├── .gitignore ├── GitHub_R_commands.Rproj ├── check_for_2_approaches.R ├── data ├── top_100_functions.jpeg ├── top_100_packages.csv └── top_2000_functions.csv ├── not_installed_packages.R └── top_functions.R /.gitignore: -------------------------------------------------------------------------------- 1 | .Rproj.user 2 | .Rhistory 3 | .RData 4 | .Ruserdata 5 | -------------------------------------------------------------------------------- /GitHub_R_commands.Rproj: -------------------------------------------------------------------------------- 1 | Version: 1.0 2 | 3 | RestoreWorkspace: Default 4 | SaveWorkspace: Default 5 | AlwaysSaveHistory: Default 6 | 7 | EnableCodeIndexing: Yes 8 | UseSpacesForTab: Yes 9 | NumSpacesForTab: 2 10 | Encoding: UTF-8 11 | 12 | RnwWeave: Sweave 13 | LaTeX: pdfLaTeX 14 | -------------------------------------------------------------------------------- /check_for_2_approaches.R: -------------------------------------------------------------------------------- 1 | library(readr) 2 | library(magrittr) 3 | library(tidyr) 4 | library(dplyr) 5 | library(stringr) 6 | 7 | content_to_check <- read_csv("data/content_clear_1.csv") 8 | 9 | #checking for 2 approaches 10 | content_trial_1 <- content_to_check[1:10000,] 11 | 12 | #first, without a bracket after 13 | 14 | #cheking max length of a function - result is 44 15 | max(nchar(functions$functions)) 16 | 17 | content_trial_1$content <- str_extract_all(content_trial_1$content, 18 | "[a-zA-Z][a-zA-Z0-9_.]{0,43}") 19 | 20 | content_trial_1 <- content_trial_1 %>% 21 | unnest(content) %>% 22 | group_by(library, content) %>% 23 | summarise(count = n()) %>% 24 | inner_join(functions, by = c("library" = "V1", "content" = "functions")) %>% 25 | arrange(desc(count)) %>% 26 | head(100) 27 | 28 | #2nd approach 29 | 30 | content_trial_2 <- content_to_check[1:10000,] 31 | 32 | 33 | content_trial_2$content <- str_extract_all(content_trial_2$content, 34 | "([a-zA-Z][a-zA-Z0-9_.]{0,43}[(])|([a-zA-Z][a-zA-Z0-9_.]{0,43}[ ][(])") 35 | 36 | content_trial_2 <- content_trial_2 %>% 37 | unnest(content) 38 | 39 | content_trial_2$content <- str_replace_all(content_trial_2$content, c(" " = "", "[(]" = "")) 40 | 41 | content_trial_2 <- content_trial_2 %>% 42 | group_by(library, content) %>% 43 | summarise(count = n()) %>% 44 | inner_join(functions, by = c("library" = "V1", "content" = "functions")) %>% 45 | arrange(desc(count)) %>% 46 | head(100) 47 | 48 | 49 | 50 | difference <- content_trial_1 %>% 51 | full_join(content_trial_2, by = c("library", "content")) %>% 52 | mutate(difference = round((count.x - count.y)/count.y,2)) %>% 53 | filter(difference > 0.2) %>% 54 | arrange(desc(difference)) 55 | 56 | colnames(difference) <- c("library", "function", "Count 1 approach", "Count 2 approach", "Difference") 57 | 58 | difference %>% 59 | View() 60 | 61 | #checking other 10000 rows due to unexpected variations with h2o package 62 | 63 | 64 | content_test_1 <- content_to_check[10000:20000,] 65 | 66 | #first, without a bracket after 67 | 68 | 69 | 70 | content_test_1$content <- str_extract_all(content_test_1$content, 71 | "[a-zA-Z][a-zA-Z0-9_.]{0,43}") 72 | 73 | content_test_1 <- content_test_1 %>% 74 | unnest(content) %>% 75 | group_by(library, content) %>% 76 | summarise(count = n()) %>% 77 | inner_join(functions, by = c("library" = "V1", "content" = "functions")) %>% 78 | arrange(desc(count)) %>% 79 | head(100) 80 | 81 | #2nd approach 82 | 83 | content_test_2 <- content_to_check[10000:20000,] 84 | 85 | 86 | content_test_2$content <- str_extract_all(content_test_2$content, 87 | "([a-zA-Z][a-zA-Z0-9_.]{0,43}[(])|([a-zA-Z][a-zA-Z0-9_.]{0,43}[ ][(])") 88 | 89 | content_test_2 <- content_test_2 %>% 90 | unnest(content) 91 | 92 | content_test_2$content <- str_replace_all(content_test_2$content, c(" " = "", "[(]" = "")) 93 | 94 | content_test_2 <- content_test_2 %>% 95 | group_by(library, content) %>% 96 | summarise(count = n()) %>% 97 | inner_join(functions, by = c("library" = "V1", "content" = "functions")) %>% 98 | arrange(desc(count)) %>% 99 | head(100) 100 | 101 | 102 | 103 | difference2 <- content_test_1 %>% 104 | full_join(content_test_2, by = c("library", "content")) %>% 105 | mutate(difference = round((count.x - count.y)/count.y,2)) %>% 106 | filter(difference > 0.2) %>% 107 | arrange(desc(difference)) 108 | 109 | colnames(difference2) <- c("library", "function", "Count 1 approach", "Count 2 approach", "Difference") 110 | 111 | difference2 %>% 112 | View() 113 | -------------------------------------------------------------------------------- /data/top_100_functions.jpeg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/v-kozhevnikov/GitHub_R_commands/6bdbbbad9dd4c1c385b1ee2ae475388b0418ea04/data/top_100_functions.jpeg -------------------------------------------------------------------------------- /data/top_100_packages.csv: -------------------------------------------------------------------------------- 1 | lib_content,count 2 | ggplot2,18033 3 | dplyr,11216 4 | plyr,6126 5 | shiny,5711 6 | data.table,5541 7 | reshape2,4410 8 | stringr,3762 9 | RColorBrewer,3289 10 | knitr,3161 11 | tidyr,3098 12 | testthat,2901 13 | scales,2783 14 | MASS,2685 15 | gridExtra,2586 16 | grid,2435 17 | rgl,2295 18 | lubridate,2157 19 | Matrix,2154 20 | rgdal,2100 21 | caret,2092 22 | igraph,2090 23 | raster,2086 24 | lattice,2054 25 | magrittr,1939 26 | parallel,1931 27 | h2o,1867 28 | sp,1727 29 | devtools,1703 30 | readr,1693 31 | jsonlite,1553 32 | tidyverse,1488 33 | Hmisc,1465 34 | RCurl,1451 35 | randomForest,1447 36 | XML,1373 37 | foreach,1309 38 | maptools,1260 39 | reshape,1233 40 | car,1222 41 | OpenMx,1213 42 | doParallel,1202 43 | xlsx,1112 44 | methods,1083 45 | e1071,1051 46 | gplots,1044 47 | hamcrest,1018 48 | foreign,990 49 | fields,981 50 | zoo,955 51 | tm,942 52 | ape,930 53 | mvtnorm,897 54 | maps,875 55 | lme4,869 56 | doMC,866 57 | RMySQL,822 58 | httr,818 59 | ggmap,786 60 | rjson,757 61 | glmnet,755 62 | plotly,754 63 | rpart,751 64 | optparse,750 65 | leaflet,732 66 | ggthemes,723 67 | xtable,719 68 | vegan,717 69 | DT,702 70 | Rcpp,700 71 | survival,682 72 | rgeos,669 73 | readxl,656 74 | psych,646 75 | gdata,627 76 | doBy,618 77 | stats,611 78 | Cairo,610 79 | oce,605 80 | boot,598 81 | GenomicRanges,597 82 | plotrix,589 83 | RPostgreSQL,581 84 | limma,565 85 | sqldf,542 86 | nlme,541 87 | ROCR,537 88 | xgboost,533 89 | tools,517 90 | pls,508 91 | cluster,502 92 | rstan,499 93 | xts,498 94 | DESeq2,492 95 | microbenchmark,492 96 | RODBC,487 97 | quantmod,485 98 | RSQLite,479 99 | shinydashboard,476 100 | cowplot,475 101 | rvest,474 102 | -------------------------------------------------------------------------------- /data/top_2000_functions.csv: 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shiny,sidebarPanel,2247 502 | base,local,2240 503 | base,quit,2240 504 | shiny,renderText,2233 505 | lme4,glmer,2222 506 | h2o,h2o.cbind,2215 507 | base,asNamespace,2204 508 | shiny,actionButton,2197 509 | base,conditionMessage,2193 510 | gridExtra,grid.arrange,2193 511 | Matrix,which,2187 512 | raster,t,2183 513 | tidyr,gather,2180 514 | plyr,dlply,2175 515 | OpenMx,mxEval,2168 516 | shiny,observe,2164 517 | base,trunc,2160 518 | shiny,fluidPage,2147 519 | knitr,knit,2116 520 | base,NextMethod,2115 521 | dplyr,bind_rows,2113 522 | caret,trainControl,2101 523 | base,save.image,2070 524 | maps,map,2066 525 | base,topenv,2053 526 | shiny,shinyServer,2047 527 | base,replace,2043 528 | base,iconv,2039 529 | base,complex,2028 530 | shiny,observeEvent,2023 531 | base,rep_len,2015 532 | base,as.array,2012 533 | base,lower.tri,2011 534 | readr,read_csv,2005 535 | Hmisc,binconf,2004 536 | shiny,checkboxInput,2002 537 | graphics,curve,1993 538 | raster,hist,1984 539 | nlme,corARMA,1972 540 | graphics,legend,1969 541 | base,lgamma,1958 542 | shiny,shinyUI,1951 543 | grid,gpar,1947 544 | base,within,1943 545 | h2o,apply,1943 546 | randomForest,randomForest,1937 547 | dplyr,desc,1928 548 | igraph,degree,1926 549 | ROCR,plot,1909 550 | base,regmatches,1901 551 | shiny,icon,1901 552 | sp,coordinates,1900 553 | base,emptyenv,1899 554 | raster,merge,1888 555 | shiny,hr,1887 556 | rpart,rpart,1884 557 | base,objects,1870 558 | raster,text,1866 559 | base,lengths,1863 560 | h2o,is.factor,1858 561 | fields,rdist,1855 562 | XML,newXMLNode,1851 563 | base,system2,1848 564 | base,trimws,1846 565 | base,call,1844 566 | base,row,1832 567 | base,col,1831 568 | sp,CRS,1831 569 | OpenMx,mxData,1823 570 | knitr,knit2html,1822 571 | raster,levels,1804 572 | parallel,clusterExport,1803 573 | base,det,1783 574 | h2o,h2o.dct,1776 575 | ggplot2,scale_y_discrete,1746 576 | shinydashboard,box,1741 577 | base,upper.tri,1739 578 | data.table,rbindlist,1733 579 | base,as.raw,1732 580 | shiny,h5,1727 581 | base,cbind.data.frame,1726 582 | base,is.call,1723 583 | dplyr,inner_join,1719 584 | grid,pushViewport,1719 585 | base,textConnection,1709 586 | h2o,h2o.createFrame,1709 587 | base,find.package,1697 588 | shiny,textInput,1697 589 | stats,rnorm,1696 590 | base,oldClass,1668 591 | h2o,h2o.table,1665 592 | base,charToRaw,1654 593 | lattice,strip.custom,1654 594 | shiny,verbatimTextOutput,1651 595 | ROCR,performance,1638 596 | shiny,renderDataTable,1634 597 | base,baseenv,1633 598 | base,make.names,1633 599 | h2o,h2o.interaction,1632 600 | h2o,h2o.levels,1628 601 | graphics,mtext,1609 602 | raster,subset,1602 603 | devtools,install_github,1598 604 | shiny,dataTableOutput,1597 605 | ggplot2,scale_size,1588 606 | shiny,need,1584 607 | gridExtra,tableGrob,1583 608 | plyr,summarise,1573 609 | base,ordered,1567 610 | graphics,points,1557 611 | plotly,toRGB,1551 612 | base,path.expand,1542 613 | ape,read.dna,1536 614 | shiny,helpText,1532 615 | base,acos,1530 616 | shiny,textOutput,1529 617 | grid,grid.newpage,1528 618 | shiny,sidebarLayout,1520 619 | reshape2,dcast,1514 620 | caret,confusionMatrix,1512 621 | base,startsWith,1510 622 | reshape,melt,1508 623 | Matrix,mean,1507 624 | Matrix,readMM,1506 625 | plyr,rename,1504 626 | parallel,parLapply,1500 627 | raster,extent,1493 628 | raster,stack,1492 629 | base,is.double,1489 630 | XML,getNodeSet,1477 631 | ggplot2,geom_violin,1468 632 | stringr,str_replace,1465 633 | raster,projectRaster,1463 634 | shiny,radioButtons,1461 635 | base,svd,1452 636 | base,labels,1448 637 | base,is.environment,1441 638 | base,file.rename,1439 639 | base,qr,1434 640 | base,writeBin,1434 641 | shiny,titlePanel,1431 642 | igraph,vcount,1428 643 | base,sample.int,1427 644 | tidyr,spread,1421 645 | plyr,l_ply,1419 646 | base,match.fun,1411 647 | base,anyDuplicated,1401 648 | base,sys.call,1400 649 | base,Sys.setlocale,1399 650 | base,Encoding,1386 651 | shiny,downloadHandler,1375 652 | base,parent.env,1372 653 | base,aperm,1363 654 | h2o,is.h2o,1350 655 | ape,unroot,1347 656 | methods,representation,1344 657 | raster,match,1344 658 | plyr,join,1342 659 | base,nargs,1339 660 | h2o,h2o.confusionMatrix,1335 661 | shiny,wellPanel,1335 662 | ape,write.tree,1328 663 | base,noquote,1326 664 | shiny,downloadButton,1322 665 | base,dput,1317 666 | dplyr,distinct,1317 667 | RCurl,getURL,1314 668 | e1071,svm,1312 669 | testthat,test_check,1312 670 | base,log1p,1307 671 | sp,summary,1300 672 | base,gl,1292 673 | base,as.single,1289 674 | base,Recall,1287 675 | parallel,clusterEvalQ,1286 676 | base,jitter,1283 677 | lubridate,year,1281 678 | base,is.name,1278 679 | base,gamma,1271 680 | base,choose,1264 681 | ggplot2,geom_rect,1261 682 | dplyr,tbl_df,1260 683 | gplots,heatmap.2,1249 684 | raster,as.factor,1249 685 | dplyr,count,1248 686 | raster,ncol,1236 687 | base,sinpi,1230 688 | grid,grid.layout,1225 689 | Matrix,Matrix,1220 690 | base,list.dirs,1217 691 | sp,proj4string,1211 692 | h2o,h2o.deeplearning,1209 693 | h2o,h2o.gainsLift,1208 694 | base,all.vars,1198 695 | raster,extract,1195 696 | rvest,html_nodes,1194 697 | base,url,1190 698 | Matrix,writeMM,1190 699 | base,raw,1177 700 | shiny,renderTable,1173 701 | ggplot2,scale_fill_gradientn,1171 702 | stringr,str_c,1171 703 | plotly,add_trace,1170 704 | base,is.primitive,1156 705 | nlme,intervals,1156 706 | raster,readIniFile,1147 707 | sp,merge,1146 708 | shiny,tabsetPanel,1144 709 | dplyr,starts_with,1134 710 | base,gzfile,1130 711 | h2o,h2o.runif,1129 712 | stringr,str_trim,1128 713 | graphics,segments,1122 714 | foreign,read.dbf,1120 715 | ape,write.dna,1118 716 | base,as.expression,1112 717 | base,is.atomic,1111 718 | ggplot2,theme_minimal,1110 719 | stats,runif,1102 720 | base,rawToChar,1096 721 | plotly,mutate,1094 722 | base,atan2,1092 723 | base,norm,1090 724 | cowplot,ggsave,1089 725 | ggplot2,theme_set,1087 726 | shiny,renderPrint,1086 727 | methods,slot,1084 728 | ROCR,prediction,1080 729 | doBy,summaryBy,1078 730 | methods,signature,1065 731 | car,Anova,1061 732 | raster,zoom,1057 733 | testthat,context,1054 734 | methods,getClass,1050 735 | zoo,as.Date,1049 736 | ggplot2,scale_fill_discrete,1044 737 | Matrix,crossprod,1040 738 | ggplot2,expand_limits,1039 739 | ggplot2,ggplot_build,1039 740 | base,kronecker,1038 741 | base,sys.parent,1035 742 | shiny,tableOutput,1035 743 | data.table,melt.data.table,1034 744 | MASS,mvrnorm,1030 745 | shiny,validate,1028 746 | shiny,updateNumericInput,1025 747 | xtable,xtable,1023 748 | base,atan,1022 749 | base,eval.parent,1017 750 | raster,calc,1015 751 | raster,quantile,1015 752 | caret,createDataPartition,1009 753 | base,findInterval,1002 754 | lattice,levelplot,994 755 | httr,content,993 756 | base,interaction,992 757 | dplyr,funs,991 758 | Matrix,solve,988 759 | lubridate,ymd,984 760 | base,Im,978 761 | lme4,fixef,976 762 | base,asin,968 763 | Matrix,all.equal,968 764 | h2o,round,965 765 | stringr,str_sub,965 766 | raster,values,962 767 | dplyr,intersect,959 768 | base,as.call,957 769 | base,open,955 770 | base,mget,953 771 | pls,plsr,950 772 | raster,as.matrix,942 773 | dplyr,setdiff,941 774 | base,rle,940 775 | lattice,panel.text,937 776 | base,prettyNum,932 777 | shiny,htmlOutput,932 778 | stringr,str_split,929 779 | OpenMx,mxFitFunctionML,926 780 | base,packageStartupMessage,922 781 | testthat,equals,921 782 | lattice,panel.xyplot,919 783 | Matrix,summary,917 784 | base,units,916 785 | igraph,ecount,916 786 | ggplot2,margin,915 787 | sp,spplot,915 788 | base,warnings,913 789 | lattice,bwplot,913 790 | base,isS4,909 791 | base,debug,905 792 | shiny,shinyApp,904 793 | stringr,str_extract,902 794 | shiny,img,900 795 | tm,Corpus,899 796 | raster,crop,898 797 | testthat,expect_false,894 798 | grid,grid.draw,892 799 | base,sys.frame,891 800 | base,force,890 801 | Matrix,format,887 802 | base,sort.list,883 803 | igraph,graph.data.frame,882 804 | httr,GET,879 805 | methods,getClassDef,879 806 | base,dyn.load,875 807 | ggplot2,scale_size_manual,874 808 | base,tabulate,873 809 | plyr,mapvalues,872 810 | leaflet,leaflet,870 811 | h2o,h2o.rm,868 812 | base,Sys.which,866 813 | grid,grid.text,866 814 | readxl,read_excel,865 815 | sp,spTransform,865 816 | data.table,setkeyv,861 817 | base,sequence,855 818 | methods,setGeneric,853 819 | methods,as,849 820 | shiny,h2,848 821 | base,tan,845 822 | base,readChar,840 823 | dplyr,tbl,835 824 | lattice,splom,826 825 | OpenMx,omxCheckError,826 826 | base,chol2inv,825 827 | base,T,824 828 | base,Conj,821 829 | base,tanh,819 830 | base,alist,818 831 | shiny,updateSelectInput,813 832 | base,is.array,811 833 | OpenMx,omxCheckEquals,808 834 | base,as.symbol,804 835 | scales,rescale,803 836 | psych,describe,802 837 | survival,coxph,800 838 | gridExtra,arrangeGrob,798 839 | lme4,ranef,798 840 | tm,stopwords,791 841 | base,is.complex,789 842 | base,read.dcf,784 843 | h2o,h2o.predict,784 844 | base,setequal,783 845 | base,file.create,778 846 | tm,VectorSource,775 847 | dplyr,do,772 848 | base,loadNamespace,766 849 | ggplot2,scale_color_discrete,766 850 | data.table,setcolorder,759 851 | pls,R2,756 852 | mvtnorm,rmvnorm,755 853 | base,getNamespace,753 854 | base,Mod,752 855 | DT,renderDataTable,750 856 | lubridate,month,750 857 | base,F,744 858 | shiny,code,736 859 | igraph,graph.adjacency,734 860 | base,is.symbol,733 861 | base,simplify2array,732 862 | dplyr,slice,732 863 | h2o,sd,731 864 | ape,as.DNAbin,728 865 | h2o,h2o.match,726 866 | base,as.table,725 867 | h2o,h2o.merge,724 868 | base,rbind.data.frame,723 869 | base,bitwShiftR,722 870 | base,beta,721 871 | base,is.object,720 872 | dplyr,contains,719 873 | foreign,write.dbf,719 874 | OpenMx,mxOption,718 875 | h2o,cor,717 876 | base,file.choose,715 877 | jsonlite,toJSON,715 878 | methods,getGeneric,715 879 | base,bitwShiftL,711 880 | base,args,710 881 | car,vif,710 882 | ggplot2,ggplot_gtable,710 883 | h2o,signif,710 884 | ggplot2,geom_area,709 885 | base,getNamespaceInfo,708 886 | stats,predict,708 887 | base,capabilities,705 888 | ggplot2,scale_fill_gradient2,705 889 | Matrix,colSums,704 890 | optparse,OptionParser,704 891 | XML,xmlValue,704 892 | survival,survfit,703 893 | caret,varImp,702 894 | h2o,var,702 895 | ggplot2,fortify,700 896 | OpenMx,omxCheckTrue,698 897 | ggplot2,geom_raster,697 898 | knitr,kable,692 899 | base,is.expression,691 900 | optparse,parse_args,690 901 | ggplot2,geom_errorbarh,685 902 | shiny,span,682 903 | ggplot2,coord_fixed,679 904 | h2o,h2o.ifelse,677 905 | base,Vectorize,676 906 | base,cumprod,670 907 | stringr,str_split_fixed,667 908 | shinydashboard,menuItem,666 909 | base,package_version,661 910 | shiny,h6,660 911 | scales,alpha,658 912 | base,Sys.getlocale,657 913 | h2o,use.package,655 914 | ggplot2,ggplotGrob,651 915 | h2o,h2o.ls,651 916 | Matrix,rowSums,651 917 | tidyr,separate,651 918 | base,R.Version,645 919 | base,is.unsorted,643 920 | shiny,headerPanel,643 921 | ggplot2,stat_function,642 922 | methods,packageSlot,642 923 | shinydashboard,tabItem,642 924 | base,geterrmessage,641 925 | base,getRversion,641 926 | base,seek,641 927 | shiny,fileInput,640 928 | caret,postResample,639 929 | ggplot2,scale_linetype_manual,637 930 | graphics,hist,630 931 | rvest,html_text,629 932 | XML,xpathSApply,628 933 | base,pairlist,625 934 | methods,extends,625 935 | base,next,622 936 | h2o,h2o.splitFrame,622 937 | base,is.ordered,621 938 | tm,content_transformer,618 939 | dplyr,collect,617 940 | base,simpleError,616 941 | raster,head,615 942 | base,version,614 943 | plotrix,pyramid.plot,612 944 | base,list2env,610 945 | base,make.unique,610 946 | lattice,trellis.par.set,609 947 | raster,brick,609 948 | XML,source,607 949 | OpenMx,mxExpectationNormal,603 950 | base,ISOdate,600 951 | h2o,h2o.glm,600 952 | plyr,llply,600 953 | scales,date_format,600 954 | plotly,group_by,599 955 | ggplot2,arrow,598 956 | base,serialize,596 957 | XML,xmlAttrs,596 958 | shiny,reactiveValues,594 959 | ggplot2,coord_equal,593 960 | plotly,select,593 961 | dplyr,first,591 962 | h2o,h2o.insertMissingValues,587 963 | grid,textGrob,585 964 | lattice,panel.abline,582 965 | shiny,checkboxGroupInput,581 966 | base,loadedNamespaces,580 967 | dplyr,data_frame,579 968 | DT,dataTableOutput,579 969 | dplyr,select_,578 970 | base,months,577 971 | base,Sys.unsetenv,574 972 | base,isOpen,572 973 | XML,xmlTreeParse,569 974 | base,chartr,566 975 | base,isNamespace,562 976 | ape,base.freq,560 977 | dplyr,glimpse,558 978 | tm,DocumentTermMatrix,557 979 | base,file.access,556 980 | Matrix,diff,555 981 | parallel,mcmapply,555 982 | boot,boot,551 983 | base,RNGkind,548 984 | base,unserialize,547 985 | sp,SpatialPoints,545 986 | leaflet,addProviderTiles,544 987 | readr,write_csv,544 988 | base,pipe,541 989 | raster,rasterize,541 990 | testthat,expect_equivalent,541 991 | dplyr,full_join,539 992 | base,bitwAnd,537 993 | DT,datatable,537 994 | base,strtoi,533 995 | base,factorial,530 996 | fields,cover.design,528 997 | shiny,updateTextInput,528 998 | xlsx,write.xlsx,528 999 | base,mat.or.vec,526 1000 | base,Sys.getpid,526 1001 | base,withCallingHandlers,526 1002 | nlme,ACF,525 1003 | ggplot2,geom_step,524 1004 | graphics,matplot,523 1005 | base,max.col,522 1006 | h2o,h2o.getModel,520 1007 | base,as.numeric_version,511 1008 | cowplot,plot_grid,511 1009 | h2o,h2o.impute,510 1010 | h2o,h2o.rbind,509 1011 | zoo,zoo,504 1012 | base,sys.function,503 1013 | dplyr,n_distinct,503 1014 | ggthemes,theme_tufte,503 1015 | base,digamma,500 1016 | dplyr,group_by_,499 1017 | ggplot2,coord_map,499 1018 | plotly,arrange,499 1019 | base,as.data.frame.matrix,498 1020 | base,is.language,498 1021 | igraph,simplify,498 1022 | plyr,summarize,498 1023 | dplyr,ends_with,497 1024 | stats,poly,494 1025 | shiny,req,493 1026 | ggplot2,geom_linerange,492 1027 | graphics,axis,492 1028 | base,print.default,490 1029 | shiny,h1,490 1030 | h2o,h2o.mse,488 1031 | caret,getTrainPerf,486 1032 | sp,Polygons,484 1033 | dplyr,lag,483 1034 | lattice,densityplot,483 1035 | scales,date_breaks,483 1036 | methods,show,482 1037 | rgl,plot3d,481 1038 | ggplot2,scale_colour_discrete,478 1039 | caret,preProcess,477 1040 | Matrix,head,475 1041 | reshape,cast,471 1042 | base,endsWith,470 1043 | base,lockBinding,468 1044 | ggplot2,geom_curve,468 1045 | Hmisc,rcorr,467 1046 | Hmisc,describe,466 1047 | Matrix,Diagonal,466 1048 | base,weekdays,465 1049 | h2o,h2o.deepfeatures,465 1050 | lattice,panel.levelplot,465 1051 | base,parseNamespaceFile,463 1052 | base,regexec,460 1053 | lattice,barchart,460 1054 | graphics,boxplot,458 1055 | base,shell,457 1056 | data.table,dcast,457 1057 | plotly,summarise,457 1058 | XML,readHTMLTable,456 1059 | sp,Polygon,455 1060 | raster,aggregate,454 1061 | base,backsolve,453 1062 | base,invokeRestart,453 1063 | plotly,ggplotly,453 1064 | tm,TermDocumentMatrix,453 1065 | fields,quilt.plot,450 1066 | graphics,title,450 1067 | base,abbreviate,449 1068 | raster,projection,448 1069 | base,charmatch,445 1070 | base,zapsmall,444 1071 | shiny,withProgress,444 1072 | h2o,h2o.group_by,443 1073 | raster,image,443 1074 | raster,mask,443 1075 | base,unlockBinding,442 1076 | tidyr,extract,442 1077 | base,break,441 1078 | base,bindingIsLocked,440 1079 | base,data.class,440 1080 | base,rowsum,440 1081 | plotrix,draw.arc,440 1082 | shiny,selectizeInput,440 1083 | leaflet,addTiles,438 1084 | randomForest,importance,438 1085 | XML,htmlParse,438 1086 | base,getNamespaceName,437 1087 | xml2,xml_add_child,437 1088 | base,file.size,434 1089 | ape,ladderize,434 1090 | ape,dist.dna,432 1091 | h2o,h2o.getFutureModel,432 1092 | MASS,ginv,428 1093 | XML,saveXML,428 1094 | car,qqPlot,425 1095 | base,trace,424 1096 | h2o,h2o.ddply,421 1097 | rpart,prune,421 1098 | plyr,laply,419 1099 | igraph,get.edgelist,418 1100 | sp,bbox,418 1101 | h2o,year,417 1102 | base,as.complex,414 1103 | shiny,pageWithSidebar,414 1104 | sp,SpatialPolygons,414 1105 | shiny,eventReactive,413 1106 | nlme,fixef,411 1107 | shiny,em,410 1108 | base,as.octmode,408 1109 | OpenMx,print,408 1110 | OpenMx,mxComputeOnce,407 1111 | shiny,updateSliderInput,407 1112 | ggplot2,theme_light,406 1113 | h2o,h2o.anyFactor,406 1114 | methods,elNamed,405 1115 | base,packageHasNamespace,404 1116 | caret,createFolds,403 1117 | cluster,pam,402 1118 | base,bitwOr,400 1119 | base,strtrim,400 1120 | ape,node.depth.edgelength,400 1121 | methods,showMethods,400 1122 | dplyr,summarise_each,396 1123 | base,seq.Date,394 1124 | base,expm1,392 1125 | lattice,histogram,392 1126 | shiny,updateCheckboxInput,392 1127 | cowplot,save_plot,391 1128 | base,if,390 1129 | httr,POST,389 1130 | stringr,str_match,387 1131 | shiny,navbarPage,386 1132 | sp,over,386 1133 | plyr,desc,385 1134 | raster,cellStats,385 1135 | base,get0,384 1136 | cowplot,draw_plot,384 1137 | dplyr,tibble,384 1138 | e1071,naiveBayes,384 1139 | shiny,incProgress,384 1140 | ggplot2,scale_colour_gradient,383 1141 | ggplot2,scale_colour_gradientn,382 1142 | grid,arrow,378 1143 | foreign,read.spss,377 1144 | igraph,erdos.renyi.game,377 1145 | base,cospi,375 1146 | MASS,lda,375 1147 | base,Negate,374 1148 | zoo,coredata,374 1149 | base,qr.R,372 1150 | ggplot2,scale_x_datetime,372 1151 | ggplot2,theme_grey,372 1152 | foreign,read.dta,370 1153 | lme4,VarCorr,370 1154 | raster,crs,370 1155 | fields,image.plot,369 1156 | ggplot2,theme_gray,369 1157 | h2o,h2o.describe,369 1158 | DBI,dbConnect,368 1159 | ggplot2,alpha,368 1160 | Matrix,tcrossprod,368 1161 | ggplot2,layer,367 1162 | maptools,readShapePoly,367 1163 | Matrix,sparseMatrix,367 1164 | zoo,index,367 1165 | raster,ncell,366 1166 | DBI,dbGetQuery,365 1167 | randomForest,varImpPlot,365 1168 | data.table,year,364 1169 | lubridate,ymd_hms,364 1170 | ggplot2,scale_alpha_manual,363 1171 | gdata,read.xls,362 1172 | h2o,h2o.nacnt,362 1173 | MASS,stepAIC,362 1174 | h2o,h2o.find_row_by_threshold,361 1175 | base,is.recursive,360 1176 | purrr,map,360 1177 | base,as.difftime,358 1178 | base,file.show,358 1179 | ape,root,357 1180 | sp,SpatialPointsDataFrame,357 1181 | h2o,h2o.auc,356 1182 | XML,xmlRoot,355 1183 | devtools,load_all,354 1184 | ggplot2,scale_linetype_discrete,354 1185 | magrittr,extract,354 1186 | base,Sys.chmod,353 1187 | methods,validObject,352 1188 | base,qr.coef,351 1189 | h2o,h2o.tabulate,351 1190 | plotly,renderPlotly,351 1191 | XML,xmlSApply,351 1192 | base,sort.int,350 1193 | OpenMx,mxComputeSequence,350 1194 | base,bitwXor,349 1195 | lubridate,days,349 1196 | data.table,fwrite,348 1197 | plotly,plotlyOutput,348 1198 | base,agrep,347 1199 | base,determinant,346 1200 | base,atanh,345 1201 | testthat,expect_warning,345 1202 | base,qr.Q,344 1203 | methods,getPackageName,344 1204 | tm,inspect,344 1205 | shinydashboard,dashboardHeader,343 1206 | shinydashboard,dashboardPage,343 1207 | ape,multi2di,342 1208 | shinydashboard,dashboardSidebar,342 1209 | stringr,str_pad,342 1210 | utils,str,342 1211 | testthat,is_equivalent_to,341 1212 | base,dget,340 1213 | plyr,rbind.fill,340 1214 | shinydashboard,dashboardBody,340 1215 | base,path.package,339 1216 | base,c,339 1217 | base,unz,337 1218 | base,sys.calls,336 1219 | data.table,setDT,335 1220 | MASS,select,335 1221 | rpart,rpart.control,334 1222 | base,file.mtime,333 1223 | rvest,html_table,333 1224 | ggplot2,map_data,332 1225 | tm,removeSparseTerms,332 1226 | base,asinh,331 1227 | base,l10n_info,330 1228 | base,library,330 1229 | grid,popViewport,330 1230 | raster,nlayers,330 1231 | methods,callGeneric,329 1232 | dplyr,one_of,328 1233 | readr,col_character,328 1234 | h2o,h2o.std_coef_plot,327 1235 | sp,bpy.colors,327 1236 | boot,boot.ci,326 1237 | base,shell.exec,325 1238 | lme4,getME,325 1239 | methods,isClass,325 1240 | readr,read_delim,324 1241 | base,cosh,321 1242 | lubridate,floor_date,321 1243 | dplyr,rename_,320 1244 | ggplot2,scale_color_gradient,319 1245 | stringr,str_count,319 1246 | igraph,delete.vertices,318 1247 | scales,math_format,317 1248 | ggplot2,scale_colour_hue,315 1249 | igraph,graph,315 1250 | raster,cut,315 1251 | dplyr,union,314 1252 | graphics,barplot,314 1253 | raster,getValues,314 1254 | base,margin.table,313 1255 | shiny,runApp,313 1256 | shiny,tagList,313 1257 | ape,cophenetic.phylo,311 1258 | leaflet,addPolygons,311 1259 | base,ISOdatetime,310 1260 | ape,read.nexus,310 1261 | dplyr,mutate_each,310 1262 | Matrix,drop,310 1263 | tools,file_path_sans_ext,309 1264 | Hmisc,wtd.quantile,308 1265 | base,setNamespaceInfo,307 1266 | OpenMx,nrow,307 1267 | igraph,graph.formula,306 1268 | base,isBaseNamespace,305 1269 | h2o,h2o.r2,305 1270 | raster,boxplot,305 1271 | sp,gridded,305 1272 | base,xor,304 1273 | methods,el,304 1274 | h2o,h2o.target_encode_create,303 1275 | igraph,membership,303 1276 | raster,select,303 1277 | rgdal,readGDAL,303 1278 | graphics,identify,302 1279 | igraph,write.graph,302 1280 | Matrix,show,302 1281 | ggplot2,geom_pointrange,300 1282 | base,is.raw,299 1283 | base,closeAllConnections,298 1284 | doBy,orderBy,298 1285 | lubridate,mdy,298 1286 | base,as.pairlist,297 1287 | base,format.pval,297 1288 | h2o,h2o.shutdown,297 1289 | Rcpp,sourceCpp,297 1290 | igraph,get.adjacency,296 1291 | Matrix,colMeans,296 1292 | dplyr,anti_join,295 1293 | grDevices,dev.off,295 1294 | ggplot2,coord_polar,294 1295 | h2o,h2o.which,293 1296 | stringr,str_length,292 1297 | XML,newXMLCommentNode,292 1298 | lubridate,hour,291 1299 | shiny,includeMarkdown,291 1300 | dplyr,transmute,290 1301 | base,isSymmetric,289 1302 | graphics,image,289 1303 | methods,getGenerics,289 1304 | XML,xmlParse,289 1305 | MASS,fitdistr,288 1306 | shinydashboard,valueBox,288 1307 | base,gzcon,287 1308 | ggthemes,geom_rangeframe,287 1309 | h2o,h2o.prcomp,285 1310 | OpenMx,mxConstraint,285 1311 | base,as.hexmode,284 1312 | dplyr,rowwise,284 1313 | lubridate,day,284 1314 | testthat,skip_on_cran,284 1315 | base,cummax,283 1316 | base,sinh,282 1317 | base,unloadNamespace,282 1318 | plotly,subplot,282 1319 | plotrix,plotCI,281 1320 | scales,trans_format,281 1321 | stats,quantile,281 1322 | base,environmentName,280 1323 | base,evalq,280 1324 | nlme,gls,280 1325 | base,as.ordered,279 1326 | mvtnorm,dmvnorm,279 1327 | plyr,revalue,279 1328 | grid,grid.rect,278 1329 | OpenMx,mxFitFunctionAlgebra,278 1330 | grid,grid.lines,277 1331 | h2o,h2o.sd,277 1332 | h2o,h2o.var,277 1333 | igraph,clusters,277 1334 | base,besselI,276 1335 | base,enc2utf8,276 1336 | base,rapply,275 1337 | ggplot2,autoplot,273 1338 | stringr,str_extract_all,273 1339 | xml2,xml_attr,272 1340 | methods,classMetaName,271 1341 | base,qr.qty,270 1342 | igraph,get.data.frame,270 1343 | car,outlierTest,269 1344 | scales,pretty_breaks,269 1345 | dplyr,row_number,267 1346 | doParallel,stopImplicitCluster,265 1347 | rvest,html_attr,265 1348 | base,conditionCall,263 1349 | leaflet,leafletOutput,263 1350 | base,intToUtf8,262 1351 | h2o,h2o.mean,262 1352 | OpenMx,mxFactor,262 1353 | base,reg.finalizer,261 1354 | leaflet,renderLeaflet,261 1355 | plotly,add_markers,261 1356 | base,formatDL,260 1357 | ggplot2,scale_shape_discrete,260 1358 | lubridate,dmy,260 1359 | ggplot2,scale_x_reverse,259 1360 | sp,spDistsN1,259 1361 | base,dump,257 1362 | base,library.dynam.unload,257 1363 | ggplot2,last_plot,257 1364 | ggplot2,scale_colour_gradient2,257 1365 | ggplot2,scale_y_reverse,257 1366 | lattice,trellis.par.get,257 1367 | igraph,read.graph,256 1368 | ggplot2,geom_density2d,255 1369 | methods,isVirtualClass,255 1370 | base,polyroot,254 1371 | h2o,h2o.randomForest,254 1372 | shiny,includeHTML,253 1373 | base,encodeString,249 1374 | DBI,dbDisconnect,249 1375 | igraph,graph_from_data_frame,249 1376 | testthat,is_identical_to,249 1377 | Hmisc,cut2,248 1378 | dplyr,bind_cols,247 1379 | leaflet,addCircleMarkers,247 1380 | stats,glm,247 1381 | methods,formalArgs,246 1382 | stats,median,246 1383 | testthat,is_true,246 1384 | base,getNativeSymbolInfo,245 1385 | shinydashboard,valueBoxOutput,245 1386 | igraph,graph.edgelist,243 1387 | optparse,print_help,243 1388 | base,sys.nframe,242 1389 | ggplot2,stat_contour,242 1390 | raster,xyFromCell,242 1391 | survival,survreg,242 1392 | ggplot2,geom_rug,241 1393 | leaflet,setView,241 1394 | stats,nls,241 1395 | h2o,h2o.getTypes,240 1396 | e1071,impute,239 1397 | h2o,h2o.F1,239 1398 | h2o,h2o.find_threshold_by_max_metric,239 1399 | h2o,h2o.giniCoef,239 1400 | data.table,key,238 1401 | ggplot2,geom_dotplot,238 1402 | sp,SpatialPolygonsDataFrame,238 1403 | plotrix,std.error,237 1404 | raster,shapefile,237 1405 | sp,sp.theme,237 1406 | XML,addChildren,237 1407 | base,comment,236 1408 | ggplot2,annotation_custom,236 1409 | graphics,pairs,236 1410 | igraph,induced.subgraph,236 1411 | nlme,VarCorr,236 1412 | raster,colSums,236 1413 | base,packageEvent,234 1414 | car,leveneTest,234 1415 | car,recode,234 1416 | zoo,rollapply,234 1417 | h2o,h2o.sdev,233 1418 | Matrix,qr,233 1419 | zoo,rollmean,233 1420 | h2o,log,232 1421 | base,lbeta,231 1422 | ggthemes,theme_few,231 1423 | h2o,h2o.varimp_plot,231 1424 | stats,rpois,231 1425 | base,sys.source,230 1426 | h2o,h2o.download_pojo,230 1427 | base,asS4,229 1428 | base,trigamma,229 1429 | caret,rfe,229 1430 | ggplot2,scale_fill_distiller,229 1431 | graphics,persp,229 1432 | methods,removeClass,229 1433 | base,Position,228 1434 | igraph,betweenness,228 1435 | stats,cor,228 1436 | ggplot2,geom_col,227 1437 | nlme,gsummary,227 1438 | RCurl,close,227 1439 | readr,read_tsv,227 1440 | rvest,html_node,227 1441 | base,sys.frames,226 1442 | car,scatterplot,226 1443 | ggplot2,scale_fill_continuous,226 1444 | h2o,h2o.mean_residual_deviance,226 1445 | lubridate,yday,226 1446 | base,Arg,225 1447 | base,environmentIsLocked,225 1448 | igraph,graph.ring,225 1449 | Hmisc,label,224 1450 | base,qr.solve,223 1451 | ggplot2,scale_colour_continuous,223 1452 | graphics,layout,223 1453 | nlme,ranef,223 1454 | scales,trans_breaks,223 1455 | stats,sd,223 1456 | caret,nearZeroVar,222 1457 | XML,xmlGetAttr,222 1458 | rgl,open3d,221 1459 | OpenMx,omxNot,220 1460 | base,library.dynam,218 1461 | h2o,h2o.mean_per_class_error,218 1462 | methods,getMethod,218 1463 | survival,strata,218 1464 | testthat,expect_output,218 1465 | tidyr,unite,218 1466 | base,is.pairlist,217 1467 | dplyr,recode,217 1468 | dplyr,top_n,217 1469 | h2o,h2o.startLogging,217 1470 | plyr,idata.frame,217 1471 | tm,findFreqTerms,217 1472 | RCurl,postForm,216 1473 | ggplot2,scale_color_identity,215 1474 | scales,muted,215 1475 | base,besselY,214 1476 | psych,corr.test,214 1477 | testthat,expect_gt,214 1478 | base,is.R,213 1479 | caret,rfeControl,213 1480 | dplyr,sample_n,213 1481 | xml2,xml_children,213 1482 | base,bzfile,212 1483 | ggplot2,scale_fill_grey,212 1484 | stats,rt,212 1485 | base,socketConnection,211 1486 | Matrix,kronecker,211 1487 | rpart,printcp,211 1488 | base,strrep,210 1489 | base,writeChar,210 1490 | graphics,rug,210 1491 | lubridate,wday,210 1492 | h2o,h2o.target_encode_apply,209 1493 | methods,isGeneric,209 1494 | reshape,rename,209 1495 | leaflet,addMarkers,208 1496 | utils,example,208 1497 | methods,methodsPackageMetaName,207 1498 | raster,setZ,207 1499 | sp,layout.north.arrow,206 1500 | stats,coef,206 1501 | base,rcond,205 1502 | ggplot2,scale_size_continuous,205 1503 | lme4,glmerControl,205 1504 | base,cummin,204 1505 | base,stdin,202 1506 | cluster,fanny,202 1507 | dplyr,if_else,202 1508 | MASS,rlm,202 1509 | reshape2,acast,202 1510 | sp,spsample,202 1511 | dplyr,between,201 1512 | MASS,glm.nb,201 1513 | zoo,as.yearmon,201 1514 | caret,findCorrelation,200 1515 | graphics,matlines,200 1516 | grDevices,rainbow,200 1517 | igraph,transitivity,200 1518 | raster,tail,200 1519 | sp,layout.scale.bar,200 1520 | igraph,plot.igraph,199 1521 | leaflet,leafletProxy,199 1522 | utils,install.packages,199 1523 | base,setHook,198 1524 | psych,alpha,198 1525 | raster,rasterFromXYZ,198 1526 | Matrix,unname,197 1527 | raster,rowSums,197 1528 | shiny,submitButton,197 1529 | base,identity,196 1530 | shiny,parseQueryString,196 1531 | base,is.qr,195 1532 | raster,getData,195 1533 | rgl,points3d,195 1534 | dplyr,pull,194 1535 | lubridate,hours,194 1536 | parallel,clusterSetRNGStream,194 1537 | car,spreadLevelPlot,193 1538 | OpenMx,mxComputeReportDeriv,193 1539 | psych,describeBy,193 1540 | stats,aggregate,192 1541 | stringr,str_locate,192 1542 | base,dyn.unload,191 1543 | DT,JS,191 1544 | ggplot2,borders,191 1545 | testthat,is_a,191 1546 | car,crPlots,190 1547 | dplyr,matches,190 1548 | h2o,trunc,190 1549 | shinydashboard,renderValueBox,190 1550 | XML,xpathApply,190 1551 | h2o,h2o.exportFile,189 1552 | h2o,h2o.removeAll,189 1553 | gsubfn,list,188 1554 | MASS,qda,188 1555 | base,getHook,187 1556 | gplots,colorpanel,187 1557 | igraph,graph.empty,187 1558 | igraph,union,187 1559 | MASS,kde2d,187 1560 | base,lockEnvironment,186 1561 | httr,add_headers,186 1562 | tm,DirSource,186 1563 | base,xtfrm,185 1564 | raster,which.max,185 1565 | base,print,184 1566 | car,avPlots,184 1567 | dplyr,summarise_all,184 1568 | dplyr,tally,184 1569 | foreign,write.dta,184 1570 | jsonlite,unbox,184 1571 | devtools,document,183 1572 | raster,scale,183 1573 | shiny,includeScript,183 1574 | ggthemes,extended_range_breaks,182 1575 | nlme,corAR1,182 1576 | base,readRenviron,181 1577 | methods,callNextMethod,181 1578 | scales,percent_format,181 1579 | cluster,daisy,180 1580 | OpenMx,omxCheckWarning,180 1581 | stats,pnorm,180 1582 | base,delayedAssign,179 1583 | base,print.data.frame,179 1584 | data.table,shift,179 1585 | Matrix,chol,179 1586 | stringr,str_to_lower,179 1587 | base,write.dcf,178 1588 | igraph,ends,178 1589 | lattice,dotplot,177 1590 | lattice,wireframe,177 1591 | plyr,adply,177 1592 | shiny,updateSelectizeInput,177 1593 | base,psigamma,176 1594 | car,Boxplot,176 1595 | shiny,setProgress,176 1596 | shinydashboard,menuSubItem,176 1597 | igraph,as.undirected,175 1598 | rgl,par3d,175 1599 | stats,hclust,175 1600 | dplyr,everything,174 1601 | base,pi,173 1602 | e1071,tune,173 1603 | OpenMx,omxSelectCols,172 1604 | ggplot2,stat_ecdf,171 1605 | grid,rectGrob,171 1606 | h2o,h2o.quantile,171 1607 | base,as.function,170 1608 | base,tanpi,170 1609 | base,traceback,169 1610 | dplyr,src_sqlite,169 1611 | foreach,getDoParWorkers,169 1612 | methods,kronecker,169 1613 | XML,xmlSize,169 1614 | base,gctorture,168 1615 | ggplot2,scale_size_discrete,168 1616 | igraph,modularity,168 1617 | leaflet,addLegend,168 1618 | raster,rasterToPoints,168 1619 | readr,col_double,168 1620 | base,is.table,167 1621 | shiny,includeCSS,167 1622 | tools,file_ext,167 1623 | ggplot2,stat_count,166 1624 | survival,pspline,166 1625 | h2o,h2o.round,165 1626 | h2o,h2o.signif,165 1627 | plyr,mdply,165 1628 | readr,col_number,165 1629 | base,xzfile,164 1630 | lubridate,years,164 1631 | plyr,round_any,164 1632 | RCurl,url.exists,164 1633 | dplyr,filter_,163 1634 | ggplot2,scale_fill_hue,163 1635 | raster,resample,163 1636 | base,unsplit,162 1637 | devtools,use_data,162 1638 | base,is.loaded,161 1639 | ape,nj,161 1640 | caret,dummyVars,161 1641 | ggplot2,scale_alpha_continuous,161 1642 | lattice,panel.points,161 1643 | maptools,readShapeSpatial,161 1644 | methods,setIs,161 1645 | readr,locale,161 1646 | rpart,plotcp,161 1647 | shiny,bootstrapPage,161 1648 | base,qr.qy,160 1649 | base,rawConnection,160 1650 | ape,plot.phylo,160 1651 | dplyr,mutate_,160 1652 | igraph,add.edges,160 1653 | igraph,is.directed,160 1654 | raster,setValues,160 1655 | shinydashboard,sidebarMenu,160 1656 | utils,file_test,160 1657 | base,all.names,159 1658 | base,default.stringsAsFactors,159 1659 | dplyr,add_rownames,159 1660 | e1071,skewness,159 1661 | ggplot2,geom_label,159 1662 | ggplot2,guide_colorbar,159 1663 | lubridate,now,159 1664 | maps,map.scale,159 1665 | zoo,na.locf,159 1666 | Matrix,sparse.model.matrix,158 1667 | stringr,str_replace_na,158 1668 | XML,newXMLDoc,158 1669 | base,eapply,157 1670 | data.table,month,157 1671 | data.table,setorder,157 1672 | data.table,uniqueN,157 1673 | grid,grobTree,157 1674 | parallel,parSapply,157 1675 | shiny,absolutePanel,157 1676 | stringr,str_wrap,157 1677 | base,getNamespaceExports,156 1678 | h2o,h2o.strsplit,156 1679 | lattice,panel.loess,156 1680 | cowplot,ggdraw,155 1681 | dplyr,sql,155 1682 | ggplot2,theme_void,155 1683 | h2o,log1p,155 1684 | httr,stop_for_status,155 1685 | igraph,set.vertex.attribute,155 1686 | shiny,withMathJax,155 1687 | tm,findAssocs,155 1688 | base,as.package_version,154 1689 | knitr,render_jekyll,154 1690 | stats,spectrum,154 1691 | xml2,xml_find_all,154 1692 | base,registerS3method,153 1693 | cluster,clusplot,153 1694 | dplyr,right_join,153 1695 | ggplot2,geom_blank,153 1696 | testthat,describe,153 1697 | XML,xmlNode,153 1698 | base,besselJ,152 1699 | base,prmatrix,152 1700 | graphics,contour,152 1701 | h2o,log10,152 1702 | Hmisc,Ecdf,152 1703 | shiny,showModal,152 1704 | h2o,log2,151 1705 | methods,getClasses,151 1706 | methods,slotNames,151 1707 | RColorBrewer,display.brewer.all,151 1708 | boot,cv.glm,150 1709 | ggthemes,theme_hc,150 1710 | methods,isClassDef,150 1711 | readr,read_rds,150 1712 | stats,fitted,150 1713 | ggplot2,coord_trans,149 1714 | gplots,barplot2,149 1715 | h2o,h2o.cor,149 1716 | h2o,h2o.varimp,149 1717 | lattice,panel.lines,149 1718 | OpenMx,vec2diag,149 1719 | plyr,numcolwise,149 1720 | base,file.exists,148 1721 | gdata,trim,148 1722 | ggplot2,annotation_logticks,148 1723 | ggplot2,stat_density2d,148 1724 | h2o,h2o.columns_by_type,148 1725 | h2o,h2o.kurtosis,148 1726 | h2o,h2o.median,148 1727 | h2o,h2o.skewness,148 1728 | methods,setClassUnion,148 1729 | scales,percent,148 1730 | shiny,modalDialog,148 1731 | stats,dist,148 1732 | stringr,fixed,148 1733 | base,seq.POSIXt,147 1734 | ape,rtt,147 1735 | igraph,diameter,147 1736 | base,acosh,146 1737 | base,numeric_version,146 1738 | fields,US,146 1739 | h2o,h2o.sub,146 1740 | igraph,edges,146 1741 | XML,xmlToList,146 1742 | base,subset.data.frame,145 1743 | DBI,dbSendQuery,145 1744 | ggplot2,scale_shape,145 1745 | httr,config,145 1746 | MASS,polr,145 1747 | readr,parse_number,145 1748 | caret,RMSE,144 1749 | stringr,regex,144 1750 | tools,md5sum,144 1751 | base,grepRaw,143 1752 | lubridate,today,143 1753 | readr,cols,143 1754 | shinydashboard,tabItems,143 1755 | stats,arima,143 1756 | base,julian,142 1757 | ape,is.binary.tree,142 1758 | data.table,is.data.table,142 1759 | methods,getFunction,142 1760 | readr,col_integer,142 1761 | dplyr,copy_to,141 1762 | h2o,h2o.trim,140 1763 | Matrix,det,140 1764 | OpenMx,omxGetParameters,140 1765 | OpenMx,omxSelectRows,140 1766 | rvest,html_session,140 1767 | utils,glob2rx,140 1768 | base,lchoose,139 1769 | dplyr,dense_rank,139 1770 | igraph,layout.fruchterman.reingold,139 1771 | igraph,list.vertex.attributes,139 1772 | lubridate,parse_date_time,139 1773 | lubridate,setdiff,139 1774 | OpenMx,mxComputeNewtonRaphson,139 1775 | OpenMx,ncol,139 1776 | plyr,colwise,139 1777 | scales,comma,139 1778 | shiny,safeError,139 1779 | tools,compactPDF,139 1780 | base,Find,138 1781 | base,importIntoEnv,138 1782 | igraph,gorder,138 1783 | leaflet,makeIcon,138 1784 | lubridate,interval,138 1785 | rgl,axes3d,138 1786 | base,besselK,137 1787 | base,isNamespaceLoaded,137 1788 | base,lfactorial,137 1789 | ggplot2,scale_size_area,137 1790 | h2o,h2o.setLevels,137 1791 | igraph,get.vertex.attribute,137 1792 | raster,reclassify,137 1793 | stats,density,137 1794 | XML,xmlChildren,137 1795 | XML,xmlClone,137 1796 | zoo,na.approx,137 1797 | ggplot2,theme_update,136 1798 | h2o,h2o.summary,136 1799 | igraph,delete.edges,136 1800 | methods,allNames,136 1801 | OpenMx,omxQuotes,136 1802 | xlsx,createSheet,136 1803 | caret,R2,135 1804 | plyr,aaply,135 1805 | ape,as.phylo,134 1806 | h2o,h2o.grep,134 1807 | h2o,h2o.nchar,134 1808 | h2o,h2o.rank_within_group_by,134 1809 | h2o,h2o.tokenize,134 1810 | h2o,h2o.tolower,134 1811 | lattice,panel.grid,134 1812 | XML,htmlTreeParse,134 1813 | xml2,xml_find_first,134 1814 | base,as.data.frame.list,133 1815 | base,tracingState,133 1816 | dplyr,lead,133 1817 | dplyr,tribble,133 1818 | Matrix,tril,133 1819 | OpenMx,mxComputeStandardError,133 1820 | tools,pkgVignettes,133 1821 | caret,resamples,132 1822 | igraph,degree.distribution,132 1823 | tm,removeWords,132 1824 | dplyr,as_tibble,131 1825 | h2o,h2o.distance,131 1826 | h2o,h2o.entropy,131 1827 | h2o,h2o.fillna,131 1828 | h2o,h2o.gsub,131 1829 | h2o,h2o.isnumeric,131 1830 | h2o,h2o.lstrip,131 1831 | h2o,h2o.rmse,131 1832 | h2o,h2o.rstrip,131 1833 | h2o,h2o.stringdist,131 1834 | h2o,h2o.substring,131 1835 | h2o,h2o.toupper,131 1836 | igraph,shortest.paths,131 1837 | Matrix,tail,131 1838 | plotly,add_lines,131 1839 | shiny,updateTabsetPanel,131 1840 | testthat,throws_error,131 1841 | base,all.equal.numeric,130 1842 | devtools,install,130 1843 | MASS,fractions,130 1844 | methods,getSlots,130 1845 | OpenMx,omxSelectRowsAndCols,130 1846 | optparse,add_option,130 1847 | plotly,rename,130 1848 | stats,t.test,130 1849 | dplyr,last,129 1850 | graphics,polygon,129 1851 | h2o,h2o.saveModel,129 1852 | OpenMx,mxFactorScores,129 1853 | dplyr,as_data_frame,128 1854 | ggplot2,lims,128 1855 | igraph,is.simple,128 1856 | leaflet,addCircles,128 1857 | Matrix,image,128 1858 | methods,selectSuperClasses,128 1859 | OpenMx,diag2vec,128 1860 | raster,which.min,128 1861 | shiny,outputOptions,128 1862 | tools,list_files_with_type,128 1863 | xlsx,addDataFrame,128 1864 | base,bindtextdomain,127 1865 | e1071,tune.svm,127 1866 | ggthemes,theme_fivethirtyeight,127 1867 | shiny,actionLink,127 1868 | ggplot2,stat_ellipse,126 1869 | methods,prototype,126 1870 | OpenMx,mxFitFunctionMultigroup,126 1871 | tm,VCorpus,126 1872 | xlsx,read.xlsx2,126 1873 | base,qr.resid,125 1874 | car,scatter3d,125 1875 | igraph,graph.full,125 1876 | leaflet,markerClusterOptions,125 1877 | NCmisc,prv,125 1878 | raster,as.list,125 1879 | shiny,singleton,125 1880 | base,file.mode,124 1881 | dplyr,rbind_list,124 1882 | methods,assignClassDef,124 1883 | methods,defaultPrototype,124 1884 | OpenMx,mxExpectationRAM,124 1885 | OpenMx,omxSetParameters,124 1886 | parallel,clusterApply,124 1887 | base,getElement,123 1888 | grDevices,png,123 1889 | methods,rbind2,123 1890 | raster,plotRGB,123 1891 | rgl,rgl.postscript,123 1892 | tibble,add_column,123 1893 | cluster,silhouette,122 1894 | h2o,h2o.predict_leaf_node_assignment,122 1895 | nlme,varIdent,122 1896 | raster,rasterOptions,122 1897 | base,attr.all.equal,121 1898 | base,kappa,121 1899 | base,La.svd,121 1900 | e1071,tune.control,121 1901 | Hmisc,errbar,121 1902 | MASS,bcv,121 1903 | Matrix,nearPD,121 1904 | base,forwardsolve,120 1905 | zoo,na.spline,120 1906 | base,format.default,119 1907 | base,srcfilecopy,119 1908 | shiny,dateRangeInput,119 1909 | base,file.append,118 1910 | base,sink.number,118 1911 | base,require,118 1912 | gridExtra,grid.table,118 1913 | methods,existsMethod,118 1914 | base,cut.Date,117 1915 | ggplot2,geom_map,117 1916 | ggplot2,scale_alpha,117 1917 | mvtnorm,dmvt,117 1918 | base,namespaceImportFrom,116 1919 | base,signalCondition,116 1920 | igraph,list.edge.attributes,116 1921 | OpenMx,mxCI,116 1922 | tools,vignetteEngine,116 1923 | xml2,read_xml,116 1924 | base,getLoadedDLLs,115 1925 | base,makeActiveBinding,115 1926 | base,qr.fitted,115 1927 | base,repeat,115 1928 | Hmisc,impute,115 1929 | rgl,text3d,115 1930 | cluster,agnes,114 1931 | igraph,closeness,114 1932 | survival,survdiff,114 1933 | bigrquery,query_exec,113 1934 | gplots,redgreen,113 1935 | graphics,filled.contour,113 1936 | grDevices,pdf,113 1937 | Matrix,update,113 1938 | cowplot,draw_label,112 1939 | ggplot2,geom_freqpoly,112 1940 | h2o,h2o.cummax,112 1941 | h2o,h2o.cummin,112 1942 | h2o,h2o.cumprod,112 1943 | h2o,h2o.cumsum,112 1944 | Matrix,cBind,112 1945 | raster,rasterToPolygons,112 1946 | graphics,rect,111 1947 | grid,gList,111 1948 | sp,Line,111 1949 | h2o,h2o.partialPlot,110 1950 | igraph,random.graph.game,110 1951 | base,addNA,109 1952 | base,as.data.frame.vector,109 1953 | car,scatterplotMatrix,109 1954 | h2o,h2o.mae,109 1955 | h2o,h2o.make_metrics,109 1956 | h2o,h2o.rmsle,109 1957 | Matrix,drop0,109 1958 | Matrix,rowMeans,109 1959 | NCmisc,must.use.package,109 1960 | OpenMx,mxExpectationGREML,109 1961 | Hmisc,subplot,108 1962 | MASS,write.matrix,108 1963 | OpenMx,mxComputeGradientDescent,108 1964 | plotly,get_figure,108 1965 | igraph,vertex_attr,107 1966 | leaflet,addLayersControl,107 1967 | stats,residuals,107 1968 | stringr,word,107 1969 | base,file.symlink,106 1970 | base,Sys.timezone,106 1971 | maptools,readShapePoints,106 1972 | RCurl,getURLContent,106 1973 | zoo,read.zoo,106 1974 | grid,upViewport,105 1975 | httr,oauth_endpoints,105 1976 | leaflet,leafletOptions,105 1977 | proto,proto,105 1978 | rgl,surface3d,105 1979 | stats,na.omit,105 1980 | base,memDecompress,104 1981 | ggplot2,waiver,104 1982 | h2o,h2o.transform,104 1983 | h2o,h2o.word2vec,104 1984 | igraph,get.edge.attribute,104 1985 | OpenMx,mxExpectationBA81,104 1986 | plyr,daply,104 1987 | shiny,navbarMenu,104 1988 | shiny,runGitHub,104 1989 | xml2,xml_add_sibling,104 1990 | fields,tim.colors,103 1991 | grDevices,colorRampPalette,103 1992 | lubridate,minute,103 1993 | raster,area,103 1994 | stats,aov,103 1995 | base,format.Date,102 1996 | base,license,102 1997 | boot,inv.logit,102 1998 | graphics,panel.smooth,102 1999 | graphics,stem,102 2000 | igraph,add.vertices,102 2001 | iterators,iter,102 2002 | -------------------------------------------------------------------------------- /not_installed_packages.R: -------------------------------------------------------------------------------- 1 | library(readr) 2 | library(magrittr) 3 | library(tidyr) 4 | library(dplyr) 5 | library(stringr) 6 | 7 | #checking for non-uploaded packages 8 | content_trial_3 <- content_r[1:10000,] 9 | 10 | content_trial_3 <- content_trial_3 %>% 11 | mutate(lib_content = str_extract_all(content, "(library\\([^\\(]+\\)|library \\([^\\(]+\\)|loadNamespace\\([^\\(]+\\)|loadNamespace \\([^\\(]+\\)|require\\([^\\(]+\\)|require \\([^\\(]+\\)|requireNamespace\\([^\\(]+\\)|requireNamespace \\([^\\(]+\\))")) 12 | 13 | content_trial_3 <- content_trial_3 %>% 14 | unnest(lib_content) 15 | 16 | content_trial_3$lib_content <- gsub( 17 | ",.*$", "", 18 | str_replace_all( 19 | str_extract(content_trial_3 $lib_content, "\\([^()]+\\)"), 20 | c("\"" = "", "\'" = "", "\\(" = "", "\\)" = "") 21 | ) 22 | ) 23 | 24 | content_trial_3$content <- str_extract_all(content_trial_3$content, "([a-zA-Z][a-zA-Z0-9_.]{0,43}[(])|([a-zA-Z][a-zA-Z0-9_.]{0,43}[ ][(])") 25 | 26 | content_trial_3 <- content_trial_3 %>% 27 | unnest(content) 28 | 29 | content_trial_3$content <- str_replace_all(content_trial_3$content, c(" " = "", "[(]" = "")) 30 | 31 | #checking with packages 32 | 33 | content_trial_3_packs <- content_trial_3 %>% 34 | group_by(lib_content, content) %>% 35 | summarise(count = n()) %>% 36 | inner_join(functions, by = c("lib_content" = "V1", "content" = "functions")) %>% 37 | arrange(desc(count)) %>% 38 | head(1000) 39 | 40 | #checking without packages 41 | content_trial_3_no_packs <- content_trial_3 %>% 42 | group_by(content) %>% 43 | summarise(count = n()) %>% 44 | inner_join(functions, by = c("content" = "functions")) %>% 45 | arrange(desc(count)) %>% 46 | head(1000) 47 | 48 | 49 | difference_without_packages <- content_trial_3_packs %>% 50 | full_join(content_trial_3_no_packs, by = "content") 51 | 52 | colnames(difference_without_packages) <- c("Package", "Function", "Count with packages", "Count without packages", "Package Option") 53 | 54 | View(difference_without_packages) 55 | 56 | -------------------------------------------------------------------------------- /top_functions.R: -------------------------------------------------------------------------------- 1 | library(readr) 2 | library(magrittr) 3 | library(tidyr) 4 | library(dplyr) 5 | library(stringr) 6 | library(bigrquery) 7 | 8 | #getting files from Google BigQuery 9 | 10 | big_query_data <- "certain-torus-206419" 11 | 12 | sql <- "SELECT content FROM [certain-torus-206419:Github.content_copy]" 13 | 14 | destination_table <- "certain-torus-206419:Github.r_2" 15 | 16 | content_r <- query_exec(sql, project = big_query_data, useLegacySql = FALSE, 17 | destination_table = destination_table, max_pages = Inf) 18 | 19 | 20 | #getting packages used in the code 21 | 22 | content_r <- content_r %>% 23 | mutate(lib_content = str_extract_all(content, "(library\\([^\\(]+\\)|library \\([^\\(]+\\)|loadNamespace\\([^\\(]+\\)|loadNamespace \\([^\\(]+\\)|require\\([^\\(]+\\)|require \\([^\\(]+\\)|requireNamespace\\([^\\(]+\\)|requireNamespace \\([^\\(]+\\))")) 24 | 25 | libraries <- content_r[,2] %>% 26 | unnest(lib_content) 27 | 28 | libraries$lib_content <- gsub( 29 | ",.*$", "", 30 | str_replace_all( 31 | str_extract(libraries$lib_content, "\\([^()]+\\)"), 32 | c("\"" = "", "\'" = "", "\\(" = "", "\\)" = "") 33 | ) 34 | ) 35 | 36 | #counting the usage of packages 37 | 38 | packages_100 <- libraries %>% 39 | group_by(lib_content) %>% 40 | summarise(count = n()) %>% 41 | arrange(desc(count)) %>% 42 | head(100) 43 | 44 | write_csv(packages_100, "data/top_100_packages.csv") 45 | 46 | 47 | #visualisation of top 50 packages 48 | 49 | packages_100 %>% 50 | arrange(desc(count)) %>% 51 | head(40) %>% 52 | ggplot() + 53 | geom_bar(aes(reorder(lib_content, count), count), stat = "identity", fill = "lightblue") + 54 | labs(x = "R packages", y = "Usage on Github") + 55 | coord_flip() 56 | 57 | #checking which packages are not installed in my R 58 | 59 | inst_pack <- as.data.frame(installed.packages()[, 1]) 60 | colnames(inst_pack) <- c("Package") 61 | inst_pack$Package <- as.character(inst_pack$Package) 62 | 63 | missing <- anti_join(packages_100, inst_pack, by = c("lib_content" = "Package" )) 64 | 65 | #insalling packages, done manually to control the process 66 | 67 | #adding packages to the environment 68 | lapply(packages_100$lib_content, require, character.only = TRUE) 69 | 70 | #finding all installed packages with their functions 71 | functions <- sapply(search(), ls) 72 | 73 | # turning "functions" into a table with the names of packages 74 | 75 | functions <- setNames(unlist(functions, use.names=F),rep(names(functions), lengths(functions))) 76 | 77 | functions <- as.tibble( 78 | cbind( 79 | functions, names(functions) 80 | ) 81 | ) %>% 82 | filter(!(V1 %in% c(".GlobalEnv", "package:datasets") )) 83 | 84 | functions$V1 <- str_sub(functions$V1, 9) 85 | 86 | # clearing original dataset to include only lines with mentioned packages 87 | 88 | content_clear <- content_r %>% 89 | filter(!(lib_content == "character(0)")) %>% 90 | unnest(lib_content) %>% 91 | mutate( 92 | library = gsub( 93 | ",.*$", "", 94 | str_replace_all( 95 | str_extract(lib_content, "\\([^()]+\\)"), 96 | c("\"" = "", "\'" = "", "\\(" = "", "\\)" = "") 97 | ) 98 | ) 99 | ) 100 | 101 | #getting packages for the analysis 102 | 103 | packages_for_proj <- as.tibble(unique(functions$V1)) 104 | 105 | # filtering dataset to incluse only needed packages 106 | 107 | content_clear_1 <- content_clear[,c(1,3)] %>% 108 | inner_join(packages_for_proj, by = c("library" = "value")) 109 | 110 | write_csv(content_clear_1, "data/content_clear_1.csv") 111 | 112 | #splitting strings into supposedly functions 113 | 114 | 115 | content_clear_2 <- content_clear_1 116 | 117 | content_clear_2$content <- str_extract_all(content_clear_2$content, "([a-zA-Z][a-zA-Z0-9_.]{0,43}[(])|([a-zA-Z][a-zA-Z0-9_.]{0,43}[ ][(])") 118 | 119 | 120 | content_clear_2_unnested <- content_clear_2 %>% 121 | unnest(content) 122 | 123 | content_clear_2_unnested$content <- str_replace_all(content_clear_2_unnested$content, c(" " = "", "[(]" = "")) 124 | 125 | content_clear_3 <- content_clear_2_unnested %>% 126 | group_by(library,content) %>% 127 | summarise(count = n()) 128 | 129 | package_functions <- content_clear_3 %>% 130 | inner_join(functions, by = c("library" = "V1", "content" = "functions")) 131 | 132 | #visualising top 100 functions from not-base packages 133 | 134 | package_functions %>% 135 | unite(col = "Package_function",library, content, sep = "::", remove = FALSE) %>% 136 | arrange(desc(count)) %>% 137 | head(50) %>% 138 | ggplot()+ 139 | geom_bar(aes(x = reorder(Package_function, count), y = count, fill = library), stat = "identity")+ 140 | labs(x = "Functions") + 141 | scale_fill_brewer(palette = "Paired") + 142 | coord_flip() 143 | 144 | 145 | #base functions 146 | 147 | all_content <- content_r 148 | 149 | all_content$content <- str_extract_all(all_content$content, "([a-zA-Z][a-zA-Z0-9_.]{0,43}[(])|([a-zA-Z][a-zA-Z0-9_.]{0,43}[ ][(])") 150 | 151 | 152 | all_content <- all_content %>% 153 | unnest(content) 154 | 155 | all_content$content <- str_replace_all(all_content$content, c(" " = "", "[(]" = "")) 156 | 157 | all_content <- all_content %>% 158 | group_by(content) %>% 159 | summarise(count = n()) 160 | 161 | base_functions <- functions %>% 162 | filter(V1 == "base") 163 | 164 | top_base_functions <- all_content %>% 165 | inner_join(base_functions, by = c("content"="functions")) %>% 166 | arrange(desc(count)) 167 | 168 | colnames(top_base_functions)[3] <- "library" 169 | top_base_functions <- top_base_functions[,c(3,1,2)] 170 | 171 | #visualising top 50 base functions 172 | 173 | top_100_base_functions %>% 174 | arrange(desc(count)) %>% 175 | head(100) %>% 176 | View() 177 | ggplot() + 178 | geom_bar(aes(x = reorder(content, count), y = count), fill = "lightblue", stat = "identity") + 179 | labs(x = "Functions") + 180 | coord_flip() 181 | 182 | #deriving functions from all packages 183 | 184 | all_top_functions <- rbind(top_base_functions,package_functions, deparse.level = 2) 185 | 186 | all_top_functions %>% 187 | unite(col = "Package_function",library, content, sep = "::", remove = FALSE) %>% 188 | arrange(desc(count)) %>% 189 | head(100) %>% 190 | ggplot()+ 191 | geom_bar(aes(x = reorder(Package_function, count), y = count, fill = library), stat = "identity")+ 192 | labs(x = "Functions") + 193 | scale_fill_brewer(palette = "Paired") + 194 | coord_flip() 195 | 196 | ggsave("top_100_functions.jpeg",height = 16) 197 | 198 | top_2000_functions <- all_top_functions %>% 199 | arrange(desc(count)) %>% 200 | head(2000) 201 | 202 | write_csv(top_2000_functions, "top_2000_functions.csv") 203 | --------------------------------------------------------------------------------