Updated vignette to include most functions.

vignettes/toolbox.Rmd

@@ -23,3 +23,87 @@ library(stRoke)
 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.
+
+## 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}
+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",])
+```
+
+### read_redcap_tables()
+
+Reads REDCap data accounting for events and repeated instruments. Based on `library(REDCapR)` and `library(agdamsbo/REDCapRITS)`.
+
+Please see [the vignette on REDCap](https://agdamsbo.github.io/stRoke/articles/redcap.html).
+
+