From bfac0fbbba317ea452d40f0ddc2ca974828a6763 Mon Sep 17 00:00:00 2001
From: Quarto GHA Workflow Runner <quarto-github-actions-publish@example.com>
Date: Fri, 11 Oct 2024 08:39:48 +0000
Subject: [PATCH] Built site for gh-pages

---
 .nojekyll                             |  2 +-
 getting_started/create_dic.html       |  6 ++--
 reference/dictionary_sheet.html       |  4 +--
 search.json                           |  6 ++--
 site_libs/bootstrap/bootstrap.min.css |  4 +--
 sitemap.xml                           | 46 +++++++++++++--------------
 6 files changed, 33 insertions(+), 35 deletions(-)

diff --git a/.nojekyll b/.nojekyll
index d652105..cf6bd91 100644
--- a/.nojekyll
+++ b/.nojekyll
@@ -1 +1 @@
-4973d82d
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+09e6bc77
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diff --git a/getting_started/create_dic.html b/getting_started/create_dic.html
index 5c4b51d..ef5058a 100644
--- a/getting_started/create_dic.html
+++ b/getting_started/create_dic.html
@@ -220,7 +220,7 @@
     <h2 id="toc-title">Table of content</h2>
    
   <ul>
-  <li><a href="#get-the-tools-ready" id="toc-get-the-tools-ready" class="nav-link active" data-scroll-target="#get-the-tools-ready">Get the tools ready 🛠</a></li>
+  <li><a href="#sec-get-tools-ready" id="toc-sec-get-tools-ready" class="nav-link active" data-scroll-target="#sec-get-tools-ready">Get the tools ready 🛠</a></li>
   <li><a href="#grow-your-setup-file" id="toc-grow-your-setup-file" class="nav-link" data-scroll-target="#grow-your-setup-file">Grow your setup file 🌱</a>
   <ul>
   <li><a href="#create-the-variable-dictionary" id="toc-create-the-variable-dictionary" class="nav-link" data-scroll-target="#create-the-variable-dictionary">Create the variable dictionary 📘</a></li>
@@ -252,8 +252,8 @@ <h1 class="title">Create dictionary</h1>
 </header>
 
 
-<section id="get-the-tools-ready" class="level2">
-<h2 class="anchored" data-anchor-id="get-the-tools-ready">Get the tools ready 🛠</h2>
+<section id="sec-get-tools-ready" class="level2">
+<h2 class="anchored" data-anchor-id="sec-get-tools-ready">Get the tools ready 🛠</h2>
 <ol type="1">
 <li><p><a href="../getting_started/download.html#download">Download</a> the files from github to get the most updated versions and unzip it.</p></li>
 <li><p>Save the empty <strong>setup file</strong> in you working directory, locally. Open the file using Desktop Excel (web-based Excel cannot run macros).</p></li>
diff --git a/reference/dictionary_sheet.html b/reference/dictionary_sheet.html
index 8134ca7..3496a3a 100644
--- a/reference/dictionary_sheet.html
+++ b/reference/dictionary_sheet.html
@@ -1049,9 +1049,7 @@ <h5 class="anchored" data-anchor-id="formula">formula</h5>
 <section id="case_when" class="level5">
 <h5 class="anchored" data-anchor-id="case_when">case_when</h5>
 <p>Variables of control “case_when” use a specifically developed function, <code>CASE_WHEN</code>, which replaces a succession of nested <code>IF</code>. While you could write the formula with nested <code>IF</code>, <code>CASE_WHEN</code> is easier to read, thus simpler to use.</p>
-<div class="usercase">
-<p>You want to recode a variable, but you do not know which values will be generated. For example, the raw data contains a columns for the age value and a column for the age unit. You use <code>CASE_WHEN</code> to create a column “age_years”. The values which will be present in the column can take many decimal value in the range of reasonable ages.</p>
-</div>
+<p><strong>Usercase</strong> You want to recode a variable, but you do not know which values will be generated. For example, the raw data contains a columns for the age value and a column for the age unit. You use <code>CASE_WHEN</code> to create a column “age_years”. The values which will be present in the column can take many decimal value in the range of reasonable ages.</p>
 <div class="callout callout-style-default callout-important callout-titled">
 <div class="callout-header d-flex align-content-center">
 <div class="callout-icon-container">
diff --git a/search.json b/search.json
index 8e35c53..4f9afe2 100644
--- a/search.json
+++ b/search.json
@@ -245,8 +245,8 @@
     "text": "Download the files from github to get the most updated versions and unzip it.\nSave the empty setup file in you working directory, locally. Open the file using Desktop Excel (web-based Excel cannot run macros).\n\n\n\n\n\n\n\nWarning\n\n\n\nOneDrive and macro-enabled Excel files do not work well together in general. To avoid random file corruption, we advise that you work in a non synchronise folder, or that you disable OneDrive while you are writting the setup file."
   },
   {
-    "objectID": "getting_started/create_dic.html#get-the-tools-ready",
-    "href": "getting_started/create_dic.html#get-the-tools-ready",
+    "objectID": "getting_started/create_dic.html#sec-get-tools-ready",
+    "href": "getting_started/create_dic.html#sec-get-tools-ready",
     "title": "Create dictionary",
     "section": "",
     "text": "Download the files from github to get the most updated versions and unzip it.\nSave the empty setup file in you working directory, locally. Open the file using Desktop Excel (web-based Excel cannot run macros).\n\n\n\n\n\n\n\nWarning\n\n\n\nOneDrive and macro-enabled Excel files do not work well together in general. To avoid random file corruption, we advise that you work in a non synchronise folder, or that you disable OneDrive while you are writting the setup file."
@@ -515,7 +515,7 @@
     "href": "reference/dictionary_sheet.html#properties",
     "title": "Dictionary sheet: define linelist tables and their variables",
     "section": "Properties",
-    "text": "Properties\nThe properties section of the table controls variable visibility, uniqueness, and the type and format of the variable (what it contains, in which form, and in which display).\n\n\n\n\n\n\nStatus\nThis is a dropdown field that contains four options for defining the visibility of the variable. The linelist has a functionality to show or hide optional variables depending on the data needs on the field.\n\nmandatory: variable displayed by default, it cannot be hidden in the linelist\noptional, visible: variable displayed by default, it can be displayed or hidden by the linelist user\noptional, hidden: variable hidden by default, it can be displayed or hidden by the linelist user\nhidden: variable hidden by default, it cannot be displayed in the linelist\n\nVariables can be shown or hidden using the “Show/Hide” button of the linelist OutbreakTools menu in the linelist file. See the how to.\n\n\n\n\n\n\nNote on showing and hiding columns manually\n\n\n\n\n\nTechnically, the linelist user can forcefully hide/un-hide columns.\nUn-hiding hidden (usually calculated) columns is usually desirable during linelist debug or to go check data that may interest you (e.g. a hidden calculated epiweek of exit). You can hide them after consultation without consequences on the rest of the linelist.\nIt is however more dangerous to forcefully hide “mandatory” columns. These columns are often fundamental variables in the linelist, that are needed for data understanding and analyses (e.g. date of admission, age or sex). If you choose to hide one of these columns, know that some analyses might not function as expected, or not at all because they rely on the hidden columns.\nFinally, any change of column visibility that is not made via the “Hide/show variable” button of the linelist will not be recorded and migrated to a new linelist.\n\n\n\n\nExample\nDefinition in the setup file:\n\nDisplay in the linelist file:\n\n\n\n\n\nRegister Book\nThis is a yes/no dropdown menu field used to predefine the variables to be included in the register to be printed. This step is not mandatory and can be managed later, directly in the linelist file.\n\n\nPersonal Identifier\nThis is a yes/no dropdown menu field that indicates that the variable contains personal data (such as names, phone numbers etc.).\nThis column has two uses:\n\nit allows the setup developer to quickly identify variables containing personal data in its dictionary\nit is used to remove variables automatically from the exports if such a behaviour is needed (see the Exports sheet).\n\n\n\nThinking about variables\nThere are many ways of thinking about variables and of classifying them.\nIn general we can distinguished between input variables, where the user enters raw data, and calculated (or derived) variables which require no input. Both of them can be created in OutbreakTools.\nIndependently of this distinction, a variety of variables types can exist, containing numbers or text in various forms. In Excel, we will often use the types integer, decimals, dates and text.1. These types are implemented in OutbreakTools linelists.\nFor input variables, you could think of two ways of entering data: a free text approach, where user can enter the value of their choice, and a controlled (constrained) approach, where the values the user can enter are limited. In Excel, this is generally implemented through dropdown menus from which the data encoder selects a value. In OutbreakTools, there have several ways of building dropdown menus, depending on whether you know the categories in advance or not. This is what we call variable control.\nFinally, many softwares allow the user to set the way the data is displayed, which we here call variable format. For example:\n\nThe date first of January of 2023 can be displayed as “01/01/2024”, or “1/1/24” or 1-Jan-24” etc.\n\nThe number “1” could be displayed as “1” simply, or “001”\n\nThe number 0.01 could be displayed with different levels of rounding, or even as “10%” if the column contains proportions that can be displayed as percentages.\n\n\n\nVariable Type\nThis column proposes a dropdown menu field containing four options for defining the type2 of each variable:\n\nText: creates a column of text3. The entry of the text may be free or constrained by a dropdown menu.\nDate: creates a date column, whose exact format is defined in the Variable format column. The default format is jj-mmm-aaaa.\nInteger: creates an integer column\nDecimal: creates a column with decimal numbers. The number of digits after the decimal point is defined in the Variable format.\n\n\n\n\nVariable Format\nThis field is used to specify the format of the variable (which depends on its type).\nThere is a predefined dropdown list with common options, but you can enter any format by hand, as long as it is written in Excel syntax (see here and here for information).\n\nExample: for an integer to appear with at least 2 characters, enter the format: # #00\n\n\n\n\n\n\nNote\n\n\n\nNote that the default date format is jj-mmm-aaaa.\n\n\n\n\nControl\nThis is a dropdown field containing nine options for defining variables that are not free text:\n\nchoice_manual\nchoice_custom\nchoice_multiple\nlist_auto\ngeo\nhf\nformula\ncase_when\nchoice_formula\n\nThese options broadly correspond to two sorts of variables to be created:\n\ninput categorical variables with constrained values and filled via a dropdown menu\n\ncalculated variables\n\nIn OutbreakTools, the variables to fill in geographic information are treated as a special case of categorical variable and have their own dedicated control.\n\nSummary of the types of control available in OutbreakTools\n\n\n\n\n\n\n\nSort of variable\nControls\nData entry in the linelist\n\n\n\n\nCategorical\nchoice_manual, choice_custom, choice_multiple, list_auto\nDropdown menu\n\n\nGeo-related columns (a special case of categorical)\ngeo, hf\nGeoHelper or dropdown menu\n\n\nCalculated\nformula, choice_formula, case_when\nNo user input needed in these columns\n\n\n\n\n\n\nGuide to choosing variable control in OBT\n\n\n\n\n\n\n\n\nNote on data validation\n\n\n\nFor non-text variable (integers, decimals, dates) is is possible to restrict values using data validation\n\n\n\nDropdown menu variables\nThis table summarises the different options:\n\n\n\n\n\n\n\n\n\nControl\nHow to populate the dropdown menu\nWhere are values defined?\nData entry\n\n\n\n\nchoice_manual\nPredefined values\nIn the setup file, in the Choices sheet\nOne value selected from a dropdown menu\n\n\nchoice_multiple\nPredefined values\nIn the setup file, in the Choices sheet\nSeveral values selected from a dropdown menu\n\n\nchoice_custom\nUser-defined values (but see details)\nIn the Linelist file, in the Custom dropdown sheet\nOne value selected from a dropdown menu\n\n\nlist_auto\nUser-defined values but from another data column\nIn the Linelist file, in another column\nOne value selected from a dropdown menu populated by the values of another variable\n\n\n\n\nchoice_manual\nThis control creates a categorical variable with a static dropdown menu in the linelist, from which one value can be selected. The authorised values from the dropdown menu are defined in advance in the setup and cannot be modified by the users of the linelist (hence the “static” description).\nIn the setup file, we define these values in a list stored in the Choices sheet, and fill the name of that list in the Control details column.\n\n\nchoice_multiple\nThis control is similar to the “choice_manual” control, in that it creates a static dropdown menu in the linelist from predefined values entered in the setup file.\nThe difference is that in the created linelist, the user can use the dropdown menu several times to select multiple values. These values will be concatenated and stored as a chain of character. By default, the separator is a coma (“,”), but you can modify this in the control column. For example, entering choice_multiple(“_”) will use the character “_” to separate values instead of “,”.\nExample: if the user selects “Azythromicin”, then “Ampicilin” from a dropdown menu, the value “Azythromicin, Ampicilin” will be stored in the cell.\n\n\n\n\n\n\nWarning: cannot be used for analyses\n\n\n\nA choice_multiple column cannot be used in the Analyses sheets as the designer cannot predict the number of combinations the user will create, and thus cannot create tables with appropriate size.\n\n\n\n\n\n\n\n\nTip: inform the linelist user\n\n\n\nSince columns allowing multiple choices are rare in linelists in general, we advise you to use the sub-label and possibly a note to inform the linelist user that they can enter several values, and how to do it.\n\n\n\n\nchoice_custom\nThis control creates a dynamic dropdown menu in the linelist, but contrary to the previous controls, the values are not (necessarily) predefined in the setup file, but instead defined by the user. This control is useful for variables where one would like to enforce standardization of values, but the values to encode are not known in advance.\nExample: you wish to create a column containing the name of facilities patients can be transferred to. The names of these facilities is site dependent, thus unknown in advance.\nUsing this control for at least one variable adds a “Custom dropdown sheet in the linelist, where the user can fill-in values to populate the dynamic, customised dropdown menu.\nWhile by default the dropdown menu created is empty, it is possible to pre-fill it by filling the “Control Details” column with a list of choices, like for the other types of dropdowns menus (see the details on setting up dropdown menus below). The table in the Custom dropdown sheet of the linelist will still be created and future users will be able to modify it.\n\n\nlist_auto\nThis control also creates a dynamic dropdown menu, but the values come from the data entered in another column.\nExample: a linelist contains two data-entry sheets:\n\nthe first data entry sheet contains patient data\n\na second data entry sheet contains more variables for a subset of re-admitted patients.\n\nThe “list_auto” control allows to create a column on the second sheet with a dropdown menu populated dynamically with the patient IDs from the first sheet.\n\n\n\n\n\nIn the setup file, the variable used to populate the dropdown menu is defined in Control Details.\n\n\n\nSpecial case of administrative levels and health facilities\nTwo controls allow the user of the linelist to enter geographic information, or information about health facilities. While the created variables are technically dropdown menus, they are treated as a special type of variables in OubtbreakTools linelists, with dedicated tools and analyses.\nOutbreakTool linelists all have a button to import a geobase, a standardised file containing lists of administrative levels to describe places. Once the geobase is successfully imported, the values from its lists populate specific dropdown menus.\n\ngeo\nThe “geo” control indicates that geographic data is expected. In the linelist, this results in the creation of four columns, one for each administrative level, which will be populated by values imported from a geobase. The user can enter data by using the GeoHelper button in the linelist or by selecting values from the cascading dropdown menus in the linelist.\nThe “geo” control does not need additional information to be filled in the “Control Details” column.\nIn the linelist, the variable labels appear in orange cells, which means that the “GeoHelper” button can be used to fill in the corresponding cells.\nExample:\nDefinition in the setup file:\n\nDisplay in the linelist file:\n\nDisplay in the linelist file after importing a geobase (here a Nigeria geobase, note the personalisation of the labels):\n\n\n\nhf\nThe “hf” control means that the user will enter health facility names. By identifying hf data in this way, you can use the GeoHelper button in the linelist to fill in the column.\nSimilarly to the “geo” control, the “hf” control does not need additional information to be filled in the “Control Details” column.\n\n\n\n\n\n\nNote\n\n\n\nThe variable label appears in an orange cell, which means that the GeoHelper button can be used to fill in the corresponding cells.\n\n\nExample:\nDefinition in the setup file:\n\nDisplay in the linelist:\n\n\n\n\nCalculated variables\nThree controls allow the creation of calculated columns. In general, the user can define a column by providing an Excel formula 4, but the setup file also provides two custom functions, CASE_WHEN and CHOICE_FORMULA to simplify formula syntax.\n\n\n\n\n\n\n\n\n\n\nControl\nFunctions\nUse\nDefault value\nCan be used in used in analyses tables\n\n\n\n\nformula\nAny combination of Excel functions (in English)\nAnything\n\nContinuous variables: yes Categorical variables: no\n\n\ncase_when\nCASE_WHEN(Excel functions optional)\nReplaces nested Ifs\nEmpty cells; user can modify it\nNo\n\n\nchoice_formula\nCHOICE_FORMULA (Excel functions optional)\nReplaces nested IF\nEmpty character; user cannot modify it\nYes\n\n\n\n\nformula\nWhen using the “formula” control, the value displayed is calculated according to a formula defined in the Control details column of the dictionary.\n\n\ncase_when\nVariables of control “case_when” use a specifically developed function, CASE_WHEN, which replaces a succession of nested IF. While you could write the formula with nested IF, CASE_WHEN is easier to read, thus simpler to use.\n\nYou want to recode a variable, but you do not know which values will be generated. For example, the raw data contains a columns for the age value and a column for the age unit. You use CASE_WHEN to create a column “age_years”. The values which will be present in the column can take many decimal value in the range of reasonable ages.\n\n\n\n\n\n\n\nImportant: CASE_WHEN and analyses\n\n\n\nCategorical variable created with this control cannot be used in univariate or bivariate tables in analyses sheets, because the designer cannot know in advance how many modalities the variable will take, and thus cannot build the tables.\nOn the other hand, numeric variables created with this control (such as age in years) can be summarised in the analyses. Indeed, taking the mean or the median of a numeric variable variable outputs one value, so the designer knows what to expect.\n\n\n\n\n\n\n\n\nWarning\n\n\n\nTo work properly the “case_when” control must be associated with a CASE_WHENfunction in the Control details column, or the designer will not work properly because the function is not native.\n\n\n\n\n\n\n\n\nWhy not using more recent Excel functions?\n\n\n\n\n\nIf you are using a recent version of Excel, you may know the functions IFS or SWITCH. OutbreakTools does not rely on them as they are not retro-compatible with some older versions of Excel. Use a CASE_WHEN or CHOICE_FORMULA instead.\n\n\n\nRead more about writing the formula in the Control details column below.\n\n\nchoice_formula\nThis control indicates the use of the CHOICE_FORMULA function, another custom function. This function is a special case of the CASE_WHEN formula, with more constrains on it. Indeed, the values that the calculated variable can take are known in advance and predefined in the Choices sheet.\nColumns generated with this control can be used in univariate or bivariate tables, as the number of possible categories is known in advance.\nRead more about writing the formula in the Control details column below.\n\n\n\n\nControl details\nThis is a free text field, which accepts three types of values:\n\nthe name of a list (defined in the Choices sheet),\nthe name of a variable (defined in the Dictionary sheet)\na formula.\n\n\n\n\n\n\n\n\n\n\nControl type\nControl column\nValue expected in the “Control details” column\n\n\n\n\n\nStatic dropdown menu\nchoice_manual choice_custom choice_multiple\nThe name of a list that contains the authorised values defined in the Choice sheet (“List Name” column)\n\n\n\nDynamic dropdown\nlist_auto\nThe name of an existing variable\n\n\n\nCalculated\nformula case_when choice_formula\nAn Excel formula (that can contain one or | more functions, including the custom | functions CASE_WHEN and CHOICE_FORMULA)\n\n\n\n\nDefining dropdown menu categories\nWhen the controls “choice_manual”, “choice_multiple” (and optionally “choice_custom”) are selected in the Control column, you need to define the values the dropdown menu will contain (i.e. the categories).\nThese values are specified in the Choices sheet. Categories of a same variable are bundled into named lists. The name of the list is then entered in the “Control details” column of the Dictionary sheet.\n\nIn the case of “list_auto” variables, you only need to provide the name of another variable in the “Control details” column. In the linelist, the values present in the referred variable will be automatically used to populate the dropdown menu. See this How to for an example.\n\n\nFormulas\nIf you have selected “formula”, “choice_formula” or “case_when” in the Control column, you need to provide the formula to be applied in this column.\n\n\n\n\n\n\nNote\n\n\n\nThe information given in the Formula control section below are also valid for “choice_formula” and “case_when” controls as these, while based on custom functions, are still formulas.\n\n\n\nformula control\nThe formula is written in English, without an “=” sign. During compilation, the formulas will automatically be translated into the Excel language defined on the computer used to generate the linelist.\n\n\n\n\n\n\nImportant\n\n\n\nWhen writing a formula, make sure that it returns an empty value for rows without an ID, as all the rows with non-null values in it will be counted in the Analyses sheets. If your graphs show a lot of “Missing” values that do not reflect how well a column is filled, check that a calculated column is not responsible for it.\n\n\n\n\n\n\n\n\nImportant: english proof your formulas!\n\n\n\nIf your Excel is not configured to use English, pay special attention to the following:\n\nUse the English function names, such as MEAN instead of MOYENNE, or IF instead of SI.\nFunction arguments are separated by “,” in English. Beware of lingering “;” if you are used to Excel in French!\nSimilarly, English Excel uses “.” for decimals, not “,” like in French.\n\n\n\n\n\n\n\n\n\nTip: improve formual readibility\n\n\n\n\n\nIn Excel, you can use ALT+ENTRY to insert a carriage return to go to the next line. This does not affect the execution of your formulas, but greatly increases the readability. The same goes for inserting spaces around operators. Contrast these two formulas:\n\n\n\n\n\n\ncase_when control\nUse the CASE_WHEN function to replace nested IF (therefore limiting the risk of error when writing the formula), in this form:\n\nCASE_WHEN(condition1, value1,\ncondition2, value2,\ncondition3, value3,\n…, …,\nDEFAULT_VALUE)\n\nYou need at least one pair of conditions-values but the function shines when there are many pairs. As in the nested IF or in the IFS functions, the conditional statement are tested in the order they are written.\nBy default, any case that is not covered by the previous conditions will return an empty cell, unless you provide a default value (the “else”).\nExample\nYou could write a formula with nested IF to calculate an age_years column:\n\nIF(age_unit = “months”, age_value / 12, IF(age_unit = “days”, age_value / 365, IF(age_unit = “years”, age_value, IF(ISBLANK(age_unit), ““))))\n\nOr write the equivalent with CASE_WHEN:\n\nCASE_WHEN(age_unit = “months”,\nage_value / 12, age_unit = “days”,\nage_value / 365, age_unit = “years”,\nage_value)\n\n\n\n\n\n\n\nNote\n\n\n\nThe information about the more generalist “formula” control are also valid here.\n\n\n\n\nchoice_formula control\nThe CHOICE_FORMULA function is a subcase of CASE_WHEN for when we want to encode a few known modalities.\nThe pseudo-code is very similar to the CASE_WHEN function:\n\nCHOICE_FORMULA(list_values_choices,\ncondition1, value1,\ncondition2, value2,\ncondition3, value3,\n…, … )\n\nBut here, the value1, value2, value3 etc. are pre-defined in the list “list_values_choices” in the “Choices” sheet, as if these values were for a dropdown menu 5.\nSince we know exactly which modalities this variable can take, we can use it as a categorical variable in the Analyses sheet, to build a uni or a bivariate table.\nExample:\n\nCHOICE_FORMULA(list_age_group, age_years &lt; 5, “0 – 4 years”, age_years &lt; 10, “5 – 9 years, age_years &lt; 15,”10 – 14 years, age_years &lt; 20, “15 – 19 years, AND(age_years &gt;= 20, age_years &lt; 120),”20+ years” )\n\nHere, “list_age_group” corresponds to the list where the potential values to be returned are predefined; “age_years” is an existing variable that contains the age in years. The values between inverted commas (“0 – 5 years”) correspond to the possible results, predefined in “list_age_group”.\n\n\n\n\n\n\nNote\n\n\n\nThe information about the more generalist “formula” control are also valid here.\n\n\n\n\nExample\nHere is an example of a setup that codes for two input columns (age value and age unit) and three calculated columns.\n\nage_num is a numeric column, with no special control\nage_unit contains a dropdown with categories “Day”/“Month/”Year”\nage_years uses CASE_WHEN to transform the input data into the age in years and keeping the formula easy to read. This column is continous, and can be used in the analyses to calculate a mean or a median (or any relevant summary statistics)\nage_months is a simpler formula based on age_years.\nage_group uses CHOICE_FORMULA so this column can be used in univariate or bivariate tables to count the nomber of patients in each class, and to build an age pyramid.\n\n\n\n\n\n\nUnique\nThis is a yes/no dropdown menu field. If the variable should have unique values (such as the patient ID in some cases), special data validation will be applied to duplicated values."
+    "text": "Properties\nThe properties section of the table controls variable visibility, uniqueness, and the type and format of the variable (what it contains, in which form, and in which display).\n\n\n\n\n\n\nStatus\nThis is a dropdown field that contains four options for defining the visibility of the variable. The linelist has a functionality to show or hide optional variables depending on the data needs on the field.\n\nmandatory: variable displayed by default, it cannot be hidden in the linelist\noptional, visible: variable displayed by default, it can be displayed or hidden by the linelist user\noptional, hidden: variable hidden by default, it can be displayed or hidden by the linelist user\nhidden: variable hidden by default, it cannot be displayed in the linelist\n\nVariables can be shown or hidden using the “Show/Hide” button of the linelist OutbreakTools menu in the linelist file. See the how to.\n\n\n\n\n\n\nNote on showing and hiding columns manually\n\n\n\n\n\nTechnically, the linelist user can forcefully hide/un-hide columns.\nUn-hiding hidden (usually calculated) columns is usually desirable during linelist debug or to go check data that may interest you (e.g. a hidden calculated epiweek of exit). You can hide them after consultation without consequences on the rest of the linelist.\nIt is however more dangerous to forcefully hide “mandatory” columns. These columns are often fundamental variables in the linelist, that are needed for data understanding and analyses (e.g. date of admission, age or sex). If you choose to hide one of these columns, know that some analyses might not function as expected, or not at all because they rely on the hidden columns.\nFinally, any change of column visibility that is not made via the “Hide/show variable” button of the linelist will not be recorded and migrated to a new linelist.\n\n\n\n\nExample\nDefinition in the setup file:\n\nDisplay in the linelist file:\n\n\n\n\n\nRegister Book\nThis is a yes/no dropdown menu field used to predefine the variables to be included in the register to be printed. This step is not mandatory and can be managed later, directly in the linelist file.\n\n\nPersonal Identifier\nThis is a yes/no dropdown menu field that indicates that the variable contains personal data (such as names, phone numbers etc.).\nThis column has two uses:\n\nit allows the setup developer to quickly identify variables containing personal data in its dictionary\nit is used to remove variables automatically from the exports if such a behaviour is needed (see the Exports sheet).\n\n\n\nThinking about variables\nThere are many ways of thinking about variables and of classifying them.\nIn general we can distinguished between input variables, where the user enters raw data, and calculated (or derived) variables which require no input. Both of them can be created in OutbreakTools.\nIndependently of this distinction, a variety of variables types can exist, containing numbers or text in various forms. In Excel, we will often use the types integer, decimals, dates and text.1. These types are implemented in OutbreakTools linelists.\nFor input variables, you could think of two ways of entering data: a free text approach, where user can enter the value of their choice, and a controlled (constrained) approach, where the values the user can enter are limited. In Excel, this is generally implemented through dropdown menus from which the data encoder selects a value. In OutbreakTools, there have several ways of building dropdown menus, depending on whether you know the categories in advance or not. This is what we call variable control.\nFinally, many softwares allow the user to set the way the data is displayed, which we here call variable format. For example:\n\nThe date first of January of 2023 can be displayed as “01/01/2024”, or “1/1/24” or 1-Jan-24” etc.\n\nThe number “1” could be displayed as “1” simply, or “001”\n\nThe number 0.01 could be displayed with different levels of rounding, or even as “10%” if the column contains proportions that can be displayed as percentages.\n\n\n\nVariable Type\nThis column proposes a dropdown menu field containing four options for defining the type2 of each variable:\n\nText: creates a column of text3. The entry of the text may be free or constrained by a dropdown menu.\nDate: creates a date column, whose exact format is defined in the Variable format column. The default format is jj-mmm-aaaa.\nInteger: creates an integer column\nDecimal: creates a column with decimal numbers. The number of digits after the decimal point is defined in the Variable format.\n\n\n\n\nVariable Format\nThis field is used to specify the format of the variable (which depends on its type).\nThere is a predefined dropdown list with common options, but you can enter any format by hand, as long as it is written in Excel syntax (see here and here for information).\n\nExample: for an integer to appear with at least 2 characters, enter the format: # #00\n\n\n\n\n\n\nNote\n\n\n\nNote that the default date format is jj-mmm-aaaa.\n\n\n\n\nControl\nThis is a dropdown field containing nine options for defining variables that are not free text:\n\nchoice_manual\nchoice_custom\nchoice_multiple\nlist_auto\ngeo\nhf\nformula\ncase_when\nchoice_formula\n\nThese options broadly correspond to two sorts of variables to be created:\n\ninput categorical variables with constrained values and filled via a dropdown menu\n\ncalculated variables\n\nIn OutbreakTools, the variables to fill in geographic information are treated as a special case of categorical variable and have their own dedicated control.\n\nSummary of the types of control available in OutbreakTools\n\n\n\n\n\n\n\nSort of variable\nControls\nData entry in the linelist\n\n\n\n\nCategorical\nchoice_manual, choice_custom, choice_multiple, list_auto\nDropdown menu\n\n\nGeo-related columns (a special case of categorical)\ngeo, hf\nGeoHelper or dropdown menu\n\n\nCalculated\nformula, choice_formula, case_when\nNo user input needed in these columns\n\n\n\n\n\n\nGuide to choosing variable control in OBT\n\n\n\n\n\n\n\n\nNote on data validation\n\n\n\nFor non-text variable (integers, decimals, dates) is is possible to restrict values using data validation\n\n\n\nDropdown menu variables\nThis table summarises the different options:\n\n\n\n\n\n\n\n\n\nControl\nHow to populate the dropdown menu\nWhere are values defined?\nData entry\n\n\n\n\nchoice_manual\nPredefined values\nIn the setup file, in the Choices sheet\nOne value selected from a dropdown menu\n\n\nchoice_multiple\nPredefined values\nIn the setup file, in the Choices sheet\nSeveral values selected from a dropdown menu\n\n\nchoice_custom\nUser-defined values (but see details)\nIn the Linelist file, in the Custom dropdown sheet\nOne value selected from a dropdown menu\n\n\nlist_auto\nUser-defined values but from another data column\nIn the Linelist file, in another column\nOne value selected from a dropdown menu populated by the values of another variable\n\n\n\n\nchoice_manual\nThis control creates a categorical variable with a static dropdown menu in the linelist, from which one value can be selected. The authorised values from the dropdown menu are defined in advance in the setup and cannot be modified by the users of the linelist (hence the “static” description).\nIn the setup file, we define these values in a list stored in the Choices sheet, and fill the name of that list in the Control details column.\n\n\nchoice_multiple\nThis control is similar to the “choice_manual” control, in that it creates a static dropdown menu in the linelist from predefined values entered in the setup file.\nThe difference is that in the created linelist, the user can use the dropdown menu several times to select multiple values. These values will be concatenated and stored as a chain of character. By default, the separator is a coma (“,”), but you can modify this in the control column. For example, entering choice_multiple(“_”) will use the character “_” to separate values instead of “,”.\nExample: if the user selects “Azythromicin”, then “Ampicilin” from a dropdown menu, the value “Azythromicin, Ampicilin” will be stored in the cell.\n\n\n\n\n\n\nWarning: cannot be used for analyses\n\n\n\nA choice_multiple column cannot be used in the Analyses sheets as the designer cannot predict the number of combinations the user will create, and thus cannot create tables with appropriate size.\n\n\n\n\n\n\n\n\nTip: inform the linelist user\n\n\n\nSince columns allowing multiple choices are rare in linelists in general, we advise you to use the sub-label and possibly a note to inform the linelist user that they can enter several values, and how to do it.\n\n\n\n\nchoice_custom\nThis control creates a dynamic dropdown menu in the linelist, but contrary to the previous controls, the values are not (necessarily) predefined in the setup file, but instead defined by the user. This control is useful for variables where one would like to enforce standardization of values, but the values to encode are not known in advance.\nExample: you wish to create a column containing the name of facilities patients can be transferred to. The names of these facilities is site dependent, thus unknown in advance.\nUsing this control for at least one variable adds a “Custom dropdown sheet in the linelist, where the user can fill-in values to populate the dynamic, customised dropdown menu.\nWhile by default the dropdown menu created is empty, it is possible to pre-fill it by filling the “Control Details” column with a list of choices, like for the other types of dropdowns menus (see the details on setting up dropdown menus below). The table in the Custom dropdown sheet of the linelist will still be created and future users will be able to modify it.\n\n\nlist_auto\nThis control also creates a dynamic dropdown menu, but the values come from the data entered in another column.\nExample: a linelist contains two data-entry sheets:\n\nthe first data entry sheet contains patient data\n\na second data entry sheet contains more variables for a subset of re-admitted patients.\n\nThe “list_auto” control allows to create a column on the second sheet with a dropdown menu populated dynamically with the patient IDs from the first sheet.\n\n\n\n\n\nIn the setup file, the variable used to populate the dropdown menu is defined in Control Details.\n\n\n\nSpecial case of administrative levels and health facilities\nTwo controls allow the user of the linelist to enter geographic information, or information about health facilities. While the created variables are technically dropdown menus, they are treated as a special type of variables in OubtbreakTools linelists, with dedicated tools and analyses.\nOutbreakTool linelists all have a button to import a geobase, a standardised file containing lists of administrative levels to describe places. Once the geobase is successfully imported, the values from its lists populate specific dropdown menus.\n\ngeo\nThe “geo” control indicates that geographic data is expected. In the linelist, this results in the creation of four columns, one for each administrative level, which will be populated by values imported from a geobase. The user can enter data by using the GeoHelper button in the linelist or by selecting values from the cascading dropdown menus in the linelist.\nThe “geo” control does not need additional information to be filled in the “Control Details” column.\nIn the linelist, the variable labels appear in orange cells, which means that the “GeoHelper” button can be used to fill in the corresponding cells.\nExample:\nDefinition in the setup file:\n\nDisplay in the linelist file:\n\nDisplay in the linelist file after importing a geobase (here a Nigeria geobase, note the personalisation of the labels):\n\n\n\nhf\nThe “hf” control means that the user will enter health facility names. By identifying hf data in this way, you can use the GeoHelper button in the linelist to fill in the column.\nSimilarly to the “geo” control, the “hf” control does not need additional information to be filled in the “Control Details” column.\n\n\n\n\n\n\nNote\n\n\n\nThe variable label appears in an orange cell, which means that the GeoHelper button can be used to fill in the corresponding cells.\n\n\nExample:\nDefinition in the setup file:\n\nDisplay in the linelist:\n\n\n\n\nCalculated variables\nThree controls allow the creation of calculated columns. In general, the user can define a column by providing an Excel formula 4, but the setup file also provides two custom functions, CASE_WHEN and CHOICE_FORMULA to simplify formula syntax.\n\n\n\n\n\n\n\n\n\n\nControl\nFunctions\nUse\nDefault value\nCan be used in used in analyses tables\n\n\n\n\nformula\nAny combination of Excel functions (in English)\nAnything\n\nContinuous variables: yes Categorical variables: no\n\n\ncase_when\nCASE_WHEN(Excel functions optional)\nReplaces nested Ifs\nEmpty cells; user can modify it\nNo\n\n\nchoice_formula\nCHOICE_FORMULA (Excel functions optional)\nReplaces nested IF\nEmpty character; user cannot modify it\nYes\n\n\n\n\nformula\nWhen using the “formula” control, the value displayed is calculated according to a formula defined in the Control details column of the dictionary.\n\n\ncase_when\nVariables of control “case_when” use a specifically developed function, CASE_WHEN, which replaces a succession of nested IF. While you could write the formula with nested IF, CASE_WHEN is easier to read, thus simpler to use.\nUsercase You want to recode a variable, but you do not know which values will be generated. For example, the raw data contains a columns for the age value and a column for the age unit. You use CASE_WHEN to create a column “age_years”. The values which will be present in the column can take many decimal value in the range of reasonable ages.\n\n\n\n\n\n\nImportant: CASE_WHEN and analyses\n\n\n\nCategorical variable created with this control cannot be used in univariate or bivariate tables in analyses sheets, because the designer cannot know in advance how many modalities the variable will take, and thus cannot build the tables.\nOn the other hand, numeric variables created with this control (such as age in years) can be summarised in the analyses. Indeed, taking the mean or the median of a numeric variable variable outputs one value, so the designer knows what to expect.\n\n\n\n\n\n\n\n\nWarning\n\n\n\nTo work properly the “case_when” control must be associated with a CASE_WHENfunction in the Control details column, or the designer will not work properly because the function is not native.\n\n\n\n\n\n\n\n\nWhy not using more recent Excel functions?\n\n\n\n\n\nIf you are using a recent version of Excel, you may know the functions IFS or SWITCH. OutbreakTools does not rely on them as they are not retro-compatible with some older versions of Excel. Use a CASE_WHEN or CHOICE_FORMULA instead.\n\n\n\nRead more about writing the formula in the Control details column below.\n\n\nchoice_formula\nThis control indicates the use of the CHOICE_FORMULA function, another custom function. This function is a special case of the CASE_WHEN formula, with more constrains on it. Indeed, the values that the calculated variable can take are known in advance and predefined in the Choices sheet.\nColumns generated with this control can be used in univariate or bivariate tables, as the number of possible categories is known in advance.\nRead more about writing the formula in the Control details column below.\n\n\n\n\nControl details\nThis is a free text field, which accepts three types of values:\n\nthe name of a list (defined in the Choices sheet),\nthe name of a variable (defined in the Dictionary sheet)\na formula.\n\n\n\n\n\n\n\n\n\n\nControl type\nControl column\nValue expected in the “Control details” column\n\n\n\n\n\nStatic dropdown menu\nchoice_manual choice_custom choice_multiple\nThe name of a list that contains the authorised values defined in the Choice sheet (“List Name” column)\n\n\n\nDynamic dropdown\nlist_auto\nThe name of an existing variable\n\n\n\nCalculated\nformula case_when choice_formula\nAn Excel formula (that can contain one or | more functions, including the custom | functions CASE_WHEN and CHOICE_FORMULA)\n\n\n\n\nDefining dropdown menu categories\nWhen the controls “choice_manual”, “choice_multiple” (and optionally “choice_custom”) are selected in the Control column, you need to define the values the dropdown menu will contain (i.e. the categories).\nThese values are specified in the Choices sheet. Categories of a same variable are bundled into named lists. The name of the list is then entered in the “Control details” column of the Dictionary sheet.\n\nIn the case of “list_auto” variables, you only need to provide the name of another variable in the “Control details” column. In the linelist, the values present in the referred variable will be automatically used to populate the dropdown menu. See this How to for an example.\n\n\nFormulas\nIf you have selected “formula”, “choice_formula” or “case_when” in the Control column, you need to provide the formula to be applied in this column.\n\n\n\n\n\n\nNote\n\n\n\nThe information given in the Formula control section below are also valid for “choice_formula” and “case_when” controls as these, while based on custom functions, are still formulas.\n\n\n\nformula control\nThe formula is written in English, without an “=” sign. During compilation, the formulas will automatically be translated into the Excel language defined on the computer used to generate the linelist.\n\n\n\n\n\n\nImportant\n\n\n\nWhen writing a formula, make sure that it returns an empty value for rows without an ID, as all the rows with non-null values in it will be counted in the Analyses sheets. If your graphs show a lot of “Missing” values that do not reflect how well a column is filled, check that a calculated column is not responsible for it.\n\n\n\n\n\n\n\n\nImportant: english proof your formulas!\n\n\n\nIf your Excel is not configured to use English, pay special attention to the following:\n\nUse the English function names, such as MEAN instead of MOYENNE, or IF instead of SI.\nFunction arguments are separated by “,” in English. Beware of lingering “;” if you are used to Excel in French!\nSimilarly, English Excel uses “.” for decimals, not “,” like in French.\n\n\n\n\n\n\n\n\n\nTip: improve formual readibility\n\n\n\n\n\nIn Excel, you can use ALT+ENTRY to insert a carriage return to go to the next line. This does not affect the execution of your formulas, but greatly increases the readability. The same goes for inserting spaces around operators. Contrast these two formulas:\n\n\n\n\n\n\ncase_when control\nUse the CASE_WHEN function to replace nested IF (therefore limiting the risk of error when writing the formula), in this form:\n\nCASE_WHEN(condition1, value1,\ncondition2, value2,\ncondition3, value3,\n…, …,\nDEFAULT_VALUE)\n\nYou need at least one pair of conditions-values but the function shines when there are many pairs. As in the nested IF or in the IFS functions, the conditional statement are tested in the order they are written.\nBy default, any case that is not covered by the previous conditions will return an empty cell, unless you provide a default value (the “else”).\nExample\nYou could write a formula with nested IF to calculate an age_years column:\n\nIF(age_unit = “months”, age_value / 12, IF(age_unit = “days”, age_value / 365, IF(age_unit = “years”, age_value, IF(ISBLANK(age_unit), ““))))\n\nOr write the equivalent with CASE_WHEN:\n\nCASE_WHEN(age_unit = “months”,\nage_value / 12, age_unit = “days”,\nage_value / 365, age_unit = “years”,\nage_value)\n\n\n\n\n\n\n\nNote\n\n\n\nThe information about the more generalist “formula” control are also valid here.\n\n\n\n\nchoice_formula control\nThe CHOICE_FORMULA function is a subcase of CASE_WHEN for when we want to encode a few known modalities.\nThe pseudo-code is very similar to the CASE_WHEN function:\n\nCHOICE_FORMULA(list_values_choices,\ncondition1, value1,\ncondition2, value2,\ncondition3, value3,\n…, … )\n\nBut here, the value1, value2, value3 etc. are pre-defined in the list “list_values_choices” in the “Choices” sheet, as if these values were for a dropdown menu 5.\nSince we know exactly which modalities this variable can take, we can use it as a categorical variable in the Analyses sheet, to build a uni or a bivariate table.\nExample:\n\nCHOICE_FORMULA(list_age_group, age_years &lt; 5, “0 – 4 years”, age_years &lt; 10, “5 – 9 years, age_years &lt; 15,”10 – 14 years, age_years &lt; 20, “15 – 19 years, AND(age_years &gt;= 20, age_years &lt; 120),”20+ years” )\n\nHere, “list_age_group” corresponds to the list where the potential values to be returned are predefined; “age_years” is an existing variable that contains the age in years. The values between inverted commas (“0 – 5 years”) correspond to the possible results, predefined in “list_age_group”.\n\n\n\n\n\n\nNote\n\n\n\nThe information about the more generalist “formula” control are also valid here.\n\n\n\n\nExample\nHere is an example of a setup that codes for two input columns (age value and age unit) and three calculated columns.\n\nage_num is a numeric column, with no special control\nage_unit contains a dropdown with categories “Day”/“Month/”Year”\nage_years uses CASE_WHEN to transform the input data into the age in years and keeping the formula easy to read. This column is continous, and can be used in the analyses to calculate a mean or a median (or any relevant summary statistics)\nage_months is a simpler formula based on age_years.\nage_group uses CHOICE_FORMULA so this column can be used in univariate or bivariate tables to count the nomber of patients in each class, and to build an age pyramid.\n\n\n\n\n\n\nUnique\nThis is a yes/no dropdown menu field. If the variable should have unique values (such as the patient ID in some cases), special data validation will be applied to duplicated values."
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diff --git a/site_libs/bootstrap/bootstrap.min.css b/site_libs/bootstrap/bootstrap.min.css
index 498e476..df36657 100644
--- a/site_libs/bootstrap/bootstrap.min.css
+++ b/site_libs/bootstrap/bootstrap.min.css
@@ -1,4 +1,4 @@
-@import"https://fonts.googleapis.com/css2?family=Lato:ital,wght@0,400;0,700;1,400&display=swap";:root{--primary: #2c3e50;--primary_light: #E4EDF3;--primary_light_inline: #E4EDF3;--secondary: #A1B8CF;--secondary_bg: #F5F9FB;--dark_grey: #C5C5C5;--light_grey: #F8F8F8;--light_blue_bg:#bcdfeb;--light_green_bg: #f1f9f1;--dark_green_bg:#002800 }/*!
+@import"https://fonts.googleapis.com/css2?family=Lato:ital,wght@0,400;0,700;1,400&display=swap";:root{--green_hightlight: #20be9f;--dark_blue: #2c3e50;--grey_code: #2c3e501a}/*!
  * Bootstrap  v5.3.1 (https://getbootstrap.com/)
  * Copyright 2011-2023 The Bootstrap Authors
  * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)
@@ -9,4 +9,4 @@
 * we also add `bright-[color]-` synonyms for the `-[color]-intense` classes since
 * that seems to be what ansi_up emits
 *
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diff --git a/sitemap.xml b/sitemap.xml
index 39f1828..1c486ff 100644
--- a/sitemap.xml
+++ b/sitemap.xml
@@ -2,94 +2,94 @@
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-    <lastmod>2024-10-09T18:38:59.742Z</lastmod>
+    <lastmod>2024-10-11T08:38:47.030Z</lastmod>
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     <loc>https://epicentre-msf.github.io/test-obt-doc-website/how_to/import_geobase.html</loc>
-    <lastmod>2024-10-09T18:38:59.758Z</lastmod>
+    <lastmod>2024-10-11T08:38:47.042Z</lastmod>
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     <loc>https://epicentre-msf.github.io/test-obt-doc-website/how_to/show_hide_variables.html</loc>
-    <lastmod>2024-10-09T18:38:59.758Z</lastmod>
+    <lastmod>2024-10-11T08:38:47.042Z</lastmod>
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-    <lastmod>2024-10-09T18:38:59.790Z</lastmod>
+    <lastmod>2024-10-11T08:38:47.078Z</lastmod>
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-    <lastmod>2024-10-09T18:38:59.830Z</lastmod>
+    <lastmod>2024-10-11T08:38:47.114Z</lastmod>
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-    <lastmod>2024-10-09T18:38:59.790Z</lastmod>
+    <lastmod>2024-10-11T08:38:47.078Z</lastmod>
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-    <lastmod>2024-10-09T18:38:59.790Z</lastmod>
+    <lastmod>2024-10-11T08:38:47.078Z</lastmod>
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-    <lastmod>2024-10-09T18:38:59.730Z</lastmod>
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-    <lastmod>2024-10-09T18:38:59.730Z</lastmod>
+    <lastmod>2024-10-11T08:38:47.014Z</lastmod>
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     <loc>https://epicentre-msf.github.io/test-obt-doc-website/about.html</loc>
-    <lastmod>2024-10-09T18:38:59.642Z</lastmod>
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-    <lastmod>2024-10-09T18:38:59.642Z</lastmod>
+    <lastmod>2024-10-11T08:38:46.926Z</lastmod>
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     <loc>https://epicentre-msf.github.io/test-obt-doc-website/tutorial.html</loc>
-    <lastmod>2024-10-09T18:38:59.830Z</lastmod>
+    <lastmod>2024-10-11T08:38:47.114Z</lastmod>
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     <loc>https://epicentre-msf.github.io/test-obt-doc-website/Options.html</loc>
-    <lastmod>2024-10-09T18:38:59.582Z</lastmod>
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-    <lastmod>2024-10-09T18:38:59.642Z</lastmod>
+    <lastmod>2024-10-11T08:38:46.930Z</lastmod>
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-    <lastmod>2024-10-09T18:38:59.742Z</lastmod>
+    <lastmod>2024-10-11T08:38:47.026Z</lastmod>
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-    <lastmod>2024-10-09T18:38:59.730Z</lastmod>
+    <lastmod>2024-10-11T08:38:47.014Z</lastmod>
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-    <lastmod>2024-10-09T18:38:59.790Z</lastmod>
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-    <lastmod>2024-10-09T18:38:59.790Z</lastmod>
+    <lastmod>2024-10-11T08:38:47.078Z</lastmod>
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-    <lastmod>2024-10-09T18:38:59.790Z</lastmod>
+    <lastmod>2024-10-11T08:38:47.078Z</lastmod>
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-    <lastmod>2024-10-09T18:38:59.830Z</lastmod>
+    <lastmod>2024-10-11T08:38:47.114Z</lastmod>
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     <loc>https://epicentre-msf.github.io/test-obt-doc-website/how_to/migrate_setup.html</loc>
-    <lastmod>2024-10-09T18:38:59.758Z</lastmod>
+    <lastmod>2024-10-11T08:38:47.042Z</lastmod>
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-    <lastmod>2024-10-09T18:38:59.758Z</lastmod>
+    <lastmod>2024-10-11T08:38:47.042Z</lastmod>
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-    <lastmod>2024-10-09T18:38:59.742Z</lastmod>
+    <lastmod>2024-10-11T08:38:47.030Z</lastmod>
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