diff --git a/.gitignore b/.gitignore index 09d5605..4e9f112 100644 --- a/.gitignore +++ b/.gitignore @@ -38,3 +38,4 @@ vignettes/*.pdf .DS_Store obstinit.Rproj +docs diff --git a/DESCRIPTION b/DESCRIPTION index 153862c..4539acc 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -18,7 +18,9 @@ Imports: tidyr, data.table, ggforce, - cli + cli, + lubridate, + tidyverse Suggests: testthat (>= 3.0.0) Config/testthat/edition: 3 diff --git a/_pkgdown.yml b/_pkgdown.yml deleted file mode 100644 index f9e6632..0000000 --- a/_pkgdown.yml +++ /dev/null @@ -1,4 +0,0 @@ -url: https://obianalysts-umich.github.io/obstinit/ -template: - bootstrap: 5 - diff --git a/docs/404.html b/docs/404.html index 3b4256b..04e6f56 100644 --- a/docs/404.html +++ b/docs/404.html @@ -4,76 +4,89 @@ - + Page not found (404) • obstinit - - - + + + - + + - - Skip to contents + -
-
-
-

Page not found (404)

+ +
+ + + +
+
+
+

Page not found (404)

Content not found. Please use links in the navbar. -
+
+ + +
- + diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 784d439..0a10ed1 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -1,59 +1,69 @@ -License • obstinitLicense • obstinit - Skip to contents + -
-
-
-

License

+ +
+
+
+

License

YEAR: 2023
 COPYRIGHT HOLDER: obstinit authors
-
+
+ + + - + diff --git a/docs/LICENSE.html b/docs/LICENSE.html index 539cac6..f2113ce 100644 --- a/docs/LICENSE.html +++ b/docs/LICENSE.html @@ -1,38 +1,40 @@ -MIT License • obstinitMIT License • obstinit - Skip to contents + -
-
-
-

MIT License

+ +
+
+
+

MIT License

@@ -43,21 +45,29 @@

THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

-
+
+ + + - + diff --git a/docs/authors.html b/docs/authors.html index aac0538..ea68214 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -1,41 +1,43 @@ -Authors and Citation • obstinitAuthors and Citation • obstinit - Skip to contents + -
-
-
-

Authors and Citation

-
+
+
+
+
+

Authors

+
-
-

Authors

  • Thea B. Author, maintainer. @@ -46,39 +48,45 @@

    Authors

+
+
+

Citation

+ +
+
-
-

Citation

-

-

B T, Chen X (2023). +

B T, Chen X (2023). obstinit: OBI Internal Tool Package. -R package version 0.0.0.9000, https://obianalysts-umich.github.io/obstinit/. +R package version 0.0.0.9000, https://obianalysts-umich.github.io/obstinit/.

- 
@Manual{,
+    
@Manual{,
   title = {obstinit: OBI Internal Tool Package},
   author = {Thea B and Xilin Chen},
   year = {2023},
   note = {R package version 0.0.0.9000},
   url = {https://obianalysts-umich.github.io/obstinit/},
 }

-
-
+
- + diff --git a/docs/index.html b/docs/index.html index fb9c5a1..8e8e1dd 100644 --- a/docs/index.html +++ b/docs/index.html @@ -4,53 +4,58 @@ - - + OBI Internal Tool Package • obstinit - - - + + + - + + - - Skip to contents + -
-
-
+ +
+ + + + +
+
+

obstinit

@@ -130,7 +135,7 @@

Other data processingExample workflow - reading in data, structuring data, and plotting control chart in ggplot 

-library(obstinit)
+library(obstinit)
 library(tidyverse)
 
 obi = read_current_data()
@@ -167,7 +172,10 @@ 
Status updates
-
+
-
+

Developed by Thea B, Xilin Chen.

-
+

Site built with pkgdown 2.0.7.

-
+
+ diff --git a/docs/pkgdown.js b/docs/pkgdown.js index 5fccd9c..6f0eee4 100644 --- a/docs/pkgdown.js +++ b/docs/pkgdown.js @@ -2,30 +2,70 @@ (function($) { $(function() { - $('nav.navbar').headroom(); + $('.navbar-fixed-top').headroom(); - Toc.init({ - $nav: $("#toc"), - $scope: $("main h2, main h3, main h4, main h5, main h6") + $('body').css('padding-top', $('.navbar').height() + 10); + $(window).resize(function(){ + $('body').css('padding-top', $('.navbar').height() + 10); }); - if ($('#toc').length) { - $('body').scrollspy({ - target: '#toc', - offset: $("nav.navbar").outerHeight() + 1 - }); + $('[data-toggle="tooltip"]').tooltip(); + + var cur_path = paths(location.pathname); + var links = $("#navbar ul li a"); + var max_length = -1; + var pos = -1; + for (var i = 0; i < links.length; i++) { + if (links[i].getAttribute("href") === "#") + continue; + // Ignore external links + if (links[i].host !== location.host) + continue; + + var nav_path = paths(links[i].pathname); + + var length = prefix_length(nav_path, cur_path); + if (length > max_length) { + max_length = length; + pos = i; + } } - // Activate popovers - $('[data-bs-toggle="popover"]').popover({ - container: 'body', - html: true, - trigger: 'focus', - placement: "top", - sanitize: false, - }); + // Add class to parent
  • , and enclosing
  • if in dropdown + if (pos >= 0) { + var menu_anchor = $(links[pos]); + menu_anchor.parent().addClass("active"); + menu_anchor.closest("li.dropdown").addClass("active"); + } + }); + + function paths(pathname) { + var pieces = pathname.split("/"); + pieces.shift(); // always starts with / + + var end = pieces[pieces.length - 1]; + if (end === "index.html" || end === "") + pieces.pop(); + return(pieces); + } + + // Returns -1 if not found + function prefix_length(needle, haystack) { + if (needle.length > haystack.length) + return(-1); - $('[data-bs-toggle="tooltip"]').tooltip(); + // Special case for length-0 haystack, since for loop won't run + if (haystack.length === 0) { + return(needle.length === 0 ? 0 : -1); + } + + for (var i = 0; i < haystack.length; i++) { + if (needle[i] != haystack[i]) + return(i); + } + + return(haystack.length); + } /* Clipboard --------------------------*/ @@ -38,7 +78,7 @@ if(ClipboardJS.isSupported()) { $(document).ready(function() { - var copyButton = ""; + var copyButton = ""; $("div.sourceCode").addClass("hasCopyButton"); @@ -49,108 +89,20 @@ $('.btn-copy-ex').tooltip({container: 'body'}); // Initialize clipboard: - var clipboard = new ClipboardJS('[data-clipboard-copy]', { + var clipboardBtnCopies = new ClipboardJS('[data-clipboard-copy]', { text: function(trigger) { return trigger.parentNode.textContent.replace(/\n#>[^\n]*/g, ""); } }); - clipboard.on('success', function(e) { + clipboardBtnCopies.on('success', function(e) { changeTooltipMessage(e.trigger, 'Copied!'); e.clearSelection(); }); - clipboard.on('error', function() { + clipboardBtnCopies.on('error', function() { changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy'); }); - }); } - - /* Search marking --------------------------*/ - var url = new URL(window.location.href); - var toMark = url.searchParams.get("q"); - var mark = new Mark("main#main"); - if (toMark) { - mark.mark(toMark, { - accuracy: { - value: "complementary", - limiters: [",", ".", ":", "/"], - } - }); - } - - /* Search --------------------------*/ - /* Adapted from https://github.com/rstudio/bookdown/blob/2d692ba4b61f1e466c92e78fd712b0ab08c11d31/inst/resources/bs4_book/bs4_book.js#L25 */ - // Initialise search index on focus - var fuse; - $("#search-input").focus(async function(e) { - if (fuse) { - return; - } - - $(e.target).addClass("loading"); - var response = await fetch($("#search-input").data("search-index")); - var data = await response.json(); - - var options = { - keys: ["what", "text", "code"], - ignoreLocation: true, - threshold: 0.1, - includeMatches: true, - includeScore: true, - }; - fuse = new Fuse(data, options); - - $(e.target).removeClass("loading"); - }); - - // Use algolia autocomplete - var options = { - autoselect: true, - debug: true, - hint: false, - minLength: 2, - }; - var q; -async function searchFuse(query, callback) { - await fuse; - - var items; - if (!fuse) { - items = []; - } else { - q = query; - var results = fuse.search(query, { limit: 20 }); - items = results - .filter((x) => x.score <= 0.75) - .map((x) => x.item); - if (items.length === 0) { - items = [{dir:"Sorry 😿",previous_headings:"",title:"No results found.",what:"No results found.",path:window.location.href}]; - } - } - callback(items); -} - $("#search-input").autocomplete(options, [ - { - name: "content", - source: searchFuse, - templates: { - suggestion: (s) => { - if (s.title == s.what) { - return `${s.dir} >
    ${s.title}
    `; - } else if (s.previous_headings == "") { - return `${s.dir} >
    ${s.title}
    > ${s.what}`; - } else { - return `${s.dir} >
    ${s.title}
    > ${s.previous_headings} > ${s.what}`; - } - }, - }, - }, - ]).on('autocomplete:selected', function(event, s) { - window.location.href = s.path + "?q=" + q + "#" + s.id; - }); - }); })(window.jQuery || window.$) - - diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 28c7bc0..1a50990 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -2,8 +2,5 @@ pandoc: 3.1.1 pkgdown: 2.0.7 pkgdown_sha: ~ articles: {} -last_built: 2023-12-10T22:54Z -urls: - reference: https://obianalysts-umich.github.io/obstinit/reference - article: https://obianalysts-umich.github.io/obstinit/articles +last_built: 2023-12-11T00:05Z diff --git a/docs/reference/add_CI_values.html b/docs/reference/add_CI_values.html index 144be3d..ab498e2 100644 --- a/docs/reference/add_CI_values.html +++ b/docs/reference/add_CI_values.html @@ -1,58 +1,58 @@ -confidence interval for a rate — add_CI_values • obstinitconfidence interval for a rate — add_CI_values • obstinit - Skip to contents - - -
    -
    -
    -

    confidence interval for a rate

    - -
    add_CI_values.Rd
    +
    -
    +

    This function create upper and lower CI for observed rate. Two new variables will be added LC and UC the formula is based on 95% CI: rate+/- 1.96 x sqrt((!!var x (1-!!var))/!!n_cases)

    -
    -

    Usage

    + 
    add_CI_values(data, var, n_cases)
    -
    -

    Arguments

    +
    +

    Arguments

    var

    variable you want to sort

    @@ -62,33 +62,50 @@

    Arguments -

    Examples

    - 
    tb = tibble::tibble(cs_rate = c(0.1, 0.3),
+    
    
+    
    Examples
    
+    
    library(dplyr)
+#> 
+#> Attaching package: ‘dplyr’
+#> The following objects are masked from ‘package:stats’:
+#> 
+#>     filter, lag
+#> The following objects are masked from ‘package:base’:
+#> 
+#>     intersect, setdiff, setequal, union
+tb = tibble::tibble(cs_rate = c(0.1, 0.3),
                     n_pt_cases = c(140, 234))
 tb %>% 
  add_CI_values(var = cs_rate,
                n_cases = n_pt_cases)
-#> Error in tb %>% add_CI_values(var = cs_rate, n_cases = n_pt_cases): could not find function "%>%"
+#> # A tibble: 2 × 4
+#>   cs_rate n_pt_cases     LC    UC
+#>     <dbl>      <dbl>  <dbl> <dbl>
+#> 1     0.1        140 0.0503 0.150
+#> 2     0.3        234 0.241  0.359
                
 
    
     
    
-

    +
    + + -
    +

    Developed by Thea B, Xilin Chen.

    -
    +

    Site built with pkgdown 2.0.7.

    -
    +
    + diff --git a/docs/reference/add_benchmark.html b/docs/reference/add_benchmark.html index 91b31bd..cc9c619 100644 --- a/docs/reference/add_benchmark.html +++ b/docs/reference/add_benchmark.html @@ -1,47 +1,49 @@ -Add benchmark to plot — add_benchmark • obstinitAdd benchmark to plot — add_benchmark • obstinit - Skip to contents + -
    -
    -
    -

    Add benchmark to plot

    - -
    add_benchmark.Rd
    +
    -
    +

    this function adds a benchmark line (and optional label) to a ggplot object

    -
    -

    Usage

    + 
    add_benchmark(
   plot,
   y_int,
@@ -56,8 +58,8 @@ 
    Usage
 )
    -
    -

    Arguments

    +
    +

    Arguments

    plot

    ggplot object

    @@ -99,22 +101,26 @@

    Arguments

    +
    + +
    -
    + diff --git a/docs/reference/calculate_IA_comp.html b/docs/reference/calculate_IA_comp.html index 2507854..6be0e6d 100644 --- a/docs/reference/calculate_IA_comp.html +++ b/docs/reference/calculate_IA_comp.html @@ -1,73 +1,79 @@ -Calculate IA compliance — calculate_IA_comp • obstinitCalculate IA compliance — calculate_IA_comp • obstinit - Skip to contents + -
    -
    -
    -

    Calculate IA compliance

    - -
    calculate_IA_comp.Rd
    +
    -
    +

    Calculate IA compliance

    -
    -

    Usage

    + 
    calculate_IA_comp(df)
    -
    -

    Arguments

    +
    +

    Arguments

    df

    Data frame -- ideally, run through obstinit::create_IA_cohort first

    -
    +
    + +
    -
    +

    Developed by Thea B, Xilin Chen.

    -
    +

    Site built with pkgdown 2.0.7.

    -
    +
    + diff --git a/docs/reference/calculate_TB_comp.html b/docs/reference/calculate_TB_comp.html index 2b985ad..82a6e33 100644 --- a/docs/reference/calculate_TB_comp.html +++ b/docs/reference/calculate_TB_comp.html @@ -1,73 +1,79 @@ -Calculate TeamBirth compliance — calculate_TB_comp • obstinitCalculate TeamBirth compliance — calculate_TB_comp • obstinit - Skip to contents + -
    -
    -
    -

    Calculate TeamBirth compliance

    - -
    calculate_TB_comp.Rd
    +
    -
    +

    Calculate TeamBirth compliance

    -
    -

    Usage

    + 
    calculate_TB_comp(df)
    -
    -

    Arguments

    +
    +

    Arguments

    df

    Data frame -- usually this is the data frame read into R using data.table::fread

    -
    +
    + + -
    +

    Developed by Thea B, Xilin Chen.

    -
    +

    Site built with pkgdown 2.0.7.

    -
    +
    + diff --git a/docs/reference/calculate_cat_II_comp.html b/docs/reference/calculate_cat_II_comp.html index 38ca568..0cd8592 100644 --- a/docs/reference/calculate_cat_II_comp.html +++ b/docs/reference/calculate_cat_II_comp.html @@ -1,73 +1,79 @@ -Calculate cat II compliance — calculate_cat_II_comp • obstinitCalculate cat II compliance — calculate_cat_II_comp • obstinit - Skip to contents + -
    -
    -
    -

    Calculate cat II compliance

    - -
    calculate_cat_II_comp.Rd
    +
    -
    +

    Calculate cat II compliance

    -
    -

    Usage

    + 
    calculate_cat_II_comp(df)
    -
    -

    Arguments

    +
    +

    Arguments

    df

    Data frame -- ideally, run through obstinit::create_cat_II_cohort first

    -
    +
    + + -
    +

    Developed by Thea B, Xilin Chen.

    -
    +

    Site built with pkgdown 2.0.7.

    -
    +
    + diff --git a/docs/reference/calculate_dys_comp.html b/docs/reference/calculate_dys_comp.html index 8dc61d8..6a1ac3a 100644 --- a/docs/reference/calculate_dys_comp.html +++ b/docs/reference/calculate_dys_comp.html @@ -1,52 +1,54 @@ -Calculate dystocia compliance — calculate_dys_comp • obstinitCalculate dystocia compliance — calculate_dys_comp • obstinit - Skip to contents + -
    -
    -
    -

    Calculate dystocia compliance

    - -
    calculate_dys_comp.Rd
    +
    -
    +

    To calculate dystocia compliance, overall and by type

    -
    -

    Usage

    + 
    calculate_dys_comp(df, include_types = F)
    -
    -

    Arguments

    +
    +

    Arguments

    df

    A data frame, preferably one that has already been run through obstint::create_obi_cohort()

    @@ -56,22 +58,26 @@

    Arguments

    +
    + +
    -
    + diff --git a/docs/reference/create_90_day_lock_dt.html b/docs/reference/create_90_day_lock_dt.html index 9f11be0..1e0c6a8 100644 --- a/docs/reference/create_90_day_lock_dt.html +++ b/docs/reference/create_90_day_lock_dt.html @@ -1,73 +1,79 @@ -Create OBI case lock dates — create_90_day_lock_dt • obstinitCreate OBI case lock dates — create_90_day_lock_dt • obstinit - Skip to contents + -
    -
    -
    -

    Create OBI case lock dates

    - -
    create_90_day_lock_dt.Rd
    +
    -
    +

    Create OBI case lock dates

    -
    -

    Usage

    + 
    create_90_day_lock_dt()
    -
    -

    Arguments

    +
    +

    Arguments

    df

    Data frame -- usually this is the data frame read into R using data.table::fread

    -
    +
    + +
    -
    +

    Developed by Thea B, Xilin Chen.

    -
    +

    Site built with pkgdown 2.0.7.

    -
    +
    + diff --git a/docs/reference/create_IA_cohort.html b/docs/reference/create_IA_cohort.html index 8462780..b0f3ae0 100644 --- a/docs/reference/create_IA_cohort.html +++ b/docs/reference/create_IA_cohort.html @@ -1,52 +1,54 @@ -Create IA cohort — create_IA_cohort • obstinitCreate IA cohort — create_IA_cohort • obstinit - Skip to contents + -
    -
    -
    -

    Create IA cohort

    - -
    create_IA_cohort.Rd
    +
    -
    +

    Create IA cohort

    -
    -

    Usage

    + 
    create_IA_cohort(df, limit_to_IA_sites = F)
    -
    -

    Arguments

    +
    +

    Arguments

    df

    Data frame -- usually this is the data frame read into R using data.table::fread

    @@ -56,22 +58,26 @@

    Arguments

    +
    + +
    -
    + diff --git a/docs/reference/create_cat_II_cohort.html b/docs/reference/create_cat_II_cohort.html index 25d9aad..af5f059 100644 --- a/docs/reference/create_cat_II_cohort.html +++ b/docs/reference/create_cat_II_cohort.html @@ -1,52 +1,54 @@ -Create cat II cohort — create_cat_II_cohort • obstinitCreate cat II cohort — create_cat_II_cohort • obstinit - Skip to contents + -
    -
    -
    -

    Create cat II cohort

    - -
    create_cat_II_cohort.Rd
    +
    -
    +

    Create cat II cohort

    -
    -

    Usage

    + 
    create_cat_II_cohort(df, limit_to_catII_sites = F)
    -
    -

    Arguments

    +
    +

    Arguments

    df

    Data frame -- usually this is the data frame read into R using data.table::fread

    @@ -56,22 +58,26 @@

    Arguments

    +
    + +
    -
    + diff --git a/docs/reference/create_caterpillar_df.html b/docs/reference/create_caterpillar_df.html index 6e3716c..52e8c36 100644 --- a/docs/reference/create_caterpillar_df.html +++ b/docs/reference/create_caterpillar_df.html @@ -1,52 +1,54 @@ -Create a data frame for caterpillar plots — create_caterpillar_df • obstinitCreate a data frame for caterpillar plots — create_caterpillar_df • obstinit - Skip to contents + -
    -
    -
    -

    Create a data frame for caterpillar plots

    - -
    create_caterpillar_df.Rd
    +
    -
    +

    this function creates a data frame to be used for caterpillar plots where each row is a site name. The df includes a numerator, denominator, and rate for the variable of interest, as well as a 95% CI (bounded by 0 and 1) for the rate.

    -
    -

    Usage

    + 
    create_caterpillar_df(df, num_var, denom_var, group_var = site_name)
    -
    -

    Arguments

    +
    +

    Arguments

    df

    Data frame -- usually this is obi_cohort

    @@ -64,22 +66,26 @@

    Arguments

    +
    + +
    -
    + diff --git a/docs/reference/create_ctrl_df.html b/docs/reference/create_ctrl_df.html index e341cd2..52ff0f3 100644 --- a/docs/reference/create_ctrl_df.html +++ b/docs/reference/create_ctrl_df.html @@ -1,53 +1,53 @@ -Structure OBI data for plotting control charts — create_ctrl_df • obstinitStructure OBI data for plotting control charts — create_ctrl_df • obstinit - Skip to contents - - -
    -
    -
    -

    Structure OBI data for plotting control charts

    - -
    create_ctrl_df.Rd
    +
    -
    +

    This function takes in a data frame row per observation like OBI data. It then summarize the numerator and denominator of a rate of interest. This function also use control chart principles to calculate CIs and flag alerts.

    -
    -

    Usage

    + 
    create_ctrl_df(
   df,
   date_var,
@@ -61,8 +61,8 @@ 
    Usage
 )
    -
    -

    Arguments

    +
    +

    Arguments

    df

    A data frame, for example OBI export data

    @@ -100,33 +100,33 @@

    Arguments -

    Value

    +
    +

    Value

    An tibble with the aggridated numerator and denominator by input date variable

    -
    -

    Examples

    - -
    -

    +
    + +
    -
    +

    Developed by Thea B, Xilin Chen.

    -
    +

    Site built with pkgdown 2.0.7.

    -
    +
    + diff --git a/docs/reference/create_dystocia_cohort.html b/docs/reference/create_dystocia_cohort.html index 674c98f..d4a5895 100644 --- a/docs/reference/create_dystocia_cohort.html +++ b/docs/reference/create_dystocia_cohort.html @@ -1,73 +1,79 @@ -Create dystocia cohort — create_dystocia_cohort • obstinitCreate dystocia cohort — create_dystocia_cohort • obstinit - Skip to contents + -
    -
    -
    -

    Create dystocia cohort

    - -
    create_dystocia_cohort.Rd
    +
    -
    +

    To create dystocia compliance cohort

    -
    -

    Usage

    + 
    create_dystocia_cohort(df)
    -
    -

    Arguments

    +
    +

    Arguments

    df

    A data frame, preferably one that has already been run through obstint::create_obi_cohort()

    -
    +
    + +
    -
    +

    Developed by Thea B, Xilin Chen.

    -
    +

    Site built with pkgdown 2.0.7.

    -
    +
    + diff --git a/docs/reference/create_obi_cohort.html b/docs/reference/create_obi_cohort.html index b834f0a..2d4cb7c 100644 --- a/docs/reference/create_obi_cohort.html +++ b/docs/reference/create_obi_cohort.html @@ -1,12 +1,5 @@ -Create OBI cohort of locked, complete cases for most analyses — create_obi_cohort • obstinitCreate OBI cohort of locked, complete cases for most analyses — create_obi_cohort • obstinit - Skip to contents - - -
    -
    -
    -

    Create OBI cohort of locked, complete cases for most analyses

    - -
    create_obi_cohort.Rd
    +
    -
    +

    this function does

    1. include case ≥2020-01-01 based on infant date of birth

    2. include case if case is complete using flg_complete

    3. create case_locked varaible using 90 days lock

      4. @@ -58,13 +54,12 @@

    4. create mdhhs_id character variable with leading 0's

    -
    -

    Usage

    + 
    create_obi_cohort(df, limit_to_locked = T)
    -
    -

    Arguments

    +
    +

    Arguments

    df

    Data frame -- usually this is the data frame read into R using data.table::fread

    @@ -74,22 +69,26 @@

    Arguments

    +
    + +
    -
    + diff --git a/docs/reference/create_pv_response_dt.html b/docs/reference/create_pv_response_dt.html index bf57582..05dc968 100644 --- a/docs/reference/create_pv_response_dt.html +++ b/docs/reference/create_pv_response_dt.html @@ -1,12 +1,5 @@ -create patient voice response data — create_pv_response_dt • obstinitcreate patient voice response data — create_pv_response_dt • obstinit - Skip to contents - - -
    -
    -
    -

    create patient voice response data

    - -
    create_pv_response_dt.Rd
    +
    -
    +

    combine patient contact log with survey response data

    • cohort: pts who received pro survey emails

    • added var:

      • pro_response: pts who completed pro survey (opt out pts also consider complete)

      • pts choose to opt out: survey_informed_consent_b_0 ==0

    -
    -

    Usage

    + 
    create_pv_response_dt(obi_dt, pro_survey_expired = FALSE)
    -
    -

    Arguments

    +
    +

    Arguments

    obi_dt

    OBI nightly export data

    @@ -72,44 +67,48 @@

    Arguments -

    Value

    +
    +

    Value

    a data frame with variables: patientid, site_name, infant_dob_dt, complete_pro_survey_flg, survey_informed_consent_b_0

    -
    -

    Details

    +
    +

    Details

    this function read in pro survey data from

    • survey response: P:/OBI_abstracted_data/Current_Data/data/input/pro_6_week_postpartum.csv

    • contact log pts who received emails: P:/OBI_abstracted_data/Current_Data/data/input/contactlog.csv

    -
    -

    Examples

    - 
    obi_dt <- read_current_data() |> 
+    
    
+    
    Examples
    
+    
    if (FALSE) {
+obi_dt <- read_current_data() |> 
   create_obi_cohort(limit_to_locked = FALSE) 
-#> Error in df %>% mutate(infant_dob_dt = lubridate::dmy_hms(infant_dob_dt),     case_lock_dt = lubridate::date(infant_dob_dt) + days(90),     case_locked = ifelse(case_lock_dt < lubridate::today(), 1,         0), across(c(starts_with("opioid_e"), starts_with("opioid_dose"),         starts_with("opioid_quantity_no"), starts_with("opioid_unit")),         ~ifelse(discharge_opioid_e == 1, .x, NA)), mdhhs_id = case_when(external_mdhhs_site_id ==         4001 ~ "04001", external_mdhhs_site_id == 8001 ~ "08001",         external_mdhhs_site_id == 9005 ~ "09005", TRUE ~ as.character(external_mdhhs_site_id))): could not find function "%>%"
 create_pv_response_dt(obi_dt) 
-#> Error in data.table::fread("/Volumes/nur-kanelow/OBI_abstracted_data/Current_Data/data/input/pro_6_week_postpartum.csv"): File '/Volumes/nur-kanelow/OBI_abstracted_data/Current_Data/data/input/pro_6_week_postpartum.csv' does not exist or is non-readable. getwd()=='/Users/xilinchen/Documents/repos/obstinit/docs/reference'
+}
  
 
    
     
    
-

    +
    + +
    -
    +

    Developed by Thea B, Xilin Chen.

    -
    +

    Site built with pkgdown 2.0.7.

    -
    +
    + diff --git a/docs/reference/index.html b/docs/reference/index.html index 7885ff1..47988f8 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -1,191 +1,167 @@ -Function reference • obstinitFunction reference • obstinit - Skip to contents + -
    -
    -
    -

    Function reference

    -
    +
      +
      +
      -
      -

      All functions

      - - -
      - - - +
      +
      +
      +

      Reference

      +
      -
      - - add_CI_values() -
      -
      confidence interval for a rate
      -
      - - add_benchmark() -
      -
      Add benchmark to plot
      -
      - - calculate_IA_comp() -
      -
      Calculate IA compliance
      -
      - - calculate_TB_comp() -
      -
      Calculate TeamBirth compliance
      -
      - - calculate_cat_II_comp() -
      -
      Calculate cat II compliance
      -
      - - calculate_dys_comp() -
      -
      Calculate dystocia compliance
      -
      - - create_90_day_lock_dt() -
      -
      Create OBI case lock dates
      -
      - - create_IA_cohort() -
      -
      Create IA cohort
      -
      - - create_cat_II_cohort() -
      -
      Create cat II cohort
      -
      - - create_caterpillar_df() -
      -
      Create a data frame for caterpillar plots
      -
      - - create_ctrl_df() -
      -
      Structure OBI data for plotting control charts
      -
      - - create_dystocia_cohort() -
      -
      Create dystocia cohort
      -
      - - create_obi_cohort() -
      -
      Create OBI cohort of locked, complete cases for most analyses
      -
      - - create_pv_response_dt() -
      -
      create patient voice response data
      -
      - - plot_caterpillar_chart() -
      -
      Plot caterpillar chart
      -
      - - plot_ctrl_chart() -
      -
      Plot control chart
      -
      - - plot_ctrl_hchart() -
      -
      Plot interactive ctrl chart using highcharter package
      -
      - - read_crosswalk() -
      -
      Read in OBI crosswalk
      -
      - - read_current_data() -
      -
      Read current OBI data
      -
      - - send_email() -
      -
      send emails from R
      -
      - - sites_w_all_years_dt() -
      -
      Limit dataset to hospitals that have data for all years 2020 - max year of your choice
      -
      - - sort_muti_selection() -
      -
      sort multiple selected varible as list
      -
      - - sort_muti_selection_var() -
      -
      sort multiple selected variable in dataset
      -
      - - structure_data() -
      -
      Structure OBI data for plotting control charts
      -
      - - theme_obi() -
      -
      Add OBI ggplot theme
      -
      -
      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      +

      All functions

      +

      +
      +

      add_CI_values()

      +

      confidence interval for a rate

      +

      add_benchmark()

      +

      Add benchmark to plot

      +

      calculate_IA_comp()

      +

      Calculate IA compliance

      +

      calculate_TB_comp()

      +

      Calculate TeamBirth compliance

      +

      calculate_cat_II_comp()

      +

      Calculate cat II compliance

      +

      calculate_dys_comp()

      +

      Calculate dystocia compliance

      +

      create_90_day_lock_dt()

      +

      Create OBI case lock dates

      +

      create_IA_cohort()

      +

      Create IA cohort

      +

      create_cat_II_cohort()

      +

      Create cat II cohort

      +

      create_caterpillar_df()

      +

      Create a data frame for caterpillar plots

      +

      create_ctrl_df()

      +

      Structure OBI data for plotting control charts

      +

      create_dystocia_cohort()

      +

      Create dystocia cohort

      +

      create_obi_cohort()

      +

      Create OBI cohort of locked, complete cases for most analyses

      +

      create_pv_response_dt()

      +

      create patient voice response data

      +

      plot_caterpillar_chart()

      +

      Plot caterpillar chart

      +

      plot_ctrl_chart()

      +

      Plot control chart

      +

      plot_ctrl_hchart()

      +

      Plot interactive ctrl chart using highcharter package

      +

      read_crosswalk()

      +

      Read in OBI crosswalk

      +

      read_current_data()

      +

      Read current OBI data

      +

      send_email()

      +

      send emails from R

      +

      sites_w_all_years_dt()

      +

      Limit dataset to hospitals that have data for all years 2020 - max year of your choice

      +

      sort_muti_selection()

      +

      sort multiple selected varible as list

      +

      sort_muti_selection_var()

      +

      sort multiple selected variable in dataset

      +

      structure_data()

      +

      Structure OBI data for plotting control charts

      +

      theme_obi()

      +

      Add OBI ggplot theme

      + + +
      -
      +

      Developed by Thea B, Xilin Chen.

      -
      +

      Site built with pkgdown 2.0.7.

      -
      +
      + diff --git a/docs/reference/plot_caterpillar_chart.html b/docs/reference/plot_caterpillar_chart.html index dd647e5..d2edb1f 100644 --- a/docs/reference/plot_caterpillar_chart.html +++ b/docs/reference/plot_caterpillar_chart.html @@ -1,47 +1,49 @@ -Plot caterpillar chart — plot_caterpillar_chart • obstinitPlot caterpillar chart — plot_caterpillar_chart • obstinit - Skip to contents + -
      -
      -
      -

      Plot caterpillar chart

      - -
      plot_caterpillar_chart.Rd
      +
      -
      +

      this function plots a caterpillar chart using the dataframe created by create_caterpillar_df()

      -
      -

      Usage

      + 
      plot_caterpillar_chart(
   df,
   y_var = rate,
@@ -53,8 +55,8 @@ 
      Usage
 )
      -
      -

      Arguments

      +
      +

      Arguments

      df

      Data frame created by create_caterpillar_df()

      @@ -84,22 +86,26 @@

      Arguments

      +
      + +
      -
      + diff --git a/docs/reference/plot_ctrl_chart.html b/docs/reference/plot_ctrl_chart.html index f9c1240..8a97b68 100644 --- a/docs/reference/plot_ctrl_chart.html +++ b/docs/reference/plot_ctrl_chart.html @@ -1,52 +1,54 @@ -Plot control chart — plot_ctrl_chart • obstinitPlot control chart — plot_ctrl_chart • obstinit - Skip to contents + -
      -
      -
      -

      Plot control chart

      - -
      plot_ctrl_chart.Rd
      +
      -
      +

      Plot control chart

      -
      -

      Usage

      + 
      plot_ctrl_chart(df, plot_center_line = T)
      -
      -

      Arguments

      +
      +

      Arguments

      df

      A data frame in wide format, created by the structure_data function

      @@ -56,22 +58,26 @@

      Arguments

      +
      + +
      -
      + diff --git a/docs/reference/plot_ctrl_hchart.html b/docs/reference/plot_ctrl_hchart.html index ef999a4..87e229a 100644 --- a/docs/reference/plot_ctrl_hchart.html +++ b/docs/reference/plot_ctrl_hchart.html @@ -1,52 +1,54 @@ -Plot interactive ctrl chart using highcharter package — plot_ctrl_hchart • obstinitPlot interactive ctrl chart using highcharter package — plot_ctrl_hchart • obstinit - Skip to contents + -
      -
      -
      -

      Plot interactive ctrl chart using highcharter package

      - -
      plot_ctrl_hchart.Rd
      +
      -
      +

      Plot interactive ctrl chart using highcharter package

      -
      -

      Usage

      + 
      plot_ctrl_hchart(df, title, ymin = NA, ymax = NA)
      -
      -

      Arguments

      +
      +

      Arguments

      df

      A data frame - should be in the structure of obstinit::structure_data

      @@ -56,22 +58,26 @@

      Arguments

      +
      + +
      -
      + diff --git a/docs/reference/read_crosswalk.html b/docs/reference/read_crosswalk.html index a128480..a11738f 100644 --- a/docs/reference/read_crosswalk.html +++ b/docs/reference/read_crosswalk.html @@ -1,66 +1,73 @@ -Read in OBI crosswalk — read_crosswalk • obstinitRead in OBI crosswalk — read_crosswalk • obstinit - Skip to contents + -
      -
      -
      -

      Read in OBI crosswalk

      - -
      read_crosswalk.Rd
      +
      -
      +

      this function reads the current OBI crosswalk file. This file contains information on hospital variables like teaching status, as well as group 1 status and color.

      -
      -

      Usage

      + 
      read_crosswalk()
      -
      +
      + +
      -
      +

      Developed by Thea B, Xilin Chen.

      -
      +

      Site built with pkgdown 2.0.7.

      -
      +
      + diff --git a/docs/reference/read_current_data.html b/docs/reference/read_current_data.html index 78463c6..2d2fa0b 100644 --- a/docs/reference/read_current_data.html +++ b/docs/reference/read_current_data.html @@ -1,66 +1,73 @@ -Read current OBI data — read_current_data • obstinitRead current OBI data — read_current_data • obstinit - Skip to contents + -
      -
      -
      -

      Read current OBI data

      - -
      read_current_data.Rd
      +
      -
      +

      read OBI analytic data from Turbo

      -
      -

      Usage

      + 
      read_current_data()
      -
      +
      + +
      -
      +

      Developed by Thea B, Xilin Chen.

      -
      +

      Site built with pkgdown 2.0.7.

      -
      +
      + diff --git a/docs/reference/send_email.html b/docs/reference/send_email.html index 11bc8b4..f676acd 100644 --- a/docs/reference/send_email.html +++ b/docs/reference/send_email.html @@ -1,47 +1,49 @@ -send emails from R — send_email • obstinitsend emails from R — send_email • obstinit - Skip to contents + -
      -
      -
      -

      send emails from R

      - -
      send_email.Rd
      +
      -
      +

      send or save draft emails from R

      -
      -

      Usage

      + 
      send_email(
   email_message = "<p> This is an automatic message. </p> <p> OBI analytics team </p> ",
   email_to = "obianalysts@umich.edu",
@@ -51,8 +53,8 @@ 
      Usage
 )
      -
      -

      Arguments

      +
      +

      Arguments

      email_message

      your email body; use html code for breaks and hyperlinks

      @@ -73,37 +75,40 @@

      Arguments

      -
      -

      Value

      +
      +

      Value

      a message in the console

      -
      -

      Examples

      - 
      send_email(email_message = "<p> This is an automatic message. </p> <p> OBI analytics team </p>")
-#> ℹ This function was only tested using outlook app
-#> Error in send_email(email_message = "<p> This is an automatic message. </p> <p> OBI analytics team </p>"): this function only works on Windows, see package RDCOMClient
-#> requirement.
+    
      
+    
      Examples
      
+    
      if (FALSE) {
+send_email(email_message = "<p> This is an automatic message. </p> <p> OBI analytics team </p>")
+}
 
      
     
      
-
      +
      + +
      -
      +

      Developed by Thea B, Xilin Chen.

      -
      +

      Site built with pkgdown 2.0.7.

      -
      +
      + diff --git a/docs/reference/sites_w_all_years_dt.html b/docs/reference/sites_w_all_years_dt.html index 0eb4b4d..29f95c6 100644 --- a/docs/reference/sites_w_all_years_dt.html +++ b/docs/reference/sites_w_all_years_dt.html @@ -1,73 +1,79 @@ -Limit dataset to hospitals that have data for all years 2020 - max year of your choice — sites_w_all_years_dt • obstinitLimit dataset to hospitals that have data for all years 2020 - max year of your choice — sites_w_all_years_dt • obstinit - Skip to contents + -
      -
      -
      -

      Limit dataset to hospitals that have data for all years 2020 - max year of your choice

      - -
      sites_w_all_years_dt.Rd
      +
      -
      +

      Limit dataset to hospitals that have data for all years 2020 - max year of your choice

      -
      -

      Usage

      + 
      sites_w_all_years_dt(df, max_year)
      -
      -

      Arguments

      +
      +

      Arguments

      df

      Data frame -- usually this is OBI's current, processed data read into R using data.table::fread. Preferably this has already been run through obstinit::create_obi_cohort()

      -
      +
      + + -
      +

      Developed by Thea B, Xilin Chen.

      -
      +

      Site built with pkgdown 2.0.7.

      -
      +
      + diff --git a/docs/reference/sort_muti_selection.html b/docs/reference/sort_muti_selection.html index f189b40..ea00805 100644 --- a/docs/reference/sort_muti_selection.html +++ b/docs/reference/sort_muti_selection.html @@ -1,83 +1,88 @@ -sort multiple selected varible as list — sort_muti_selection • obstinitsort multiple selected varible as list — sort_muti_selection • obstinit - Skip to contents + -
      -
      -
      -

      sort multiple selected varible as list

      - -
      sort_muti_selection.Rd
      +
      -
      +

      multiple selected varibales shouldn't have different values based on order for example, 1|2 euqal to 2|1. This function short the numbers

      -
      -

      Usage

      + 
      sort_muti_selection(var)
      -
      -

      Arguments

      +
      +

      Arguments

      var

      variable you want to sort

      -
      -

      Examples

      +
      +

      Examples

      val = "8,1,0,3"
 sort_muti_selection(val)
 #> Error in sort_muti_selection(val): could not find function "sort_muti_selection"
      -
      +
      + + -
      +

      Developed by Thea B, Xilin Chen.

      -
      +

      Site built with pkgdown 2.0.7.

      -
      +
      + diff --git a/docs/reference/sort_muti_selection_var.html b/docs/reference/sort_muti_selection_var.html index b8389c1..ce40b7b 100644 --- a/docs/reference/sort_muti_selection_var.html +++ b/docs/reference/sort_muti_selection_var.html @@ -1,84 +1,90 @@ -sort multiple selected variable in dataset — sort_muti_selection_var • obstinitsort multiple selected variable in dataset — sort_muti_selection_var • obstinit - Skip to contents + -
      -
      -
      -

      sort multiple selected variable in dataset

      - -
      sort_muti_selection_var.Rd
      +
      -
      +

      multiple selected varibales shouldn't have different values based on order for example, 1|2 euqal to 2|1. This function short the numbers

      -
      -

      Usage

      + 
      sort_muti_selection_var(var)
      -
      -

      Arguments

      +
      +

      Arguments

      var

      variable you want to sort

      -
      -

      Examples

      +
      +

      Examples

      df <- tibble(col = c("{1|2}", "{2|1}", "{3|2|1}", "{2|3|1}", "{2|1|3}"))
-#> Error in tibble(col = c("{1|2}", "{2|1}", "{3|2|1}", "{2|3|1}", "{2|1|3}")): could not find function "tibble"
 df %>% mutate(new = sort_muti_selection_var(col))
-#> Error in df %>% mutate(new = sort_muti_selection_var(col)): could not find function "%>%"
+#> Error in mutate(., new = sort_muti_selection_var(col)): ℹ In argument: `new = sort_muti_selection_var(col)`.
+#> Caused by error in `str_extract_all()`:
+#> ! could not find function "str_extract_all"
      -
      +
      + + -
      +

      Developed by Thea B, Xilin Chen.

      -
      +

      Site built with pkgdown 2.0.7.

      -
      +
      + diff --git a/docs/reference/structure_data.html b/docs/reference/structure_data.html index 0a8d6c2..e038c27 100644 --- a/docs/reference/structure_data.html +++ b/docs/reference/structure_data.html @@ -1,53 +1,53 @@ -Structure OBI data for plotting control charts — structure_data • obstinitStructure OBI data for plotting control charts — structure_data • obstinit - Skip to contents - - -
      -
      -
      -

      Structure OBI data for plotting control charts

      - -
      structure_data.Rd
      +
      -
      +

      This function takes in a data frame row per observation like OBI data. It then summarize the numerator and denominator of a rate of interest. This function also use control chart principles to calculate CIs and flag alerts.

      -
      -

      Usage

      + 
      structure_data(
   df,
   date_var,
@@ -61,8 +61,8 @@ 
      Usage
 )
      -
      -

      Arguments

      +
      +

      Arguments

      df

      A data frame, for example OBI export data

      @@ -100,33 +100,49 @@

      Arguments -

      Value

      +
      +

      Value

      An tibble with the aggridated numerator and denominator by input date variable

      -
      -

      Examples

      - +
      +

      Examples

      + 
      # It might take a min to load OBI data
+if (FALSE) {
+library(tidyverse)
+OBI_data = read_current_data()
+structure_data(
+ df = OBI_data,
+ date_var = infant_dob_dt,
+ num_var = cesarean,
+ den_var = birth
+ )
+ }
+ 
+
      -

      +
      + + -
      +

      Developed by Thea B, Xilin Chen.

      -
      +

      Site built with pkgdown 2.0.7.

      -
      +
      + diff --git a/docs/reference/theme_obi.html b/docs/reference/theme_obi.html index 2fbdd02..4611b7e 100644 --- a/docs/reference/theme_obi.html +++ b/docs/reference/theme_obi.html @@ -1,47 +1,49 @@ -Add OBI ggplot theme — theme_obi • obstinitAdd OBI ggplot theme — theme_obi • obstinit - Skip to contents + -
      -
      -
      -

      Add OBI ggplot theme

      - -
      theme_obi.Rd
      +
      -
      +

      Add OBI ggplot theme

      -
      -

      Usage

      + 
      theme_obi(
   x_axis_title_size = 12,
   x_axis_text_size = 10,
@@ -58,8 +60,8 @@ 
      Usage
 )
      -
      -

      Arguments

      +
      +

      Arguments

      x_axis_title_size

      Size for x axis title. Default is 12.

      @@ -109,22 +111,26 @@

      Arguments

      +
      + +
      -
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