From 3ad5c27b5491d2b86ace551ba984601cd216e71f Mon Sep 17 00:00:00 2001 From: Abinaya Yogasekaram <73252787+ayogasekaram@users.noreply.github.com> Date: Tue, 19 Sep 2023 11:21:12 -0400 Subject: [PATCH] 57 reorganize tlg@main (#117) closes #57 --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Joe Zhu --- book/generate-index.R | 24 +++++++++++++++++-- book/graphs/{other => efficacy}/fstg01.qmd | 0 book/graphs/{other => efficacy}/fstg02.qmd | 0 book/graphs/{other => efficacy}/mmrmg01.qmd | 0 book/graphs/{other => efficacy}/mmrmg02.qmd | 0 .../{pharmacokinetic => ada}/adal02.qmd | 0 .../{other => adverse-events}/ael01.qmd | 0 .../{other => adverse-events}/ael01_nollt.qmd | 0 .../{other => adverse-events}/ael02.qmd | 0 .../{other => adverse-events}/ael02_ed.qmd | 0 .../{other => adverse-events}/ael03.qmd | 0 .../{other => adverse-events}/ael04.qmd | 0 book/listings/{other => con-med}/cml01.qmd | 0 .../listings/{other => con-med}/cml02a_gl.qmd | 0 .../listings/{other => con-med}/cml02b_gl.qmd | 0 .../listings/{other => disposition}/dsl01.qmd | 0 .../listings/{other => disposition}/dsl02.qmd | 0 book/listings/{other => dsur}/dsur4.qmd | 0 book/listings/{other => ecg}/egl01.qmd | 0 book/listings/{other => efficacy}/oncl01.qmd | 0 book/listings/{other => exposure}/exl01.qmd | 0 .../listings/{other => lab-results}/lbl01.qmd | 0 .../{other => lab-results}/lbl01_rls.qmd | 0 .../{other => lab-results}/lbl02a.qmd | 0 .../{other => lab-results}/lbl02a_rls.qmd | 0 .../{other => lab-results}/lbl02b.qmd | 0 .../{other => medical-history}/mhl01.qmd | 0 .../listings/{other => vital-signs}/vsl01.qmd | 0 .../{pharmacokinetic => ada}/adat01.qmd | 0 .../{pharmacokinetic => ada}/adat02.qmd | 0 .../{pharmacokinetic => ada}/adat03.qmd | 0 .../{pharmacokinetic => ada}/adat04a.qmd | 0 .../{pharmacokinetic => ada}/adat04b.qmd | 0 book/tables/{safety => con-med}/cmt01.qmd | 0 book/tables/{safety => con-med}/cmt01a.qmd | 0 book/tables/{safety => con-med}/cmt01b.qmd | 0 book/tables/{safety => con-med}/cmt02_pt.qmd | 0 book/tables/{safety => deaths}/dtht01.qmd | 0 book/tables/{safety => demography}/dmt01.qmd | 0 .../{other => disclosures}/disclosurest01.qmd | 0 .../{safety => disclosures}/eudrat01.qmd | 0 .../{safety => disclosures}/eudrat02.qmd | 0 book/tables/{safety => disposition}/dst01.qmd | 0 book/tables/{safety => disposition}/pdt01.qmd | 0 book/tables/{safety => disposition}/pdt02.qmd | 0 book/tables/{safety => ecg}/egt01.qmd | 0 book/tables/{safety => ecg}/egt02.qmd | 0 book/tables/{safety => ecg}/egt03.qmd | 0 book/tables/{safety => ecg}/egt04.qmd | 0 book/tables/{safety => ecg}/egt05_qtcat.qmd | 0 book/tables/{other => efficacy}/aovt02.qmd | 0 book/tables/{other => efficacy}/aovt03.qmd | 0 book/tables/{other => efficacy}/cmht01.qmd | 0 book/tables/{other => efficacy}/ratet01.qmd | 0 book/tables/{other => efficacy}/rbmit01.qmd | 0 book/tables/{safety => exposure}/ext01.qmd | 0 .../{safety => medical-history}/mht01.qmd | 0 book/tables/{other => rmp}/rmpt01.qmd | 0 book/tables/{other => rmp}/rmpt03.qmd | 0 book/tables/{other => rmp}/rmpt04.qmd | 0 book/tables/{other => rmp}/rmpt05.qmd | 0 book/tables/{other => rmp}/rmpt06.qmd | 0 book/tables/{safety => vital-signs}/vst01.qmd | 0 book/tables/{safety => vital-signs}/vst02.qmd | 0 64 files changed, 22 insertions(+), 2 deletions(-) rename book/graphs/{other => efficacy}/fstg01.qmd (100%) rename book/graphs/{other => efficacy}/fstg02.qmd (100%) rename book/graphs/{other => efficacy}/mmrmg01.qmd (100%) rename book/graphs/{other => efficacy}/mmrmg02.qmd (100%) rename book/listings/{pharmacokinetic => ada}/adal02.qmd (100%) rename book/listings/{other => adverse-events}/ael01.qmd (100%) rename book/listings/{other => adverse-events}/ael01_nollt.qmd (100%) rename book/listings/{other => adverse-events}/ael02.qmd (100%) rename book/listings/{other => adverse-events}/ael02_ed.qmd (100%) rename book/listings/{other => adverse-events}/ael03.qmd (100%) rename book/listings/{other => adverse-events}/ael04.qmd (100%) rename book/listings/{other => con-med}/cml01.qmd (100%) rename book/listings/{other => con-med}/cml02a_gl.qmd (100%) rename book/listings/{other => con-med}/cml02b_gl.qmd (100%) rename book/listings/{other => disposition}/dsl01.qmd (100%) rename book/listings/{other => disposition}/dsl02.qmd (100%) rename book/listings/{other => dsur}/dsur4.qmd (100%) rename book/listings/{other => ecg}/egl01.qmd (100%) rename book/listings/{other => efficacy}/oncl01.qmd (100%) rename book/listings/{other => exposure}/exl01.qmd (100%) rename book/listings/{other => lab-results}/lbl01.qmd (100%) rename book/listings/{other => lab-results}/lbl01_rls.qmd (100%) rename book/listings/{other => lab-results}/lbl02a.qmd (100%) rename book/listings/{other => lab-results}/lbl02a_rls.qmd (100%) rename book/listings/{other => lab-results}/lbl02b.qmd (100%) rename book/listings/{other => medical-history}/mhl01.qmd (100%) rename book/listings/{other => vital-signs}/vsl01.qmd (100%) rename book/tables/{pharmacokinetic => ada}/adat01.qmd (100%) rename book/tables/{pharmacokinetic => ada}/adat02.qmd (100%) rename book/tables/{pharmacokinetic => ada}/adat03.qmd (100%) rename book/tables/{pharmacokinetic => ada}/adat04a.qmd (100%) rename book/tables/{pharmacokinetic => ada}/adat04b.qmd (100%) rename book/tables/{safety => con-med}/cmt01.qmd (100%) rename book/tables/{safety => con-med}/cmt01a.qmd (100%) rename book/tables/{safety => con-med}/cmt01b.qmd (100%) rename book/tables/{safety => con-med}/cmt02_pt.qmd (100%) rename book/tables/{safety => deaths}/dtht01.qmd (100%) rename book/tables/{safety => demography}/dmt01.qmd (100%) rename book/tables/{other => disclosures}/disclosurest01.qmd (100%) rename book/tables/{safety => disclosures}/eudrat01.qmd (100%) rename book/tables/{safety => disclosures}/eudrat02.qmd (100%) rename book/tables/{safety => disposition}/dst01.qmd (100%) rename book/tables/{safety => disposition}/pdt01.qmd (100%) rename book/tables/{safety => disposition}/pdt02.qmd (100%) rename book/tables/{safety => ecg}/egt01.qmd (100%) rename book/tables/{safety => ecg}/egt02.qmd (100%) rename book/tables/{safety => ecg}/egt03.qmd (100%) rename book/tables/{safety => ecg}/egt04.qmd (100%) rename book/tables/{safety => ecg}/egt05_qtcat.qmd (100%) rename book/tables/{other => efficacy}/aovt02.qmd (100%) rename book/tables/{other => efficacy}/aovt03.qmd (100%) rename book/tables/{other => efficacy}/cmht01.qmd (100%) rename book/tables/{other => efficacy}/ratet01.qmd (100%) rename book/tables/{other => efficacy}/rbmit01.qmd (100%) rename book/tables/{safety => exposure}/ext01.qmd (100%) rename book/tables/{safety => medical-history}/mht01.qmd (100%) rename book/tables/{other => rmp}/rmpt01.qmd (100%) rename book/tables/{other => rmp}/rmpt03.qmd (100%) rename book/tables/{other => rmp}/rmpt04.qmd (100%) rename book/tables/{other => rmp}/rmpt05.qmd (100%) rename book/tables/{other => rmp}/rmpt06.qmd (100%) rename book/tables/{safety => vital-signs}/vst01.qmd (100%) rename book/tables/{safety => vital-signs}/vst02.qmd (100%) diff --git a/book/generate-index.R b/book/generate-index.R index bb630c99aa..2fd8e3c71a 100755 --- a/book/generate-index.R +++ b/book/generate-index.R @@ -37,21 +37,41 @@ cat( # Tables section_header("Tables") +create_subsection("./tables/ada", "ADA") create_subsection("./tables/adverse-events", "Adverse Events") +create_subsection("./tables/con-med", "Concomitant Medications") +create_subsection("./tables/deaths", "Deaths") +create_subsection("./tables/demography", "Demography") +create_subsection("./tables/disclosures", "Disclosures") +create_subsection("./tables/disposition", "Disposition") +create_subsection("./tables/ecg", "ECG") create_subsection("./tables/efficacy", "Efficacy") +create_subsection("./tables/exposure", "Exposure") create_subsection("./tables/lab-results", "Lab Results") +create_subsection("./tables/medical-history", "Medical History") create_subsection("./tables/pharmacokinetic", "Pharmacokinetic") +create_subsection("./tables/rmp", "Risk Management Plan") create_subsection("./tables/safety", "Safety") -create_subsection("./tables/other", "Other") +create_subsection("./tables/vital-signs", "Vital Signs") # Listings section_header("Listings") +create_subsection("./listings/ada", "ADA") +create_subsection("./listings/adverse-events", "Adverse Events") +create_subsection("./listings/con-med", "Concomitant Medications") +create_subsection("./listings/disposition", "Disposition") +create_subsection("./listings/dsur", "Development Safety Update Report") +create_subsection("./listings/ecg", "ECG") +create_subsection("./listings/exposure", "Exposure") +create_subsection("./listings/lab-results", "Lab Results") +create_subsection("./listings/medical-history", "Medical History") create_subsection("./listings/pharmacokinetic", "Pharmacokinetic") -create_subsection("./listings/other", "Other") +create_subsection("./listings/vital-signs", "Vital Signs") # Graphs section_header("Graphs") +create_subsection("./graphs/efficacy", "Efficacy") create_subsection("./graphs/pharmacokinetic", "Pharmacokinetic") create_subsection("./graphs/other", "Other") diff --git a/book/graphs/other/fstg01.qmd b/book/graphs/efficacy/fstg01.qmd similarity index 100% rename from book/graphs/other/fstg01.qmd rename to book/graphs/efficacy/fstg01.qmd diff --git a/book/graphs/other/fstg02.qmd b/book/graphs/efficacy/fstg02.qmd similarity index 100% rename from book/graphs/other/fstg02.qmd rename to book/graphs/efficacy/fstg02.qmd diff --git a/book/graphs/other/mmrmg01.qmd b/book/graphs/efficacy/mmrmg01.qmd similarity index 100% rename from book/graphs/other/mmrmg01.qmd rename to book/graphs/efficacy/mmrmg01.qmd diff --git a/book/graphs/other/mmrmg02.qmd b/book/graphs/efficacy/mmrmg02.qmd similarity index 100% rename from book/graphs/other/mmrmg02.qmd rename to book/graphs/efficacy/mmrmg02.qmd diff --git a/book/listings/pharmacokinetic/adal02.qmd b/book/listings/ada/adal02.qmd similarity index 100% rename from book/listings/pharmacokinetic/adal02.qmd rename to book/listings/ada/adal02.qmd diff --git a/book/listings/other/ael01.qmd b/book/listings/adverse-events/ael01.qmd similarity index 100% rename from book/listings/other/ael01.qmd rename to book/listings/adverse-events/ael01.qmd diff --git a/book/listings/other/ael01_nollt.qmd b/book/listings/adverse-events/ael01_nollt.qmd similarity index 100% rename from book/listings/other/ael01_nollt.qmd rename to book/listings/adverse-events/ael01_nollt.qmd diff --git a/book/listings/other/ael02.qmd b/book/listings/adverse-events/ael02.qmd similarity index 100% rename from book/listings/other/ael02.qmd rename to book/listings/adverse-events/ael02.qmd diff --git a/book/listings/other/ael02_ed.qmd b/book/listings/adverse-events/ael02_ed.qmd similarity index 100% rename from book/listings/other/ael02_ed.qmd rename to book/listings/adverse-events/ael02_ed.qmd diff --git a/book/listings/other/ael03.qmd b/book/listings/adverse-events/ael03.qmd similarity index 100% rename from book/listings/other/ael03.qmd rename to book/listings/adverse-events/ael03.qmd diff --git a/book/listings/other/ael04.qmd b/book/listings/adverse-events/ael04.qmd similarity index 100% rename from book/listings/other/ael04.qmd rename to book/listings/adverse-events/ael04.qmd diff --git a/book/listings/other/cml01.qmd b/book/listings/con-med/cml01.qmd similarity index 100% rename from book/listings/other/cml01.qmd rename to book/listings/con-med/cml01.qmd diff --git a/book/listings/other/cml02a_gl.qmd b/book/listings/con-med/cml02a_gl.qmd similarity index 100% rename from book/listings/other/cml02a_gl.qmd rename to book/listings/con-med/cml02a_gl.qmd diff --git a/book/listings/other/cml02b_gl.qmd b/book/listings/con-med/cml02b_gl.qmd similarity index 100% rename from book/listings/other/cml02b_gl.qmd rename to book/listings/con-med/cml02b_gl.qmd diff --git a/book/listings/other/dsl01.qmd b/book/listings/disposition/dsl01.qmd similarity index 100% rename from book/listings/other/dsl01.qmd rename to book/listings/disposition/dsl01.qmd diff --git a/book/listings/other/dsl02.qmd b/book/listings/disposition/dsl02.qmd similarity index 100% rename from book/listings/other/dsl02.qmd rename to book/listings/disposition/dsl02.qmd diff --git a/book/listings/other/dsur4.qmd b/book/listings/dsur/dsur4.qmd similarity index 100% rename from book/listings/other/dsur4.qmd rename to book/listings/dsur/dsur4.qmd diff --git a/book/listings/other/egl01.qmd b/book/listings/ecg/egl01.qmd similarity index 100% rename from book/listings/other/egl01.qmd rename to book/listings/ecg/egl01.qmd diff --git a/book/listings/other/oncl01.qmd b/book/listings/efficacy/oncl01.qmd similarity index 100% rename from book/listings/other/oncl01.qmd rename to book/listings/efficacy/oncl01.qmd diff --git a/book/listings/other/exl01.qmd b/book/listings/exposure/exl01.qmd similarity index 100% rename from book/listings/other/exl01.qmd rename to book/listings/exposure/exl01.qmd diff --git a/book/listings/other/lbl01.qmd b/book/listings/lab-results/lbl01.qmd similarity index 100% rename from book/listings/other/lbl01.qmd rename to book/listings/lab-results/lbl01.qmd diff --git a/book/listings/other/lbl01_rls.qmd b/book/listings/lab-results/lbl01_rls.qmd similarity index 100% rename from book/listings/other/lbl01_rls.qmd rename to book/listings/lab-results/lbl01_rls.qmd diff --git a/book/listings/other/lbl02a.qmd b/book/listings/lab-results/lbl02a.qmd similarity index 100% rename from book/listings/other/lbl02a.qmd rename to book/listings/lab-results/lbl02a.qmd diff --git a/book/listings/other/lbl02a_rls.qmd b/book/listings/lab-results/lbl02a_rls.qmd similarity index 100% rename from book/listings/other/lbl02a_rls.qmd rename to book/listings/lab-results/lbl02a_rls.qmd diff --git a/book/listings/other/lbl02b.qmd b/book/listings/lab-results/lbl02b.qmd similarity index 100% rename from book/listings/other/lbl02b.qmd rename to book/listings/lab-results/lbl02b.qmd diff --git a/book/listings/other/mhl01.qmd b/book/listings/medical-history/mhl01.qmd similarity index 100% rename from book/listings/other/mhl01.qmd rename to book/listings/medical-history/mhl01.qmd diff --git a/book/listings/other/vsl01.qmd b/book/listings/vital-signs/vsl01.qmd similarity index 100% rename from book/listings/other/vsl01.qmd rename to book/listings/vital-signs/vsl01.qmd diff --git a/book/tables/pharmacokinetic/adat01.qmd b/book/tables/ada/adat01.qmd similarity index 100% rename from book/tables/pharmacokinetic/adat01.qmd rename to book/tables/ada/adat01.qmd diff --git a/book/tables/pharmacokinetic/adat02.qmd b/book/tables/ada/adat02.qmd similarity index 100% rename from book/tables/pharmacokinetic/adat02.qmd rename to book/tables/ada/adat02.qmd diff --git a/book/tables/pharmacokinetic/adat03.qmd b/book/tables/ada/adat03.qmd similarity index 100% rename from book/tables/pharmacokinetic/adat03.qmd rename to book/tables/ada/adat03.qmd diff --git a/book/tables/pharmacokinetic/adat04a.qmd b/book/tables/ada/adat04a.qmd similarity index 100% rename from book/tables/pharmacokinetic/adat04a.qmd rename to book/tables/ada/adat04a.qmd diff --git a/book/tables/pharmacokinetic/adat04b.qmd b/book/tables/ada/adat04b.qmd similarity index 100% rename from book/tables/pharmacokinetic/adat04b.qmd rename to book/tables/ada/adat04b.qmd diff --git a/book/tables/safety/cmt01.qmd b/book/tables/con-med/cmt01.qmd similarity index 100% rename from book/tables/safety/cmt01.qmd rename to book/tables/con-med/cmt01.qmd diff --git a/book/tables/safety/cmt01a.qmd b/book/tables/con-med/cmt01a.qmd similarity index 100% rename from book/tables/safety/cmt01a.qmd rename to book/tables/con-med/cmt01a.qmd diff --git a/book/tables/safety/cmt01b.qmd b/book/tables/con-med/cmt01b.qmd similarity index 100% rename from book/tables/safety/cmt01b.qmd rename to book/tables/con-med/cmt01b.qmd diff --git a/book/tables/safety/cmt02_pt.qmd b/book/tables/con-med/cmt02_pt.qmd similarity index 100% rename from book/tables/safety/cmt02_pt.qmd rename to book/tables/con-med/cmt02_pt.qmd diff --git a/book/tables/safety/dtht01.qmd b/book/tables/deaths/dtht01.qmd similarity index 100% rename from book/tables/safety/dtht01.qmd rename to book/tables/deaths/dtht01.qmd diff --git a/book/tables/safety/dmt01.qmd b/book/tables/demography/dmt01.qmd similarity index 100% rename from book/tables/safety/dmt01.qmd rename to book/tables/demography/dmt01.qmd diff --git a/book/tables/other/disclosurest01.qmd b/book/tables/disclosures/disclosurest01.qmd similarity index 100% rename from book/tables/other/disclosurest01.qmd rename to book/tables/disclosures/disclosurest01.qmd diff --git a/book/tables/safety/eudrat01.qmd b/book/tables/disclosures/eudrat01.qmd similarity index 100% rename from book/tables/safety/eudrat01.qmd rename to book/tables/disclosures/eudrat01.qmd diff --git a/book/tables/safety/eudrat02.qmd b/book/tables/disclosures/eudrat02.qmd similarity index 100% rename from book/tables/safety/eudrat02.qmd rename to book/tables/disclosures/eudrat02.qmd diff --git a/book/tables/safety/dst01.qmd b/book/tables/disposition/dst01.qmd similarity index 100% rename from book/tables/safety/dst01.qmd rename to book/tables/disposition/dst01.qmd diff --git a/book/tables/safety/pdt01.qmd b/book/tables/disposition/pdt01.qmd similarity index 100% rename from book/tables/safety/pdt01.qmd rename to book/tables/disposition/pdt01.qmd diff --git a/book/tables/safety/pdt02.qmd b/book/tables/disposition/pdt02.qmd similarity index 100% rename from book/tables/safety/pdt02.qmd rename to book/tables/disposition/pdt02.qmd diff --git a/book/tables/safety/egt01.qmd b/book/tables/ecg/egt01.qmd similarity index 100% rename from book/tables/safety/egt01.qmd rename to book/tables/ecg/egt01.qmd diff --git a/book/tables/safety/egt02.qmd b/book/tables/ecg/egt02.qmd similarity index 100% rename from book/tables/safety/egt02.qmd rename to book/tables/ecg/egt02.qmd diff --git a/book/tables/safety/egt03.qmd b/book/tables/ecg/egt03.qmd similarity index 100% rename from book/tables/safety/egt03.qmd rename to book/tables/ecg/egt03.qmd diff --git a/book/tables/safety/egt04.qmd b/book/tables/ecg/egt04.qmd similarity index 100% rename from book/tables/safety/egt04.qmd rename to book/tables/ecg/egt04.qmd diff --git a/book/tables/safety/egt05_qtcat.qmd b/book/tables/ecg/egt05_qtcat.qmd similarity index 100% rename from book/tables/safety/egt05_qtcat.qmd rename to book/tables/ecg/egt05_qtcat.qmd diff --git a/book/tables/other/aovt02.qmd b/book/tables/efficacy/aovt02.qmd similarity index 100% rename from book/tables/other/aovt02.qmd rename to book/tables/efficacy/aovt02.qmd diff --git a/book/tables/other/aovt03.qmd b/book/tables/efficacy/aovt03.qmd similarity index 100% rename from book/tables/other/aovt03.qmd rename to book/tables/efficacy/aovt03.qmd diff --git a/book/tables/other/cmht01.qmd b/book/tables/efficacy/cmht01.qmd similarity index 100% rename from book/tables/other/cmht01.qmd rename to book/tables/efficacy/cmht01.qmd diff --git a/book/tables/other/ratet01.qmd b/book/tables/efficacy/ratet01.qmd similarity index 100% rename from book/tables/other/ratet01.qmd rename to book/tables/efficacy/ratet01.qmd diff --git a/book/tables/other/rbmit01.qmd b/book/tables/efficacy/rbmit01.qmd similarity index 100% rename from book/tables/other/rbmit01.qmd rename to book/tables/efficacy/rbmit01.qmd diff --git a/book/tables/safety/ext01.qmd b/book/tables/exposure/ext01.qmd similarity index 100% rename from book/tables/safety/ext01.qmd rename to book/tables/exposure/ext01.qmd diff --git a/book/tables/safety/mht01.qmd b/book/tables/medical-history/mht01.qmd similarity index 100% rename from book/tables/safety/mht01.qmd rename to book/tables/medical-history/mht01.qmd diff --git a/book/tables/other/rmpt01.qmd b/book/tables/rmp/rmpt01.qmd similarity index 100% rename from book/tables/other/rmpt01.qmd rename to book/tables/rmp/rmpt01.qmd diff --git a/book/tables/other/rmpt03.qmd b/book/tables/rmp/rmpt03.qmd similarity index 100% rename from book/tables/other/rmpt03.qmd rename to book/tables/rmp/rmpt03.qmd diff --git a/book/tables/other/rmpt04.qmd b/book/tables/rmp/rmpt04.qmd similarity index 100% rename from book/tables/other/rmpt04.qmd rename to book/tables/rmp/rmpt04.qmd diff --git a/book/tables/other/rmpt05.qmd b/book/tables/rmp/rmpt05.qmd similarity index 100% rename from book/tables/other/rmpt05.qmd rename to book/tables/rmp/rmpt05.qmd diff --git a/book/tables/other/rmpt06.qmd b/book/tables/rmp/rmpt06.qmd similarity index 100% rename from book/tables/other/rmpt06.qmd rename to book/tables/rmp/rmpt06.qmd diff --git a/book/tables/safety/vst01.qmd b/book/tables/vital-signs/vst01.qmd similarity index 100% rename from book/tables/safety/vst01.qmd rename to book/tables/vital-signs/vst01.qmd diff --git a/book/tables/safety/vst02.qmd b/book/tables/vital-signs/vst02.qmd similarity index 100% rename from book/tables/safety/vst02.qmd rename to book/tables/vital-signs/vst02.qmd