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112 lines
4.3 KiB
Plaintext
112 lines
4.3 KiB
Plaintext
---
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title: "Toolbox"
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output: rmarkdown::html_vignette
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vignette: >
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%\VignetteIndexEntry{Toolbox}
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%\VignetteEngine{knitr::rmarkdown}
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%\VignetteEncoding{UTF-8}
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---
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```{r, include = FALSE}
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knitr::opts_chunk$set(
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collapse = TRUE,
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comment = "#>"
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)
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```
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```{r setup}
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library(stRoke)
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```
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# A toolbox
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My own toolbox in my small workshop is a mix of some old, worn, well proven tools and some newcomers. This package should be seen as something like that.
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I have tried to collect tools and functions from other packages that I use regularly in addition to functions that I have written myself to fill use cases, that I have not been able to find solutions to elsewhere.
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In documenting and testing the package, I have used [OpenAI's](https://beta.openai.com/overview) chatgpt with [gpttools](https://jameshwade.github.io/gpttools/). The chatgpt is an interesting tool, that is in no way perfect, but it helps with tedious tasks. Both `gpttools` and [`gptstudio`](https://michelnivard.github.io/gptstudio/) are interesting implementations in R and RStudio.
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## CPR manipulations {#cpr-intro}
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Note that, if handled, CPR numbers (social security numbers) should be handled with care as they a considered highly sensitive data.
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The CPR number is structured as _DDMMYY-XXXX_, with the 1st _X_ designating decade of birth, the last _X_ designate binary gender (not biological sex) dependent on even/uneven as female/male, and the last for digits are used in a modulus calculation to verify the validity of the CPR number. Foreigners and unidentified persons are given temporary CPR numbers including letters.
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More information can be found on [cpr.dk](https://cpr.dk).
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Note, that all CPR numbers used in examples are publicly known or non-organic.
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### age_calc()
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The age_calc() function was created as a learning exercise and functions similarly to `lubridate::time_length()`.
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```{r age_calc-example}
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(age <- age_calc(as.Date("1945-10-23"),as.Date("2018-09-30")))
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trunc(age)
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```
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### cpr_check()
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Checks validity of CPR numbers according to the [modulus 11 rule](https://cpr.dk/cpr-systemet/opbygning-af-cpr-nummeret). Note that due to limitations in the possible available CPR numbers, this rule [does not apply to all CPR numbers after 2007](https://cpr.dk/cpr-systemet/personnumre-uden-kontrolciffer-modulus-11-kontrol).
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```{r cpr_check-example}
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cpr_check(c("2310450637", "010190-2000", "010115-4000","300450-1030","010150-4021", "010150-4AA1"))
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```
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Including CPR numbers with letters gives a warning and `NA`, as it can not be checked by the modulus 11 function. Should be used with care, see the message.
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### cpr_dob()
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Extracts date of birth (DOB) from a CPR number. Accounts for the decade of birth. [See earlier](#cpr-intro).
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```{r cpr_dob-example}
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cpr_dob(c("2310450637", "010190-2000", "010115-4000","300450-1030","010150-4021"))
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```
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### cpr_female()
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Gives logical vector of whether female gender from last digit of CPR.
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```{r cpr_female-example}
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table(cpr_female(stRoke::cprs[,1]))
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```
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## Plotting
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### ci_plot()
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Plots odds ratios with 95 % confidence intervals. Performs binary logistic regression for outcome factors with two (2) levels and ordinal logistic regression for outcome factors with more than two levels. Mind relevant assumptions.
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Outputs ggplot element for further manipulation.
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```{r ci_plot-example}
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data(talos)
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talos[,"mrs_1"]<-factor(talos[,"mrs_1"],ordered=TRUE)
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ci_plot(ds = talos, x = "rtreat", y = "mrs_1", vars = c("hypertension","diabetes"))
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```
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### generic_stroke()
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For learning purposes. Uses annonymized data from the [TALOS trial](https://doi.org/10.1161/STROKEAHA.117.020067) to output a Table 1 (with `gtsummary::tbl_summary()`), plotting the so-called grotta-bars based on mRS scores (with `rankinPlot::grottaBar()`) and a ordinal logistic regression model plot (with `stRoke::ci_plot()`).
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```{r generic_stroke-example}
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generic_stroke(stRoke::talos, "rtreat", "mrs_6", variables = c("hypertension","diabetes","civil"))
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```
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### index_plot()
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Used for plotting scores from a multi dimensional patient test.
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```{r index_plot-example}
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index_plot(stRoke::score[score$event=="A",])
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```
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### read_redcap_tables()
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Reads REDCap data accounting for events and repeated instruments. Based on `library(REDCapR)` and `library(agdamsbo/REDCapRITS)`.
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Please see [the vignette on REDCap](https://agdamsbo.github.io/stRoke/articles/redcap.html).
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