From a535f63acd75aca36d498f5a3156ed0dcc985380 Mon Sep 17 00:00:00 2001 From: CJ Yetman Date: Tue, 17 Dec 2024 11:31:34 -0500 Subject: [PATCH 1/6] use a mermaid flowchart --- vignettes/cookbook_running_the_analysis.Rmd | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/vignettes/cookbook_running_the_analysis.Rmd b/vignettes/cookbook_running_the_analysis.Rmd index 3d6cc228..49b16845 100644 --- a/vignettes/cookbook_running_the_analysis.Rmd +++ b/vignettes/cookbook_running_the_analysis.Rmd @@ -29,7 +29,11 @@ The PACTA for Supervisors analysis consists of four main steps: The following diagram illustrates the structure of the workflow: ```{r workflow_structure, echo=FALSE, fig.cap='Fig. 1: Structure of the Workflow', fig.align='center', out.width='200px'} -knitr::include_graphics("../man/figures/p4s_workflow_structure.png") +DiagrammeR::mermaid("graph TD + id1("prepare_abcd()") --> id2("match_loanbooks()") + id2("match_loanbooks()") --> id3("prioritise_and_diagnose()") + id3("prioritise_and_diagnose()") --> id4("analyse()") +") ``` As the diagram shows, there is a logical sequence to how to run the functions. For any of the functions to work, the previous functions must have been run already and their outputs must be accessible as inputs to the next functions. If you want to keep different versions of the calculations, i.e. you want to avoid overwriting past outputs, you will have to (1) ensure that each run is done with a new value for the corresponding output directory set in the `config.yml` and (2) that the relevant function refers to the appropriate directories of upstream outputs. For example, if you want to run the analysis twice and keep both results, all `dir_*` entries of the `config.yml` should remain identical for both runs, except for the `dir_analysis` entry, which should be different for each run. From 89e65e3faa9f5c03dbb3dfcb2a639a699ad81226 Mon Sep 17 00:00:00 2001 From: CJ Yetman Date: Tue, 17 Dec 2024 11:35:06 -0500 Subject: [PATCH 2/6] Update DESCRIPTION --- DESCRIPTION | 1 + 1 file changed, 1 insertion(+) diff --git a/DESCRIPTION b/DESCRIPTION index 43292234..c3909f71 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -60,6 +60,7 @@ Depends: License: MIT + file LICENSE RoxygenNote: 7.3.2 Suggests: + DiagrammeR, gt, knitr, pkgdown, From cb282f09835d9b8dbb4531567e65830492a6c4cd Mon Sep 17 00:00:00 2001 From: CJ Yetman Date: Tue, 17 Dec 2024 11:37:56 -0500 Subject: [PATCH 3/6] Update cookbook_running_the_analysis.Rmd --- vignettes/cookbook_running_the_analysis.Rmd | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/vignettes/cookbook_running_the_analysis.Rmd b/vignettes/cookbook_running_the_analysis.Rmd index 49b16845..f9141116 100644 --- a/vignettes/cookbook_running_the_analysis.Rmd +++ b/vignettes/cookbook_running_the_analysis.Rmd @@ -29,11 +29,11 @@ The PACTA for Supervisors analysis consists of four main steps: The following diagram illustrates the structure of the workflow: ```{r workflow_structure, echo=FALSE, fig.cap='Fig. 1: Structure of the Workflow', fig.align='center', out.width='200px'} -DiagrammeR::mermaid("graph TD +DiagrammeR::mermaid('graph TD id1("prepare_abcd()") --> id2("match_loanbooks()") id2("match_loanbooks()") --> id3("prioritise_and_diagnose()") id3("prioritise_and_diagnose()") --> id4("analyse()") -") +') ``` As the diagram shows, there is a logical sequence to how to run the functions. For any of the functions to work, the previous functions must have been run already and their outputs must be accessible as inputs to the next functions. If you want to keep different versions of the calculations, i.e. you want to avoid overwriting past outputs, you will have to (1) ensure that each run is done with a new value for the corresponding output directory set in the `config.yml` and (2) that the relevant function refers to the appropriate directories of upstream outputs. For example, if you want to run the analysis twice and keep both results, all `dir_*` entries of the `config.yml` should remain identical for both runs, except for the `dir_analysis` entry, which should be different for each run. From bc26b72e5a2133028eedbba172b7de7121b10875 Mon Sep 17 00:00:00 2001 From: CJ Yetman Date: Tue, 17 Dec 2024 11:43:24 -0500 Subject: [PATCH 4/6] Update cookbook_running_the_analysis.Rmd --- vignettes/cookbook_running_the_analysis.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/vignettes/cookbook_running_the_analysis.Rmd b/vignettes/cookbook_running_the_analysis.Rmd index f9141116..af21b48c 100644 --- a/vignettes/cookbook_running_the_analysis.Rmd +++ b/vignettes/cookbook_running_the_analysis.Rmd @@ -28,7 +28,7 @@ The PACTA for Supervisors analysis consists of four main steps: The following diagram illustrates the structure of the workflow: -```{r workflow_structure, echo=FALSE, fig.cap='Fig. 1: Structure of the Workflow', fig.align='center', out.width='200px'} +```{r workflow_structure, echo=FALSE, fig.cap='Fig. 1: Structure of the Workflow', fig.align='center'} DiagrammeR::mermaid('graph TD id1("prepare_abcd()") --> id2("match_loanbooks()") id2("match_loanbooks()") --> id3("prioritise_and_diagnose()") From 18d8fd4f2e6ed728c323c27a2f84995e99f5e50f Mon Sep 17 00:00:00 2001 From: CJ Yetman Date: Tue, 17 Dec 2024 11:44:13 -0500 Subject: [PATCH 5/6] Delete man/figures/p4s_workflow_structure.png --- man/figures/p4s_workflow_structure.png | Bin 7370 -> 0 bytes 1 file changed, 0 insertions(+), 0 deletions(-) delete mode 100644 man/figures/p4s_workflow_structure.png diff --git a/man/figures/p4s_workflow_structure.png b/man/figures/p4s_workflow_structure.png deleted file mode 100644 index 45eb606dedc6769c546d9a12272ac6fd412672ca..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 7370 zcmc(DXH*kRv~2(p2wl4L8hVi;Jyc2P9YmUfpwc4(p#?-K0s;vwv;az%CMZOZA}9$c zks?S9N)V-LXhuq|_pWPsWZMxwqx zdM}cutoat$4aQZw~ zh%c7AuIzSZ4R`3X`ya6Dbk=*fWcG+GSO=G9A3ZviMTB?D_J?b)nNtk^KcnD`nzgH--r`=~dz?n5&gPj{)#2a3Md4ffYu3M3JH8Rymg*4ck)&lQ0XQg&x` z9@qI-lEqj|WkYGggGDVXP6*skLH73$t1cCfg~}m=PJK$h-I>`HgUt9eB#63>za|Be z&2y23lMxm1kQrfah@t6d4A~VMEGc9*RJ3#Rb4O76y)NmnFoxVM7)6E-YP{VZm)W@Q)cqc~kYk9f#Pv z9L%ZCycPp!r;B0t$ZnIs{TEkbm)?WGT*((bo?7n!=StgahZMj&qkaJ48vhumz zM4=%4(mFmNz|STPUN-Mr-$|xq!6ec+nF*OmfoaKLXG~*LgiG!#(%*W9Z+yah&%1~r zv-9zQ`cW0}#1a-p=BZOrdWN4EPQE4{*!_viyJw-C2d}Hl%%e;;;=_W0O^gRr?-B(Mp#UoKeGA!dr<*oU8EdKqt9Tv9ddaC;3ACWjv+ zIfx%!+V~h(a`ZKxM~VS-2~%R`!4?{Fr~Erd3q-4x_t_Y|DN>1_4n~r)Q#3%P?On4= zPbehOBOm&^`&T1e>P@4PG;194ZA14)ftLfEEidCGpFc??vSlIVf{tO(Ok1gjNz-rH(I(_|T3eQkO6(4P{& zL;utc*?VR3vguy&$^Zm-a1Nfk%i{&uj3mq8g?F4>768jrcsk?0n!r$K6Iv=P*At^s zO((a9|AhKAEYSo(_9IUkORV499XHc!NFaBMH$u2BAHm`!Gg&`%WpxJ%!&k5%lYH_E!lGX@ypE?GnQ`BBY7t;!>6By ztk}snkaS&do+a!oK|AsW`?QsIk!3SCjk{qnf9mVYC#Q=19YA38F@EDj4wndXsJrk* zm*UW0q93bL&&c<^#P6$&&ZveNSC?fzlbkXEO4D^tRH} z@qM{7>^I$@`zcTDMw6nNxANmA;L-PH#6aB zSGzk?rN2IH!Ml{$AM$k>nlc&S2PQ0UZr3>D~AagwJGKU~9$;!%M<|7U_| zGab?R+e27VPI@XHEL$1Tnp41k>*ha+&)5|12gzc<>V4IKpY9u{yHc;1{I3Ucg1M*l zOnyNFKE=!I7MBr7!l*rTuOG}16+MaHeYMz1`ooOET>s0{gi(?o)B=pr`tL~*GCAt- zGW@EwNFZ4oHGO>$zQLjv|wkqWY z0-u2odTwEB-G`%&o5-}X8o>O?COKv3_&keoYi}-3p^|t9(R9%`a>#xCkr z?U7Y6eVJV;6fsgK=kTBx1qmcS##5}9)pRg;J(+cN_z3BL3f6l3KTMQTVcl990Kk`@ zL_Cn%3Z=d9-RVsBZ;Sf}VR*RJsbeGdc=b2p+tF|Yy}4{r{Yr*KHs7*V0=2a<&Zv2t z17%xRz(!<+$-U}Ip z9tU%UoTrMzS?e7`T`I4z|2gGU0tk-c2cD|W9@tdj6^h1c+_=fgbc>p*6OXL>&aH4i zjK{sWP3P;4q_V;eW(sA${v=p>t7o6sr)MTUMng4JvuN(2s-kxSB|Ep@>&0VQzQ#=i2cax` z#wEgD_e%N*q((?jzC6Aa!=HPLbyy1{WONF}HzjcnHMFE9M6WWNk5@jLPJfoC zDk$+`gJYI8mv>G8Ye3`fRURysDw?hfh#JmJDq5FLi(Wc^|1CS;D-Sw`&plD==X~v& zr!FQ%0B_3!q7IfoQPR+soHr%iE3s@87vJDbj9*f7cWG$q>*ZeHxko~Sw{<3Iyt0it zy&m&d9<9;Rgth6@b>DjQiJid|u$tA|aEN0acoh#L-r?FNdA(Vn`);5_$>LrqgLuAs z7_+pngIF-^2e?EC7#Mq6@jYnZN1KkjG%Y5(vZ(eE{s!UPS0K1xPA1q7?8A-4k zNZfSKd&l(aT~do2nQr>2cv6Xt*;mvspWfV~nFJ45sHt*Np}v#3$m0*+stFO#L~-}T zC~Fz!eiTxn$(LSW_^QS7pqE_X`Hxb|&PbxxBH;5F{hNZRF`XzA-34tgihTI&@Lhg@ z!9{!+hQ>N^)eUex4>!y4c3Bwf%ZLyM85H%h`x;f#b8vkS4_ZXcA|#HI(q96CFPINB z<(AnW-UivWG@@=X6wHBQT>@(YmUz?Sfnq-`WOi^1E8U{vU00*#0#_u$Mq+|BeraKu zSk~@LfF{oIPthY4`J``*qK-=yrM)n4vTW~M# zymCxcbFSS}hHbdp(<>lxfRqZ0Gg`DaXgS}Q=S9Y4lX>(d*nIll<~IN2oegihNu^3k zFBo`gY1<50$+CS^_C|i%aZ2jGUWr;vvOcrZvS8%7wm3&}@8hY0D81)P#zp?~cjoJINY1q*3&!s4 zKbl>u_J(v6r=Dz~?lK$=tvQtMxSldbp5ON##DNQkc1k9|Rvk$Ob80K#O~mq_t;Eg@u;KkKL2o>XZPhKZ7hkU{KJwRG)N zC4w+piCo|(;wovqBIH=yrg-ar&m@IJAb7WK9?Z_7gR)PshMj?ZR}u}880vaRb9t8k)}0B_22TY~O)tRRMw&Z6kILN5;Nxiu z)DG*Uk5Xa4b1w3t^M|>q#+^&(qkviOcxro)R6OuRb{RfA9o%E}+DavRbB@#Z^Wis< zr7qC;aHx}I!e)QYtTSZkaXDdZkp1dN;?N-^hPB$)y>_wb?L>FEe9;>Z!`tO2zgI$n z;}DpsM3T?*v2Q^_l!b+X3fm{&i_1E!R3bFy5aI!qfYNl@0kXXFnE=1=pms{<+-Ewj zMw-;D!L*gpFN1(X))ldcPV>juA*g&m|SuL@>SE7=_9{SV*Ah208i8z+H_LC!77RyAjNT+Ps zi{x}~8f!OTo5x&@97E1j!kT3k{W%_mFy#$Rx`Cj1=O?H7rJ3#rX`9SRO>!{b;mpv+ z`0}6ckWxOAx6Tp{(zWt1hh^h7jXeX*KUgAy;|NSievLvCp@}39vwIbXN1Pvk1q=Gi ztw9SMDvs`i%PR%oW}hoq*aLiQFx06K^qrNm@t}T?OT2?`C*wU&+k7tE-kxB#)11io ztkI=!Tj>4s?<=}X@TNSU zF6Bw0pUYUEvu<)(?(VPX2vGhdU{qRK%luiQ?n=#Q8o)P;CO*)oepD&Q88#Q213&DM=%58Lxj4XYX#x9@+kWa-G%A}sf9%T-9PzJo~ksv&*=c5 z8#e&oMD0WAES;27Qlqc^I3mi`@ylI9QIQ?u*-FI?)DCjHY;>{{8un{?DnE!46KtDD zekGfeEWpIu>W!cu)D8C?&wtfz6UF3fkA+>mv1$z8^$tF7o!C?si(yse!>$emyaP3V zFH<@1$B;AncI~AzoOz(B)|0>oxQ-=HZ8w5c5-+jm(FcqRyX>VtYq7BgRQh0H5q}OV z7o7%@O9Sb*5OtpXTP2Gz=Z_SxXkDH2%FI7Dno@MK<>d$(J&0!p+=GWR=Z}$b*kc}} zq6gUq^oCP3_Au!8m6wN-Mh-Qj%|(%~K5vZP6wgw20Mky_+GB4nKlw0WA9@e{gGW_& zQRoo5dKRt%%pZf$CZeyJkCty~b?tFwR)oK^Setdg4e5d9cjb(9&hj;LTRf}VU>jE>X|?OVT$gE_0W7Y~)}%1q zhIA#2mG+pAUh`BG(qtyAA$iq_MlC1eL{7PfqxeEEVmp8(W4Y?eVLZ4XFaST6w`E(U zUm13(EHZxglRUc;V_dAW?cIm@^-h)Xbl>uc!E&ypyF+oCXpKMDqiP^J!eaFS$>car zzY>Mny%$2NI}JwIe0(>@K_HItnBo>PH&5d13;FZn5qri`?z-wziM45zG1ha>K}Xs$ zwZeRs*qu>tV|^{w1Ep^8le>K?!m++=MmcG-4oPiSBnfVd5ywQyc~|#Z!;FJy_~}RG zzMQx>OYe(~)%3LoS*Wm@I0%ifm+?8YJdyJHJURIi*0y**m3xv(b$eLaNeS2E)A*i6 zT>rF5(~o;?*sWZ@cdvWDH|zL-@{9XhBzc!y{R-4nJI?hSx^Z&iiYi>b9iiVf9@5w> z-c)-BHyXT0I)eWqbeI=174TtP18=_6j;nly3Eg=tXgRhxIgO`!Twr;IUsC43g)`ph zccMlmeq>zYocLIVwo1Umea&|c^;hywl68W^*n4i8NDe1P+cp=6LA+qwFfSgA2O)Ps6f^Rv6b90VA#vf4Q2$%g zG#>H0+YL_v;)&vvL;}j^v3cm_$L1oa*2oh+u#z;~np{TG!QVx$OA(+ID18vz_Ma7$ ztP>Z#20RAG(O^8{XY&&m*i&Pu`UD zIgU4m7CnyNl03?5H8q5ZQ|5Q_1o0yVFiFb%od{`4F@^_3ng5ojhab_0fhfAek_bsr zr!EjBJvKRdj?!^PE^m7*}ZH?S=`Kg5#2(7vS4Zk_r+{JgVC><7pA-q}1g<{|Wz z9(XkP6!9Jje)uJg1;LjZ?MS_82v3arWW3sUe6VTzZaT%@k^Mfz+(jHdxd%~t-ngfE zMfG{MjZ-+9*OSJt*?=Vs10kqs7MwHM6@Iu*tk^NAvdL`-J=w z0AtwBb3>l&yhH*fPGxZe(hy_4GcdfejI2VdVAhVsT?7P^y357t2`s8M$EL z)YEZ!sh?tp0{GPkaCE5$CWz%v&|TnhP9~}QD*hNMTr_N?Cuqhv1qdpC@ibk5TF|X{ zzZ25uaY-hP_z&o6B(Fh|xz*RxKp->Mzx4e%U%2y8SVGx$y%St$Lr z)!)MZTF3D%>w9h&wiWIqWghI_Q&=**F8SoVk9<84Z)5S3Q4zoG7ger<%J-9zJT8XmJgh-tOLc|djqI9;1$^gN#Qp73>-z&41H$G4VZf{}lO9NEwdD zlHi_X@?HF1H|gJ#njlSBMHXSKDn_JLz(x8wR^ExqaFL?kle7Qy7rSI*L^~?Fmhg{a zmQA=6@V6)dSYA*c(W`U0eWChZuYCZ`KXR&&-L2DiShj;#_xi|!ukJLLDdi)odNE}G z%9E%z!jm$lQH1@!En~=LaPV3NIdPP0?KD592k<@ABs-NMPT=pe2mm#=HES{Pz5g#Y C-GABu From f59471d3be740bc4b8e9b07c745ea2c1bfb93a02 Mon Sep 17 00:00:00 2001 From: CJ Yetman Date: Fri, 20 Dec 2024 09:07:01 -0500 Subject: [PATCH 6/6] styling --- vignettes/cookbook_running_the_analysis.Rmd | 15 +++++++++++---- 1 file changed, 11 insertions(+), 4 deletions(-) diff --git a/vignettes/cookbook_running_the_analysis.Rmd b/vignettes/cookbook_running_the_analysis.Rmd index af21b48c..f8ade4ad 100644 --- a/vignettes/cookbook_running_the_analysis.Rmd +++ b/vignettes/cookbook_running_the_analysis.Rmd @@ -29,10 +29,17 @@ The PACTA for Supervisors analysis consists of four main steps: The following diagram illustrates the structure of the workflow: ```{r workflow_structure, echo=FALSE, fig.cap='Fig. 1: Structure of the Workflow', fig.align='center'} -DiagrammeR::mermaid('graph TD - id1("prepare_abcd()") --> id2("match_loanbooks()") - id2("match_loanbooks()") --> id3("prioritise_and_diagnose()") - id3("prioritise_and_diagnose()") --> id4("analyse()") +DiagrammeR::mermaid(' + graph TB; + id1("prepare_abcd()") --> id2("match_loanbooks()"); + id2("match_loanbooks()") --> id3("prioritise_and_diagnose()"); + id3("prioritise_and_diagnose()") --> id4("analyse()"); + classDef nodeStyle fill: #45cfcc, stroke: #000, stroke-width: 2px; + class id1,id2,id3,id4 nodeStyle; + click id1 "../reference/prepare_abcd.html"; + click id2 "../reference/match_loanbooks.html"; + click id3 "../reference/prioritise_and_diagnose.html"; + click id4 "../reference/analyse.html"; ') ```