From 79cc1ecf077d7cac6a786f9ad637df597355c9ae Mon Sep 17 00:00:00 2001 From: prise6 Date: Sun, 21 Jun 2015 02:29:01 +0200 Subject: [PATCH] Update manual --- data-raw/sepsis.R | 4 +++- data/sepsis.rdata | Bin 6406 -> 6411 bytes man/VT.difft.Rd | 16 +++++++++++++--- man/VT.object.Rd | 2 +- man/VT.tree.Rd | 2 +- man/sepsis.Rd | 39 +++++++++++++++++++-------------------- man/vt.data.Rd | 28 ++++++++++++++++++++++++++++ 7 files changed, 65 insertions(+), 26 deletions(-) create mode 100644 man/vt.data.Rd diff --git a/data-raw/sepsis.R b/data-raw/sepsis.R index 2207871..8426590 100644 --- a/data-raw/sepsis.R +++ b/data-raw/sepsis.R @@ -22,7 +22,9 @@ sum(is.na(sepsis.csv$survival)) # For futures computation i need to impute missing values # I use random forest imputation with randomForest package with simple parameters # I need to make survival field as factor -sepsis.csv$survival <- factor(sepsis.csv$survival, levels = 0:1) +sepsis.csv$survival <- factor(sepsis.csv$survival, levels = 0:1) +# reproducibility: +set.seed(123) sepsis.imp <- with(sepsis.csv, rfImpute(y = survival, x = sepsis.csv[, -1], iter = 5, ntree = 500)) str(sepsis.imp) diff --git a/data/sepsis.rdata b/data/sepsis.rdata index bd883b8df60d3bdd7cd2969c445954c6f20af708..55b91ea698b9c3ede75d2f3eea56524c72b4aa74 100644 GIT binary patch delta 5967 zcmW-idpy$%(gN?9XgZ2O*$O1bU06ou_b zwaR5ha+@uexo6}qwroS#%r?8nwx)V58mr? z_f*m7-mI)pa&2Y8*(l4HNE5+uyV1MbH{P0`-E(5#P3l0?lmwc>VyhwY=9ozS-K1zZ zDWxCNFHr&jF@D*hOI$NnJo)LhefkU4n{x;qvQ+b-RI~eChWU%pL$}T0DI+VYnSJ}u z?k98<+)!4gsDAD2s#ajVKp%CVg@Uj zTR8^{43CjEOlpF)z18$UcDcaJZj&Suo`D>R38b*v;^O| z7?U*;YF9fPVgI3g6#9)FPO1^}+ z%LBU0uwuo{C;sJA9~LontJxQIO|wjHAXHw{hMJ`ae{90fxfGr zK)UCf`#aC8SOaA+F@_>Ru+shP}5zn>Q6s z$s3wwS&e(RC@N~JKFfUiU;E7$jkdW6N;so?n^0Y@_GdcnR>7H<30x9~|D&~0TpA3E zNBux+rhnF-jV@cgyH;(AP!0<3#=r{Y2ltjdg1ssKcE0=Q=$C|J%AvmsVE{@JaSxFT z_58k&=;2>7Mf;5|lNv;I2ld;)6ie&)U(1iC6$%VF&i3YvxxQVj){`(}d3SbD(z7k? zO=AlSS*K!7A8RbuM3rC{HpJMsOU{B5pAUK3td#c-;^&9XlD)-S$phZXiFw}Q#fUBv zq>emPneboK)>zYw0R#gIw4Wsu8R7Q83Vla%BB#vw>z2Z#UB`;dd4ZUMjhBPeO>1zt z!Rsa6z>13_Mo7rN5hfweh@+udAH=4Qzo5$bG>E0+v8HJCoPle* zZ|C%3ea4uJGNC_%DB;4WalL5|wW=P*ynf{&cbO1GX{=hf59nu;CcM47wnFJIO8tcVUZ-Q8-rhCmRfX87(5ZFns%!a7_{0j)_J}#O>sSg#zpZ86)z| zmiZ7ndbb05ffi^Q_-5_C$6J)IHP6@|n+tZ|7lcjUz}N{XOv69wLeh&0LkqTfshK-Wtz)V z%Uo~zON3;Sc{H7!Yv+E2#D9VncUR9}4e!1#XyJ-|N6R z9e~OKwL?)~k|V8x!Q!B}TA1zzY0fN>^9WaxG)CoJhwIKbpgO1@;0q*Ph?WSR@&tP=-}ro`6lo^raXIy;?12 zdmNOElm{{=5ET}zC5V9hhzb)~%u;xnC6(aBMDY?;X70IXnB}j_-y;) zp-n7_!ZUr|K@&i0II*ka|Qdss)RcQV5jqL?xthqf@lt8P4G|KB!dCVwf9xVk!=>3HAPz4#Md z8bYmpYY8OpoNkOfsT)BVMuXD9Gi@Tl}vl8ND zE>u)UIz#>*+!zv?N3c9^&NlgnG9t>3r(ib+-f!B}*-QQ8?Q?5Or=SHAdAi==MECgJ zqwM2-`#VeRxoaA}{O)01_L3yF#hR8I7YKd^3U`Wt!(OlXQN-uYk*pnx!E_h#df)V` zMc;PH$`4ZPTY^(gB^AB6LNMOj;e8`BEn&d?M-VY=4ej;5iTLC0)psVgo$EH@9@yx_ zwD&7G81U=eIs@@>jq6&H`!0me<c^_;$X?Vw=W_YQCD3lzzOv1dkDhjPe#jGc zQ*83Tg`5{DUeMX+@w$C*+++@zWd-sH&_pxVH{ZJY0LG=m{Yxjw7%=iqq_AL%x?Mj0 z%9LhE`eQNA(%hFd>TDPF#h2Ak;{d`?0V|PDKPzY%r^yK!V>o8A<7aQXe_}WyCh>P> ztF|#6)p9FMyMVziTo$PM3ijWX*Cawx=GQK9rYW8xnVzpsQ@o-8%Za38EB16i?)5J| zswXtV8A}hm)8rm{o&dgyvml3p1QBex~fN44yl!nbU1pLAvEW%YH}(~8wUnUFT_!gy&LfT#6%=2U4$8qchLy?fo`(s zA{{3L_~Q^`gn*ZEQ`_dJdzF2L^|U-!VosTUo^PFEi~Lo6rA{-fGY!j2Hr>83(x~}* zOq*}{ucn86f&Pr#xE%(9ynnTInW=eu87zW7Q>Sh!5x7Fi-Prt?jo;295;#;?L> z3Ca160)OfbZ&8@+(cA(Vo@Jl1)lm=~VGK@BTRoKB`iwt>7Yqd_+jygI5R?86pZHy~ z0mg}9?Lov%xLzsX*;;X;v9G)(<{4**9WfsWGAGu*HMl`}!?X2ECyjwALJ&>(ZPjVo%!J*L(aMVj6@aQ6LRNgJnvfSly9?N% z(Kr)fyQAQmMH0Lkpp6G5F)wQ-#>UfZNOCYy-)@KMX?%gtW-ui%Sq=Oul-nnHE*fm) z+c->s8W75;=7CtEZ~F!z(3h%sX21eJin$=$&~39kYp|4x;@~p07sS^|vKqf&3g3}G z*6t=u>w~JZ9yrTxEL$&!c(=PV*D@YpW*bgmZ}zEy^-}Q^*OQ=1qE|0wiy}eaam8^M zhs}v!+jKpRm+2O*9!nWgANNPwRngN$7)o^WW{|>a+d@i=q#=>C+J=-G@~6%#iQh1S z3137qDq<=bJN^736ld!|q{%zV$(s4k4$&}C&O91%XeP5>kV;qmcxscv{jV#u8>c4% zir=P#u2rbkK-uqa&wWbM&z0Vrj@1^10s5VP6cu!q0Lo{STOO;orW9PW&MKO!I_bE& zj?!$mOz6}P_0M>p0X8RMC9e&}STbc2N0bPOM}9mU8!EboVNMT$>ezU3P$CNz<1sVH zX`62za9_E`h@B8h`dlC!Vd71fk3ogNX!9 z@#k-~j&4FFqmDUF`5^H{pFyUR#D^jGllUlf1ExowzogDp%1}?Rq(m}1x2&GuIsQ){ znYl*1z_o*#k|KPXw0O>M;w!?8hsCl*U5eX7fMvvUG7S>2{XHQ;R`R^hOqH?K71Es- z)N1%glI(f~_A9W!PSsZXOAl{Hp9XPvtBqP5<_OA(wJGPo6<$LQqb8cC0GzVAS@?#z z)haRdD|F)b26H=TJ7x4SvO8KoX_RMcw9COq#gz)r_P~_oN!9(A>IfwMAY^=oYoymu zJNQ5@IJ^tqMcWG5Owaddi)HPkTC9H9s@n}sFiHiz zRj=i}UJhAtO~}4Z?@<2sH-zElBFx8?*b+7$B=!~oSFM6wtG&hY zHlg;E2YUCWch0;PW)0kUY`8fCb2Z|+=6}2`-Wtf|k=>HMl>I`}>KND|icVwgw^<&5 z_^ztr=^p9XI?@g)izE9(v*<#G4GtyrP(DQIZx|1V@1z{)+S9&4ijFe15n)tIeCvWM^ ze2_;DWh>nYS!rZ(M|rVW)&^s2z?1p*|M)#2WM2vQ7)id;mD>DPUBrLqJ2x~>st>d< z+C!%lCKx~nzULRt!|$a9c%E~3%Nwv7t>kP>d1gRCpmKrfZM0{=OfU+(d_bQMEVw;7 z8mfMorp=bxxvl1jWmkn!R#Z}T)8DHk-2M^AkL-5h~i3oCovcL_R7VM1TA zp4z=^<@lr1iv7M|-tQf~CVOu0jYaiC&iFdFT#%XaV1HQv_VCl`K&>rkac3szj-c~L zft9y72vBYZF`ZUT>HR9ZJz8l#wq#=IExsyYq7H=b0m@n5=@--9s&+ww0iNr!bs*qd zlK9bg=~VM@A0g$zMFSS7oNkSHtJ_sfduBPm74q1X^K-(J*4yB@Cm;??o0)W~`I-EL zs0R9o`NMit>*5OVDcd&1tLUadCiEWmy(_?!zw|-;;gLF-S=8vs`%XOaGV`eX505yg z+HE;{8{~rAnN?od_`AkmzHPx8uhjlD|B8*AHnG3?eY~}lxk36~_zv0QH%j3-A-6%f z`L4);({yA>{8z)yX+THt@N8L_4PO2D1f-^%l;7=$MhE_&+^+14!K&6+^SGk#z(YAA zq0{-cCh{rp05fMi}~H$uJt(V?7+fZD`uj5;jY`~6wnE4tTlKKa978uyH6#ml6mr@%$dlJjn zk76#B)P>je$B0lR;w1QNi5!Ctod*eOG#~hL5LJ{idg2d!uS2hqU3Ml&@SYzzb>OD* z_Qd6x*4!9DZ*L4y%j0@>G#cE5%NZUwr@iex!|QmwX=J7PfbxC@R~*f`KymrR z3mvX@6ash>nKG(<8EDlNJ(C?*p&f;^QMz!*tf@9(=coy@p9ngtk==0hlr4G@DI$Y9 zqBP9+lae&H`dfb{A47-Og(1T4v+D5Lyr7Dmz~bjHfqZ(U#3r$wK`EjAC~~Fc<_5)m z)KxyVB)~|ncN80zgiTBL2q|tzTKG}aHz4a9*JsIrN+GKy6MeEt*!y;XDM(@zwgI9?K-I zOn@lD&B*SxebcQjo9U0ZLgrrSQe;L2oY%qw^_RwanHw#vXtTXwlIHCoaI_fB(15Ti zHR|&0H^j2;yJLuK&NH3D%=@5=^@Ib6EX~O%7KfDc5`%s@XNXlvbIab7&|>+~)o<-7 z(Q(tvHqtO{!Ur-c4dyP(OD^^G`faDw2V(j+l?xS`CkGLBa2|QLE0WDrokQMiu2Ch& zLXU`N#$qz_^vWB6tv9@PocHQZ^h}!63%f>-rv(&wV&=nGn1H1yMkn7fs{NVJ#7)~V zMZx=@=_iW=4$Z~$YsE{VC;o{~JzbWVEh(|hyy2)ttEkoKM3q8vf8MM6yDPtzb7>@p z7(k0x_>1HF2dN7GY>ID*qslGp?GbHMGxIs_^&_W6pcvyUHB0^j&nWGn@n)_2=RCv2 zzS-LhX%-g4$qvK(I`PJoKH8LC!e9g{GyR%r>{ z=OK!DD}~zTORqz>+h*)nunvB%7yNFP{sg zf%h%!U=;>cd4%Naz`CXCRBcQ3&>|t9iNAPg)P^Aal9Ye&b+{cqoDA=YvaqKblRW?7 zJM+seOww#JF?b)^6U5}nCYRSZO#LfuwUK-#-=d@Z*QUp=M4&@n6;PbMV+io8^e2ja z8!|~9@dsa9nwyL%8dCQA*{lr3&Sjt_DQhIxOX@fU9>kdTuywk^~J6lWc(&qph-{WJH&@>~Ex$R>wYoY!Z>({xu J+OnU1`ahWeBZB|{ delta 5962 zcmW-jcU02{+lK3_En2JCQbcBI6(gcVi@dCmSgB1FC3Rq!i85p<5s?u{@@uuo9tIQ? zNGhNK*+bbx5r|>sWe*_{5(tn$$RLv>pXa;(eg3)5bFOplJMEW8zW|`LonQTbwyzZt zvagR5=)&~|A+~beMo`}l{qsh0=B<=JM$ZRAir>wAjf*-wF;$r?JQtK0vT*Ho<9|!; zgk2f^ICkq|fbNfx(mP|G;G(csB`J@!B^h-kyRIMpA@af3qCIs?aiMTJ3NF`@)s-oA zqw_<)0Mn5dORQl7Y++%rQQ(@fDQu+vg=K2-Oxd44D(nksUA6S!>y*{vr62Abn7hBZ z98_}o+VZiC8Mj91#1{7`eX9DGJ?xouW~mqUW6ov^={E5dIV>=nMyh(Mg%(&d>ZI36 z9vLieP8An<-M3=1Wn}9&O@BSjn{B=J?C4&JKRN^Z#NQjp0KA+k-lHs*D&u&IWk0yT ze*gZryB>EkJbbLj$NcQ-D#qZ)dK#b4Gz!YQQ5pJA{4tkqzxJ!xe|3E9nPEd1{%u$T zNoX+0tC5^_7fUWQbY`T_Rs$-M& zoyhc%Xz5fA9=41(D*=7yB0EgccLLFuu}KyQKWnCN0{Z{9zie_=%yM8^9XaM}(cu9U zY97mL8}k}MeL?7pXxnh#HPOqx_;B6Jef^p}U@w#D-LL07TamfPs#V*~RkKDPpP48o z7G<$5Eif>Z-qBHui{J1HclmqGZ|GG7uVCVX-P&4g_|-WFZh`Sjj-kq+w{}t_cXp1i zt;Qdnu=O)L;;dzC)AU3J;$*-Z0_Q&{Sk~&b$Ra=K_?kSEBEDk#7zgM&-mwj=^x~UA5}-;RL7Qh z4v`>#5iTkc&EY@eiroV8`X~=$RX{Zf8uhgt`}iN8?&)A^ubR(2id*`pV||&K$gyqetX<#K#T`L6Y_x~6!@NI-ZY|mhaa;4uo_^-C zX5NYJN~_))-%~Rixl)F~(EJDcn+D=e!sLYoCQDHHeB9<{Kq;G9 zQ(@ijGgG&gB-gOMfkS|>6=${DRp0OK>c4C-yfnCnwWr9a8vhH7&lnMKeLA3`P(PI= zMiz?RB9#zGRMCtfvLovA-$5*k>4T1`RKcX@wa6Uk^sg-oSA7qF895!PInoh;G42`T zR=rRh-Rr6fp$LrN9LrT3TTgwb52^!exZxCO$VFNyN@+-0@&ebp#-Dx)s&|XGL8 z&FayAcx6>O_vUDR=bIQnpl}>Hg(9}QMS1)MBS2=W1mgsp8M^AN%56%HU|;CJjf-N|Yzofk0ZSdZ*nw~z|{%DY5INeVC zty^kP+9y+4#mSmW?>!TG<4lVKv-TaCDLLKy!6{^~)S5ZC4da?CaC~9z)qHzb88<0% z|D$}~5vtpPV>?=Xw&M7Lvmv_Gll#|wibXRAUwtYL#ID?xSygBJO_-THAi$=R zwEx`!v-`#=`q4jAz<2!fj=6JHmwzyQ;V!a6tP~#AMqd_xH`+b~4@NH3sF$mDFMa#o zhcj^&cDX94{mpwb-5-sz5I_-DZ4vci%lqS==tt1a_q^vvL$OB@@%7p-uefh?5@Yaj zXY@$*$(R>e^Tgh=BYm0Hnt?v#va4lV_;&9!<#F0G=ARMU_<$F%1D?LS?ssMPtqIKc zJA)EqM&7m_P4Vchx9Q9D$ah;UOCb@*Zl37IyreDtnbpB9-;NEzEW2KJ_j2`8+`QB< zan`wBJ9F-!s~$hoE`L0{e&Y=MgQ}S3MR}q(ZmKqk4(+u0w>vWtvK#O^oo1i@>-E7= z-bwJ+JWL?hiV0w3`xyPJyS)gYiEOz$)R13h~jPuZ#}8!|a13 zTvy7geaM7jsURJ$gv34}n~PegW`qSu55m9@=xDeI@y0BTD%wo@uBlH8xhEVuh1MyA z1@&<6FYHAMay7@?#Em7(dP0Am*X|*)u}EmQ5S<5xvb}D~@3ebcFA_yB= zt}{JB<12%7EOir+x{?4A$7ohiefQ;jjIe`0Q6wTKd=r~a+zb{$(2nJtX1(7vS|grI zUGxxTZejBn8ln}j?o=R^kMbVIsWi-pmbGU+A0Tujdzd&f>l{vi{skg#3iAt~x08Yd(9u2A5di+*FFJkVwqghdkBupf3-Ij0T(SGGxWV5!u zp?ufdZNMhUZ&6b)$r?^rm1z|ZlIG$Pp4mj*FU>cjm_AwQJ=Y(r9q+NH1D^$*xM&iR zQvv${;4A35pF4XQM&l|&ckS;8OYEm{1}?+?4zllYN3Q(?LcI?$OxL=0z9ThF8s1vS{{>{7Kl20MlGp&e~;WC#cqpTlT4LAVPx+@qSi}(i^ccCcI$N}ol~*AKg|;6K^WD?&$h8oXgpaX zq%D&Eu#MB310QZxWxkAzokSWDB4at9ZGw^f(&5nQ_i6f`AleBDHxwbMzKEerPc%tfoK<8jk{&9~N_A$0xy3rm2iU*~;# zg%kOS?T))o=QnUxowu5lMB-dyJA9Qx&<6vq*jfa{X4cDsxlHFsLK zz!!8)I*$@o!EEQy9Hc`rLut=#<;Ap#<_{0~Qv)|LZsUk#aaf^wk_Y?q)xwWRcy=s9 zq_V^OMKQO@1f;%o(aJf#aN<$>q zx(7Sp!+)sfM>M2v-?%Dzz_v=*U3PV`s^n+Y1(3a#n?vC5h*st2$pe#JFa15x>LIB}WZG89_}RKwpyT8;+i@`jqM={qdFu zpzWbYeMji2Y0!Rq9&oY5#LD7dQ^NgZ=6_Md?AP`R?D);suw?xSkTOG^JkGwtGhZ8N zy$tb?aL_l$|CZBNg&$F`;XA3=TXe@nnU1o{iM zs^n;3a1f-fNc>Q!#rBMM*N9_J8Uylcgn6?|n^l_L{OIp*ey1!~+YS*7vSyjYO!c$G zFEXXe!zv>7>Bc(Fsgf~7_&eN++(-Ufnu){PyUUWZE`qkzg8H0IYurFV57S|B(Dd|( z(8s7Su0LIGQXsjXIoe;hY{iF5w#3+2I*4yGniTT9MJg>}%ExqSo#3a4 z)3*wf^?TDIfge504(RtL#?>!eB=*&<_B==7&$m=7Qtr)>@`91*4j*x)>LB^Jb2+nq zvVJtRB#{SIUbhfWRJAW|n#-)Mvl??E-)u3`Xojc>E42y#dGtVM9*URiRyewMJ)tJ% z&+75Xaa0*Hpl`7~h!zA=9(Tk=_Bm5dC}$Bmt0W-CllSwcXM9z(HDn<`*EF=9-@e!y zjZVwr=h7v|gze0RQ72spWiczrUOo)!hxbQ_ePX5RwmUXAV691JOgy)q5YDwA!rzkPI!|F@&yGf0uTvK2i3K`UWl{fr6=hQT z0Em&bV<>r5koAk1dhE_+gg$VG{rY{=^BNe?ztq3L(cK+Ck@sfZjbZIHv-QHXli<}NbwH$CrX9kkD&;a#=r1f+@O;$5GkWc$L0+78fN)r;(@9AMawctXQ z&Nb*|ncZfoMNLi%9HTohehY+|Vag0gpWf^Y{z9x7=EuoYftc)orP)Y z2K8b+WlJupHO!nkEzt$7YdofO&cLMsF{GvG$ItCIRwmOjyNELkHs^m>1K}Ja8m;o>d6huV)@&{68gXcbTpCpi1F82ryiRE4lD{IZQR@7OdWX<2Y^xzK1_xByrr%Czaqgm@XS~ zx953&q^SQWN|9THf72gw_vwNELaHrwJ2t|}xWKKH03y2-pCQsXJkgtlUr~TDkX|T_ z0ZB;xw`&i7JC6qPi9d{p0qkxPV2T5%^#VPoJzI@ws$|4E6`h$jWp5fV;REJ+;{09i z7U9QS)oGr2<^uhvMc08+ysVeq8!+{QLykDdkLbu@=uRVB`W*9RQ^x zbUo|<8Fm_4TJ>^%5yTzb2yZ7|Hh0+`sc(){{jYx6e;EbhQl`>=-d*f8(Q(b`Wz>PK82*4u9KYE@wGfvPMMG`hYy(#(XtN#P&J{)8K diff --git a/man/VT.difft.Rd b/man/VT.difft.Rd index 4b36f71..f178fde 100644 --- a/man/VT.difft.Rd +++ b/man/VT.difft.Rd @@ -10,8 +10,14 @@ A reference class to represent difference between twin1 and twin2 \details{ Difft are calculated depending on the favorable outcome chosen. It is the second level of the outcome. For example, if the outcome is 0 and 1, the -favorable outcome is 1. Then, \deqn{difft_i = twin1_i - twin2_i IF T_i = -1} \deqn{ difft_i = twin2_i - twin1_i IF T_i = 0} +favorable outcome is 1. Then, \deqn{difft_i = twin1_i - twin2_i if T_i = 1} +\deqn{ difft_i = twin2_i - twin1_i if T_i = 0}. +So \emph{absolute} method is : +\deqn{P(Y = 1 | T = 1) - P(Y = 1 | T =0)} +So \emph{relative} method is : +\deqn{P(Y = 1 | T = 1)/P(Y = 1 | T =0)} +So \emph{absolute} method is : +\deqn{logit(P(Y = 1 | T = 1)) - logit(P(Y = 1 | T =0))} } \section{Fields}{ @@ -22,6 +28,9 @@ favorable outcome is 1. Then, \deqn{difft_i = twin1_i - twin2_i IF T_i = \item{\code{twin2}}{vector of \eqn{E(Y|T = another treatment)}} +\item{\code{method}}{Method available to compute difft : c("absolute", "relative", +"logit"). Absolute is default value. See details.} + \item{\code{difft}}{vector of difference between twin1 and twin2} }} \section{Methods}{ @@ -30,6 +39,7 @@ favorable outcome is 1. Then, \deqn{difft_i = twin1_i - twin2_i IF T_i = \item{\code{computeDifft()}}{Compute difference between twin1 and twin2. See details.} }} \seealso{ -\code{\link{VT.forest}}, \code{\link{VT.forest.one}}, \code{\link{VT.forest.double}} +\code{\link{VT.forest}}, \code{\link{VT.forest.one}}, + \code{\link{VT.forest.double}} } diff --git a/man/VT.object.Rd b/man/VT.object.Rd index 3094fe6..1698021 100644 --- a/man/VT.object.Rd +++ b/man/VT.object.Rd @@ -40,7 +40,7 @@ treatments.} \item{\code{getFormula()}}{Return formula : Y~T+X1+...+Xp. Usefull for cforest function.} -\item{\code{getIncidences()}}{Return incidence table of data.} +\item{\code{getIncidences(rule = NULL)}}{Return incidence table of data if rule set to NULL. Otherwise return incidence for the rule.} \item{\code{getX(interactions = T, trt = NULL)}}{Return predictors (T,X,X*T,X*(1-T)). Or (T,X) if interactions is FALSE. If trt is not NULL, return predictors for T = trt} diff --git a/man/VT.tree.Rd b/man/VT.tree.Rd index 7fe0bb4..2aea263 100644 --- a/man/VT.tree.Rd +++ b/man/VT.tree.Rd @@ -70,7 +70,7 @@ screening field} \item{\code{getInfos()}}{Return infos about tree} \item{\code{getRules(only.leaf = F, only.fav = F, tables = T, verbose = T, - compete = F)}}{Retrun subgroups discovered by the tree. See details.} + compete = F)}}{Return subgroups discovered by the tree. See details.} \item{\code{run(...)}}{Compute tree with rpart parameters} }} diff --git a/man/sepsis.Rd b/man/sepsis.Rd index d9509e7..0e1b14c 100644 --- a/man/sepsis.Rd +++ b/man/sepsis.Rd @@ -4,22 +4,17 @@ \name{sepsis} \alias{sepsis} \title{Clinical Trial for Sepsis desease} -\format{454 patients and 13 variables. -\describe{ - \item{survival}{binary outcome} - \item{THERAPY}{1 for active treatment, 0 for control treatment} - \item{TIMFIRST}{Time from first sepsis-organ fail to start drug} - \item{AGE}{Patient age in years} - \item{BLLPLAT}{Baseline local platelets} - \item{blSOFA}{Sum of baselin sofa (cardiovascular, hematology, hepaticrenal, and respiration scores)} - \item{BLLCREAT}{Base creatinine} - \item{ORGANNUM}{Number of baseline organ failures} - \item{PRAPACHE}{Pre-infusion apache-ii score} - \item{BLGCS}{Base GLASGOW coma scale score} - \item{BLIL6}{Baseline serum IL-6 concentration} - \item{BLADL}{Baseline activity of daily living score} - \item{BLLBILI}{Baseline local bilirubin} -}} +\format{470 patients and 13 variables. \describe{ \item{survival}{binary + outcome} \item{THERAPY}{1 for active treatment, 0 for control treatment} + \item{TIMFIRST}{Time from first sepsis-organ fail to start drug} + \item{AGE}{Patient age in years} \item{BLLPLAT}{Baseline local platelets} + \item{blSOFA}{Sum of baselin sofa (cardiovascular, hematology, + hepaticrenal, and respiration scores)} \item{BLLCREAT}{Base creatinine} + \item{ORGANNUM}{Number of baseline organ failures} + \item{PRAPACHE}{Pre-infusion apache-ii score} \item{BLGCS}{Base GLASGOW + coma scale score} \item{BLIL6}{Baseline serum IL-6 concentration} + \item{BLADL}{Baseline activity of daily living score} + \item{BLLBILI}{Baseline local bilirubin} }} \source{ \url{http://biopharmnet.com/wiki/Software_for_subgroup_identification_and_analysis} } @@ -27,21 +22,25 @@ data(sepsis) } \description{ -Simulated clinical trial with two groups treatment about sepsis desease. See details. +Simulated clinical trial with two groups treatment about sepsis desease. See +details. } \details{ This dataset is taken from \href{http://biopharmnet.com/wiki/Software_for_subgroup_identification_and_analysis}{SIDES method}. -\code{Sepsis} contains simulated data on 454 subjects with a binary outcome +\code{Sepsis} contains simulated data on 470 subjects with a binary outcome survival, that stores survival status for patient after 28 days of treatment, value of 1 for subjects who died after 28 days and 0 otherwise. There are 11 covariates, listed below, all of which are numerical variables. Note that contrary to the original dataset used in SIDES, missing values have -been imputed by random forest \code{(randomForest::rfImpute())} +been imputed by random forest \code{(randomForest::rfImpute())}. See file +data-raw/sepsis.R for more details. -True subgroup is \emph{PRAPACHE <= 26 & AGE <= 49.80} +True subgroup is \emph{PRAPACHE <= 26 & AGE <= 49.80}. \emph{NOTE:} This +subgroup is defined with the \emph{lower} event rate (survival = 1) in +treatement arm. } diff --git a/man/vt.data.Rd b/man/vt.data.Rd new file mode 100644 index 0000000..43ddf47 --- /dev/null +++ b/man/vt.data.Rd @@ -0,0 +1,28 @@ +% Generated by roxygen2 (4.1.1): do not edit by hand +% Please edit documentation in R/object.wrapper.R +\name{vt.data} +\alias{vt.data} +\title{Initialize virtual twins data} +\usage{ +vt.data(dataset, outcome.field, treatment.field, interactions = TRUE, ...) +} +\arguments{ +\item{dataset}{data.frame representing RCT's} + +\item{outcome.field}{name of the outcome's field in \code{dataset}} + +\item{treatment.field}{name of the treatment's field in \code{dataset}} + +\item{interactions}{logical. If running VirtualTwins with treatment's +interactions, set to TRUE (default value)} + +\item{...}{parameters of \code{\link{VT.object}}} +} +\value{ +\code{VT.object} +} +\description{ +\code{vt.data} is a wrapper of \code{\link{formatRCTDataset}} and +\code{\link{VT.object}}. +} +