdatFile))
-      fvFile <- tdatFile
-    else if (file.exists(datFile))
-      fvFile <- datFile
-    else
-      stop('No datafiles found, please verify the integrity of the chosen files')
-
-    # NOTE: preference on data file for the alignment by FV: dat > tdat > cdat
+    # NOTE: preference on data file from coco: dat > tdat > cdat
     if (file.exists(datFile))
       rtFile <- datFile
     else if (file.exists(tdatFile))
       rtFile <- tdatFile
     else if (file.exists(cdatFile))
       # TODO: perhaps turn on `subsampling` here as this would take quite some time
       rtFile <- cdatFile
+    else
+      stop('No datafiles found, please verify the integrity of the chosen files')
 
     read_raw <- switch(
       format,
@@ -101,22 +93,21 @@ DataSet <- function(info, verbose = F, maximization = NULL, format = IOHprofiler
     )
 
     RT_raw <- read_raw(rtFile, subsampling)
-    FV_raw <- read_raw(fvFile, subsampling)
 
     if (is.null(maximization)) {
       if (verbose)
         warning("Did not find maximization / minimization, auto-detecting based on
                 function value progression")
       # TODO: idxTarget should be set depending on the data format
       idxTarget <- 2
-      cond <- unique(lapply(FV_raw, function(FV) FV[1, idxTarget] >= FV[nrow(FV), idxTarget]))
+      cond <- unique(lapply(RT_raw, function(FV) FV[1, idxTarget] >= FV[nrow(FV), idxTarget]))
       if (length(cond) > 1)
         stop('The detected maximization differs in multiple runs')
       maximization <- cond
     }
 
     RT <- align_running_time(RT_raw, format = format, maximization = maximization)
-    FV <- align_function_value(FV_raw, format = format)
+    FV <- align_function_value(RT_raw, format = format)
 
     PAR <- list(
       'by_FV' = RT[names(RT) != 'RT'],
@@ -148,9 +139,9 @@ DataSet <- function(info, verbose = F, maximization = NULL, format = IOHprofiler
     # TODO: clean up these if-statements: Function to set idxTarget and n_data_column?
     # `idxTarget` is a global variable?
     if (format == TWO_COL)
-      finalFV <- set_names(sapply(FV_raw, function(d) d[nrow(d), idxTarget - 1]), NULL)
+      finalFV <- set_names(sapply(RT_raw, function(d) d[nrow(d), idxTarget - 1]), NULL)
     else
-      finalFV <- set_names(sapply(FV_raw, function(d) d[nrow(d), idxTarget]), NULL)
+      finalFV <- set_names(sapply(RT_raw, function(d) d[nrow(d), idxTarget]), NULL)
 
     if (any(finalFV != info$finalFV) && verbose)
       warning('Inconsitent finalFvalue in *.info file and *.dat file')
@@ -168,9 +159,9 @@ DataSet <- function(info, verbose = F, maximization = NULL, format = IOHprofiler
                    maximization = maximization, suite = suite, ID = info$algId))
     )
     if (isTRUE(info$constrained) || full_sampling) {
-      FV_raw_mat <- matrix(nrow = nrow(FV), ncol = length(FV_raw))
-      for (idx in seq(length(FV_raw))) {
-        FV_raw_mat[,idx] = FV_raw[[idx]][,2]
+      FV_raw_mat <- matrix(nrow = nrow(FV), ncol = length(RT_raw))
+      for (idx in seq(length(RT_raw))) {
+        FV_raw_mat[,idx] = RT_raw[[idx]][,2]
       }
       temp$FV_raw_mat <- FV_raw_mat
       attr(temp, 'contains_full_FV') <- TRUE