This code provides examples of visualizations like those on MERMAID Explore that show information about bleaching severity (from the bleaching protocol).
Getting summary sample event data from MERMAID
The following code downloads summary sample event data from MERMAID using the mermaidr package (documentation can be found at https://data-mermaid.github.io/mermaidr/). The summary sample events contain all surveys (i.e. sample events) that have permissions of “public summary” or “public”.
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rm(list =ls()) #remove past stored objectsoptions(scipen =999) #turn off scientific notation#### Load packages and libraries ###### If this is the first time using mermaidr, install the package through "remotes"# install.packages("remotes")# remotes::install_github("data-mermaid/mermaidr")# install.packages("tidyverse")# install.packages("plotly") # install.packages("htmlwidgets")library(mermaidr) #package to download data from datamermaid.orglibrary(tidyverse) #package that makes it easier to work with datalibrary(plotly) #for interactive plottinglibrary(htmlwidgets) #for saving plots at html files#### Get data from MERMAID for creating aggregate visualizations ####allMermaidSampEventsTBL <- mermaidr::mermaid_get_summary_sampleevents()
Barplot - # coral colonies by bleaching severity
This code creates a barplot showing the total number of coral colonies across all surveys (summary sample events) that have been found to be in each of seven levels of bleaching severity. It also includes code to show the total number of coral colonies observed at the top of the plot.
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### Consolidating the bleaching severity data from the summary sample eventsbleachTotalColoniesSummTBL <- allMermaidSampEventsTBL %>%filter(!is.na(colonies_bleached_count_total_avg)) %>%mutate(NumColoniesTotal = colonies_bleached_count_total_avg * colonies_bleached_sample_unit_count) %>%summarise(TotalColoniesNormal =sum(NumColoniesTotal * colonies_bleached_percent_normal_avg/100),TotalColoniesPale =sum(NumColoniesTotal * colonies_bleached_percent_pale_avg/100),TotalColonies0to20 =sum(NumColoniesTotal * colonies_bleached_percent_20_avg/100),TotalColonies20to50 =sum(NumColoniesTotal * colonies_bleached_percent_50_avg/100),TotalColonies50to80 =sum(NumColoniesTotal * colonies_bleached_percent_80_avg/100),TotalColonies80to100 =sum(NumColoniesTotal * colonies_bleached_percent_100_avg/100),TotalColoniesDead =sum(NumColoniesTotal * colonies_bleached_percent_dead_avg/100))## create fixed label and color mapping for the bleaching categoriesbleachLabels <-factor(x =c("Normal", "Pale", "0-20%", "20-50%", "50-80%", "80-100%", "Dead"),levels =c("Normal", "Pale", "0-20%", "20-50%", "50-80%", "80-100%", "Dead"))bleachColorMap <-setNames(object =c("#3c6e9a", "#6288ad", "#85a3c1", "#a8bed5", "#cbdaea", "#eff7ff", "#b4b4b4", "black"),nm =levels(bleachLabels))bleachingAggBarplot <-plot_ly(x = bleachLabels,y =as.numeric(bleachTotalColoniesSummTBL[1,]),type ="bar",color = bleachLabels,colors = bleachColorMap,height =450,hovertemplate =paste('Bleaching severity: %{x}','<br>%{y:.0f} colonies','<extra></extra>')) %>%config(displayModeBar =TRUE,displaylogo =FALSE,modeBarButtonsToRemove =c('zoom','pan', 'select', 'zoomIn', 'zoomOut','autoScale', 'resetScale', 'lasso2d','hoverClosestCartesian', 'hoverCompareCartesian')) %>%layout(showlegend =FALSE,bargap =0.1,xaxis =list(title ="Bleaching severity",linecolor ="black",linewidth =2),yaxis =list(title ="Number of coral colonies",linecolor ="black", # Set the y-axis line color to blacklinewidth =2),annotations =list(list(x =0, y =1.15, text ="BLEACHING", showarrow =FALSE, xref ='paper', yref ='paper', xanchor ='left', yanchor ='top',font =list(size =20)),list(x =0, y =1.08,text =paste0(round(sum(allMermaidSampEventsTBL$colonies_bleached_count_total_avg*allMermaidSampEventsTBL$colonies_bleached_sample_unit_count,na.rm = T))," Colonies"),showarrow =FALSE, xref ='paper', yref ='paper', xanchor ='left', yanchor ='top',font =list(size =12)) ),margin =list(t =50, b =75)) # Increase top margin to create more space for title and subtitle# Visualize the plotbleachingAggBarplot
Time series - % of coral colonies by year and bleaching severity
Stacked barplots showing the percent cover (y-axis) by year (x-axis), with different colors representing each of the seven bleaching severity levels (Normal, Pale, 0-20%, 20-50%, 50-80%, 80-100%, Dead).
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### Get the relevant data for bleaching severitybleachPercColoniesYearSummTBL <- allMermaidSampEventsTBL %>%filter(!is.na(colonies_bleached_count_total_avg)) %>%mutate(NumColoniesTotal = colonies_bleached_count_total_avg * colonies_bleached_sample_unit_count,year =year(sample_date)) %>%group_by(year) %>%summarise(TotalColoniesNormal =sum(NumColoniesTotal * colonies_bleached_percent_normal_avg/100),TotalColoniesPale =sum(NumColoniesTotal * colonies_bleached_percent_pale_avg/100),TotalColonies0to20 =sum(NumColoniesTotal * colonies_bleached_percent_20_avg/100),TotalColonies20to50 =sum(NumColoniesTotal * colonies_bleached_percent_50_avg/100),TotalColonies50to80 =sum(NumColoniesTotal * colonies_bleached_percent_80_avg/100),TotalColonies80to100 =sum(NumColoniesTotal * colonies_bleached_percent_100_avg/100),TotalColoniesDead =sum(NumColoniesTotal * colonies_bleached_percent_dead_avg/100),TotalAllColonies =sum(NumColoniesTotal)) %>%ungroup() %>%mutate(PercColoniesNormal = TotalColoniesNormal/TotalAllColonies*100,PercColoniesPale = TotalColoniesPale/TotalAllColonies*100,PercColonies0to20 = TotalColonies0to20/TotalAllColonies*100,PercColonies20to50 = TotalColonies20to50/TotalAllColonies*100,PercColonies50to80 = TotalColonies50to80/TotalAllColonies*100,PercColonies80to100 = TotalColonies80to100/TotalAllColonies*100,PercColoniesDead = TotalColoniesDead/TotalAllColonies*100)bleachingTimeSeriesBarplot <-plot_ly(data = bleachPercColoniesYearSummTBL,x =~year,y =~PercColoniesNormal,type ='bar',name ="Normal",marker =list(color ="#3c6e9a"),height =450,hovertemplate =paste('Bleaching severity: %{fullData.name}','<br>Year: %{x}','<br>%{y:.1f}% of colonies','<extra></extra>')) %>%add_trace(y =~PercColoniesPale,name ="Pale",marker =list(color ="#6288ad")) %>%add_trace(y =~PercColonies0to20,name ="0-20%",marker =list(color ="#85a3c1")) %>%add_trace(y =~PercColonies20to50,name ="20-50%",marker =list(color ="#a8bed5")) %>%add_trace(y =~PercColonies50to80,name ="50-80%",marker =list(color ="#cbdaea")) %>%add_trace(y =~PercColonies80to100,name ="80-100%",marker =list(color ="#eff7ff")) %>%add_trace(y =~PercColoniesDead,name ="Dead",marker =list(color ="#b4b4b4")) %>%config(displayModeBar =TRUE,displaylogo =FALSE,modeBarButtonsToRemove =c('zoom','pan', 'select', 'zoomIn', 'zoomOut','autoScale', 'resetScale', 'lasso2d','hoverClosestCartesian','hoverCompareCartesian')) %>%layout(barmode ="stack",bargap =0.1,yaxis =list(title ="% of Colonies",linecolor ="black",hoverformat ='.2f',tickvals =seq(0, 100, by =10), # Set y-axis tick valuesticktext =seq(0, 100, by =10),linewidth =2),xaxis =list(title ="Year",linecolor ="black", # Set the x-axis line color to blacklinewidth =2),annotations =list(list(x =0, y =1.15, text ="BLEACHING", showarrow =FALSE,xref ='paper', yref ='paper', xanchor ='left', yanchor ='top',font =list(size =20)),list(x =0, y =1.08,text =paste0(round(sum( allMermaidSampEventsTBL$colonies_bleached_count_total_avg * allMermaidSampEventsTBL$colonies_bleached_sample_unit_count,na.rm = T))," Colonies"),showarrow =FALSE, xref ='paper', yref ='paper', xanchor ='left', yanchor ='top',font =list(size =12)) ),legend =list(title =list(text ="Bleaching severity:"),orientation ="h",xanchor ="center",x =0.5, y =-0.2),margin =list(t =50, b =75)) # Increase top margin to create more space for title and subtitle# Visualize the plotbleachingTimeSeriesBarplot
Stacked Single Barplot - % of coral colonies by bleaching severity (single bleaching survey)
Code to create a single stacked barplot showing the percent cover (y-axis) for each of the seven levels of bleaching severity levels: Normal, Pale, 0-20%, 20-50%, 50-80%, 80-100%, Dead (each represented by a different color). This code shows an example with a single survey (i.e. sample event) but could be adapted to apply to multiple surveys and sites. In this example I have intentionally selected a sample event that has each bleaching severity level represented but this is not the case for all sample events.
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### Bleaching severity data for a single sample event bleachSurveySingleSeTBL <- allMermaidSampEventsTBL %>%filter(colonies_bleached_count_total_avg >0) %>%mutate(NumColoniesTotal = colonies_bleached_count_total_avg * colonies_bleached_sample_unit_count) %>%filter(project =="Semporna PCA"& site =="SWV (Restoration Site 2)")bleachingSeveritySingleSeBarplot <-plot_ly(data = bleachSurveySingleSeTBL[1,],x =1,y =~colonies_bleached_percent_normal_avg,type ='bar',hovertemplate =paste('%{meta}','<br>%{y:.1f}% of colonies','<extra></extra>'),name =paste0("Normal (", bleachSurveySingleSeTBL$ colonies_bleached_percent_normal_avg[1],"%)"),meta ="Normal",marker =list(color ="#3c6e9a"),height =450,width =500) %>%add_trace(y =~colonies_bleached_percent_pale_avg,name =paste0("Pale (", bleachSurveySingleSeTBL$ colonies_bleached_percent_pale_avg[1], "%)"),meta ="Pale",marker =list(color ="#6288ad")) %>%add_trace(y =~colonies_bleached_percent_20_avg,name =paste0("0-20% bleached (", bleachSurveySingleSeTBL$ colonies_bleached_percent_20_avg[1], "%)"),meta ="0-20% bleached",marker =list(color ="#85a3c1")) %>%add_trace(y =~colonies_bleached_percent_50_avg,name =paste0("20-50% bleached (", bleachSurveySingleSeTBL$ colonies_bleached_percent_50_avg[1], "%)"),meta ="20-50% bleached",marker =list(color ="#a8bed5")) %>%add_trace(y =~colonies_bleached_percent_80_avg,name =paste0("50-80% bleached (", bleachSurveySingleSeTBL$ colonies_bleached_percent_80_avg[1], "%)"),meta ="50-80% bleached",marker =list(color ="#cbdaea")) %>%add_trace(y =~colonies_bleached_percent_100_avg,name =paste0("80-100% bleached (", bleachSurveySingleSeTBL$ colonies_bleached_percent_100_avg[1], "%)"),meta ="80-100% bleached",marker =list(color ="#eff7ff")) %>%add_trace(y =~colonies_bleached_percent_dead_avg,name =paste0("Recently dead (", bleachSurveySingleSeTBL$ colonies_bleached_percent_dead_avg[1], "%)"),meta ="Recently dead",marker =list(color ="#b4b4b4")) %>%config(displayModeBar =TRUE,displaylogo =FALSE,modeBarButtonsToRemove =c('zoom','pan', 'select', 'zoomIn', 'zoomOut','autoScale', 'resetScale', 'lasso2d','hoverClosestCartesian','hoverCompareCartesian')) %>%layout(barmode ="stack",bargap =0,yaxis =list(title ="% of colonies",linecolor ="black",linewidth =2,range =c(0,100.2),tickvals =seq(0, 100, by =10), # Set y-axis tick valuesticksuffix ="%"),xaxis =list(title ="",linecolor ="black", # Set the x-axis line color to blacklinewidth =2,showticklabels=FALSE),annotations =list(list(x =0, y =1.15, text ="BLEACHING - SEVERITY", showarrow =FALSE,xref ='paper', yref ='paper', xanchor ='left', yanchor ='top',font =list(size =20)),list(x =0, y =1.08,text =paste0(bleachSurveySingleSeTBL$NumColoniesTotal[1]," Colonies"),showarrow =FALSE, xref ='paper', yref ='paper', xanchor ='left', yanchor ='top',font =list(size =12)) ),margin =list(t =50, b =75))# Visualize the plotbleachingSeveritySingleSeBarplot
