First draft for text description of the data #69
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Relates to #35 |
…uture improvements. Added description of raw data. National Patient Register only for now.
Moved changes section to #78
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changed the title
…same recnum value is repeated for all diagnoses for that specific contact.
vignettes/algorithm_logic.Rmd
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| in future revisions. Refer to the other vignettes for background | ||
| information and a more general description of the algorithm. |
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You could add links to specific vignettes with relevant information here?
vignettes/algorithm_data.Rmd
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| ## Contents | ||
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| This document describes the structure of the data components processed |
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I have used the word "data sources". Do we prefer "data components"? Or "data objects" as in the title? I think it makes sense to align this, so the same words are used for the same things throughout the documentation :)
vignettes/algorithm_data.Rmd
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| In a future revision, the algorithm can also utilise the Danish Medical | ||
| Birth Register to extend the period of time of valid inclusions further | ||
| back in time compared to what is possible using obstetric codes from the | ||
| National Patient Register. |
vignettes/algorithm_data.Rmd
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| assumes that raw data is stored/structured in the most common format for | ||
| raw data provided on Statistics Denmark's servers (from our experience). |
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Maybe add which specific formats you are talking about here? :)
vignettes/algorithm_data.Rmd
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| `d_inddto`/`dato_start`. | ||
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| - Named `lpr_adm` in the LPR2-formatted data prior to 2019, and | ||
| `kontakter` in contact-based LPR3-formatted data from 2019 |
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Do you want to use the English abbreviation DNPR?
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Maybe also add what the abbreviation comes from? I.e., Landspatientregisteret?
Or do we assume readers know this?
Co-authored-by: Signe Kirk Brødbæk <40836345+signekb@users.noreply.github.com>
| rlang::check_installed("glue") | ||
| rlang::check_installed("knitr") |
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Whenever you use a function from a package that you set as "suggests" as a dependency, you need to include a check function to inform the user to install these packages if they are not installed. So that's what these do (when you use use_package("packagename", "suggests"), it tells you exactly what to do)
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| variable_description |> | ||
| dplyr::select( | ||
| .data$register_name, |
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I think I mentioned this already, but the .data$ is used to masked the variable so that CRAN doesn't warn of "undeclared variables". Since we declare this placeholder variable ".data" already.
| the `dw_ek_kontakt` variable (LPR3 data). | ||
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| ```{r} | ||
| for (register in osdc:::get_register_abbrev()) { |
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While I almost always suggest not to use for loops, this is one of those cases that you need to, since these functions are used to create Markdown text, and it doesn't really work in a "functional" way.
| register, | ||
| caption = glue::glue("Variables and their descriptions within the `{register}` register.") | ||
| ) |> | ||
| print() |
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You need to print because only the last thing in a for loop is output, but we want all these things to output.
| ```{r, include = FALSE} | ||
| knitr::opts_chunk$set( | ||
| echo = FALSE, | ||
| results = "asis", |
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This tells knitr to treat all the output as plain text rather than as code output text
| sources: | ||
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| ```{r, results='asis'} | ||
| osdc:::registers_as_md_table("Danish registers used in the OSDC algorithm.") |
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The triple-colons is because this is an internal function/object or what is going on here?
Also, a note to my future self: you need to build the package in order to access internal objects
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haah yes! Or use Ctrl-Shift-L to load the package. And yea, ::: accesses all internal objects in a package, neat trick!
Just want some feedback on the current format before I fill out the remaining sections describing the raw data with similar content.
I suspect @lwjohnst86 will want to automate the data source descriptions at some point. Then we might have to add a column with the english register names to the variable description csv.