methods and results part 2

content/60.methods.md

@@ -161,20 +161,20 @@ The workflow file is available from <https://github.com/greenelab/covid19-review
 The Python package versions are available in <https://github.com/greenelab/covid19-review/blob/external-resources/environment.yml>.<!-- To Do: These files are archived with [Zenodo?](...). -->
 Data about worldwide cases and deaths from the COVID-19 Data Repository by the Center for Systems Science and Engineering at Johns Hopkins University [@https://github.com/CSSEGISandData/COVID-19/tree/master/csse_covid_19_data/csse_covid_19_time_series] were read using a Python script. <!-- To Do: replace figure reference with manuscript reference or reference figure conditionally based on template variable [to generate Figure @fig:csse-deaths.] -->
 Similarly, the clinical trials statistics and figure were generated based on data from the University of Oxford Evidence-Based Medicine Data Lab's COVID-19 TrialsTracker [@doi:10.5281/zenodo.3732709]. <!-- TODO: replace figure reference with manuscript reference or reference figure conditionally based on template variable [Figure @fig:ebm-trials] -->
+The evolution of this figure over time is shown in Figure @fig:ebm-trials.
 Information about vaccine distribution was extracted from Our World In Data [@url:https://github.com/owid/covid-19-data].
-Figure 1 (above) also uses this approach to dynamically integrate data directly from the CORD-19 dataset [@arxiv:2004.10706].
-<!--To Do: Flow chart of data integration? We could have a summary figure showing all of the external data sources that are integrated into the manuscript. We have icons for MSSM reviews, JHU data, etc. at the top. That flows into a GitHub repo, which also takes input from all the contributors. Then the output of the repo is the manuscript and other CI artifacts.-->
-
-<!-- To Do: example of how the auto-updated figures changed between an early version and most recent version to demonstrate the importance of having current data visualized--> July 7, 2020 compared to current ().
+Figure 1 (above) also uses this approach to dynamically integrate data directly from the CORD-19 dataset [@arxiv:2004.10706].<!--To Do: Flow chart of data integration? We could have a summary figure showing all of the external data sources that are integrated into the manuscript. We have icons for MSSM reviews, JHU data, etc. at the top. That flows into a GitHub repo, which also takes input from all the contributors. Then the output of the repo is the manuscript and other CI artifacts.-->
 
 ![
 **Change in the COVID-19 clinical trials figure over time.**
 When we first produced this figure on July 7, 2020, there were 3,733 clincial trials in the University of Oxford Evidence-Based Medicine Data Lab's COVID-19 TrialsTracker [@doi:10.5281/zenodo.3732709].
 As of {{ebm_date_pretty}}, it contains {{ebm_all_trials}}.
-We were also able to easily reconfigure the figure to emphasize interventional trials based on the recommendation of a collaborator who is a clinician.
+We were also able to easily reconfigure the figure prior to journal submission to emphasize interventional trials based on the recommendation of a collaborator who is a clinician.
 This figure is included in an analysis of pharmaceutical development efforts during COVID-19 [@arxiv:2103.02723].
 ]((images/ebmdatalab-trials-original.png){{ebm_trials_figure}} "COVID-19 clinical trials"){#fig:ebm-trials secno=1}
 
+<!--To Do: Discussion of the absurd number of references?-->
+
 #### Updates to Manubot
 
 The scite integration and spell-checking functionalities have been integrated into the current release of Manubot <!--To Do: Link-->.