diff --git a/index.html b/index.html index 172c747e..cb611492 100644 --- a/index.html +++ b/index.html @@ -57,13 +57,17 @@ -

This package is the backbone of the FreesearchR, a free and open-source browser based data exploration and analysis tool for clinicians and researchers with publication ready output.

-

This package and the FreesearchR-tool is part of a larger initiative to democratize health data analysis and remove barriers for clinicians to engage in health research.

-

the FreesearchR-tool is online and accessible here: link to the app freely hosted on shinyapps.io. All feedback is welcome and can be shared as a GitHub issue.

-

Initiatives for funding continued development of the tool and surrounding initiatives is ongoing.

+

This package is the backbone of the FreesearchR, a free and open-source browser based data exploration and analysis tool intended to democratise clinical research by assisting any researcher to easily evaluate and analyse data and export publication ready results.

+

The FreesearchR-tool is online and accessible here: link to the app freely hosted on shinyapps.io. All feedback is welcome and can be shared as a GitHub issue. Any suggestions on collaboration is much welcomed. Please reach out!

Motivation

+

This app has the following simple goals:

+
    +

  1. help the health clinician getting an overview of data in quality improvement projects and clinical research

    2. +

  2. help learners get a good start analysing data and coding in R

    3. +

  3. ease quick data overview and basic visualisations for any clinical researcher

    4. +

Install locally diff --git a/pkgdown.yml b/pkgdown.yml index 9948425f..90782cff 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -3,7 +3,7 @@ pkgdown: 2.1.1 pkgdown_sha: ~ articles: FreesearchR: FreesearchR.html -last_built: 2025-04-14T10:38Z +last_built: 2025-04-15T15:13Z urls: reference: https://agdamsbo.github.io/FreesearchR/reference article: https://agdamsbo.github.io/FreesearchR/articles diff --git a/reference/add_class_icon.html b/reference/add_class_icon.html index f6220322..b7626c68 100644 --- a/reference/add_class_icon.html +++ b/reference/add_class_icon.html @@ -1,5 +1,5 @@ -Convert class grid column to icon — add_class_icon • FreesearchR +Convert class grid column to icon — add_class_icon • FreesearchR Skip to contents @@ -42,7 +42,7 @@

Usage

- 
add_class_icon(grid, column = "class")
+ 
add_class_icon(grid, column = "class", fun = class_icons)
@@ -68,10 +68,8 @@ overview_vars() |> toastui::datagrid() |> add_class_icon() -
-
-
-
+#> Error: grid_columns: Variable(s) class are not valid columns in data passed to datagrid() +

diff --git a/reference/add_sparkline.html b/reference/add_sparkline.html index 8707db49..bedff1f1 100644 --- a/reference/add_sparkline.html +++ b/reference/add_sparkline.html @@ -75,10 +75,10 @@ toastui::datagrid() |> add_sparkline() grid -
-
+
+
-
+ diff --git a/reference/align_axes.html b/reference/align_axes.html new file mode 100644 index 00000000..4ba3f165 --- /dev/null +++ b/reference/align_axes.html @@ -0,0 +1,80 @@ + +Aligns axes between plots — align_axes • FreesearchR + Skip to contents + + +
+
+
+ +

Aligns axes between plots

+ Source: R/data_plots.R +
align_axes.Rd
+
+ +
+

Aligns axes between plots

+
+ +
+

Usage

+ 
align_axes(...)
+
+ +
+

Arguments

+ + +
...
+

ggplot2 objects or list of ggplot2 objects

+ +
+
+

Value

+

list of ggplot2 objects

+
+ +
+ + +
+ + + + + + + diff --git a/reference/argsstring2list.html b/reference/argsstring2list.html index 25efbd49..06c4111d 100644 --- a/reference/argsstring2list.html +++ b/reference/argsstring2list.html @@ -58,6 +58,18 @@

list

+
+

Examples

+ 
argsstring2list("A=1:5,b=2:4")
+#> $A
+#> [1] 1 2 3 4 5
+#> 
+#> $b
+#> [1] 2 3 4
+#> 
+
+
+
diff --git a/reference/class_icons.html b/reference/class_icons.html new file mode 100644 index 00000000..d46c84d2 --- /dev/null +++ b/reference/class_icons.html @@ -0,0 +1,363 @@ + +Get data class icons — class_icons • FreesearchR + Skip to contents + + +
+
+
+ +

Get data class icons

+ Source: R/data-summary.R +
class_icons.Rd
+
+ +
+

Get data class icons

+
+ +
+

Usage

+ 
class_icons(x)
+
+ +
+

Arguments

+ + +
x
+

character vector of data classes

+ +
+
+

Value

+

list

+
+ +
+

Examples

+ 
"numeric" |> class_icons()|> str()
+#> List of 3
+#>  $ name    : chr "i"
+#>  $ attribs :List of 3
+#>   ..$ class     : chr "fas fa-calculator"
+#>   ..$ role      : chr "presentation"
+#>   ..$ aria-label: chr "calculator icon"
+#>  $ children: list()
+#>  - attr(*, "class")= chr "shiny.tag"
+#>  - attr(*, "browsable_html")= logi TRUE
+#>  - attr(*, "html_dependencies")=List of 1
+#>   ..$ :List of 10
+#>   .. ..$ name      : chr "font-awesome"
+#>   .. ..$ version   : chr "6.5.2"
+#>   .. ..$ src       :List of 1
+#>   .. .. ..$ file: chr "fontawesome"
+#>   .. ..$ meta      : NULL
+#>   .. ..$ script    : NULL
+#>   .. ..$ stylesheet: chr [1:2] "css/all.min.css" "css/v4-shims.min.css"
+#>   .. ..$ head      : NULL
+#>   .. ..$ attachment: NULL
+#>   .. ..$ package   : chr "fontawesome"
+#>   .. ..$ all_files : logi TRUE
+#>   .. ..- attr(*, "class")= chr "html_dependency"
+mtcars |> sapply(class) |> class_icons() |> str()
+#> List of 11
+#>  $ mpg :List of 3
+#>   ..$ name    : chr "i"
+#>   ..$ attribs :List of 3
+#>   .. ..$ class     : chr "fas fa-calculator"
+#>   .. ..$ role      : chr "presentation"
+#>   .. ..$ aria-label: chr "calculator icon"
+#>   ..$ children: list()
+#>   ..- attr(*, "class")= chr "shiny.tag"
+#>   ..- attr(*, "browsable_html")= logi TRUE
+#>   ..- attr(*, "html_dependencies")=List of 1
+#>   .. ..$ :List of 10
+#>   .. .. ..$ name      : chr "font-awesome"
+#>   .. .. ..$ version   : chr "6.5.2"
+#>   .. .. ..$ src       :List of 1
+#>   .. .. .. ..$ file: chr "fontawesome"
+#>   .. .. ..$ meta      : NULL
+#>   .. .. ..$ script    : NULL
+#>   .. .. ..$ stylesheet: chr [1:2] "css/all.min.css" "css/v4-shims.min.css"
+#>   .. .. ..$ head      : NULL
+#>   .. .. ..$ attachment: NULL
+#>   .. .. ..$ package   : chr "fontawesome"
+#>   .. .. ..$ all_files : logi TRUE
+#>   .. .. ..- attr(*, "class")= chr "html_dependency"
+#>  $ cyl :List of 3
+#>   ..$ name    : chr "i"
+#>   ..$ attribs :List of 3
+#>   .. ..$ class     : chr "fas fa-calculator"
+#>   .. ..$ role      : chr "presentation"
+#>   .. ..$ aria-label: chr "calculator icon"
+#>   ..$ children: list()
+#>   ..- attr(*, "class")= chr "shiny.tag"
+#>   ..- attr(*, "browsable_html")= logi TRUE
+#>   ..- attr(*, "html_dependencies")=List of 1
+#>   .. ..$ :List of 10
+#>   .. .. ..$ name      : chr "font-awesome"
+#>   .. .. ..$ version   : chr "6.5.2"
+#>   .. .. ..$ src       :List of 1
+#>   .. .. .. ..$ file: chr "fontawesome"
+#>   .. .. ..$ meta      : NULL
+#>   .. .. ..$ script    : NULL
+#>   .. .. ..$ stylesheet: chr [1:2] "css/all.min.css" "css/v4-shims.min.css"
+#>   .. .. ..$ head      : NULL
+#>   .. .. ..$ attachment: NULL
+#>   .. .. ..$ package   : chr "fontawesome"
+#>   .. .. ..$ all_files : logi TRUE
+#>   .. .. ..- attr(*, "class")= chr "html_dependency"
+#>  $ disp:List of 3
+#>   ..$ name    : chr "i"
+#>   ..$ attribs :List of 3
+#>   .. ..$ class     : chr "fas fa-calculator"
+#>   .. ..$ role      : chr "presentation"
+#>   .. ..$ aria-label: chr "calculator icon"
+#>   ..$ children: list()
+#>   ..- attr(*, "class")= chr "shiny.tag"
+#>   ..- attr(*, "browsable_html")= logi TRUE
+#>   ..- attr(*, "html_dependencies")=List of 1
+#>   .. ..$ :List of 10
+#>   .. .. ..$ name      : chr "font-awesome"
+#>   .. .. ..$ version   : chr "6.5.2"
+#>   .. .. ..$ src       :List of 1
+#>   .. .. .. ..$ file: chr "fontawesome"
+#>   .. .. ..$ meta      : NULL
+#>   .. .. ..$ script    : NULL
+#>   .. .. ..$ stylesheet: chr [1:2] "css/all.min.css" "css/v4-shims.min.css"
+#>   .. .. ..$ head      : NULL
+#>   .. .. ..$ attachment: NULL
+#>   .. .. ..$ package   : chr "fontawesome"
+#>   .. .. ..$ all_files : logi TRUE
+#>   .. .. ..- attr(*, "class")= chr "html_dependency"
+#>  $ hp  :List of 3
+#>   ..$ name    : chr "i"
+#>   ..$ attribs :List of 3
+#>   .. ..$ class     : chr "fas fa-calculator"
+#>   .. ..$ role      : chr "presentation"
+#>   .. ..$ aria-label: chr "calculator icon"
+#>   ..$ children: list()
+#>   ..- attr(*, "class")= chr "shiny.tag"
+#>   ..- attr(*, "browsable_html")= logi TRUE
+#>   ..- attr(*, "html_dependencies")=List of 1
+#>   .. ..$ :List of 10
+#>   .. .. ..$ name      : chr "font-awesome"
+#>   .. .. ..$ version   : chr "6.5.2"
+#>   .. .. ..$ src       :List of 1
+#>   .. .. .. ..$ file: chr "fontawesome"
+#>   .. .. ..$ meta      : NULL
+#>   .. .. ..$ script    : NULL
+#>   .. .. ..$ stylesheet: chr [1:2] "css/all.min.css" "css/v4-shims.min.css"
+#>   .. .. ..$ head      : NULL
+#>   .. .. ..$ attachment: NULL
+#>   .. .. ..$ package   : chr "fontawesome"
+#>   .. .. ..$ all_files : logi TRUE
+#>   .. .. ..- attr(*, "class")= chr "html_dependency"
+#>  $ drat:List of 3
+#>   ..$ name    : chr "i"
+#>   ..$ attribs :List of 3
+#>   .. ..$ class     : chr "fas fa-calculator"
+#>   .. ..$ role      : chr "presentation"
+#>   .. ..$ aria-label: chr "calculator icon"
+#>   ..$ children: list()
+#>   ..- attr(*, "class")= chr "shiny.tag"
+#>   ..- attr(*, "browsable_html")= logi TRUE
+#>   ..- attr(*, "html_dependencies")=List of 1
+#>   .. ..$ :List of 10
+#>   .. .. ..$ name      : chr "font-awesome"
+#>   .. .. ..$ version   : chr "6.5.2"
+#>   .. .. ..$ src       :List of 1
+#>   .. .. .. ..$ file: chr "fontawesome"
+#>   .. .. ..$ meta      : NULL
+#>   .. .. ..$ script    : NULL
+#>   .. .. ..$ stylesheet: chr [1:2] "css/all.min.css" "css/v4-shims.min.css"
+#>   .. .. ..$ head      : NULL
+#>   .. .. ..$ attachment: NULL
+#>   .. .. ..$ package   : chr "fontawesome"
+#>   .. .. ..$ all_files : logi TRUE
+#>   .. .. ..- attr(*, "class")= chr "html_dependency"
+#>  $ wt  :List of 3
+#>   ..$ name    : chr "i"
+#>   ..$ attribs :List of 3
+#>   .. ..$ class     : chr "fas fa-calculator"
+#>   .. ..$ role      : chr "presentation"
+#>   .. ..$ aria-label: chr "calculator icon"
+#>   ..$ children: list()
+#>   ..- attr(*, "class")= chr "shiny.tag"
+#>   ..- attr(*, "browsable_html")= logi TRUE
+#>   ..- attr(*, "html_dependencies")=List of 1
+#>   .. ..$ :List of 10
+#>   .. .. ..$ name      : chr "font-awesome"
+#>   .. .. ..$ version   : chr "6.5.2"
+#>   .. .. ..$ src       :List of 1
+#>   .. .. .. ..$ file: chr "fontawesome"
+#>   .. .. ..$ meta      : NULL
+#>   .. .. ..$ script    : NULL
+#>   .. .. ..$ stylesheet: chr [1:2] "css/all.min.css" "css/v4-shims.min.css"
+#>   .. .. ..$ head      : NULL
+#>   .. .. ..$ attachment: NULL
+#>   .. .. ..$ package   : chr "fontawesome"
+#>   .. .. ..$ all_files : logi TRUE
+#>   .. .. ..- attr(*, "class")= chr "html_dependency"
+#>  $ qsec:List of 3
+#>   ..$ name    : chr "i"
+#>   ..$ attribs :List of 3
+#>   .. ..$ class     : chr "fas fa-calculator"
+#>   .. ..$ role      : chr "presentation"
+#>   .. ..$ aria-label: chr "calculator icon"
+#>   ..$ children: list()
+#>   ..- attr(*, "class")= chr "shiny.tag"
+#>   ..- attr(*, "browsable_html")= logi TRUE
+#>   ..- attr(*, "html_dependencies")=List of 1
+#>   .. ..$ :List of 10
+#>   .. .. ..$ name      : chr "font-awesome"
+#>   .. .. ..$ version   : chr "6.5.2"
+#>   .. .. ..$ src       :List of 1
+#>   .. .. .. ..$ file: chr "fontawesome"
+#>   .. .. ..$ meta      : NULL
+#>   .. .. ..$ script    : NULL
+#>   .. .. ..$ stylesheet: chr [1:2] "css/all.min.css" "css/v4-shims.min.css"
+#>   .. .. ..$ head      : NULL
+#>   .. .. ..$ attachment: NULL
+#>   .. .. ..$ package   : chr "fontawesome"
+#>   .. .. ..$ all_files : logi TRUE
+#>   .. .. ..- attr(*, "class")= chr "html_dependency"
+#>  $ vs  :List of 3
+#>   ..$ name    : chr "i"
+#>   ..$ attribs :List of 3
+#>   .. ..$ class     : chr "fas fa-calculator"
+#>   .. ..$ role      : chr "presentation"
+#>   .. ..$ aria-label: chr "calculator icon"
+#>   ..$ children: list()
+#>   ..- attr(*, "class")= chr "shiny.tag"
+#>   ..- attr(*, "browsable_html")= logi TRUE
+#>   ..- attr(*, "html_dependencies")=List of 1
+#>   .. ..$ :List of 10
+#>   .. .. ..$ name      : chr "font-awesome"
+#>   .. .. ..$ version   : chr "6.5.2"
+#>   .. .. ..$ src       :List of 1
+#>   .. .. .. ..$ file: chr "fontawesome"
+#>   .. .. ..$ meta      : NULL
+#>   .. .. ..$ script    : NULL
+#>   .. .. ..$ stylesheet: chr [1:2] "css/all.min.css" "css/v4-shims.min.css"
+#>   .. .. ..$ head      : NULL
+#>   .. .. ..$ attachment: NULL
+#>   .. .. ..$ package   : chr "fontawesome"
+#>   .. .. ..$ all_files : logi TRUE
+#>   .. .. ..- attr(*, "class")= chr "html_dependency"
+#>  $ am  :List of 3
+#>   ..$ name    : chr "i"
+#>   ..$ attribs :List of 3
+#>   .. ..$ class     : chr "fas fa-calculator"
+#>   .. ..$ role      : chr "presentation"
+#>   .. ..$ aria-label: chr "calculator icon"
+#>   ..$ children: list()
+#>   ..- attr(*, "class")= chr "shiny.tag"
+#>   ..- attr(*, "browsable_html")= logi TRUE
+#>   ..- attr(*, "html_dependencies")=List of 1
+#>   .. ..$ :List of 10
+#>   .. .. ..$ name      : chr "font-awesome"
+#>   .. .. ..$ version   : chr "6.5.2"
+#>   .. .. ..$ src       :List of 1
+#>   .. .. .. ..$ file: chr "fontawesome"
+#>   .. .. ..$ meta      : NULL
+#>   .. .. ..$ script    : NULL
+#>   .. .. ..$ stylesheet: chr [1:2] "css/all.min.css" "css/v4-shims.min.css"
+#>   .. .. ..$ head      : NULL
+#>   .. .. ..$ attachment: NULL
+#>   .. .. ..$ package   : chr "fontawesome"
+#>   .. .. ..$ all_files : logi TRUE
+#>   .. .. ..- attr(*, "class")= chr "html_dependency"
+#>  $ gear:List of 3
+#>   ..$ name    : chr "i"
+#>   ..$ attribs :List of 3
+#>   .. ..$ class     : chr "fas fa-calculator"
+#>   .. ..$ role      : chr "presentation"
+#>   .. ..$ aria-label: chr "calculator icon"
+#>   ..$ children: list()
+#>   ..- attr(*, "class")= chr "shiny.tag"
+#>   ..- attr(*, "browsable_html")= logi TRUE
+#>   ..- attr(*, "html_dependencies")=List of 1
+#>   .. ..$ :List of 10
+#>   .. .. ..$ name      : chr "font-awesome"
+#>   .. .. ..$ version   : chr "6.5.2"
+#>   .. .. ..$ src       :List of 1
+#>   .. .. .. ..$ file: chr "fontawesome"
+#>   .. .. ..$ meta      : NULL
+#>   .. .. ..$ script    : NULL
+#>   .. .. ..$ stylesheet: chr [1:2] "css/all.min.css" "css/v4-shims.min.css"
+#>   .. .. ..$ head      : NULL
+#>   .. .. ..$ attachment: NULL
+#>   .. .. ..$ package   : chr "fontawesome"
+#>   .. .. ..$ all_files : logi TRUE
+#>   .. .. ..- attr(*, "class")= chr "html_dependency"
+#>  $ carb:List of 3
+#>   ..$ name    : chr "i"
+#>   ..$ attribs :List of 3
+#>   .. ..$ class     : chr "fas fa-calculator"
+#>   .. ..$ role      : chr "presentation"
+#>   .. ..$ aria-label: chr "calculator icon"
+#>   ..$ children: list()
+#>   ..- attr(*, "class")= chr "shiny.tag"
+#>   ..- attr(*, "browsable_html")= logi TRUE
+#>   ..- attr(*, "html_dependencies")=List of 1
+#>   .. ..$ :List of 10
+#>   .. .. ..$ name      : chr "font-awesome"
+#>   .. .. ..$ version   : chr "6.5.2"
+#>   .. .. ..$ src       :List of 1
+#>   .. .. .. ..$ file: chr "fontawesome"
+#>   .. .. ..$ meta      : NULL
+#>   .. .. ..$ script    : NULL
+#>   .. .. ..$ stylesheet: chr [1:2] "css/all.min.css" "css/v4-shims.min.css"
+#>   .. .. ..$ head      : NULL
+#>   .. .. ..$ attachment: NULL
+#>   .. .. ..$ package   : chr "fontawesome"
+#>   .. .. ..$ all_files : logi TRUE
+#>   .. .. ..- attr(*, "class")= chr "html_dependency"
+
+
+
+ + +
+ + + + + + + diff --git a/reference/create_baseline.html b/reference/create_baseline.html index ce0b1673..2fb67136 100644 --- a/reference/create_baseline.html +++ b/reference/create_baseline.html @@ -84,7 +84,6 @@

Examples

mtcars |> create_baseline(by.var = "gear", add.p = "yes" == "yes")
-#> Setting theme "JAMA"
 

 
   
@@ -172,6 +171,59 @@ N = 5
+    
Characteristic
 0 (0)
 1 (20)
 
1 Kruskal-Wallis rank sum test; Fisher’s exact test
create_baseline(default_parsing(mtcars), by.var = "am", add.p = FALSE, add.overall = FALSE, theme = "lancet")
+

+
+  
+      
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+    
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+
CharacteristicFALSE

+N = 191		TRUE

+N = 131
mpg17·3 (14·7 – 19·2)22·8 (21·0 – 30·4)
cyl

    43 (16%)8 (62%)
    64 (21%)3 (23%)
    812 (63%)2 (15%)
disp276 (168 – 360)120 (79 – 160)
hp175 (110 – 205)109 (66 – 113)
drat3·15 (3·07 – 3·70)4·08 (3·85 – 4·22)
wt3·52 (3·44 – 3·85)2·32 (1·94 – 2·78)
qsec17·82 (17·05 – 19·44)17·02 (16·46 – 18·61)
vs7 (37%)7 (54%)
gear

    315 (79%)0 (0%)
    44 (21%)8 (62%)
    50 (0%)5 (38%)
carb

    13 (16%)4 (31%)
    26 (32%)4 (31%)
    33 (16%)0 (0%)
    47 (37%)3 (23%)
    60 (0%)1 (7·7%)
    80 (0%)1 (7·7%)
1 Median (IQR); n (%)