mirror of
https://github.com/agdamsbo/stRoke.git
synced 2024-10-29 19:01:53 +01:00
142 lines
4.7 KiB
Plaintext
142 lines
4.7 KiB
Plaintext
---
|
|
title: "Toolbox"
|
|
date: "`r Sys.Date()`"
|
|
output: rmarkdown::html_vignette
|
|
vignette: >
|
|
%\VignetteIndexEntry{Toolbox}
|
|
%\VignetteEngine{knitr::rmarkdown}
|
|
%\VignetteEncoding{UTF-8}
|
|
---
|
|
|
|
```{r, include = FALSE}
|
|
knitr::opts_chunk$set(
|
|
collapse = TRUE,
|
|
comment = "#>"
|
|
)
|
|
```
|
|
|
|
```{r setup}
|
|
library(stRoke)
|
|
```
|
|
|
|
# A toolbox
|
|
|
|
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.
|
|
|
|
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.
|
|
|
|
In documenting and testing the package, I have used [OpenAI's](https://platform.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.
|
|
|
|
## CPR manipulations {#cpr-intro}
|
|
|
|
Note that, if handled, CPR numbers (social security numbers) should be handled with care as they a considered highly sensitive data.
|
|
|
|
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.
|
|
|
|
More information can be found on [cpr.dk](https://cpr.dk).
|
|
|
|
Note, that all CPR numbers used in examples are publicly known or non-organic.
|
|
|
|
### age_calc()
|
|
|
|
The age_calc() function was created as a learning exercise and functions similarly to `lubridate::time_length()`.
|
|
|
|
```{r age_calc-example}
|
|
(age <- age_calc(as.Date("1945-10-23"), as.Date("2018-09-30")))
|
|
trunc(age)
|
|
```
|
|
|
|
### cpr_check()
|
|
|
|
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).
|
|
|
|
```{r cpr_check-example}
|
|
cpr_check(
|
|
c(
|
|
"2310450637",
|
|
"010190-2000",
|
|
"010115-4000",
|
|
"300450-1030",
|
|
"010150-4021",
|
|
"010150-4AA1"
|
|
)
|
|
)
|
|
```
|
|
|
|
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.
|
|
|
|
### cpr_dob()
|
|
|
|
Extracts date of birth (DOB) from a CPR number. Accounts for the decade of birth. [See earlier](#cpr-intro).
|
|
|
|
```{r cpr_dob-example}
|
|
cpr_dob(c(
|
|
"2310450637",
|
|
"010190-2000",
|
|
"010115-4000",
|
|
"300450-1030",
|
|
"010150-4021"
|
|
))
|
|
```
|
|
|
|
### cpr_female()
|
|
|
|
Gives logical vector of whether female gender from last digit of CPR.
|
|
|
|
```{r cpr_female-example}
|
|
table(cpr_female(stRoke::cprs[, 1]))
|
|
```
|
|
|
|
## Plotting
|
|
|
|
### ci_plot()
|
|
|
|
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.
|
|
|
|
Outputs ggplot element for further manipulation.
|
|
|
|
```{r ci_plot-example}
|
|
data(talos)
|
|
talos[, "mrs_1"] <- factor(talos[, "mrs_1"], ordered = TRUE)
|
|
ci_plot(
|
|
ds = talos,
|
|
x = "rtreat",
|
|
y = "mrs_1",
|
|
vars = c("hypertension", "diabetes")
|
|
)
|
|
```
|
|
|
|
### generic_stroke()
|
|
|
|
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()`).
|
|
|
|
```{r generic_stroke-example}
|
|
generic_stroke(stRoke::talos,
|
|
"rtreat",
|
|
"mrs_6",
|
|
variables = c("hypertension", "diabetes", "civil"))
|
|
```
|
|
|
|
### index_plot()
|
|
|
|
Used for plotting scores from a multi dimensional patient test.
|
|
|
|
```{r index_plot-example}
|
|
index_plot(stRoke::score[score$event == "A", ])
|
|
```
|
|
|
|
### win_prob()
|
|
|
|
The `win_prob()` is an implementation of the Tournament Method for calculating the probability of winning as suggested by [Zou et al 2022](https://doi.org/10.1161/STROKEAHA.121.037744). The authors has included a spreadsheet as supplementary materials. This function aims to mimic that functionality. The function also includes a `print()` extension for nice printing.
|
|
|
|
```{r win_prob-example}
|
|
win_prob(
|
|
data = stRoke::talos,
|
|
response = "mrs_6",
|
|
group = "rtreat",
|
|
sample.size = TRUE,
|
|
print.tables = TRUE
|
|
)
|
|
```
|
|
|