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

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!

+

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.

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 90782cff..9948425f 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -3,7 +3,7 @@ pkgdown: 2.1.1 pkgdown_sha: ~ articles: FreesearchR: FreesearchR.html -last_built: 2025-04-15T15:13Z +last_built: 2025-04-14T10:38Z 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 b7626c68..f6220322 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", fun = class_icons)
+ 
add_class_icon(grid, column = "class")
@@ -68,8 +68,10 @@ 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 bedff1f1..8707db49 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 deleted file mode 100644 index 4ba3f165..00000000 --- a/reference/align_axes.html +++ /dev/null @@ -1,80 +0,0 @@ - -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 06c4111d..25efbd49 100644 --- a/reference/argsstring2list.html +++ b/reference/argsstring2list.html @@ -58,18 +58,6 @@

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 deleted file mode 100644 index d46c84d2..00000000 --- a/reference/class_icons.html +++ /dev/null @@ -1,363 +0,0 @@ - -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

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list

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- -
-

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"
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- - - - - - - diff --git a/reference/create_baseline.html b/reference/create_baseline.html index 2fb67136..ce0b1673 100644 --- a/reference/create_baseline.html +++ b/reference/create_baseline.html @@ -84,6 +84,7 @@

Examples

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

 
   
@@ -171,59 +172,6 @@ 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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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 (%)