117 lines
5.9 KiB
Text
117 lines
5.9 KiB
Text
---
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title: "Physical activity and sequelae after stroke"
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subtitle: "PhD Midterm Evaluation"
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format:
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titlepage-mod-pdf:
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include-in-header:
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text: |
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\usepackage[document]{ragged2e}
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\usepackage{pdfpages}
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\usepackage{setspace}
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\onehalfspacing
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editor: source
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bibliography: references.bib
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---
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<!-- Help: https://nmfs-opensci.github.io/quarto_titlepages/ -->
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<!-- ### State of the art report -->
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{{< include StateoftheArt.qmd >}}
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```{r include=FALSE}
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# Possibly a better option, but more focused on glossaries
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# library(glossary)
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# glossary_path("glossary.yml")
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# glossary_popup("hover")
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# glossary_style(color = "purple",
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# text_decoration = "underline",
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# def_bg = "#333",
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# def_color = "white")
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```
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# PhD status
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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}.
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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).
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Below I will go through the three different projects in my PhD.
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{{< include a-predict.qmd >}}
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{{< include b-longterm.qmd >}}
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{{< include c-lifestyle.qmd >}}
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# Publications
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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.
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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.
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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.
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## Other publicized work
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```{r}
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#| include: false
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#| message: false
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#| fig-cap: The total downloads of maintained *R* packages.
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library(cranlogs)
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library(tidyverse)
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downs <- cran_downloads(
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packages = c("stRoke", "REDCapCAST"),
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from = "2023-01-01",
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to = Sys.Date()
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) |> group_by(package) |> summarise(downloads = sum(count))
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# downs |> knitr::kable()
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# downs |> filter(package=="stRoke") |> select(downloads) |> c()
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```
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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.
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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.
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### Documentation on working with MRI data
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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.
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# Research plans for the remaining PhD study
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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.
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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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<!-- Ref: https://phd.health.au.dk/doingaphd/ordinaryphd/evaluations/midtermevaluation/ -->
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<!-- ### The scientific report -->
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<!-- The scientific report, approximately five pages in total, has to include: -->
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<!-- - A "State of the Art" description (one-two pages) of the research area at hand describing the present international scientific knowledge including references to recent relevant scientific literature -->
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<!-- - A status of the supervised research project including provisional results and a discussion of these -->
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<!-- - Any publications resulting from the PhD student's own work needs to be listed -->
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<!-- - A discussion of the research plans for the remaining PhD study period -->
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<!-- There are no requirements as to font, type size or spacing, but the report needs to be in English. The scientific report has to be uploaded in MyPhD. -->
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{{< pagebreak >}}
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# References {.unnumbered}
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::: {#refs}
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:::
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# List of Abbrevations {.unnumbered}
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\printacronyms
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# Appendicies
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{{< include appendicies.qmd >}}
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