From 7bede225a1d41fa575ee7c2577c9f3bba337340c Mon Sep 17 00:00:00 2001 From: Will Beasley Date: Tue, 25 Feb 2020 01:38:37 -0600 Subject: [PATCH] 1st analysis ref #2 --- .../figure-png/scatterplots-1.png | Bin 0 -> 19640 bytes .../month-performance-1/month-performance-1.R | 140 ++ .../month-performance-1.Rmd | 145 ++ .../month-performance-1.html | 1804 +++++++++++++++++ .../month-performance-1.md | 226 +++ config.yml | 26 +- data-public/raw/month-performance.csv | 5 + 7 files changed, 2322 insertions(+), 24 deletions(-) create mode 100644 analysis/month-performance-1/figure-png/scatterplots-1.png create mode 100644 analysis/month-performance-1/month-performance-1.R create mode 100644 analysis/month-performance-1/month-performance-1.Rmd create mode 100644 analysis/month-performance-1/month-performance-1.html create mode 100644 analysis/month-performance-1/month-performance-1.md create mode 100644 data-public/raw/month-performance.csv diff --git a/analysis/month-performance-1/figure-png/scatterplots-1.png b/analysis/month-performance-1/figure-png/scatterplots-1.png new file mode 100644 index 0000000000000000000000000000000000000000..4480db60c1d4b7c10b95f4692a1a594590c8a797 GIT binary patch literal 19640 zcmb5W2Ut^Gw=Eosf=Y>kg7l(*bP?&zPzC9|OYgmRRGM@}K&c|V3y27zN*C$91_-@| zCN02S@q5qt@BRLJ&$%~`KE`Axd+)X8nrnaF)|`gFuK{F@Lc-oeIn$5IV?nsb?DAX^=B5i2bpRRONsXa)-TQ2 z*Q861k7VP%*(Br%rr22q21TdF^t z#tHs~goFp({S3cb~7<>w7H~l$FPAt6`-BrWFIc zrD}yCdM011^hzmWWVTqbLt9=B*jAsMmlGygP!r)bjgE|t-X{nnGAhwv^*h>FE+3N8 zGB&2ArRDOx`|3+|wPvA)>A}Kd0yAC;5217wwk3hGl9H0y;7(>DaQD~f=dmD=Iyzht z2tLG!H^aXE6$2K>lVBB5FLgcEO4rZir9{v4o3mQj~#un4Uy zh7x$gXD|OuJ6)k#iBtI;_Bm&&tol1*C`DFubp@*GRsnGQNM&%H^ucP-es zxN#7*HB|#Y-bkI|NI?D=8`DaZ&mC>Qa^5HCsi=vq%}U@L;aU|gz9IG#)8wYf7y-8Q75 zuUU({n8Vrsws*tCR#8ghMNLM7&3UN$dE;$3FTMd)XL_L!d>559Y{eGPMDXm_A1aaf zl#IJ)J*gb3q=_HjpGi+<9XuUPKWv0uMo zm!g5+f7rIVx3?D^!;Ert{QtS8GKLX z*3TU-R6*|VEGA=XWFx;66&0a1lda`@g3R%k-FpL}6fBW`LHjai-CR*p4^v1rcq-T_DJY863QxEm*=0BCYiW^VUnYBf|E|N%r!R}gx8&+$Z(q_RPon6N zkX1MbrO5OAJ_T>LnQnNSKjJMylalu^bx#W}YLA%v_>uflHWmp34@t>W+F4F3DXF$m z^ZT7Hyt9|T5q*T-=}Ov0Mt$Or_Vy#T)x3%|@c6uSLAMnsOesUehUZflF>RymXwh7Q zUwBxUP6l6$HhXX|R+R`0+-@SeOuC7(~@N;q?HaD)@n&NT*{w?~mx9o$4#?%(D41>Y9b z*YD2|8so5H8KUN7W@5GN$a%yihMJ#E$Y+>+1!YL+K6BsIb=zCaRjxJYlaUPA-I*0$ zFTFM`ZRhA1c($G|7;C2chdAiujangk)A)+w_U*@hf41^715>^feE9I;+O2y~*py+H zepBE@$PE$(M#dZTW}UHyRhGSAB{3Td}xp_+68yy`TA0I!qqigl+ zJFWP)#H8>p7Wu>(@zpRq5}xx2Lv~!=$S*%(k`Mi)C^!?x#cO1Yk6XKkpBLKjUbt=P z{a!iHyc@LxSI$=R8ah{dHr1u7t9$?M-R1NWuOs$*w-kr(h;MH7*jC%}8a7R*B7cO1 zg+)f*Oz6&0E9Bwfsq@$zThaN_I;Iv-#=t4|oP?S!`=RgD7sI9_Xh6A916nhsYh!a0 ziA1)SF{sF)p`vjnA90q$V5~0FJFGzR?Eo95Rr4!2@2NEHk7G&NSPZHG0Cv)Ik7-aX01~=$$15Wnw#}s zFiB?9XY2b;1g%bb(BO*5#dacVz4sO;tE}|(_03F8!FRt-=YXJaKE1d{a#vbsjCfrM zilTeOnY=ku>!zuxNfXD+$?1riZ^8D|!-n9Jg73gaoO&+&ycUam|NcElv{_nSV{P{! z!4kp2;hbf;xyxIVRZpKjp#}9ULVk}}qEX1jnuI{?Cz`*Hshy)Y`-I{W5TwY$zIv|7u z)6LU+W1f7*!S}`&TLYi}!GJ4*OXA*$1wqS$*RV0Kos@!)4PZWxItQPSzW)5EBdGci0l|TU!Tpa481`T&w zP1P%vS*3&oe}$svoiJxX;oyp#5DOt75cG8{;>%!g2M}?|X313;<}em;Te_G_paU0( zPn_-qfqZEl=fuB`dG-niix^u1947JkS#zuAGt9G>u;$j?C3m6zOz}9(U^IsWha(97 z9u0=22@7+g*V13Fi?nhRg|}K(-Kd7;4?jxi7KkOW4Q=ULcR%ZU|0K1SjMKo{-d=-+ zbbWoju&|I<(NBa1KpE3_fyh1YEl=S*!tX6EX+6t}H5B>7lY1}YyUnp3zhcFjkguaF zwU=CL$-`P!TFrFFkbC$7A_8EMexJ>M{dC?Yg@};wE~<;Wr;=B(Sc5f7i+oEUR=s$1 z%^x|r?U^Y5u*JCEjJ@ZVIZt4*jg8Ivi7g($R6~M^X4QJR2R%mbUNEV%CQkT!qvr~P zTi+mm^aOlwp+F5x>Litxm0^ZfA|BQ(sqeq4FD)H9ye{?6E3H>2o{f8hv6wNT3k}AD zO>O!k1(dP}BMiyF&@1747s3rzQ%7y@!g(Q(lM5(nDAW&xgS*KIESakDVEgx{CtzDt z+rb3e6clymHRfG8JZz&o&i!D@3ZFH5xj5{c@|kzVcXi2CL}5dMmBNE}EC0UxNV3`M z*$;3j5W0CdDJIMy#E477zq9d~5ZB*X67$}-TUfLun8}7vOElxrVh(G*OF#eS24>Rc zwPDS8cz<7WdL2ycj)|RM1eWUU&;G)QpRKLu$Ge&D-@nF$&q*Q_h1FSeKsb!Vg3KR3 zYsP~j`f5&2PA)IbJKNeK3`rpn+=saS5~yu|1tq1vU%ze=6O+MNAP{_0eD8NY!U%kN zF!rB5eKIjIF(tbOfjlF|;-YX`)t8f#(*nD&ZyhWPiaCCb0g7Tkc{YZIh90dCGjnjn zQ6l)>L6|s&oZQE5bi=G8h}5g#U3SbpKyK5|hlXP=8%m9B zB=`5WAcM77#(H{nffv4)k6XFH=CL_mUNdR`#PYYClF~|Y9F3^&uMdxy5^T1os^7hP z2Y?B(Gmbe#fGYMOz==ln0xYri*_hK{%dcKXe>G_ZfT=_L5`a#@SjLbE`|lGI6Nzlv zXN|7Y-yI~wi5mV)*{$|x_T!=bb{qI@h8~FL2qQgpUtCu=YcQZ$j2*N6f?P8W5ZA(t zzr@S^VS3*Nqb9%Oox5yWP?$a6bna?Suce!e%ys$@3`)c7+7&wWK~(N{sEx@zAixySj&2oX{>bDeCI-xG7&Tl_|OB2E8W+S8*8D zeXFe%6cYTmkQfC81xclSL^443TwGinE!GxJ?*n^n;KfQhrr+ z_0jQYD^JF+H;D0z6CZy)-||;JJn}1^@JEsFdzPts_%?&k3(Y}8;j>9|yA&Jm^}qUw zWYpEw9jx|)F9U-EP@c53^lez6*W*{+%dQ?3h&5Yo0;IEmvwa?6EYg6J?5g620cTw2 za7&a;N>X2hDY=YL)7D+VbfsA2*He^E(p^t)XR6Lhd$_VH+T=h<)7bcGtE#{8bR`vi z_3}-N^V&exJ4V?ejiTOE{#}6fPxqHOlZ$h5+AOQ?-o3j$UBe|T3~y`{V_-0Ci?|(i zk7Lp6A|PEXK!}|^T6qi+dE_0tdp2Swkn}O*`Mb={v`%Ce%P+shG>eIis{Ga`H+}ET zNT`Zi)%PqH6&Dwmm06NAadL7#eX3cib=61wa2{M~uG%9&qJElISo2c&OICw~Hod)K z^`3&@dP4U|OVr()(jd|^SxNL26cnVSLjIEjR$%V0deR;{BVa{f=VT9g?b@|uvE?|? zlXPLPd!(e^SGybTbuP$`y|}2zNO^gAkl|QJ-By0nhop)444Lx~(u({{EdcQQlrm zB+SHsGx;l4P_5wXCH~3&{(gm7r*F_qjS~V8oqL=Ha>MRm=^yXRHcali){d3xACIUj z-^O6M-w#o@3dRyw%>+@f|j+zO?m#lHv7xTt@8n4~g^@kcHF%*NL}JEcjAO z3k$m!oLLfoMbn6KrHN#uypMLr1G%4}lx^}8rR~pbPQP-pSfrkwUbIYh&oZF!AQi5x z4ix@uE$uifIMEQ-0z!wgX3kwypO#&hMc-%mtYd>wKQ}o1xttt6A>ol&u1c8DHgzuz z&_D2bhi(GQ%*mgi&Iy=B%G%nR!sEY61lth4f-9D?YGorMvw-BCXu>lhqYjs}%S9hn9yY&; zn80F?LnT<=-|~hwzSySGtZ~a%7NFjqsp>bW(WDVCda)+{^7pnoewhd{1kxg_ z=iq82pJ+KhA-utQW+0+!DICBe!kUuJ5~)Jfs*|F4dv^aUI+YSp%HMK9hy|e&c+NY2 zgP!Mp`iz@|Yuro{Q$y}^CtIEYS0BKqb2xQLV)6vQWjYQKo@Am8%%_%%8~pa?sWzP`+|zG{KD9{bqzS5e+2d5D?sgQCqQDFm|8VA3a)+;%bD}utIM9q!EGOw_5Y2 zykLrIR|60jK4V((nV6>e3P@jc1YstJzM?&q`AX^ghMdVgZmzCvMK>iX|Gt;5ls~-g zxiz7xqr>9K0SN{JOGlMt0YDj17Y;5q5Rvd@m=f;C$iQbgJ?SCAl7|qwf~~DBuz@~g zVzT9>NXcvH8GM8{Z}oTl0Pm4jWlAXQb;T74&IC%7gq(W5QiFR|yXjugL&%+Q%=e3o zh4)&X1F5CG3}3?awFhyA2|0YWOob&xFROI{z)FHv{OX@CSKWmKV@cqV5(}R2QY|)V zRa3G%Is&mkaYJhjPfh(o@WeI|`n$PR?Vh}S`_`q_U}!S#*jr@i)S|p=8|bEpPC`3GM^E@r6sk-G2{GrTz$2zf`}mP1p?eXDtOAe9%2+Bv22VrC`!|@l@QG_vBWDTNPH%`-zzF^9|%IwTsr+NI1(>^_4a}w z;%en?@I9IWs+zL+MVpJk?p#BA*)0iI%mn8|L_~mee+LH6+!;e@#Y+K%pW{C$$UMJ* z6j%~xE2&QPahj}}^74^-rI(9QTvF^eBvQWO5kr1*Q^YVObemRaXlb2s*66VRXrc@BNHOA(rPgU$cGCxi*9?TL!)uU}QR^dOK`@Bx+9aAI+n zMck_s^y$HLjT09eTPwXUl?m+S;UG5kOI6qy=wca>2%6b|+3m)-5-obhy`U-|yd~a85|~ zGt5N+UJig(ni6x6&lJ!G!~)LD&CLOC_}5Z>31XvE>mbg8=l&421nEa}kdpsRcy$kT zL-D0<143L{TH1K)V1Hkz>H)}UKtHyu@)4mygaTw|I*LQ5NPW%!`SWf`Vo~#&>1lS5 zot`LQ2h(W*QRf6@5@s^R-n3Z;mny`Qs1&++0;H6tvyEZ^eYIH=1KIE)uc!8qogmqe zkdRpLq+#Jg)n&2DRaj_z*XWxPu_1=RFPK^_93a@wWP?oe^Yh0?M^8&hA#2zpwnw?E zN08<#p{X~SPptYtZt*{!_43*ri}}K`yZ@Gi*)z}t0{t*FJPe@F@X%2Gc-_K+D?cP~ zOto1#l`kf59Uuw5p6M5{*C42=rXX=?RX~;;k{IW)&?VWyR=Q(eoz#%|$ULQVR?iz? zHsDxS+cgLx8W8~@p)>eyqunvWAn4*K-QX?+_i_HPuDW__=G$>=UN9~gNu3Pji@9-f&&UmPPyU>dA<>DwG@XhnV957!3QzF$LCd1B9P zdk*vVilh8QA<&s$Jw0H#o&DMFIc|AE;0BHYmkkC~X=@0Qlbg;b2sEZlUs@se0(3Hf zJ7Dcx7(IaC5>`#lbGTe%XbM&Ka~a%Rd?JOAWNK{uK5 z@$+162)_JZ%6!Q}7iXcHWFd`NM^nTnNl8f@`rm&TlqDMnPI}eK=jwg8pDZ_q_gbbt zHVZpuBFUDG%iyuNNpIetAxg>bc<3!sQBl#}-oCJ~@L#YU5fQZ4r7L9KODG+q{u?(1 zQpAKoO)GRT3fYez0u`Is@o9f>F6*wQzB}lr=J%xwA8(F3R!y3knQ509tiuQXC4QGT zUHZDa9|E#87j$*ubFkt7=n(+w<3@hlV6mPC2kkZ-GbyHoxZ~k-0*yL1H`h4mqT1`N zQhrZ=KUu{Ch|NX;afY&2EV7ugXNQ236H^Jy3#SJHeW@uBlj#5dq)8?lB+Pv-P*njTNznR$nR$F-q(8-Vl3s3`4nqiuH~fYr~AHjmE(MIorTsVTi!Bg< zAnRE|*0!`yEMEW(_i%lf)^{zd+HO24F%dIZJxLtszTPnG#t?6jj7REu{`=j`1g$`)1e6p&?11w>7FJf{8v9Q>)cE8h-F?Wp8&9IXEY=l>#3E<@*#m*(ZdX>jGL#S2Jb*S=Aek^SFwppI zRp>j`E+^?bu1{92{tUe}US@dChS13$j-lj_4KmQs&`?wR>5>NS!wAt>Q31wwh*xp= zFip@6pPpGcgZI-5kl&4~Z8gE_k(887S6a=r17t*1RdtRLOS>Oa^XfHD!NI53Do)IN za4iJ-rseaft;?GOzP}s>t@Q-xw|RL?u&!@5!&3n+IyyQq*lXiW66Jt^0Du2_z``Oy zJttS~ZEtudcl4n3$hteMG#>e5V`IZJv+gHz-xb%pZgVuDWu9_oqs?%h@l^*ve}3z^ z$tUT^p`oFjS-3iBVrFL0QrGQE_{+_)QlMVUjl&JffcDy(E}RU#bN4PF5Q4F-fe$3+ z4*~;%KrXB_29*xufTP48%UE(MvVN%3(^F#6!vV1FK~_xWGQM2Pj@to4#&4L<$Hlb^ zPyry*+AO4C<%0Da5)bxXAexF_91fF8=jPwIlK2jMoZ{E?fUhvz+%2P6?tu-KZY z!12nzhJRBgd(fOmmp$p%FL}iBy{PtO*SDB$)x(|W5-?5xq-H_Xy~4qBY&g=2>ulxz zO`ALITGi&Msin0D4aomV?`td|h2TU;9(s6qbjHzwHREn*XqdV!$C(V!<{!Ya zLFhARZa4`@?cNGs3-IWmKdY>)q?ZgcIMV<(3D%fkAXm|S)?HU&jRYLFjQ zEU+ZBzYMRt3(W!@-M=4>6|4hxB!G)(MZDvK(lRiQxsj0(z;S`R-86C?(vtu6>%g|> zv^`(oVr;T|-T)3RzCje&w>AE?yX}rv)bG@7a;k1%#h3Io+!KY!_5SB}=F)dp!l3C? z?+|EX02Bgg%2XQ*Lj9*D=<;-R?#2Oaz~NwlYPMx>%IM6@R`O2(z6(cfFQ>ji=*nWT z16y8S1Jy=T@|Cu?BtS$W=YH7?N)#tXo{(VA-2D9Hq@)Z%x4b{eZ5XH|lp@^(;s&7F zLEeiNJlbe#;Xg;?#^akuICw;d`YsTt`=4Eevg$}~_}R&{GfxhDZ=w5O z>zr}x7Y%`?D_QY;LTgY!aI*^4^CJzhA7~PnenE|^H1K7E@Zfbw&`t^&Ih2=9#B$Oe! z$Er7_UHm%4S{q=D)YM-&`S~^9zC~yf2b(XbsYB=<#3H8*^2ZjOUv>g4@fUFd(GiRz zP#^BV)VD@JCH`Mt0P-*!TiYqPmlIgp|B2stUp7OMdyY<5Gf7~44pZMiHUwx33+MV@ zsO8SvO$3>*F(uFY`t@sWZo6%@8fosJHBdf*;4TsQ_iS8EXdXU3KA;yqd?=lz5@ARb z?EaT`WXr@9m6eIPEK2$K_yF)&<2VaAmGh>~KiCrNgWv(~ijtBNs71uoLI660z2Vuj zR};BdaA|OFq=)xj` z*$6y;2G+O4Vtf&A{4&0`RF-(9aTByUNwN3T%{oSY5r{=5qa60wd*rR8_HZzUh->0< zKu;tOyZu*BbTNP{Uvp_bFy;hbdBt?cIkYAAibNiBTu&u?kC7wWd-hASh0eFf2XCXI zgx%Lv08h9Zr_q+v?p#=b?Sm3gIVmyJldDZsw>EO^nu+^=ttpNg3P>33}&1I3#9t;T&k1`|; zCS6cw1(^W=Zb|&N5fO4A=w7@aASMP-&e(r1^zY*MgP~dfhyCFHnSuen^O}{N-5ov) zG&03}Cs)@>orhR*Bp3$uuS~q4FzvtlPaY>*(lMMFr5z zU!7oRq)@$`6AOZm;aYTn_Wk zcZ+`l6mYFF1Av4Nun(vxWPbc;T{UU>`{TQ`wBJoH0pn25d-3?w3%l{MnCR#i&!68H z4-}zqTX1IAtu)_T#NhmN!v`3%&M+u}Xlho2(nZtN#V&XqBipIcEL=OaZ0C=i>asdN2mQf{bYII&ZzIIO@EW@4EFgAyf?OZYCxLBw0-mB@=WYYmy1zdffN$jD;`@XIJ6l^R5pR2q?c6Wg8@#rUM4 zUIAbvSiwY{F6=$~`Z1ICjt&mn^X*{KW@WV)=f3^D?D~8)xq%_f#GD66N?OuD+&rC#Q!+{ZvptsvTNdhhqe16BO^fp4~R?}?*K&2 zTUQ|FkW1>d1T{*G=1xIL398=aJTK%gt|eKdD={~X0{P=j%Roz1qPzuQZ5NKx&~21WXFd zGu73Pf`WpaoDifyDD1IS9~G>tJAoOvq5xLVF4Y?a0>!|9O8&6Vx-BT^fYNI$dE}Q9 zkDEX!3s-JUo=2AUpkhe^Z=F3Y|A77cqEb7gx09^X??o@EU4q`f+k zb*dwQ0U&q`pyQtGIH337%Xc{XmR*6}$#G|E>w!c>3W#Z93QUrLkWBB z@RAb%>o*g^M8``XWq60f!f_r;1ST*2d;UXJ%Gr6+%PDO(7bL1%VaeyTLji`vEZgbD7cgP7N$(+fB0c$zSsiE$1>yB<)Z zIAT1AOVL_oDtBNQCzFpmZ0hS9QOwOW1TWlSQk8{F=6d3sh?Cxas^;Gp4dtHx6{bkhipDzGUyZbikr zH;-$lpSUk0JL=r-UxdZ{I8at~5l6KAadMLtyV$$$V)sU3KK%=*RWS)AL0>=C&FgJ;GaY3-|G9khh%Bd`*dOrB}~OQ+V)+2b3_|h=W~|xhIS7Yi7=2=TnDvPWA&iA9NKJtah6{yvEUuFk#-NX*vMZFaK z19OO(8<=lMwPPm4#KqCE*xs&{Wg7eJud4}A{g6IpM|URFJjwX8TYBrg=?`b$S)_Ur zLe#pah*^&#Z!|92@S&6nNMW4c0#*~4+A0^y;^>RYXvHt&U`P|zWnGIu&=x`%W4X4;d_ZMk6UxZ9&!EG ztAn7x%bLY3{{G)hr*me)HU14dr?uq)oSq&~=fkk;yGR)`66V(5J|~&8cz+IvlP)f* z_r?vcI(6N2WBoP}5BnScY}9ER@8<9)x;K-+7)(i~*>8+WSrW37=91&Hgx$*D4f0{k zDyTT-3iQ!KV2xkV(&y}U-N>JJjcGJP)kR6)nauZfWzQ2iNDJnp`m6#_ML&@2#wVZN-l&a6%? z%iDa#9wrwM(BO41;Ho0Kjr|t(i(|+8qi1y?A-FI(hX$j&_ojSyAFjKh{8ML2n*867 z@n3;BCAaH~G`x))uj+NL+|Sf@IZha#{+jxw1iqkt<0h^0oY-N~c{?W|w(8!N4>KEE zY^ETGCp|R6z|re6#ARGD)wOP8tAk6NF(j=}NciF%-cE+U{%S*E&hh*p6CU-NxUZ{P z+zhn+>atNw)|&a!#b@lZopi}f?0bsC#YWzzL(9T^mz`Jb5}zL->Sj%=b?m>dB;AYa zk;Z=;9dXh_5>?(!IppKSx*ohby`<(#_(06T)l2LmcEaP?=Lp5_{foz9jKX4!`X#1x za?;XLfDA?`7pkzBeXDq^=S1tD#>b~bIb8@oFL`L40Bjv)@8|9FO_%sI@&KYunY z{RlWiKrv1XX!Vc*&F4b%r&YW8e**sAD!0fy|Ec9FaY+2G=PoH6iZAtrfcQD>m#cot zphzXT^Oa1lcB{jRNqe48zwh4b5WjmjnZeP4P6)AJ@|eOVPxB9Aor0XkxiH_z=ke1= zr=w4ceXTs4?ClSoOO6YdLcZr?KeMfG&6f2Io3!_QOtY(=&MyKIV}R_8!Tup{c(p|@ zn(_pG=3UNt+J-0oR*xd0ycdOvC49YrwOwnXG1$-^r&BWawrbbz$x9;tFdw+uDm9Jz zO7H$O>T`Wf@h#58#6+MG>6QN3&^}s-a@*B8{N8SwWuup?W_WQEe!Y0KXwbT?4CaqU zag!4O!JR4L@KLEk1^cG6z)5LdSy|spZg-SvuG(a=Hdjz0Q;IlypzHDh*Qrs_Jw1JW zP{ZP*g>}*16F;r7G6uyAP?;$3aHRsCQa*DzVY1)Pny*S4&(el1V-@98rEh-k`y3X0 z?2)zq0oEbY)@I^;0&6zz>mJTui-$V6zj&eXVWK*M7;87m2CR)*E#h#0eM<{{CxPrD>J5?(V;ZIS1O`tzjIr+Wx^gO0?OG^9lKy2R^ex+~Gx;+-oS`sH=1G3f$fI4xym=C>?a|cExkSaU~e7 z$Tv0yzDIs-9BXgFjUPSc+{sgw22VX7cC^RP1~dc*ps4Z3g009q9BbG}Z)Rz&IST-& z+R6e=T{_Xa;rl>%9ko4bI3b0?{=dTIh9_Lu`?0ht5cn`a7r7^g0lGEQK+68> zGVy@VViOU^A~}-{fXfX%=jrYJV}6s=IrJH*%uszfb`_wah`H{EayX&+QUg{+arGNA za0Mp(6A}P-V+?b*i3ZP2$vc)^Z(w|Q$oysFo0%v50+a%4TQUZgUEWd2D2A zZw&cH8d696c3wD4(p09fEB3t`-P^EtNqi46Hl)L*9WuAKG`)Utv#pHibqArBvhe=V zF_7;V{7{9V#mNmY{6c}C9b#qi!4Z2?a;7Jx(})cHq@)is&p}2MJyE`D{MtDW%Ia!lP>2C1mRUCB4Ybm6E z&ftNk4KzXq@mNsm@_@f+_d>#ux=$3hu&~a1A+a+vk0mm%z~{*h$0vctgE@sEtjv$2 z<%i7VdylA(0IDpnrL{p=tTI4=}YARIL=`q<-F=3Ezrjt=)S*h;FF;e4em zG-AtG6$)=8G(`O7&{i2jfh+ErG#^`V9BOBF&^M60wlTxYQzy$-J~-Di3WfZxGRc0| zJLs)8JSsDneQ|aG;w3eP&?KcR#8Gr{xT-ub-4Fua!M73B#39itg``tArJKtI>v4Br{{1aY+_~YHK>qgpelZQ} zFZlY-)@zpsOF;*OskVI?Gw|xIo}g8Pf2Q~7v*zc@iqt^}L$5g@o8J*X2jZ`0@iq;P z+MPTvQ7!qYRxdJGO?~J%cTqnaCs59bQ}BBA@bDa~!K&!h>||OhkJZ;9zZ)H}FW2Mx z@ilC|{$%%sMO1vZJ!ZC3+Bpw%f%6Uu!6Hg)-z9|~a+34=|H2u(G26zeV*XJY(Q&#F zwd?BEUxOB@+E?gRp^n}vqdj? z>E?5wD0C{PFPeW)X~l7H-987S%m3Txr*YPAvdkSvtIaX5%%;;UvUV0i>>JXdolJne z_)E5wKU38(HAt%go)B)|;NyD;wu|Rmu5<&Re)notkFvK~=6EPXN0Gp(@Y$K% z+$@f+i4zbP;-ULlSb@7ZJ-$Pk3>)P!A9eied*H{R?9AvSO3sYu+oC_#GD1P|`_<;f zm4D@4m9m@fah8p4d#xLen=4Iv3?*qxKc9cydIFc&K|e~O8Rr|OH7fdY9183E;E;JX zBL1zS0{s9U#PNw9lbHTodVhU6{}R>}+mP!dcEuAUt^(`22r{Cx1*ELL)oit~!7i!c z&M|`eSc#ej-#hpZ^-2BGz&LGm>XEyt7NXQHV=YPaW8QMi)5Mg5z6Nnz+`^+&vCF3Z z8j-zu#z|3Mv4gYymJ2tV`-UES{`T(Cn4tC#?|eUQL_Jd8L>q>8HXo#A9MGqsos0ht z`GAc$02LA+DT#18A1}U;RUT`z_@PH35F4Y|w>9R)l4p$?z(aKOUHBRMt#0dg#wx@p z^Xlp8Bz4Ov_H2qn0#Ivjn6Id5NXlpv-la`hJKnSPo`>;kJA;uV3OESbTW^pgl}|HY zrl0qTp03_Rj&>?EHQMYvnLS&HGE{o`tl9Y2vS;}$YIhf`oJP)lTdvsH*mFJ0 zo=w%44cl<9n*t)vS*d?cGtAR3XMFWISDT8Q-{1A7Ngg&Wp;d9$ckPQ1&8+u1nU3q2 zInH5K`-+qqXcsUn3(M>1=AY3R2x=Cl9Fvu?KRu`qH~aDhl$fxw#YLE6;4W>S>#GCr z(}0jdB$Q-cTvUYorpo0ZW!8PAUFWm?ZkNB1v6>xe<2VwRS{w1DAV}P=|8vFgzGJ=q z)&|`?8ktR~-*_P;#1m;k-jKDhhet~v^4sWS%>l_g$r#MaJ1fIU2zz%1r-PK!p~BI6P{?}+p$Zxpk4p3~n%kkoMFj zx!}gIgOK>0H!>E7aLe(|;+m^XuJPFe@3>ctZDsh_*EU^}9gQfdGdn6Xo`fH_F)9m-7 z;?EukUp^>~PO9Oh^s2woR{U^}S=Z;I`KoO-HR8fYeOvH8hkBfHi@VEM-6f;+~0FL?w{P?%}cxuLPY;>s~b%d*^tE=n# z6;(2bKGeK>j|roD)VCsM+M~|Se6IjE!>iwYuBD!^AkMaesIkXUs>CkOt=OsJ&nywD zlqJc{wyvEvajND!{tb6TOL7&tMB{O0@$-rtjBA5s%*`jG&|_Yz6keOVJoVZxBjB)q zs=yjE<)=i%f{N4BrGe!C1eR6Y4$_GzDxsu#`f%#?H?h+i@d}wT{HGWeHD>c<_r!WR zZ#>dUB+5p8VC*MZ^2!k{s%AAQlr<3uGN4}4%dztGiqi+^`v@P4(22i_45Jh$KZZl~ z5d%qvS(=Gc=XT!P5HF){ytExv1nE&N>PD9+#=(>h`$PZi&5Ax@q%vnfhogYA0n zZyyF;OFztmvOA`n&vaBmWJ`{b;j zr^0g+5t<}qpV1HJ#3DPkX{u2c;7fHWzrl4ZQx~n3CB<{2`{AoxMk&aAeHMW-yY`m=;a{ zqk4~%oXJj4$H|NC6rdOdKDFDy9$=EicbVcy6yLEf613yH&-lg6y->9BdTg7NFW0y3 zYLg0GFWQNqvNKaN^#o2nJ^;f}_5Lq%WK*f)Xlbmt()ge9cY?NMu(wYwNu9JE?;Y!`f$g`u6k-^#WKv~zpp*q2{Qpz3z&;0b5G(%#6f;++XIkiuFtw>rY^AG zQ>ePEXLw;&p;KnrYZyGdPB0WjccXnM=gM=|jVx|gTiV)UA6nD8^YzmcJkoo!O;UGX z3Hy`4@H<@`Yf??fVRCkM#nan6^X;V49^1V|py_z1i2qk?Qm2%3c-OM0tX)()j|kV* z+i;qL%=j>5XuDlYD0ZdI8*4X-caB$Fs8dpi&CTLzoH=c^D}3 z1GNSeQGj`+r?0Q9ygV)<0(gSjzDP#_Ptdfq^VuQ5JJcQ?#|wgu2g44#4gLp=<$1@n zb5m2S3EhWQL;)2WZ_)aegpGR{#ky`}^UeamA6bsBE8A>c-Bnyq=RX`1bd|OSnm=Hb z!s;tHWo-GDGVGKiR+Z$FRY=FA)VC#`=@-N&YVt)>5 zt->O}cjD-186mC|3)qR%X{#|Hdf4N3Rbhks(96f2E_0kl9ou)xS?~?AcRy0?BV?W- zu#g+5GjY1x7&#TsAK)fXtHvJxPx|)WIO9!_i99ieAoFgOe-w^ zyONIEJ6tx^4V5k=;@oxnbHMoQg;l`ljf+V$Q!?z9Ebl+{35j<*`_u0Ihh$sReOjr* z&a0TM*mujpwGpsjeU7}ZDC-KgoA}lVa4Ll8$;v%94XKW9@dr`SatXA$9W@g!-vt1XYhSgaq#x;R-rGJ$%D@)o+g?b>=BM$2aXsA@*DJ^4>!R)i_Lh&U%cW z*23^{L7UFTNFi`m)?ZzopFRX-S9bv_U=D*~pe!0Cr>OW4(@=PLcnHj3M{5ha=Nivh z=5><{LE-ckSABe9qBQ;^E-qu>B{IG`({{IdU2f5nR5-dZZX9G-ss;RnUWfoMP}A>8 z=4v`Df>3offD_?+cY|h21h75Bu^nz}0Q2k%jB)sGUJ$t~987FqOR+yhr$Loks@6f0pQb!OQ($^9m5+Z^|wf2i& zp@9)eL0%s8Km0UaS_PL5?$5B!ef>$lh+7XwO+9E941uQP^`{H-2cl0pX@mTyzS%f6 zU3{Ndej^UdDi)TO`|EuP-R8hDXVsrkT2OGZ-@|3>yPmt;lMGHnCFpA25q%$&s3)y5 zrRx+(TDgJ$3tV_AztbPi5^(t8uyQ8GLYU#_2)r4^TBQsjq@eq7qT)?Z%P}HI9C!s? zSg-FL0;eP}%+CI(J%mda@Fxz?h|uSNy7kwuC}05w{t11!XQ@oK&q62}utScGjC{j1 zDFC2=*6h4N4;p#EBP2dU)GtFkC<7@#^?P@J$yKnY(&3&f6>~zjQkuXZh=@zBP0$ha z5z3IxRxF7JECK2U1|t3^&X=7aO2H*)7is|TLPXUS^akuN`{0*I+ytnuzsahuu69B+ znrac4erA!+Qu#*7pBz|&FAc-$cS#$yB_t-^1#K3fQ$GL2Cmv9Q2L^u?(oqluoiu(W zy_*fjhd<&g-OVj58V>q|`BG!V-DL1hbpI@MCyX1o#Tb=0@t$J=b27$G3x0zF`0)(R z*smJ0)C#W?Qhf8;odZ#T@$R4Sy!#BSzsFmX2azs}>^G>tT!GDMr9acy*tq{nM_+%_ z6AmmW=ZEWVpqC-49fmLHvGL*9I<@6xL17_%2$irWJ0qiHNo7kWXt)555@0%i8YlwH z@?LX3%pxNGz~c?(8T^a~Xv}&T0=Bx9^WCQ8ZgXJP@^T9X9Rb_~pzVbQCYLD|0A^vu zUFZfqXtvoJ&L_S~0XG1;V?d+ntty^}1>e3M_HZ?&33=GUUEJ2aqEvR-N>h97|7GC* z+kKv^=F>^-ML;DG53K~gV9am7B$%%BrY2`(7^$jOn6^iP-?G>^@+}@cn}0(LScdx6 zehaMu=QxA6uPKkYyMkL`Dv@1e47`}V#4%YfUDua~+$0d_Wk4dmUs zqg{?2KfaewRB6+;ZO>#mE`Ip%!NA1iiK)80tZZ&iizLE~_y@`pJ;KAMckEbKT~lLY zYO1Q_rFnYO9>!^@z((Zx^ZtTAe_xr<*w|RK6L^Zsnyvfx?F;kz`{wQAYC(P$r-TRU zEjKf|{y%U99tr|HO95D5g=jsEy;%Q^{Z)OQh>VQPoS8E>=30ZdWc|OIz_HNDMu4NS zaehGRVok0;moHDwy$x)G0?$vnH}&4Vd$(^#zb{`Jv{6S}sPl)fKd?qAiE{B;I_Y|; zkeZ?#N6Uc&{x>!y{uBE9`}gkL+rTQn*IZ9&Wyq^{@76`F?eegjFE1_qdG@*~QL(Y5 zvD@R;&!0Qj*T?725#Ptl1z@f<*gyF$FlNr3^Lw1FA=aInm)CXT>C>f;Er4rrKUUOK zR$7Vy7d~$N`n7cJ*T;{Ol_qw$Ee7uHQYtDa2+$A#<|Ct-b7s$eyuy7ll99m1z=f7G t@xX+-fHM$ykd=V|E3jR_jE8waTvqGOweKHi024I>gQu&X%Q~loCIANoY_tFX literal 0 HcmV?d00001 diff --git a/analysis/month-performance-1/month-performance-1.R b/analysis/month-performance-1/month-performance-1.R new file mode 100644 index 0000000..117ef05 --- /dev/null +++ b/analysis/month-performance-1/month-performance-1.R @@ -0,0 +1,140 @@ +rm(list = ls(all.names = TRUE)) # Clear the memory of variables from previous run. This is not called by knitr, because it's above the first chunk. + +# ---- load-sources ------------------------------------------------------------ +#Load any source files that contain/define functions, but that don't load any other types of variables +# into memory. Avoid side effects and don't pollute the global environment. +# source("SomethingSomething.R") + +# ---- load-packages ----------------------------------------------------------- +library(ggplot2) #For graphing +import::from("magrittr", "%>%") +requireNamespace("dplyr") +# requireNamespace("RColorBrewer") +# requireNamespace("scales") #For formating values in graphs +# requireNamespace("mgcv) #For the Generalized Additive Model that smooths the longitudinal graphs. +# requireNamespace("TabularManifest") # remotes::install_github("Melinae/TabularManifest") + +# ---- declare-globals --------------------------------------------------------- +options(show.signif.stars=F) #Turn off the annotations on p-values +config <- config::get() + +palette_dark <- list( # http://colrd.com/image-dna/50489/ + # "#141e1f", # black + "boundary" = "#3e525c", # dark gray + "post" = "#27403a", # dark green + "pre" = "#804d1e" # dark brown + # "#77b6c4", # light blue + # "post" = "#185f63", # lighter green + # "pre" = "#c5873e" # lighter brown +) +palette_light <- list( # http://colrd.com/image-dna/50489/ + # "#141e1f", # black + "boundary" = "#3e525c", # dark gray + # "post" = "#27403a", # dark green + # "pre" = "#804d1e", # dark brown + # "#77b6c4", # light blue + "post" = "#185f63", # lighter green + "pre" = "#c5873e" # lighter brown +) +# OuhscMunge::readr_spec_aligned(config$path_month_raw) + +col_types <- readr::cols_only( + `month` = readr::col_date(format = ""), + `phase` = readr::col_character(), + `stroke_numerator` = readr::col_integer(), + `stroke_denominator` = readr::col_integer(), + `antithromb_numerator` = readr::col_integer(), + `antithromb_denominator` = readr::col_integer(), + `anticoag_numerator` = readr::col_integer(), + `anticoag_denominator` = readr::col_integer(), + `statin_numerator` = readr::col_integer(), + `statin_denominator` = readr::col_integer(), + `smoking_numerator` = readr::col_integer(), + `smoking_denominator` = readr::col_integer(), + `cumulative_numerator` = readr::col_integer(), + `cumulative_denominator` = readr::col_integer() +) + +# ---- load-data --------------------------------------------------------------- +ds <- readr::read_csv(config$path_month_raw, col_types = col_types) + +# ---- tweak-data -------------------------------------------------------------- +ds <- + ds %>% + dplyr::mutate( + post = dplyr::recode(phase, "pre" = 0L, "post" = 1L), + phase = factor(phase, levels = c("pre", "post")), + ) %>% + dplyr::mutate( + stroke_proportion = stroke_numerator / stroke_denominator , + antithromb_proportion = antithromb_numerator / antithromb_denominator , + anticoag_proportion = anticoag_numerator / anticoag_denominator , + statin_proportion = statin_numerator / statin_denominator , + smoking_proportion = smoking_numerator / smoking_denominator , + cumulative_proportion = cumulative_numerator / cumulative_denominator , + ) %>% + dplyr::mutate( + stroke_label = sprintf("%4.0f%% (%2i of %2i)", stroke_proportion * 100, stroke_numerator , stroke_denominator ), + antithromb_label = sprintf("%4.0f%% (%2i of %2i)", antithromb_proportion * 100, antithromb_numerator , antithromb_denominator ), + anticoag_label = sprintf("%4.0f%% (%2i of %2i)", anticoag_proportion * 100, anticoag_numerator , anticoag_denominator ), + statin_label = sprintf("%4.0f%% (%2i of %2i)", statin_proportion * 100, statin_numerator , statin_denominator ), + smoking_label = sprintf("%4.0f%% (%2i of %2i)", smoking_proportion * 100, smoking_numerator , smoking_denominator ), + cumulative_label = sprintf("%4.0f%% (%2i of %2i)", cumulative_proportion * 100, cumulative_numerator , cumulative_denominator ), + ) + +# ---- marginals --------------------------------------------------------------- +# # Inspect continuous variables +# histogram_continuous(d_observed=ds, variable_name="quarter_mile_sec", bin_width=.5, rounded_digits=1) +# # slightly better function: TabularManifest::histogram_continuous(d_observed=ds, variable_name="quarter_mile_sec", bin_width=.5, rounded_digits=1) +# histogram_continuous(d_observed=ds, variable_name="displacement_inches_cubed", bin_width=50, rounded_digits=1) +# +# # Inspect discrete/categorical variables +# histogram_discrete(d_observed=ds, variable_name="carburetor_count_f") +# histogram_discrete(d_observed=ds, variable_name="forward_gear_count_f") + + +# ---- scatterplots ------------------------------------------------------------ +x_breaks <- ds$month + +g1 <- + ggplot(ds, aes(x=month, y=statin_proportion, size=statin_denominator, label=statin_label, color = phase)) + + geom_text(aes(y = -Inf, size=5), angle = 90, hjust = 0) + + geom_vline(xintercept = config$intervention_start, size = 4, color = "gray70", alpha = .6) + + annotate("text", label = "intervention starts", x = config$intervention_start, y = .5, hjust = .5, angle = 90, alpha = .4) + + geom_line(size=.5, color = "gray70") + + geom_point(aes(fill = phase), shape=21, alpha = .5) + + scale_x_date(breaks = x_breaks, date_labels = "%b\n%Y") + + scale_y_continuous(labels = scales::percent_format(accuracy = 1)) + + scale_color_manual(values = palette_dark, guide = "none") + + scale_fill_manual(values = palette_light, guide = "none") + + scale_size(guide = "none") + + coord_cartesian(ylim = c(0, 1)) + + theme_light() + + theme(axis.ticks = element_blank()) + + labs(x = NULL, y = "statin") +g1 + +# g1 %+% aes(color=cylinder_count) + + +# ---- models ------------------------------------------------------------------ +m1 <- lm(statin_proportion ~ 1 + post, data=ds) +summary(m1) + +m2 <- glm( + statin_numerator / statin_denominator ~ 1 + post, + family = quasipoisson, + data = ds +) +summary(m2) + + +# ---- model-results-table ----------------------------------------------- +summary(m2)$coef %>% + knitr::kable( + digits = 2, + format = "markdown" + ) + +# Uncomment the next line for a dynamic, JavaScript [DataTables](https://datatables.net/) table. +# DT::datatable(round(summary(m2)$coef, digits = 2), options = list(pageLength = 2)) diff --git a/analysis/month-performance-1/month-performance-1.Rmd b/analysis/month-performance-1/month-performance-1.Rmd new file mode 100644 index 0000000..531b4ba --- /dev/null +++ b/analysis/month-performance-1/month-performance-1.Rmd @@ -0,0 +1,145 @@ +--- +title: Skeleton Report 1 +date: "Date: `r Sys.Date()`" +output: + # radix::radix_article: # radix is a newer alternative that has some advantages over `html_document`. + html_document: + keep_md: yes + toc: 4 + toc_float: true + number_sections: true + css: ../common/styles.css # analysis/common/styles.css +--- + +This report covers the analyses used in the ZZZ project (Marcus Mark, PI). + + +```{r, echo=F, message=F} +# cat("Working directory: ", getwd()) +library(knitr) +opts_knit$set(root.dir='../../') #Don't combine this call with any other chunk -especially one that uses file paths. +``` + + +```{r set-options, echo=F} +# cat("Working directory: ", getwd()) +report_render_start_time <- Sys.time() +opts_chunk$set( + results = 'show', + comment = NA, + tidy = FALSE, + # dpi = 400, + # out.width = "650px", #This affects only the markdown, not the underlying png file. The height will be scaled appropriately. + fig.width = 4, + fig.height = 4, + fig.path = 'figure-png/' +) + +echo_chunks <- FALSE # Toggle for debugging. +message_chunks <- FALSE # Toggle for debugging. +# options(width=100) # So the output is 25% wider than the default. +read_chunk("./analysis/month-performance-1/month-performance-1.R") # This allows knitr to call chunks tagged in the underlying *.R file. +``` + + +```{r load-sources, echo=echo_chunks, message=message_chunks} +``` + + +```{r load-packages, echo=echo_chunks, message=message_chunks} +``` + + +```{r declare-globals, echo=echo_chunks, results='show', message=message_chunks} +``` + + +```{r rmd-specific, echo=echo_chunks, message=message_chunks} +# Put presentation-specific code in here. It doesn't call a chunk in the codebehind file. +# It should be rare (and used cautiously), but sometimes it makes sense to include code in Rmd +# that doesn't live in the codebehind R file. +``` + + +```{r load-data, echo=echo_chunks, results='show', message=message_chunks} +``` + + +```{r tweak-data, echo=echo_chunks, results='show', message=message_chunks} +``` + +Summary {.tabset .tabset-fade .tabset-pills} +=========================================================================== + +Notes +--------------------------------------------------------------------------- + +1. The current report covers `r nrow(ds)` month, with `r dplyr::n_distinct(ds$phase)` unique values for `month`. + + +Unanswered Questions +--------------------------------------------------------------------------- + + + +Answered Questions +--------------------------------------------------------------------------- + + +Graphs +=========================================================================== + + +Marginals +--------------------------------------------------------------------------- + +```{r marginals, echo=echo_chunks, message=message_chunks} +``` + + +Scatterplots +--------------------------------------------------------------------------- + +```{r scatterplots, echo=echo_chunks, message=message_chunks, fig.width=7} +``` + + +Models +=========================================================================== + +Model Exploration +--------------------------------------------------------------------------- +```{r models, echo=echo_chunks, message=message_chunks} +``` + + +Final Model +--------------------------------------------------------------------------- + +```{r model-results-table, echo=echo_chunks, message=message_chunks, warning=TRUE} +``` + +In the model that includes two predictors, the slope coefficent of `Miles per gallon` is `r summary(m2)$coefficients[2,1]`. + + +Session Information {#session-info} +=========================================================================== + +For the sake of documentation and reproducibility, the current report was rendered in the following environment. Click the line below to expand. + +
+ Environment +```{r session-info, echo=FALSE} +if( requireNamespace("devtools", quietly = TRUE) ) { + devtools::session_info() +} else { + sessionInfo() +} +``` +
+ +```{r session-duration, echo=FALSE} +report_render_duration_in_seconds <- as.integer(difftime(Sys.time(), report_render_start_time, units="secs")) +``` + +Report rendered by `r Sys.info()["user"]` at `r strftime(Sys.time(), "%Y-%m-%d, %H:%M %z")` in `r report_render_duration_in_seconds` seconds. diff --git a/analysis/month-performance-1/month-performance-1.html b/analysis/month-performance-1/month-performance-1.html new file mode 100644 index 0000000..3b8a3e6 --- /dev/null +++ b/analysis/month-performance-1/month-performance-1.html @@ -0,0 +1,1804 @@ + + + + + + + + + + + + + +Skeleton Report 1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +
+
+
+
+
+ +
+ + + + + + + +

This report covers the analyses used in the ZZZ project (Marcus Mark, PI).

+ + + + + + + + +
+

1 Summary

+
+

1.1 Notes

+
    +
  1. The current report covers 4 month, with 2 unique values for month.
    2. +
+
+
+

1.2 Unanswered Questions

+
+
+

1.3 Answered Questions

+
+
+
+

2 Graphs

+
+

2.1 Marginals

+
+
+

2.2 Scatterplots

+

+
+
+
+

3 Models

+
+

3.1 Model Exploration

+

+Call:
+lm(formula = statin_proportion ~ 1 + post, data = ds)
+
+Residuals:
+         1          2          3          4 
+-1.364e-01  1.364e-01 -1.388e-17 -1.388e-17 
+
+Coefficients:
+            Estimate Std. Error t value Pr(>|t|)
+(Intercept)  0.86364    0.09642   8.957   0.0122
+post         0.13636    0.13636   1.000   0.4226
+
+Residual standard error: 0.1364 on 2 degrees of freedom
+Multiple R-squared:  0.3333,    Adjusted R-squared:      0 
+F-statistic:     1 on 1 and 2 DF,  p-value: 0.4226
+

+Call:
+glm(formula = statin_numerator/statin_denominator ~ 1 + post, 
+    family = quasipoisson, data = ds)
+
+Deviance Residuals: 
+      1        2        3        4  
+-0.1509   0.1431   0.0000   0.0000  
+
+Coefficients:
+            Estimate Std. Error t value Pr(>|t|)
+(Intercept)  -0.1466     0.1116  -1.313    0.320
+post          0.1466     0.1524   0.962    0.438
+
+(Dispersion parameter for quasipoisson family taken to be 0.0215311)
+
+    Null deviance: 0.063216  on 3  degrees of freedom
+Residual deviance: 0.043243  on 2  degrees of freedom
+AIC: NA
+
+Number of Fisher Scoring iterations: 4
+
+
+

3.2 Final Model

+ + + + + + + + + + + + + + + + + + + + + + + + + + +
EstimateStd. Errort valuePr(>|t|)
(Intercept)-0.150.11-1.310.32
post0.150.150.960.44
+

In the model that includes two predictors, the slope coefficent of Miles per gallon is 0.1466035.

+
+
+
+

4 Session Information

+

For the sake of documentation and reproducibility, the current report was rendered in the following environment. Click the line below to expand.

+
+

Environment

+
─ Session info ───────────────────────────────────────────────────────────────
+ setting  value                       
+ version  R version 3.6.2 (2019-12-12)
+ os       Ubuntu 19.10                
+ system   x86_64, linux-gnu           
+ ui       X11                         
+ language (EN)                        
+ collate  en_US.UTF-8                 
+ ctype    en_US.UTF-8                 
+ tz       America/Chicago             
+ date     2020-02-25                  
+
+─ Packages ───────────────────────────────────────────────────────────────────
+ package     * version date       lib source        
+ assertthat    0.2.1   2019-03-21 [1] CRAN (R 3.6.2)
+ backports     1.1.5   2019-10-02 [1] CRAN (R 3.6.2)
+ callr         3.4.2   2020-02-12 [1] CRAN (R 3.6.2)
+ cli           2.0.1   2020-01-08 [1] CRAN (R 3.6.2)
+ colorspace    1.4-1   2019-03-18 [1] CRAN (R 3.6.2)
+ config        0.3     2018-03-27 [1] CRAN (R 3.6.2)
+ crayon        1.3.4   2017-09-16 [1] CRAN (R 3.6.2)
+ desc          1.2.0   2018-05-01 [1] CRAN (R 3.6.2)
+ devtools      2.2.2   2020-02-17 [1] CRAN (R 3.6.2)
+ digest        0.6.25  2020-02-23 [1] CRAN (R 3.6.2)
+ dplyr         0.8.4   2020-01-31 [1] CRAN (R 3.6.2)
+ ellipsis      0.3.0   2019-09-20 [1] CRAN (R 3.6.2)
+ evaluate      0.14    2019-05-28 [1] CRAN (R 3.6.2)
+ fansi         0.4.1   2020-01-08 [1] CRAN (R 3.6.2)
+ farver        2.0.3   2020-01-16 [1] CRAN (R 3.6.2)
+ fs            1.3.1   2019-05-06 [1] CRAN (R 3.6.2)
+ ggplot2     * 3.2.1   2019-08-10 [1] CRAN (R 3.6.2)
+ glue          1.3.1   2019-03-12 [1] CRAN (R 3.6.2)
+ gtable        0.3.0   2019-03-25 [1] CRAN (R 3.6.2)
+ highr         0.8     2019-03-20 [1] CRAN (R 3.6.2)
+ hms           0.5.3   2020-01-08 [1] CRAN (R 3.6.2)
+ htmltools     0.4.0   2019-10-04 [1] CRAN (R 3.6.2)
+ import        1.1.0   2015-06-22 [1] CRAN (R 3.6.2)
+ knitr       * 1.28    2020-02-06 [1] CRAN (R 3.6.2)
+ labeling      0.3     2014-08-23 [1] CRAN (R 3.6.2)
+ lazyeval      0.2.2   2019-03-15 [1] CRAN (R 3.6.2)
+ lifecycle     0.1.0   2019-08-01 [1] CRAN (R 3.6.2)
+ magrittr      1.5     2014-11-22 [1] CRAN (R 3.6.2)
+ memoise       1.1.0   2017-04-21 [1] CRAN (R 3.6.2)
+ munsell       0.5.0   2018-06-12 [1] CRAN (R 3.6.2)
+ pillar        1.4.3   2019-12-20 [1] CRAN (R 3.6.2)
+ pkgbuild      1.0.6   2019-10-09 [1] CRAN (R 3.6.2)
+ pkgconfig     2.0.3   2019-09-22 [1] CRAN (R 3.6.2)
+ pkgload       1.0.2   2018-10-29 [1] CRAN (R 3.6.2)
+ prettyunits   1.1.1   2020-01-24 [1] CRAN (R 3.6.2)
+ processx      3.4.2   2020-02-09 [1] CRAN (R 3.6.2)
+ ps            1.3.2   2020-02-13 [1] CRAN (R 3.6.2)
+ purrr         0.3.3   2019-10-18 [1] CRAN (R 3.6.2)
+ R6            2.4.1   2019-11-12 [1] CRAN (R 3.6.2)
+ Rcpp          1.0.3   2019-11-08 [1] CRAN (R 3.6.2)
+ readr         1.3.1   2018-12-21 [1] CRAN (R 3.6.2)
+ remotes       2.1.1   2020-02-15 [1] CRAN (R 3.6.2)
+ rlang         0.4.4   2020-01-28 [1] CRAN (R 3.6.2)
+ rmarkdown     2.1     2020-01-20 [1] CRAN (R 3.6.2)
+ rprojroot     1.3-2   2018-01-03 [1] CRAN (R 3.6.2)
+ scales        1.1.0   2019-11-18 [1] CRAN (R 3.6.2)
+ sessioninfo   1.1.1   2018-11-05 [1] CRAN (R 3.6.2)
+ stringi       1.4.6   2020-02-17 [1] CRAN (R 3.6.2)
+ stringr       1.4.0   2019-02-10 [1] CRAN (R 3.6.2)
+ testthat      2.3.1   2019-12-01 [1] CRAN (R 3.6.2)
+ tibble        2.1.3   2019-06-06 [1] CRAN (R 3.6.2)
+ tidyselect    1.0.0   2020-01-27 [1] CRAN (R 3.6.2)
+ usethis       1.5.1   2019-07-04 [1] CRAN (R 3.6.2)
+ vctrs         0.2.3   2020-02-20 [1] CRAN (R 3.6.2)
+ withr         2.1.2   2018-03-15 [1] CRAN (R 3.6.2)
+ xfun          0.12    2020-01-13 [1] CRAN (R 3.6.2)
+ yaml          2.2.1   2020-02-01 [1] CRAN (R 3.6.2)
+
+[1] /home/wibeasley/R/x86_64-pc-linux-gnu-library/3.6
+[2] /usr/local/lib/R/site-library
+[3] /usr/lib/R/site-library
+[4] /usr/lib/R/library
+
+

Report rendered by wibeasley at 2020-02-25, 01:35 -0600 in 1 seconds.

+
+ + + +
+
+ +
+ + + + + + + + + + + + + + + + diff --git a/analysis/month-performance-1/month-performance-1.md b/analysis/month-performance-1/month-performance-1.md new file mode 100644 index 0000000..e6e9bad --- /dev/null +++ b/analysis/month-performance-1/month-performance-1.md @@ -0,0 +1,226 @@ +--- +title: Skeleton Report 1 +date: "Date: 2020-02-25" +output: + # radix::radix_article: # radix is a newer alternative that has some advantages over `html_document`. + html_document: + keep_md: yes + toc: 4 + toc_float: true + number_sections: true + css: ../common/styles.css # analysis/common/styles.css +--- + +This report covers the analyses used in the ZZZ project (Marcus Mark, PI). + + + + + + + + + + + + + + + + + + + + + + + + + +Summary {.tabset .tabset-fade .tabset-pills} +=========================================================================== + +Notes +--------------------------------------------------------------------------- + +1. The current report covers 4 month, with 2 unique values for `month`. + + +Unanswered Questions +--------------------------------------------------------------------------- + + + +Answered Questions +--------------------------------------------------------------------------- + + +Graphs +=========================================================================== + + +Marginals +--------------------------------------------------------------------------- + + + + +Scatterplots +--------------------------------------------------------------------------- + +![](figure-png/scatterplots-1.png) + + +Models +=========================================================================== + +Model Exploration +--------------------------------------------------------------------------- + +``` + +Call: +lm(formula = statin_proportion ~ 1 + post, data = ds) + +Residuals: + 1 2 3 4 +-1.364e-01 1.364e-01 -1.388e-17 -1.388e-17 + +Coefficients: + Estimate Std. Error t value Pr(>|t|) +(Intercept) 0.86364 0.09642 8.957 0.0122 +post 0.13636 0.13636 1.000 0.4226 + +Residual standard error: 0.1364 on 2 degrees of freedom +Multiple R-squared: 0.3333, Adjusted R-squared: 0 +F-statistic: 1 on 1 and 2 DF, p-value: 0.4226 +``` + +``` + +Call: +glm(formula = statin_numerator/statin_denominator ~ 1 + post, + family = quasipoisson, data = ds) + +Deviance Residuals: + 1 2 3 4 +-0.1509 0.1431 0.0000 0.0000 + +Coefficients: + Estimate Std. Error t value Pr(>|t|) +(Intercept) -0.1466 0.1116 -1.313 0.320 +post 0.1466 0.1524 0.962 0.438 + +(Dispersion parameter for quasipoisson family taken to be 0.0215311) + + Null deviance: 0.063216 on 3 degrees of freedom +Residual deviance: 0.043243 on 2 degrees of freedom +AIC: NA + +Number of Fisher Scoring iterations: 4 +``` + + +Final Model +--------------------------------------------------------------------------- + + +| | Estimate| Std. Error| t value| Pr(>|t|)| +|:-----------|--------:|----------:|-------:|------------------:| +|(Intercept) | -0.15| 0.11| -1.31| 0.32| +|post | 0.15| 0.15| 0.96| 0.44| + +In the model that includes two predictors, the slope coefficent of `Miles per gallon` is 0.1466035. + + +Session Information {#session-info} +=========================================================================== + +For the sake of documentation and reproducibility, the current report was rendered in the following environment. Click the line below to expand. + +
+ Environment + +``` +─ Session info ─────────────────────────────────────────────────────────────── + setting value + version R version 3.6.2 (2019-12-12) + os Ubuntu 19.10 + system x86_64, linux-gnu + ui X11 + language (EN) + collate en_US.UTF-8 + ctype en_US.UTF-8 + tz America/Chicago + date 2020-02-25 + +─ Packages ─────────────────────────────────────────────────────────────────── + package * version date lib source + assertthat 0.2.1 2019-03-21 [1] CRAN (R 3.6.2) + backports 1.1.5 2019-10-02 [1] CRAN (R 3.6.2) + callr 3.4.2 2020-02-12 [1] CRAN (R 3.6.2) + cli 2.0.1 2020-01-08 [1] CRAN (R 3.6.2) + colorspace 1.4-1 2019-03-18 [1] CRAN (R 3.6.2) + config 0.3 2018-03-27 [1] CRAN (R 3.6.2) + crayon 1.3.4 2017-09-16 [1] CRAN (R 3.6.2) + desc 1.2.0 2018-05-01 [1] CRAN (R 3.6.2) + devtools 2.2.2 2020-02-17 [1] CRAN (R 3.6.2) + digest 0.6.25 2020-02-23 [1] CRAN (R 3.6.2) + dplyr 0.8.4 2020-01-31 [1] CRAN (R 3.6.2) + ellipsis 0.3.0 2019-09-20 [1] CRAN (R 3.6.2) + evaluate 0.14 2019-05-28 [1] CRAN (R 3.6.2) + fansi 0.4.1 2020-01-08 [1] CRAN (R 3.6.2) + farver 2.0.3 2020-01-16 [1] CRAN (R 3.6.2) + fs 1.3.1 2019-05-06 [1] CRAN (R 3.6.2) + ggplot2 * 3.2.1 2019-08-10 [1] CRAN (R 3.6.2) + glue 1.3.1 2019-03-12 [1] CRAN (R 3.6.2) + gtable 0.3.0 2019-03-25 [1] CRAN (R 3.6.2) + highr 0.8 2019-03-20 [1] CRAN (R 3.6.2) + hms 0.5.3 2020-01-08 [1] CRAN (R 3.6.2) + htmltools 0.4.0 2019-10-04 [1] CRAN (R 3.6.2) + import 1.1.0 2015-06-22 [1] CRAN (R 3.6.2) + knitr * 1.28 2020-02-06 [1] CRAN (R 3.6.2) + labeling 0.3 2014-08-23 [1] CRAN (R 3.6.2) + lazyeval 0.2.2 2019-03-15 [1] CRAN (R 3.6.2) + lifecycle 0.1.0 2019-08-01 [1] CRAN (R 3.6.2) + magrittr 1.5 2014-11-22 [1] CRAN (R 3.6.2) + memoise 1.1.0 2017-04-21 [1] CRAN (R 3.6.2) + munsell 0.5.0 2018-06-12 [1] CRAN (R 3.6.2) + pillar 1.4.3 2019-12-20 [1] CRAN (R 3.6.2) + pkgbuild 1.0.6 2019-10-09 [1] CRAN (R 3.6.2) + pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 3.6.2) + pkgload 1.0.2 2018-10-29 [1] CRAN (R 3.6.2) + prettyunits 1.1.1 2020-01-24 [1] CRAN (R 3.6.2) + processx 3.4.2 2020-02-09 [1] CRAN (R 3.6.2) + ps 1.3.2 2020-02-13 [1] CRAN (R 3.6.2) + purrr 0.3.3 2019-10-18 [1] CRAN (R 3.6.2) + R6 2.4.1 2019-11-12 [1] CRAN (R 3.6.2) + Rcpp 1.0.3 2019-11-08 [1] CRAN (R 3.6.2) + readr 1.3.1 2018-12-21 [1] CRAN (R 3.6.2) + remotes 2.1.1 2020-02-15 [1] CRAN (R 3.6.2) + rlang 0.4.4 2020-01-28 [1] CRAN (R 3.6.2) + rmarkdown 2.1 2020-01-20 [1] CRAN (R 3.6.2) + rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.6.2) + scales 1.1.0 2019-11-18 [1] CRAN (R 3.6.2) + sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.6.2) + stringi 1.4.6 2020-02-17 [1] CRAN (R 3.6.2) + stringr 1.4.0 2019-02-10 [1] CRAN (R 3.6.2) + testthat 2.3.1 2019-12-01 [1] CRAN (R 3.6.2) + tibble 2.1.3 2019-06-06 [1] CRAN (R 3.6.2) + tidyselect 1.0.0 2020-01-27 [1] CRAN (R 3.6.2) + usethis 1.5.1 2019-07-04 [1] CRAN (R 3.6.2) + vctrs 0.2.3 2020-02-20 [1] CRAN (R 3.6.2) + withr 2.1.2 2018-03-15 [1] CRAN (R 3.6.2) + xfun 0.12 2020-01-13 [1] CRAN (R 3.6.2) + yaml 2.2.1 2020-02-01 [1] CRAN (R 3.6.2) + +[1] /home/wibeasley/R/x86_64-pc-linux-gnu-library/3.6 +[2] /usr/local/lib/R/site-library +[3] /usr/lib/R/site-library +[4] /usr/lib/R/library +``` +
+ + + +Report rendered by wibeasley at 2020-02-25, 01:35 -0600 in 1 seconds. diff --git a/config.yml b/config.yml index 3659e4c..458466e 100644 --- a/config.yml +++ b/config.yml @@ -1,28 +1,6 @@ default: # To be processed by Ellis lanes - path_subject_1_raw: "data-public/raw/subject-1.csv" - path_mlm_1_raw: "data-public/raw/mlm-1.csv" - - path_car_raw: "data-public/raw/mtcar.csv" - - path_ss_county: "data-public/metadata/ss-county.csv" - - # Central Database (produced by Ellis lanes). - path_database: "data-public/derived/db.sqlite3" - - # Derived Rectangles (produced by Ellis lanes). - - # Analysis-ready datasets (produced by scribes & consumed by analyses). - - path_county_derived: "data-public/derived/county.rds" - path_county_year_derived: "data-public/derived/county-year.rds" - path_mlm_1_derived: "data-public/derived/mlm-1.rds" - - path_te_county: "data-public/derived/te/te-county.rds" - path_te_county_month: "data-public/derived/te/te-county-month.rds" - - path_car_derived: "data-public/derived/car.rds" # Actually produced by an Ellis - - path_annotation: "data-public/metadata/cqi-annotation.csv" + path_month_raw: "data-public/raw/month-performance.csv" + intervention_start: !expr as.Date("2019-11-01") path_log_flow: !expr strftime(Sys.time(), "data-unshared/log/%Y/%Y-%m/flow-%Y-%m-%d--%H-%M-%S.log") diff --git a/data-public/raw/month-performance.csv b/data-public/raw/month-performance.csv new file mode 100644 index 0000000..130e659 --- /dev/null +++ b/data-public/raw/month-performance.csv @@ -0,0 +1,5 @@ +month,phase,stroke_numerator,stroke_denominator,antithromb_numerator,antithromb_denominator,anticoag_numerator,anticoag_denominator,statin_numerator,statin_denominator,smoking_numerator,smoking_denominator,cumulative_numerator,cumulative_denominator +2019-09-15,pre,15,22,20,21,1,2,16,22,6,13,, +2019-10-15,pre,,,3,3,2,2,3,3,3,3,, +2019-11-15,post,,,1,1,0,0,1,1,0,0,, +2019-12-15,post,,,5,5,0,0,5,5,2,2,, \ No newline at end of file