Fixed data references in loadData

Galiano BioBlitz 2023.Rmd

@@ -7,13 +7,6 @@ knit: (function(inputFile, encoding) {
 
 ```{r, echo=FALSE, message=FALSE, warning=FALSE}
 source("scripts/loadData.R")
-library(tidyverse)
-records <- read.csv("tabular_data/Galiano_Island_vascular_plant_records_consolidated-prepared.csv")
-summary <- read.csv("tabular_data/Galiano_Tracheophyta_review_summary_reviewed_2024-10-07-assigned_revised.csv")
-new <- summary %>% filter(str_detect(Reporting.Status, "new")) 
-confirmed <- summary %>% filter(Reporting.Status == 'confirmed') 
-reported <- summary %>% filter(Reporting.Status == 'reported') 
-observed <- summary %>% filter(Observation == 'observed') 
 ```
 
 ## Community science contributions

docs/Galiano-BioBlitz-2023.html

@@ -2282,14 +2282,14 @@ <h1 class="title toc-ignore">Galiano BioBlitz 2023 outcomes: vascular
 <div id="community-science-contributions" class="section level2">
 <h2>Community science contributions</h2>
 <p>Through the combined efforts of 25 individuals, the Hunterston Farms
-naturalist community has now documented a total of 802 vascular plant
-species. Based on search efforts over the last decade, 82 percent of the
-historically reported plant diversity has been confirmed and 195 new
+naturalist community has now documented a total of 191 vascular plant
+species. Based on search efforts over the last decade, 97 percent of the
+historically reported plant diversity has been confirmed and 16 new
 species reports added to the list. Community members have now documented
-85 percent of the plant diversity known to the region on
+96 percent of the plant diversity known to the region on
 iNaturalist.</p>
-<div id="htmlwidget-91843466dcea8a9a24e3" style="width:672px;height:140px;" class="plotly html-widget"></div>
-<script type="application/json" data-for="htmlwidget-91843466dcea8a9a24e3">{"x":{"visdat":{"2aa86ade3b7f":["function () ","plotlyVisDat"]},"cur_data":"2aa86ade3b7f","attrs":{"2aa86ade3b7f":{"x":{},"y":{},"orientation":"h","marker":{"color":"#5a96d2","line":{"color":"#5a96d2","width":1}},"name":"confirmed","alpha_stroke":1,"sizes":[10,100],"spans":[1,20],"type":"bar"},"2aa86ade3b7f.1":{"x":{},"y":{},"orientation":"h","marker":{"color":"#decb90","line":{"color":"#decb90","width":1}},"name":"historic","alpha_stroke":1,"sizes":[10,100],"spans":[1,20],"type":"bar","inherit":true},"2aa86ade3b7f.2":{"x":{},"y":{},"orientation":"h","marker":{"color":"#7562b4","line":{"color":"#7562b4","width":1}},"name":"new","alpha_stroke":1,"sizes":[10,100],"spans":[1,20],"type":"bar","inherit":true}},"layout":{"height":140,"margin":{"b":40,"l":60,"t":25,"r":10},"barmode":"stack","autosize":true,"showlegend":false,"xaxis":{"domain":[0,1],"automargin":true,"title":"Species Reporting Status"},"yaxis":{"domain":[0,1],"automargin":true,"title":"","showticklabels":false,"type":"category","categoryorder":"array","categoryarray":["records"]},"meta":{"mx_widgetId":"reportingStatus"},"hovermode":"closest"},"source":"A","config":{"modeBarButtonsToAdd":["hoverclosest","hovercompare"],"showSendToCloud":false,"displayModeBar":false,"responsive":true},"data":[{"x":[169],"y":["records"],"orientation":"h","marker":{"color":"#5a96d2","line":{"color":"#5a96d2","width":1}},"name":"confirmed","type":"bar","error_y":{"color":"rgba(31,119,180,1)"},"error_x":{"color":"rgba(31,119,180,1)"},"xaxis":"x","yaxis":"y","frame":null},{"x":[6],"y":["records"],"orientation":"h","marker":{"color":"#decb90","line":{"color":"#decb90","width":1}},"name":"historic","type":"bar","error_y":{"color":"rgba(255,127,14,1)"},"error_x":{"color":"rgba(255,127,14,1)"},"xaxis":"x","yaxis":"y","frame":null},{"x":[16],"y":["records"],"orientation":"h","marker":{"color":"#7562b4","line":{"color":"#7562b4","width":1}},"name":"new","type":"bar","error_y":{"color":"rgba(44,160,44,1)"},"error_x":{"color":"rgba(44,160,44,1)"},"xaxis":"x","yaxis":"y","frame":null}],"highlight":{"on":"plotly_click","persistent":false,"dynamic":false,"selectize":false,"opacityDim":0.20000000000000001,"selected":{"opacity":1},"debounce":0},"shinyEvents":["plotly_hover","plotly_click","plotly_selected","plotly_relayout","plotly_brushed","plotly_brushing","plotly_clickannotation","plotly_doubleclick","plotly_deselect","plotly_afterplot","plotly_sunburstclick"],"base_url":"https://plot.ly"},"evals":[],"jsHooks":[]}</script>
+<div id="htmlwidget-8818f7c03a0dfee4a3ce" style="width:672px;height:140px;" class="plotly html-widget"></div>
+<script type="application/json" data-for="htmlwidget-8818f7c03a0dfee4a3ce">{"x":{"visdat":{"a0f8b7c8c4":["function () ","plotlyVisDat"]},"cur_data":"a0f8b7c8c4","attrs":{"a0f8b7c8c4":{"x":{},"y":{},"orientation":"h","marker":{"color":"#5a96d2","line":{"color":"#5a96d2","width":1}},"name":"confirmed","alpha_stroke":1,"sizes":[10,100],"spans":[1,20],"type":"bar"},"a0f8b7c8c4.1":{"x":{},"y":{},"orientation":"h","marker":{"color":"#decb90","line":{"color":"#decb90","width":1}},"name":"historic","alpha_stroke":1,"sizes":[10,100],"spans":[1,20],"type":"bar","inherit":true},"a0f8b7c8c4.2":{"x":{},"y":{},"orientation":"h","marker":{"color":"#7562b4","line":{"color":"#7562b4","width":1}},"name":"new","alpha_stroke":1,"sizes":[10,100],"spans":[1,20],"type":"bar","inherit":true}},"layout":{"height":140,"margin":{"b":40,"l":60,"t":25,"r":10},"barmode":"stack","autosize":true,"showlegend":false,"xaxis":{"domain":[0,1],"automargin":true,"title":"Species Reporting Status"},"yaxis":{"domain":[0,1],"automargin":true,"title":"","showticklabels":false,"type":"category","categoryorder":"array","categoryarray":["records"]},"meta":{"mx_widgetId":"reportingStatus"},"hovermode":"closest"},"source":"A","config":{"modeBarButtonsToAdd":["hoverclosest","hovercompare"],"showSendToCloud":false,"displayModeBar":false,"responsive":true},"data":[{"x":[169],"y":["records"],"orientation":"h","marker":{"color":"#5a96d2","line":{"color":"#5a96d2","width":1}},"name":"confirmed","type":"bar","error_y":{"color":"rgba(31,119,180,1)"},"error_x":{"color":"rgba(31,119,180,1)"},"xaxis":"x","yaxis":"y","frame":null},{"x":[6],"y":["records"],"orientation":"h","marker":{"color":"#decb90","line":{"color":"#decb90","width":1}},"name":"historic","type":"bar","error_y":{"color":"rgba(255,127,14,1)"},"error_x":{"color":"rgba(255,127,14,1)"},"xaxis":"x","yaxis":"y","frame":null},{"x":[16],"y":["records"],"orientation":"h","marker":{"color":"#7562b4","line":{"color":"#7562b4","width":1}},"name":"new","type":"bar","error_y":{"color":"rgba(44,160,44,1)"},"error_x":{"color":"rgba(44,160,44,1)"},"xaxis":"x","yaxis":"y","frame":null}],"highlight":{"on":"plotly_click","persistent":false,"dynamic":false,"selectize":false,"opacityDim":0.20000000000000001,"selected":{"opacity":1},"debounce":0},"shinyEvents":["plotly_hover","plotly_click","plotly_selected","plotly_relayout","plotly_brushed","plotly_brushing","plotly_clickannotation","plotly_doubleclick","plotly_deselect","plotly_afterplot","plotly_sunburstclick"],"base_url":"https://plot.ly"},"evals":[],"jsHooks":[]}</script>
 </div>
 <div id="authors" class="section level2">
 <h2>Authors</h2>

scripts/loadData.R

@@ -9,10 +9,13 @@ source("scripts/utils.R")
 originalSummary <- read.csv("tabular_data/Galiano_Tracheophyta_review_summary_reviewed_2024-10-07-assigned_revised.csv")
 filteredSummary <- read.csv("tabular_data/Galiano_Island_vascular_plant_records_consolidated-assigned-taxa.csv")
 
+records <- read.csv("tabular_data/Galiano_Island_vascular_plant_records_consolidated-prepared.csv")
+
 summary <- inner_join(x = originalSummary, y = filteredSummary, by = join_by(ID == id))
 
 # Subset historic, confirmed and new records
 
 new <- summary %>% filter(str_detect(Reporting.Status, "new"))
 confirmed <- summary %>% filter(Reporting.Status == "confirmed")
 reported <- summary %>% filter(Reporting.Status == "reported")
+observed <- summary %>% filter(Observation == 'observed')