From aec37980364c3b287f069fcc7322b29e730a8c98 Mon Sep 17 00:00:00 2001 From: AG Damsbo Date: Fri, 30 Sep 2022 12:57:23 +0200 Subject: [PATCH] Added the generic_stroke() function and bumped version number. --- DESCRIPTION | 4 +- NAMESPACE | 5 + R/generic_stroke.R | 43 +++ docs/404.html | 2 +- docs/authors.html | 6 +- docs/index.html | 2 +- docs/pkgdown.yml | 2 +- docs/reference/Rplot002.png | Bin 0 -> 31231 bytes docs/reference/age_calc.html | 2 +- docs/reference/cpr_check.html | 2 +- docs/reference/cpr_dob.html | 2 +- docs/reference/cpr_female.html | 2 +- docs/reference/cprs.html | 2 +- docs/reference/generic_stroke-1.png | Bin 0 -> 38675 bytes docs/reference/generic_stroke-2.png | Bin 0 -> 84364 bytes docs/reference/generic_stroke.html | 558 +++++++++++++++++++++++++++ docs/reference/index.html | 7 +- docs/reference/plot_olr-1.png | Bin 90068 -> 87613 bytes docs/reference/plot_olr.html | 2 +- docs/reference/quantile_cut.html | 6 +- docs/reference/stRoke-package.html | 2 +- docs/search.json | 2 +- docs/sitemap.xml | 3 + man/generic_stroke.Rd | 31 ++ tests/testthat/test-generic_stroke.R | 5 + 25 files changed, 671 insertions(+), 19 deletions(-) create mode 100644 R/generic_stroke.R create mode 100644 docs/reference/Rplot002.png create mode 100644 docs/reference/generic_stroke-1.png create mode 100644 docs/reference/generic_stroke-2.png create mode 100644 docs/reference/generic_stroke.html create mode 100644 man/generic_stroke.Rd create mode 100644 tests/testthat/test-generic_stroke.R diff --git a/DESCRIPTION b/DESCRIPTION index 62e4c5c..9848da5 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: stRoke Title: Tools for work in clinical stroke research -Version: 0.22.9.3 +Version: 0.22.9.4 Authors@R: person("Andreas Gammelgaard", "Damsbo", , "agdamsbo@clin.au.dk", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-7559-1154")) @@ -19,5 +19,7 @@ Language: en-US Config/testthat/edition: 3 Imports: ggplot2, + gtsummary, MASS, + rankinPlot, stats diff --git a/NAMESPACE b/NAMESPACE index baa1609..b914ecf 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -4,8 +4,13 @@ export(age_calc) export(cpr_check) export(cpr_dob) export(cpr_female) +export(generic_stroke) export(plot_olr) export(quantile_cut) import(MASS) import(ggplot2) import(stats) +importFrom(MASS,polr) +importFrom(gtsummary,add_overall) +importFrom(gtsummary,tbl_summary) +importFrom(rankinPlot,grottaBar) diff --git a/R/generic_stroke.R b/R/generic_stroke.R new file mode 100644 index 0000000..7b1d5b2 --- /dev/null +++ b/R/generic_stroke.R @@ -0,0 +1,43 @@ +utils::globalVariables(c("df","group","score","strata")) + +#' Generic stroke study outcome +#' +#' Includes table 1, grotta bars and ordinal logistic regression plot. +#' Please just use this function for illustration purposes. +#' To dos: +#' +#' @param df Data set as data frame +#' @param group Variable to group by +#' @param score Outcome measure variable +#' @param strata Optional variable to stratify by +#' @param variables String of variable names to include in adjusted OLR-analysis +#' +#' @return Returns list with three elements +#' @export +#' +#' @import ggplot2 +#' @importFrom gtsummary tbl_summary +#' @importFrom gtsummary add_overall +#' @importFrom MASS polr +#' @importFrom rankinPlot grottaBar +#' +#' @examples +#' iris$ord<-factor(sample(1:3,size=nrow(iris),replace=TRUE),ordered=TRUE) +#' generic_stroke(df=iris, group = "Species", score = "ord", variables = colnames(iris)[1:3]) +generic_stroke <- function(df, group, score, strata = NULL, variables = NULL) + { + t1<-gtsummary::tbl_summary(data = df[,c(group,variables)], + by = group) |> + gtsummary::add_overall() + + x <- table(df[,c(group, score, strata)]) + f1 <- rankinPlot::grottaBar(x = x, groupName = group, + scoreName = score, + strataName = strata, + colourScheme ="custom") + + df[,score] <- factor(df[,score],ordered = TRUE) + f2 <- plot_olr(MASS::polr(formula(paste0(score,"~.")), data=df[,c(group, score, variables)], Hess=TRUE, method="logistic"), input="model") + + list("Table 1" = t1, "Figure 1" = f1, "Figure 2" = f2) +} diff --git a/docs/404.html b/docs/404.html index 8d28b25..09ea99d 100644 --- a/docs/404.html +++ b/docs/404.html @@ -24,7 +24,7 @@ stRoke - 0.22.9.3 + 0.22.9.4 + + + + + +
+
+
+

Generic stroke study outcome

+ +
generic_stroke.Rd
+
+ +
+

Includes table 1, grotta bars and ordinal logistic regression plot. +Please just use this function for illustration purposes. +To dos:

+
+ +
+

Usage

+ 
generic_stroke(df, group, score, strata = NULL, variables = NULL)
+
+ +
+

Arguments

+
df
+

Data set as data frame

+ + +
group
+

Variable to group by

+ + +
score
+

Outcome measure variable

+ + +
strata
+

Optional variable to stratify by

+ + +
variables
+

String of variable names to include in adjusted OLR-analysis

+ +
+
+

Value

+ + +

Returns list with three elements

+
+ +
+

Examples

+ 
iris$ord<-factor(sample(1:3,size=nrow(iris),replace=TRUE),ordered=TRUE) 
+generic_stroke(df=iris, group = "Species", score = "ord", variables = colnames(iris)[1:3])
+#> Waiting for profiling to be done...
+#> $`Table 1`
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+#>     <tr>
+#>       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col"><strong>Characteristic</strong></th>
+#>       <th class="gt_col_heading gt_columns_bottom_border gt_center" rowspan="1" colspan="1" scope="col"><strong>Overall</strong>, N = 150<sup class="gt_footnote_marks">1</sup></th>
+#>       <th class="gt_col_heading gt_columns_bottom_border gt_center" rowspan="1" colspan="1" scope="col"><strong>setosa</strong>, N = 50<sup class="gt_footnote_marks">1</sup></th>
+#>       <th class="gt_col_heading gt_columns_bottom_border gt_center" rowspan="1" colspan="1" scope="col"><strong>versicolor</strong>, N = 50<sup class="gt_footnote_marks">1</sup></th>
+#>       <th class="gt_col_heading gt_columns_bottom_border gt_center" rowspan="1" colspan="1" scope="col"><strong>virginica</strong>, N = 50<sup class="gt_footnote_marks">1</sup></th>
+#>     </tr>
+#>   </thead>
+#>   <tbody class="gt_table_body">
+#>     <tr><td class="gt_row gt_left">Sepal.Length</td>
+#> <td class="gt_row gt_center">5.80 (5.10, 6.40)</td>
+#> <td class="gt_row gt_center">5.00 (4.80, 5.20)</td>
+#> <td class="gt_row gt_center">5.90 (5.60, 6.30)</td>
+#> <td class="gt_row gt_center">6.50 (6.23, 6.90)</td></tr>
+#>     <tr><td class="gt_row gt_left">Sepal.Width</td>
+#> <td class="gt_row gt_center">3.00 (2.80, 3.30)</td>
+#> <td class="gt_row gt_center">3.40 (3.20, 3.68)</td>
+#> <td class="gt_row gt_center">2.80 (2.53, 3.00)</td>
+#> <td class="gt_row gt_center">3.00 (2.80, 3.18)</td></tr>
+#>     <tr><td class="gt_row gt_left">Petal.Length</td>
+#> <td class="gt_row gt_center">4.35 (1.60, 5.10)</td>
+#> <td class="gt_row gt_center">1.50 (1.40, 1.58)</td>
+#> <td class="gt_row gt_center">4.35 (4.00, 4.60)</td>
+#> <td class="gt_row gt_center">5.55 (5.10, 5.88)</td></tr>
+#>   </tbody>
+#>   
+#>   <tfoot class="gt_footnotes">
+#>     <tr>
+#>       <td class="gt_footnote" colspan="5"><sup class="gt_footnote_marks">1</sup> Median (IQR)</td>
+#>     </tr>
+#>   </tfoot>
+#> </table>
+#> </div>
+#> 
+#> $`Figure 1`
+
+#> 
+#> $`Figure 2`
+
+#> 
+
+
+
+ + +
+

Developed by Andreas Gammelgaard Damsbo.

+
+ +
+

Site built with pkgdown 2.0.6.

+
+ +
+ + + + + + + diff --git a/docs/reference/index.html b/docs/reference/index.html index b34907b..0a51153 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -10,7 +10,7 @@ stRoke - 0.22.9.3 + 0.22.9.4