PAaSO/Midterm assesment/Midterm.qmd

---
title: "Physical activity and sequelae after stroke"
subtitle: "PhD Midterm Evaluation"
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# PhD status

My PhD project draws on two different data sets. The first data set is from the \acr{TALOS} trial[@kraglund2018], a clinical trial conducted between 2013-2016. Within by PhD, I am looking to enrich this clinical data set with data from a number of different registries. The second data set is expected to be and data from a clinical, observational study that is currently including patients. This trial is called \acr{ENIGMA}.

As part of by PhD, I have completed courses and other activities corresponding to 28.5 ECTS points (of 30 required) and have performed a total of 129.5 hours of teaching and supervision combined (of 150 hours required).

Below I will go through the three different projects in my PhD.

{{< include a-predict.qmd >}}

{{< include b-longterm.qmd >}}

{{< include c-lifestyle.qmd >}}

# Publications

As described earlier, my main publications are still pending journal submission. I have, however been involved in a few of other projects. Below, I have highlighted two articles, that I have been closely involved with.

The first article was on depressive symptoms and pre\acr{PA} after stroke within the \acr{TALOS}-cohort.[@vestergaard2023] I performed all the data management and analyses, as well as co-authoring the manuscript.

The second article is on stroke outcome for patients where the clinician abstained from acute treatment and three months outcome.[@behrndtz2022] I joined in the work to help on the data analyses and co-authoring the manuscript.

## Other publicized work

```{r}
#| include: false
#| message: false
#| fig-cap: The total downloads of maintained *R* packages.

library(cranlogs)
library(tidyverse)

downs <- cran_downloads(
    packages = c("stRoke", "REDCapCAST"),
    from = "2023-01-01",
    to = Sys.Date()
  ) |> group_by(package) |> summarise(downloads = sum(count)) 
# downs |> knitr::kable()
# downs |> filter(package=="stRoke") |> select(downloads) |> c()
```

For the \acr{ENIGMA} trial, I have been responsible for the data base creation and maintenance in REDCap.[@harris2009] All scripts used for data management has been openly shared.[@damsbo2023a] I have also improved previous work[@redcapr2023] for handling longitudinal data from REDCap and shared these improvements as an *R* package called `REDCapCAST` with different functions to ease this kind of work.[@egeler2023] In total, the `REDCapCAST` package has been downloaded `r downs |> filter(package=="REDCapCAST") |> select(downloads) |> c()` times.

Additionally, I have published a collection of useful tools and learning examples as an *R* package called `stRoke`.[@damsbo2023] The `stroke` package has been downloaded a total of `r downs |> filter(package=="stRoke") |> select(downloads) |> c()` times.

### Documentation on working with MRI data

During my exchange stay in the \acr{BBL} at \acr{UBC} led by prof. Lara Boyd, I have worked extensively with colleagues at the \acr{BBL} on developing a pipeline for translating stroke lesions into a model for studying the "dis-connectome" of lost connections between different functional areas of the brain and linking it to motor function.[@kuceyeski2013] We have used free and open source tools, and the work on the pipeline has been documented and shared openly and freely as part of the project (<https://agdamsbo.github.io/normalisation-pipeline/>). We are working on a publishing the work in a peer-reviewed journal, and the documentation will be extended to work as reference for others.

# Research plans for the remaining PhD study

I believe that the timeline for my three projects as outlined above is reasonable and leaves room for further delays to data availability as the main limiting factor, that I am not in complete control of. Overall, I plan to have the publications on my three PhD projects ready within the next year.

Regarding my other commitments as a PhD-student I am very satisfied that I have completed my exchange stay and received (almost) all ECTS points from the PhD School at the midterm time point. I will also soon have completed the necessary teaching and supervision, but will be looking forward to continuing supervision, and teaching and dissemination tasks.

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# References {.unnumbered}

::: {#refs}
:::

# List of Abbrevations {.unnumbered}

\printacronyms

# Appendicies

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