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3 Cognitive change/project-presentation.qmd
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3 Cognitive change/project-presentation.qmd
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---
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title: "Physical activity before stroke, small vessel disease and cognitive decline after stroke"
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format:
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revealjs:
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footer: "Andreas"
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slide-number: c/t
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show-slide-number: all
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toc: true
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toc-title: "Overview"
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logo: dsc_tekst.png
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theme: serif
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css: style.css
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editor: visual
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---
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## Hypothesis
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```{r}
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library(tidyverse)
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# remotes::install_github("agdamsbo/REDCapRITS")
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library(gtsummary)
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library(patchwork)
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library(REDCapRITS)
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# REDCapR::redcap_instruments(redcap_uri = "https://redcap.au.dk/api/", token = keyring::key_get("enigma_api_key"))$data
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d_list <- REDCapRITS::read_redcap_tables(
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uri = "https://redcap.au.dk/api/",
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token = keyring::key_get("enigma_api_key"),
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fields = c("record_id", "incl_by" , "incl_date"),
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forms = c(
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"klassifikation_af_primre_stroke",
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"baseline_stroke",
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"registrering",
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"baseline_nihss",
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"mrs",
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"uddannelsesniveau",
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"hjde_vgt_og_blodtryk",
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"rygeanamnese",
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"rbans",
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"iqcode",
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"eos"
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)
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)
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```
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```{r message=FALSE}
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d <- REDCapRITS::redcap_wider(d_list)
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```
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> Higher level of PA before acute ischemic stroke (AIS) is associated with decreased risk of cognitive decline after stroke independently of stroke severity and cSVD burden.
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## Data {.smaller}
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- Physical Activity Scale in the Elderly (**PASE**) questionnaire
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- Modified Rankin Scale (**mRS**)
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- Level of education
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- Informant Questionnaire on Cognitive Decline in the Elderly, short version (**IQCODE**)
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- Repeatable Battery for the Assessment of Neuropsychological Status (**RBANS**), Scandinavian version
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- Wellbeing and depressive symptoms
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- Cerebral Small vessel disease burden (**cSVD score**)
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## Education {.smaller}
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```{r education}
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# dput(levels(factor(d$education_inclusion_long)))
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d |>
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select(kon, education_inclusion_long, ) |>
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mutate(
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education_inclusion_long = factor(
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education_inclusion_long,
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levels = c(
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"Folkeskole (9-10 år)",
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"Gymnasiale/erhvervsfaglige uddannelser (11-12 år)",
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"Erhvervsakademiuddannelser (13-14 år)",
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"Professionsbachelor/universitetsbachelor (15-17 år)",
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"Kandidatuddannelser (18-19 år)",
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"PhD ( > 20 år)"
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)
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)) |>
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tbl_summary(
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by = "kon",
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missing = "ifany",
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missing_text = "Not classified",
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label = list(education_inclusion_long ~ "Level of education")
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) |>
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add_overall(
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)
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```
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## SVD scoring
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- Number of microbleeds (SWI)
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- Superficiel siderose (SWI)
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- Lacunes (3D FLAIR)
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- White matter hyperintensities (3D FLAIR)
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- Enlarged Perivascular Space (3D FLAIR)
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- Atrophy (3D T1)
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## SVD score {.scrollable}
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```{r}
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REDCapTidieR::read_redcap(
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redcap_uri = "https://redcap.au.dk/api/",
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token = keyring::key_get("enigma_api_key"),
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forms = c("svd_score")) |> REDCapTidieR::bind_tibbles()
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svd_score |> filter(svd_initials=="AGD",redcap_event=="inclusion") |> select(svd_score) |> na.omit() |> mutate(svd_score = as.numeric(svd_score)) |> tbl_summary()
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```
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## IQCODE og RBANS {.smaller}
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```{r}
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d |>
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select(kon,
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mrs_score_inclusion_long,
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iq_score,
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rbans_e_is_3_months_long,
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rbans_e_is_12_months_long
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# ,
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# svd_score
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) |>
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mutate(mrs_score_inclusion_long=factor(mrs_score_inclusion_long,labels = c("0","1","2"))) |>
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tbl_summary(
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by = "kon",
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missing = "no",
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label = list(
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mrs_score_inclusion_long~"mRS at inclusion",
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iq_score~"IQCODE score",
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rbans_e_is_3_months_long~"RBANS 3 months",
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rbans_e_is_12_months_long~"RBANS 12 months"#,
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# svd_score~"SVD score at inclusion"
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)
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) |>
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add_overall()
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```
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## RBANS plot
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```{r}
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source("/Users/au301842/ENIGMAtrial_R/src/plot_index.R")
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rbans <- d_list$rbans |>
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dplyr::select(c("record_id",
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"redcap_event_name",
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ends_with(c("_is","_lo","_up","_per")))) |>
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na.omit()|>
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dplyr::mutate(redcap_event=factor(redcap_event_name,
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levels = c("3_months","12_months"),
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labels = c("3 months","12 months"))) |>
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dplyr::tibble()
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rbans |>
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dplyr::filter(record_id %in% record_id[duplicated(record_id)]) |> # Only patients with both 3 and 12 month
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dplyr::filter(record_id %in% sample(record_id,5)) |> # 5 random patients
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# filter(record_id %in% 28:32) |> # Only specified number
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plot_index(id="redcap_event_name",facet.by = "record_id")
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```
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