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.gitignore

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*/.DS_Store
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*/wc10/
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*/simple_workflow_files/
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*/complex_workflow_files/
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.DS_Store
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Montreal201904/TiliaInstallation/Tilia_ProductKey_Montreal_201904.txt
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Montreal201904/TiliaInstallation/setup_tilia_2-1-1.exe

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AMQUA-June2022/complex_workflow.html

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AMQUA-June2022/complex_workflow.md

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---
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title: "A Not so Simple Workflow"
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author: "Simon Goring, Socorro Dominguez Vidaña"
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date: "2022-05-31"
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date: "2024-02-28"
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output:
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html_document:
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code_folding: show
@@ -63,8 +63,8 @@ stara_chron %>% as.data.frame() %>%
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```
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```{=html}
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<div id="htmlwidget-5c0c7f998e554236bca2" style="width:100%;height:auto;" class="datatables html-widget"></div>
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<script type="application/json" data-for="htmlwidget-5c0c7f998e554236bca2">{"x":{"filter":"none","vertical":false,"data":[["1","2","3"],["14589","14590","14591"],["C14 BP age with Tilia (Grimm)","CAL BP age with CLKAM (Blaauw) sigma 2","linear interpolation between neighbouring dated levels"],["linear interpolation","linear interpolation","Clam"],[2050,2000,2000],[5,400,400],[1,0,1],["2013-01-01","2013-01-01","2007-06-20"],["Radiocarbon years BP","Calibrated radiocarbon years BP","Calibrated radiocarbon years BP"],["C14 BP","CAL BP","PALYCZ"]],"container":"<table class=\"display\">\n <thead>\n <tr>\n <th> <\/th>\n <th>chronologyid<\/th>\n <th>notes<\/th>\n <th>agemodel<\/th>\n <th>ageboundolder<\/th>\n <th>ageboundyounger<\/th>\n <th>isdefault<\/th>\n <th>dateprepared<\/th>\n <th>modelagetype<\/th>\n <th>chronologyname<\/th>\n <\/tr>\n <\/thead>\n<\/table>","options":{"scrollX":"100%","columnDefs":[{"className":"dt-right","targets":[4,5,6]},{"orderable":false,"targets":0}],"order":[],"autoWidth":false,"orderClasses":false}},"evals":[],"jsHooks":[]}</script>
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<div class="datatables html-widget html-fill-item" id="htmlwidget-67933b3df0dac80d80ba" style="width:100%;height:auto;"></div>
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<script type="application/json" data-for="htmlwidget-67933b3df0dac80d80ba">{"x":{"filter":"none","vertical":false,"data":[["1","2","3"],["14589","14590","14591"],["C14 BP age with Tilia (Grimm)","CAL BP age with CLKAM (Blaauw) sigma 2","linear interpolation between neighbouring dated levels"],["linear interpolation","linear interpolation","Clam"],[2050,2000,2000],[5,400,400],[1,0,1],["2013-01-01","2013-01-01","2007-06-20"],["Radiocarbon years BP","Calibrated radiocarbon years BP","Calibrated radiocarbon years BP"],["C14 BP","CAL BP","PALYCZ"]],"container":"<table class=\"display\">\n <thead>\n <tr>\n <th> <\/th>\n <th>chronologyid<\/th>\n <th>notes<\/th>\n <th>agemodel<\/th>\n <th>ageboundolder<\/th>\n <th>ageboundyounger<\/th>\n <th>isdefault<\/th>\n <th>dateprepared<\/th>\n <th>modelagetype<\/th>\n <th>chronologyname<\/th>\n <\/tr>\n <\/thead>\n<\/table>","options":{"scrollX":"100%","columnDefs":[{"className":"dt-right","targets":[4,5,6]},{"orderable":false,"targets":0}],"order":[],"autoWidth":false,"orderClasses":false}},"evals":[],"jsHooks":[]}</script>
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```
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There are three chronologies here, but for whatever reason we've decided not to use any of them. We want to build a new one with the function `Bchronology()` from the [`Bchron` package](https://cran.r-project.org/web/packages/Bchron/vignettes/Bchron.html). First we want to see what chroncontrols we have for the prior chronologies. We're going to select the chronologies used for chronology `14591` as our template.
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```
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```{=html}
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<div id="htmlwidget-086aba428feff353477f" style="width:100%;height:auto;" class="datatables html-widget"></div>
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<script type="application/json" data-for="htmlwidget-086aba428feff353477f">{"x":{"filter":"none","vertical":false,"data":[["1","2","3","4","5"],[15771,15771,15771,15771,15771],[14591,14591,14591,14591,14591],[0,7.5,62.5,122.5,227.5],[null,5,5,5,5],[null,730,950,1320,1990],[53783,53779,53780,53781,53782],[null,610,810,1160,1850],[null,670,880,1240,1920],["Core top","Radiocarbon","Radiocarbon","Radiocarbon","Radiocarbon"]],"container":"<table class=\"display\">\n <thead>\n <tr>\n <th> <\/th>\n <th>siteid<\/th>\n <th>chronologyid<\/th>\n <th>depth<\/th>\n <th>thickness<\/th>\n <th>agelimitolder<\/th>\n <th>chroncontrolid<\/th>\n <th>agelimityounger<\/th>\n <th>chroncontrolage<\/th>\n <th>chroncontroltype<\/th>\n <\/tr>\n <\/thead>\n<\/table>","options":{"scrollX":"100%","columnDefs":[{"className":"dt-right","targets":[1,2,3,4,5,6,7,8]},{"orderable":false,"targets":0}],"order":[],"autoWidth":false,"orderClasses":false}},"evals":[],"jsHooks":[]}</script>
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<div class="datatables html-widget html-fill-item" id="htmlwidget-a22d32465c2791f4cb97" style="width:100%;height:auto;"></div>
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<script type="application/json" data-for="htmlwidget-a22d32465c2791f4cb97">{"x":{"filter":"none","vertical":false,"data":[["1","2","3","4","5"],["15771","15771","15771","15771","15771"],[14591,14591,14591,14591,14591],[0,7.5,62.5,122.5,227.5],[null,5,5,5,5],[null,730,950,1320,1990],[53783,53779,53780,53781,53782],[null,610,810,1160,1850],[null,670,880,1240,1920],["Core top","Radiocarbon","Radiocarbon","Radiocarbon","Radiocarbon"]],"container":"<table class=\"display\">\n <thead>\n <tr>\n <th> <\/th>\n <th>siteid<\/th>\n <th>chronologyid<\/th>\n <th>depth<\/th>\n <th>thickness<\/th>\n <th>agelimitolder<\/th>\n <th>chroncontrolid<\/th>\n <th>agelimityounger<\/th>\n <th>chroncontrolage<\/th>\n <th>chroncontroltype<\/th>\n <\/tr>\n <\/thead>\n<\/table>","options":{"scrollX":"100%","columnDefs":[{"className":"dt-right","targets":[2,3,4,5,6,7,8]},{"orderable":false,"targets":0}],"order":[],"autoWidth":false,"orderClasses":false}},"evals":[],"jsHooks":[]}</script>
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```
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We can look at other tools to decided how we want to manage the chroncontrols, for example, saving them and editing them using Excel or another spreadsheet program. We could add a new date by adding a new row. In this example we're just going to modify the existing ages to provide better constraints at the core top. We are setting the core top to *0 calibrated years BP*, and assuming an uncertainty of 2 years, and a thickness of 1cm.
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```{=html}
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<div id="htmlwidget-7999ecf122933dc516b6" style="width:100%;height:auto;" class="datatables html-widget"></div>
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<script type="application/json" data-for="htmlwidget-7999ecf122933dc516b6">{"x":{"filter":"none","vertical":false,"data":[["1","2","3","4","5"],[15771,15771,15771,15771,15771],[14591,14591,14591,14591,14591],[0,7.5,62.5,122.5,227.5],[1,5,5,5,5],[2,730,950,1320,1990],[53783,53779,53780,53781,53782],[-2,610,810,1160,1850],[0,670,880,1240,1920],["Core top","Radiocarbon","Radiocarbon","Radiocarbon","Radiocarbon"]],"container":"<table class=\"display\">\n <thead>\n <tr>\n <th> <\/th>\n <th>siteid<\/th>\n <th>chronologyid<\/th>\n <th>depth<\/th>\n <th>thickness<\/th>\n <th>agelimitolder<\/th>\n <th>chroncontrolid<\/th>\n <th>agelimityounger<\/th>\n <th>chroncontrolage<\/th>\n <th>chroncontroltype<\/th>\n <\/tr>\n <\/thead>\n<\/table>","options":{"scrollX":"100%","columnDefs":[{"className":"dt-right","targets":[1,2,3,4,5,6,7,8]},{"orderable":false,"targets":0}],"order":[],"autoWidth":false,"orderClasses":false}},"evals":[],"jsHooks":[]}</script>
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<div class="datatables html-widget html-fill-item" id="htmlwidget-9956323373cd0daab07b" style="width:100%;height:auto;"></div>
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<script type="application/json" data-for="htmlwidget-9956323373cd0daab07b">{"x":{"filter":"none","vertical":false,"data":[["1","2","3","4","5"],["15771","15771","15771","15771","15771"],[14591,14591,14591,14591,14591],[0,7.5,62.5,122.5,227.5],[1,5,5,5,5],[2,730,950,1320,1990],[53783,53779,53780,53781,53782],[-2,610,810,1160,1850],[0,670,880,1240,1920],["Core top","Radiocarbon","Radiocarbon","Radiocarbon","Radiocarbon"]],"container":"<table class=\"display\">\n <thead>\n <tr>\n <th> <\/th>\n <th>siteid<\/th>\n <th>chronologyid<\/th>\n <th>depth<\/th>\n <th>thickness<\/th>\n <th>agelimitolder<\/th>\n <th>chroncontrolid<\/th>\n <th>agelimityounger<\/th>\n <th>chroncontrolage<\/th>\n <th>chroncontroltype<\/th>\n <\/tr>\n <\/thead>\n<\/table>","options":{"scrollX":"100%","columnDefs":[{"className":"dt-right","targets":[2,3,4,5,6,7,8]},{"orderable":false,"targets":0}],"order":[],"autoWidth":false,"orderClasses":false}},"evals":[],"jsHooks":[]}</script>
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```
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### Extract Depth & Analysis Unit IDs

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AMQUA-June2022/simple_workflow.html

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