Code

set.seed()

In 00-simulate_data.R, you used set.seed(), which ensures reproducibility!
You made a lot of comments throughout your script and it was easy to follow along with what was going on in your code.
Preamble documentation’s prerequisites mentions scripts that need to be ran and library that needs to be installed prior to running the current script file. One suggestion I would make is maybe you could include a comment suggesting to call the install.packages function to install the required packages just in case if someone is unfamiliar with how you would install packages in R.
Overall great work with your scripts!

Paper

Introduction

The introduction is well written and interesting! It introduces your topic and the importance of assessing disease outbreaks in healthcare facilities! I also appreciate you defining terms like outbreak to get rid of misunderstandings of certain terms when people go to read your paper.

Data

The dataset used in this analysis is the 2023 installment of “Outbreaks in Toronto Healthcare Institutions” from Toronto Public Health (Toronto Public Health 2024). In Ontario, the law mandates that respiratory and gastroenteric infections in healthcare facilities are followed and that any outbreaks, regardless of verification, are reported to public health entities such as Toronto Public Health (Toronto Public Health 2024).

I like how in this part of the discuss how the dataset was obtained and the laws requiring the data being added.

Moreover, this dataset is considered to be “open data” (Toronto Public Health 2024) and can be utilized for a variety of purposes as long as an attribution statement is attached (Section A.3) and the link to the City of Toronto’s Open Data License is added (City of Toronto, n.d.b).

This part of your paper might not be necessary to include, specifically the following part: “Moreover, this dataset is considered to be “open data””). I think that just mentioning the dataset can be used for various purposes as long as an attribution statement is attached is fine.

The variables or measurements included in this analysis are “Type of Location” (named “Out- break Setting” in the original dataset), which refers to the nature of the healthcare offered at each facility; “Type of Outbreak”, which indicates whether each outbreak is respiratory, enteric, or other in nature; and “Outbreak First Known Cause” (named “Causative Agent-1” in the original dataset), which denotes the first discovered pathogen based on at least one of the outbreak’s cases (Toronto Public Health 2024)

You included both the names of the variable and also their names when used for graphs and tables, which makes it clear where you are getting your data.

Only two other datasets involving outbreaks, titled “COVID-19 Cases in Toronto” and “Daily Shelter & Overnight Service Occupancy & Capacity”, could be identified following a search of the City of Toronto’s Open Data Catalogue (City of Toronto, n.d.a). However, none of these datasets pertain specifically to healthcare settings in Toronto and were thus not used in this analysis.

Great work on mentioning datasets that you identified and explaining what you ended up not choosing them.

Using the R programming language (R Core Team 2022)

Great job on citing R!

The graph was easy to understand and clear of what the data is presenting

Discussion

In Section 2.2, it was observed that long-term care homes had the greatest proportion of the total outbreaks among healthcare facilities in Toronto in 2023 (Table 1 and Figure 1), that approximately 95% of the outbreaks were respiratory in nature (Table 2 and Figure 2), and that COVID-19 was the first known cause of a majority of the outbreaks (Table 3 and Figure 3).

I think this part can be broken up into two sentences since it’s a bit long.

All three of these results share common origins. For instance, in October 2022, the Government of Ontario removed a masking requirement for caregivers and visitors in long-term care homes (The Canadian Press 2022), whose residents are primarily at or above 65 years of age with an average age of 83 years as reported in 2018 (Ontario Centres for Learning, Research and Innovation in Long-Term Care 2018). Since individuals aged 60 years or older are more likely to experience worse health effects after contracting COVID-19, the Public Health Agency of Canada recommends that they wear a respirator or mask to limit the transmission of this pathogen (Public Health Agency of Canada 2022). As a result, it seems that the Government of Ontario did not heed this advice, possibly contributing to the large proportion of disease outbreaks (which include COVID-19) in Toronto long-term care homes in 2023. This appears to follow a long-standing trend in Ontario long-term care homes. For example, at the start of the COVID-19 pandemic, long-term care homes in Ontario experienced a sizable increase in COVID-19 cases (Casey 2020). This was potentially made worse by the fact that not all of these facilities enforced mask-wearing and that long-term care homes were passed over for personal protective equipment in favour of hospitals (Casey 2020). Moreover, the fact that several hospitals in Toronto curtailed their mask requirements in June and July of 2023 (Fox 2023) likely contributed to the large volume of respiratory disease outbreaks observed in Table 2
and Figure 2.

This discussion is great and I like how you used real life events to back up your thinking of why you think you are seeing the results you are seeing.

As a result, it seems that the Government of Ontario did not heed this advice, possibly contributing to the large proportion of disease outbreaks (which include COVID-19) in Toronto long-term care homes in 2023

I believe, “Toronto long-term care homes” should be “Toronto’s long-term care homes” instead.

Acknowledgments

I also don't think you need an acknowledgment section for your statement on your R code. You could just briefly mention it in your Appendix section.

Overall your paper is well written and your graphs are clear! Also, terrific job on citations! I noticed you cited a lot and used BibTeX and had all mentions of figures and tables linked in your paper.

bennyrochwerg / healthcare-outbreaks-toronto