Merge branch 'main' of https://github.com/steno-aarhus/darter-project

# Conflicts:
#	_quarto.yml

.github/workflows/build-website.yml

@@ -25,7 +25,7 @@ jobs:
       - name: Set up Quarto
         uses: quarto-dev/quarto-actions/setup@v2
         with:
-          tinytex: false
+          tinytex: true
 
       - name: Publish to GitHub Pages (and render)
         uses: quarto-dev/quarto-actions/publish@v2

_freeze/applications/rm/registration/execute-results/html.json

@@ -0,0 +1,14 @@
+{
+  "hash": "884f1f01a841b388e354cc87a4a2a7b1",
+  "result": {
+    "markdown": "---\n# format: docx\nexecute: \n  output: asis\n---\n\n\n\n\n# English original\n\n## Projektets type, titel og formål\n\n### Projektets titel\n\n\n{{< var project.title >}}\n\n\n\n### Projektets formål\n\nThe overall aim of this project is to identify the contributions of\nfamily and early life determinants on the development, management, and\ncare of diabetes and the diseases that may arise following a diabetes\ndiagnosis, under a life-course framework.\n\nDiabetes is a complex, multi-factorial disease. Its development depends\non the timing and accumulation of exposures throughout the life-course.\nIn addition to genetic influences, behavioral risk factors and\nsocioeconomic conditions cluster in families and are passed through\ngenerations. For instance, poor childhood socioeconomic status (SES) can\nimpact final educational attainment, adult SES, and lifestyle and\nbehavioral characteristics, which ultimately influence an individual's\nmetabolic capacity to regulate glucose and subsequent risk for diabetes.\n\nThis project will contribute to a broader and deeper understanding of\nthe role that these factors play with the development and progression of\ndiabetes. For this purpose, we will apply causal and predictive\nstatistical methods to best use the data available from the integrated\ndata sources with an overarching goal to model several potential public\nhealth strategies that might impact the prevention and management of\ndiabetes and the diseases that follow its diagnosis.\n\n## Generel beskrivelse\n\n### Registre: Angiv hvilke\n\n\n- Ældredokumentation - hjemmesygepleje i eget hjem (AEHJSP)\n- Ældredokumentation - Rehabilitering (AEREHAB)\n- Ældredokumentation genoptræning vedligeholdelsestræning (AETR)\n- Ældredokumentation visiteret hjemmehjælp frit valg (AEFV)\n- Afregning og finansiering (DRG)\n- Arbejdsklassifikationsmodulet (AKM)\n- Befolkningen (BEF)\n- Beskæftigelsesministeriets forløbsdatabase DREAM (DREAM)\n- Cancerregisteret (Cancerregisteret)\n- CPR Status (CPST)\n- Dansk Børne Diabetes Database (DBDD)\n- Dansk Vosken Diabetes Database (DVDD)\n- Det Nationale Diabetesregister (DND)\n- Detaljeret lønmodtagerdata fra e-Indkomst (BFL)\n- Diabase (Diabase)\n- Døde i Danmark (DOD)\n- Dødfødte ud fra LPR (LPRMFRDF)\n- Dødsårsagsregister (DODSAASG)\n- Dødsårssagsregistret (DODSAARS)\n- Familieindkomster (FAIK)\n- Fertilitet - børn (FTBARN)\n- Fertilitet - forælder (FTFORAEL)\n- Fertilitetsdatabasen børn (FTDB)\n- Fertilitetsdatabasen paritetsfil kvinder (FTDK)\n- Fertilitetsdatabasen paritetsfil mænd (FTDM)\n- Fraværsperioder (FRPE)\n- Historiske vandringer (VNDS)\n- Husstande og familier (FAIN)\n- IDA ansættelser (IDAN)\n- IDA persondata (IDAP)\n- Indkomst (IND)\n- Indvandrere og Efterkommere (IEPE)\n- IVF-registeret (IVF)\n- Laboratoriedatabasen (LABKA)\n- Lægemiddeldatabasen (LMDB)\n- Landspatientregistret - administrative oplysninger (LPR_ADM)\n- Landspatientregistret - ambulante besøgsdatoer (LPR_BES)\n- Landspatientregistret - diagnoser (LPR_DIAG)\n- Landspatientregistret - operationer (LPR_SKSOPR)\n- Landspatientregistret - operationer efter ICD8 klassifikationen (LPR_OPR)\n- Landspatientregistret - undersøgelser og behandlinger (LPR_SKSUBE)\n- Landspatientregistret – psykologi (LPR_PSYK)\n- Levendefødte ud fra LPR (LPRMFRLF)\n- Plejehjemsdata (PLH)\n- Register for Udvalgte Kroniske Sygdomme (RUKS)\n- Sammenhængende socialstatistik (SHSS)\n- Sammenhængende socialstatistik nettovarigheder (SSNV)\n- Sygesikring (6-cifret) (SSSY)\n- Sygesikring (sikringsgruppe) (SYSI)\n- Uddannelser (BUE) (UDDA)\n\n\n## Antal, personkategorier og oplysningstyper\n\n### Antalpersoner-new\n\n\\~8 million people\n\n### Personkategori 1\n\nWhole population (e.g., patients, healthy, dead, etc).\n\n### Oplysningstyper om personkategori 1:\n\nA lot of information on health and disease (e.g. diabetes), economics,\nsocial relationships (e.g. parents).\n\n## Sikkerhed og indsendelse\n\n### Beskriv kort de tekniske og organisatoriske sikkerhedsforanstaltninger\n\nWe have multiple national register based research projects on going at\nSteno Diabetes Center Aarhus and have dedicated personnel who are\nresponsible for managing and ensuring security of the research projects.\nMore information about our process from either Annelli Sandbæk, Adam\nHulman, or Else-Marie Dalsgaard.\n\n# Danish translation\n\n## Projektets type, titel og formål\n\n### Projektets titel\n\n\n{{< var project.title >}}\n\n\n\n### Projektets formål\n\nDet overordnede formål med dette projekt er at identificere bidragene\nfra familieforhold og betingelser tidligt i livet på udvikling,\nhåndtering og behandling af diabetes og de sygdomme, der kan opstå efter\nen diabetesdiagnose, set i løbet af hele livsforløbet.\n\nDiabetes er en kompleks, multifaktoriel sygdom. Udviklingen af diabetes\nafhænger af timingen og akkumuleringen af eksponeringer gennem hele\nlivsforløbet. Ud over genetiske forhold samler adfærdsmæssige\nrisikofaktorer og socioøkonomiske forhold sig i familier og går gennem\ngenerationer. For eksempel kan dårlig socioøkonomisk status i barndommen\npåvirke den endelige uddannelsesniveau, voksen-socioøkonomisk status og\nlivsstils- og adfærdskarakteristika, som i sidste ende påvirker et\nindivids metaboliske kapacitet til at regulere glukose og efterfølgende\nrisiko for diabetes.\n\nDette projekt vil bidrage til en bredere og dybere forståelse af den\nrolle, som disse faktorer spiller for udvikling og forværring af\ndiabetes. Til dette formål vil vi anvende kausale og prædiktive\nstatistiske metoder for bedst muligt at bruge de tilgængelige data fra\nintegrerede datakilder med det overordnede mål til at modellere\nforskellige potentielle folkesundhedsstrategier, der kan påvirke\nforebyggelsen og håndteringen af diabetes og de sygdomme, der følger\nefter diagnosen.\n\n## Generel beskrivelse\n\n### Registre: Angiv hvilke\n\n\n- Ældredokumentation - hjemmesygepleje i eget hjem (AEHJSP)\n- Ældredokumentation - Rehabilitering (AEREHAB)\n- Ældredokumentation genoptræning vedligeholdelsestræning (AETR)\n- Ældredokumentation visiteret hjemmehjælp frit valg (AEFV)\n- Afregning og finansiering (DRG)\n- Arbejdsklassifikationsmodulet (AKM)\n- Befolkningen (BEF)\n- Beskæftigelsesministeriets forløbsdatabase DREAM (DREAM)\n- Cancerregisteret (Cancerregisteret)\n- CPR Status (CPST)\n- Dansk Børne Diabetes Database (DBDD)\n- Dansk Vosken Diabetes Database (DVDD)\n- Det Nationale Diabetesregister (DND)\n- Detaljeret lønmodtagerdata fra e-Indkomst (BFL)\n- Diabase (Diabase)\n- Døde i Danmark (DOD)\n- Dødfødte ud fra LPR (LPRMFRDF)\n- Dødsårsagsregister (DODSAASG)\n- Dødsårssagsregistret (DODSAARS)\n- Familieindkomster (FAIK)\n- Fertilitet - børn (FTBARN)\n- Fertilitet - forælder (FTFORAEL)\n- Fertilitetsdatabasen børn (FTDB)\n- Fertilitetsdatabasen paritetsfil kvinder (FTDK)\n- Fertilitetsdatabasen paritetsfil mænd (FTDM)\n- Fraværsperioder (FRPE)\n- Historiske vandringer (VNDS)\n- Husstande og familier (FAIN)\n- IDA ansættelser (IDAN)\n- IDA persondata (IDAP)\n- Indkomst (IND)\n- Indvandrere og Efterkommere (IEPE)\n- IVF-registeret (IVF)\n- Laboratoriedatabasen (LABKA)\n- Lægemiddeldatabasen (LMDB)\n- Landspatientregistret - administrative oplysninger (LPR_ADM)\n- Landspatientregistret - ambulante besøgsdatoer (LPR_BES)\n- Landspatientregistret - diagnoser (LPR_DIAG)\n- Landspatientregistret - operationer (LPR_SKSOPR)\n- Landspatientregistret - operationer efter ICD8 klassifikationen (LPR_OPR)\n- Landspatientregistret - undersøgelser og behandlinger (LPR_SKSUBE)\n- Landspatientregistret – psykologi (LPR_PSYK)\n- Levendefødte ud fra LPR (LPRMFRLF)\n- Plejehjemsdata (PLH)\n- Register for Udvalgte Kroniske Sygdomme (RUKS)\n- Sammenhængende socialstatistik (SHSS)\n- Sammenhængende socialstatistik nettovarigheder (SSNV)\n- Sygesikring (6-cifret) (SSSY)\n- Sygesikring (sikringsgruppe) (SYSI)\n- Uddannelser (BUE) (UDDA)\n\n\n## Antal, personkategorier og oplysningstyper\n\n### Antalpersoner-new\n\n\\~8 mio. mennesker\n\n### Personkategori 1\n\nHele befolkningen (f.eks, patienter, raske, afdøde, etc).\n\n### Oplysningstyper om personkategori 1:\n\nMange oplysninger om sundhed og sygdom (f.eks. diabetes), økonomiske, og\nsociale forhold (f.eks. forældre).\n\n## Sikkerhed og indsendelse\n\n### Beskriv kort de tekniske og organisatoriske sikkerhedsforanstaltninger\n\nVi har flere nationale registerbaserede forskningsprojekter i gang på\nSteno Diabetes Center Aarhus og har dedikerede medarbejdere, der er\nansvarlige for at styre og sikre sikkerheden i forskningsprojekterne.\nMere information om vores proces kan indhentes fra enten Annelli Sandbæk\n(anesnd\\@rm.dk), Adam Hulman (adahul\\@rm.dk), eller Else-Marie Dalsgaard\n(elseda\\@rm.dk)\n",
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_freeze/applications/sds/application/execute-results/html.json

@@ -0,0 +1,14 @@
+{
+  "hash": "571b15aff6e263df7180a6fea8607f8a",
+  "result": {
+    "markdown": "---\ntitle: \"Application for use of Sundhedsdatastyrelsen (SDS) registers\"\n---\n\n\nFill in the below information using the [SDS application\nform](https://ds.sst.dk/ds2010/Forskerservice_CRM2/Forskerservice.aspx).\nNot all information filled into the form is present here.\n\n-   **Project number**: 708421\n\n# Project title\n\n\n{{< var project.title >}}\n\n\n\n# Abstract\n\nDiabetes is a complex, multi-factorial disease. Its development depends\non the timing and accumulation of exposures throughout the life-course.\nIn addition to genetic influences, behavioral risk factors and\nsocioeconomic conditions cluster in families and are passed through\ngenerations. The overall aim of this project is to identify the\ncontributions of family and early life determinants on the development,\nmanagement, economics, and care of diabetes and the diseases that may\narise following a diabetes diagnosis, under a life-course framework.\n\n# Registers\n\n\n\n\n- Cancerregisteret\n- DRG\n- IVF\n- LAB\n- LMDB\n- LPR_PSYK\n- PLH\n- RUKS\n",
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_freeze/applications/sds/description/execute-results/html.json

@@ -0,0 +1,14 @@
+{
+  "hash": "2f0d864a6c8bddb9fc268adc09f82c7c",
+  "result": {
+    "markdown": "---\ntitle: \"Project description\"\n---\n\n\n## Introduction\n\n<!-- Brief introduction to the area. -->\n\nDiabetes is a complex, multi-factorial disease. Its development depends\non the timing and accumulation of exposures throughout the life-course.\nIn addition to genetic influences, behavioral risk factors and\nsocioeconomic conditions cluster in families and are passed through\ngenerations. For instance, poor childhood socioeconomic status (SES) can\nimpact final educational attainment, adult SES, and lifestyle and\nbehavioral characteristics, which ultimately influence an individual's\nmetabolic capacity to regulate glucose and subsequent risk for diabetes.\n\n## Purpose\n\n<!-- The purpose of the project is briefly formulated. -->\n\nThe overall aim of this project is to identify the contributions of\nfamily and early life determinants on the development, management,\neconomics, and care of diabetes and the diseases that may arise\nfollowing a diabetes diagnosis, under a life-course framework.\n\n## The problem of the project\n\n\n```{=html}\n<!-- \nPreferably formulated as the specific question or questions to which the \nconclusion must answer.\n-->\n```\n\nSome of our questions include:\n\n1.  Are some metabolic characteristics affected more by early life\n    conditions than others?\n2.  Knowing the above and knowing an adult individual's history during\n    early life, could we intervene and target specific metabolic\n    characteristics to lower the risk for T2DM?\n3.  Do some early life conditions affect an adult individual's metabolic\n    status and risk for disease more than other conditions?\n4.  Are long-term diabetes outcomes (nephropathy, eye disease, premature\n    death) affected by treatment persistence and stability in patients\n    with psychiatric comorbidity?\n5.  To what extent does the family network (e.g. parents, grandparents,\n    siblings) and family environment influence the risk for developing\n    type 2 diabetes in adulthood?\n\n## Data and Method\n\n\n```{=html}\n<!-- \nHow will the project respond to the problem? What data will be used? How should\ndata be used?\n-->\n```\n\nWe intend to use the requested data from both SDS and DST registers, as\nwell as data from Danish cohort studies, to apply causal and predictive\nstatistical methods that best model associations for our questions and\ncompare how various public health strategies might impact the\nprevention, economics, and management of diabetes and the diseases that\nfollow its diagnosis.\n\nBecause we intend to try to answer questions that involve any\nindividual's early life and early childhood conditions, we need data on\ntheir parents. Likewise, to understand the role that the family network,\nincluding siblings and grandparents, has on diabetes risk, we need a\nlarge enough population to make these linkages and to adequately study\nthis area. Given the complicated nature of linking and constructing\nfamily networks, we need data on not just the individual but also the\nfamily in order to obtain the data we need to answer our questions.\n\n## Publication of results\n\n<!-- How and when are the results of the research planned to be published? -->\n\nWe will disseminate the results of the planned research project through\npre-print archives, conference presentations, journal articles, and\nthrough blogs and other social media outlets. Results will only be\npublished in open access scientific outlets.\n\n## Perspective\n\n<!-- What knowledge of societal relevance can this study contribute to? -->\n\nThis project will contribute to a broader and deeper understanding of\nthe role that these factors play with the development and progression of\ndiabetes.\n\nUnderstanding how early life and familial factors can influence diabetes\nprovides us with tools and knowledge to better target, intervene, and\neither prevent or manage diabetes and its complications. Considering the\nimpact that diabetes as a disease itself and its related comorbidities\nhas at the personal, public health, and economic level, any improvement\nin knowledge can have major impacts.\n\n## Ethical considerations\n\n\n```{=html}\n<!-- \nIf the project involves direct contact with citizens, for example questionnaire \nsurveys or intervention studies: What ethical considerations have been made in\nconnection with the direct involvement of citizens in the survey?\n-->\n```\n\nNo direct contact to citizens are made in this project.\n",
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_freeze/applications/sds/instructions/execute-results/html.json

@@ -0,0 +1,14 @@
+{
+  "hash": "3b6272e99f3a66f7e0adab931c6dfe00",
+  "result": {
+    "markdown": "---\nexecute:\n  eval: false\n---\n\n\n# Instructions for documents to provide to SDS\n\n## Project description\n\n\n::: {.cell}\n\n:::\n\n\nNår du søger om adgang til data via Forskerservice, skal du vedhæfte en\nprojektbeskrivelse til ansøgningen. Vi skal i Forskerservice bruge\nprojektbeskrivelsen til at vurdere, om dine ønsker om data svarer til\nprojektets problemstilling og metode. Ligeledes skal vi vurdere den\nsamfundsmæssige rele- vans af projektet. Begge dele for at vi kan\noverholde databeskyttelsesforordningen. Derfor vil en præcis\nprojektbeskrivelse hjælpe os til at give dig en bedre rådgivning i\nforbindelse med din ansøgning. Projektbeskrivelsen skal indeholde\nfølgende: Introduktion Kort indføring i området. Formål Projektets\nformål kort formuleret. Projektets problemstilling Gerne formuleret som\ndet eller de konkrete spørgsmål, som konklusionen skal svare på. Data og\nMetode Hvordan vil projektet svare på problemstillingen? Hvilke data vil\nman anvende? Hvordan skal data bruges? Offentliggørelse af resultater\nHvordan og hvornår planlægges forskningens resultater offentliggjort?\nPerspektivering Hvilken viden af samfundsmæssig relevans kan denne\nundersøgelse bidrage til? Etiske overvejelser Hvis projektet indebærer\ndirekte kontakt med borgere, for eksempel spørgeskemaunder- søgelser\neller interventionsstudier: Hvilke etiske overvejelser er der gjort i\nforbindelse med direkte inddragelse af borgere i undersøgelsen?\n\n## Extraction description\n\n\n::: {.cell}\n\n:::\n",
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_freeze/applications/sds/review/additional-requests-completed/execute-results/docx.json

@@ -0,0 +1,14 @@
+{
+  "hash": "592493b1f5c5b9eb7d63c3970dab2ca4",
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+    "markdown": "---\nformat: docx\n---\n\n\n1.  Processing of personally identifiable data\n    -   See attached documents.\n    -   Requested information:\n        -   Name of institution responsible for data: Steno Diabetes\n            Center Aarhus\n        -   Name of project manager: Annelli Sandbæk (or Adam Hulman)\n        -   Title of the project: Interplay between diabetes and\n            intergenerational transmission of health determinants over\n            the life course\n        -   End date of the project, if any: 2030-12-31 (with DST)\n2.  Payment information\n    -   E-mail payment manager: sofalb\\@rm.dk\n    -   Invoice must be sent to: Sofie Albrechtsen, Steno Diabetes\n        Center Aarhus\n    -   CVR: 29190925\n    -   EAN:\n    -   Project account: 708421\n3.  Extraction description\n    -   We've updated the extraction document with the requested\n        justifications.\n4.  ATC codes for LMDB:\n    -   We've completed the ATC code document as requested.\n",
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