clean

R/app_version.R

@@ -1 +1 @@
-app_version <- function()'250319_1306'
+app_version <- function()'250319_1327'

R/regression_plot.R

@@ -138,6 +138,6 @@ symmetrical_scale_x_log10 <- function(plot,breaks=c(1,2,3,5,10),...){
   max_abs_x <- max(abs(c(x_min,x_max)))
 
   ticks <- log10(breaks)+(ceiling(max_abs_x)-1)
-  browser()
+
   plot + ggplot2::scale_x_log10(limits=c(rx_min,rx_max),breaks=create_log_tics(10^ticks[ticks<=max_abs_x]))
 }

inst/apps/FreesearchR/app.R

@@ -10,7 +10,7 @@
 #### Current file: R//app_version.R 
 ########
 
-app_version <- function()'250319_1306'
+app_version <- function()'250319_1327'
 
 
 ########
@@ -3400,20 +3400,25 @@ plot_box_single <- function(data, x, y=NULL, seed = 2103) {
     ## THis could be optional in future
     ggplot2::geom_jitter(color = "black", size = 2, alpha = 0.9) +
     ggplot2::coord_flip() +
-    # viridis::scale_fill_viridis(discrete = discrete, option = "C") +
+    viridis::scale_fill_viridis(discrete = discrete, option = "D") +
     # ggplot2::theme_void() +
+    ggplot2::theme_bw(base_size = 24) +
     ggplot2::theme(
       legend.position = "none",
       # panel.grid.major = element_blank(),
       # panel.grid.minor = element_blank(),
       # axis.text.y = element_blank(),
       # axis.title.y = element_blank(),
-      text = ggplot2::element_text(size = 20),
+      # text = ggplot2::element_text(size = 20),
       # axis.text = ggplot2::element_blank(),
       # plot.title = element_blank(),
       panel.background = ggplot2::element_rect(fill = "white"),
       plot.background = ggplot2::element_rect(fill = "white"),
-      panel.border = ggplot2::element_blank()
+      panel.border = ggplot2::element_blank(),
+      panel.grid.major = ggplot2::element_blank(),
+      panel.grid.minor = ggplot2::element_blank(),
+      axis.line = ggplot2::element_line(colour = "black"),
+      axis.ticks = ggplot2::element_line(colour = "black")
     )
 }
 
@@ -5338,7 +5343,7 @@ symmetrical_scale_x_log10 <- function(plot,breaks=c(1,2,3,5,10),...){
   max_abs_x <- max(abs(c(x_min,x_max)))
 
   ticks <- log10(breaks)+(ceiling(max_abs_x)-1)
-  browser()
+
   plot + ggplot2::scale_x_log10(limits=c(rx_min,rx_max),breaks=create_log_tics(10^ticks[ticks<=max_abs_x]))
 }
 

inst/apps/FreesearchR/rsconnect/shinyapps.io/agdamsbo/freesearcheR.dcf

@@ -5,6 +5,6 @@ account: agdamsbo
 server: shinyapps.io
 hostUrl: https://api.shinyapps.io/v1
 appId: 13611288
-bundleId: 9961770
+bundleId: 9969300
 url: https://agdamsbo.shinyapps.io/freesearcheR/
 version: 1

inst/apps/FreesearchR/www/notes_visuals.md

@@ -1,6 +1,6 @@
 # Basic visualisations
 
-This section on plotting data is kept very minimal, and includes only the most common plot types for clinical projects.
+The goal of ***FreesearchR*** is to keep things simple. Visuals can get very complicated. We provide a selection of plots, that helps visualise typical clinical and will be enough for most use cases, and for publishing to most journals.
 
 If you want to go further, have a look at these sites with suggestions and sample code for data plotting:
 
@@ -8,4 +8,4 @@ If you want to go further, have a look at these sites with suggestions and sampl
 
 -   [*R* Graph gallery](https://r-graph-gallery.com/): Another gallery with great graphs
 
--   [grphics principles](https://graphicsprinciples.github.io/): Easy to follow recommendations for clear visuals. 
+-   [graphics principles](https://graphicsprinciples.github.io/): Easy to follow recommendations for clear visuals. 

inst/apps/FreesearchR/www/references.bib

@@ -0,0 +1,24 @@
+
+@book{andreasgammelgaarddamsbo2025,
+	title = {agdamsbo/freesearcheR: freesearcheR 25.3.1},
+	author = {Andreas Gammelgaard Damsbo, },
+	year = {2025},
+	month = {03},
+	date = {2025-03-06},
+	publisher = {Zenodo},
+	doi = {10.5281/ZENODO.14527429},
+	url = {https://zenodo.org/doi/10.5281/zenodo.14527429}
+}
+
+@article{Aam2020,
+	title = {Post-stroke Cognitive Impairment{\textemdash}Impact of Follow-Up Time and Stroke Subtype on Severity and Cognitive Profile: The Nor-COAST Study},
+	author = {Aam, Stina and Einstad, Marte Stine and Munthe-Kaas, Ragnhild and Lydersen, Stian and Ihle-Hansen, Hege and Knapskog, Anne Brita and {Ellekjær}, Hanne and Seljeseth, Yngve and Saltvedt, Ingvild},
+	year = {2020},
+	date = {2020},
+	journal = {Frontiers in Neurology},
+	pages = {1--10},
+	volume = {11},
+	number = {July},
+	doi = {10.3389/fneur.2020.00699},
+	note = {Citation Key: Aam2020}
+}

inst/apps/FreesearchR/www/report.rmd

@@ -1,8 +1,8 @@
 ---
-title: "freesearcheR data report"
+title: "FreesearchR data report"
 date: "Report generated `r gsub('(\\D)0', '\\1', format(Sys.time(), '%A, %d.%m.%Y'))`"
 format: docx
-author: freesearcheR data analysis tool
+author: FreesearchR data analysis tool
 toc: false
 params:
   data.file: NA
@@ -13,7 +13,6 @@ knitr::opts_chunk$set(echo = FALSE, message = FALSE, warning = FALSE)
 # glue::glue("{format(lubridate::today(),'%A')}, {lubridate::day(lubridate::today())}.{lubridate::month(lubridate::today())}.{lubridate::year(lubridate::today())}")
 ```
 
-
 ```{r}
 web_data <- readr::read_rds(file = params$data.file)
 library(gtsummary)
@@ -42,11 +41,11 @@ vec2sentence <- function(data, sep.word = "and") {
 
 ## Introduction
 
-Research should be free and open with easy access for all. The freesearcheR tool attempts to help lower the bar to participate in contributing to science by making guided data analysis easily accessible in the web-browser.
+Research should be free and open with easy access for all. The FreesearchR tool attempts to help lower the bar to participate in contributing to science by making guided data analysis easily accessible in the web-browser.
 
 ## Methods
 
-Analyses were conducted in the *freesearcheR* data analysis web-tool based on R version 4.4.1.
+Analyses were conducted in the *FreesearchR* data analysis web-tool based on R version 4.4.1.
 
 ## Results
 
@@ -70,3 +69,4 @@ knitr::knit_print(tbl_merge(reg_tbl))
 ## Discussion
 
 Good luck on your further work!
+