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()
Histogram - Fish biomass from summary sample events
This code creates a histogram of the fish biomass data from all the sample events available with permissions of “public summary” or “public”. It includes the total number of surveys (i.e. sample events in MERMAID) and truncates the data at 5000 kg/ha, with any surveys above that grouped into a single bar for “5000+”.
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### Fish biomass data - only use relevant data and truncate > 5000 kg/hafishbeltSurveySummTBL <- allMermaidSampEventsTBL %>%filter(!is.na(beltfish_biomass_kgha_avg)) %>%mutate(truncBiomass =ifelse(test = beltfish_biomass_kgha_avg >5000,yes =5001,no = beltfish_biomass_kgha_avg))### Create the plotfishbeltAggHist <-plot_ly(data = fishbeltSurveySummTBL,x =~truncBiomass,type ='histogram',xbins =list(start =0, size =100),marker =list(color ="#769fca"),height =450,hovertemplate =paste('Bin: %{x} kg/ha','<br>%{y} surveys','<extra></extra>')) %>%config(displayModeBar =TRUE,displaylogo =FALSE,modeBarButtonsToRemove =c('zoom','pan', 'select', 'zoomIn', 'zoomOut','autoScale', 'resetScale', 'lasso2d','hoverClosestCartesian', 'hoverCompareCartesian')) %>%layout(bargap =0.1,xaxis =list(title ="Fish biomass (kg/ha)",linecolor ="black",linewidth =2,tickmode ="array",ticktext =list("0","1000","2000","3000","4000","5000+"),tickvals =list(0, 1000, 2000, 3000, 4000, 5000)),yaxis =list(title ="Number of surveys",#type = 'log',linecolor ="black", # Set the y-axis line color to blacklinewidth =2),annotations =list(list(x =0, y =1.15, text ="FISH BIOMASS", showarrow =FALSE, xref ='paper', yref ='paper', xanchor ='left', yanchor ='top',font =list(size =20)),list(x =0, y =1.08,text =paste0(length(fishbeltSurveySummTBL$beltfish_biomass_kgha_avg)," Surveys"),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 plotfishbeltAggHist
Time series - Fish biomass by year and management
Barplots showing the average fish biomass (y-axis), each year (x-axis), colored by management (open access = green, restrictions = blue). Note that here I am using a median rather than a mean since fish biomass tends to have a non-normal distribution.
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## Get the fishbelt data and assign either "Open Access" or "Restrictions"fishbeltSurveyManagementTBL <- allMermaidSampEventsTBL %>%filter(!is.na(beltfish_biomass_kgha_avg)) %>%mutate(open_access =case_when(management_rules =="open access"~"Open Access",.default ="Restrictions"),open_access =factor(open_access,levels =c("Restrictions", "Open Access")))## Summarize to get the biomass by year and management (open access vs restricted)fishbeltBiomassByYearManagementTBL <- fishbeltSurveyManagementTBL %>%mutate(year =year(sample_date)) %>%group_by(year, open_access) %>% dplyr::summarise(MedianFishBiomass =median(beltfish_biomass_kgha_avg),.groups ="keep") managementColorMap <-setNames(object =c("#E69F00", "#70AAE6"),nm =c("Open Access", "Restrictions"))fishbeltTimeSeriesBarplot <-plot_ly(data = fishbeltBiomassByYearManagementTBL,x =~year,y =~MedianFishBiomass,color =~open_access,colors = managementColorMap,type ='bar',hovertemplate =paste('%{fullData.name}','<br>Year: %{x}','<br>%{y:.0f} kg/ha','<extra></extra>'), #Custom hover textheight =450) %>%config(displayModeBar =TRUE,displaylogo =FALSE,modeBarButtonsToRemove =c('zoom','pan', 'select', 'zoomIn', 'zoomOut','autoScale', 'resetScale', 'lasso2d','hoverClosestCartesian','hoverCompareCartesian')) %>%layout(bargap =0.1,xaxis =list(title ="Year",linecolor ="black",linewidth =2),yaxis =list(title ="Fish biomass (kg/ha)",linecolor ="black", # Set the y-axis line color to blacklinewidth =2),annotations =list(list(x =0, y =1.15, text ="FISH BIOMASS", showarrow =FALSE, xref ='paper', yref ='paper', xanchor ='left', yanchor ='top',font =list(size =20)),list(x =0, y =1.08,text =paste(length(fishbeltSurveyManagementTBL$beltfish_biomass_kgha_avg)," Surveys"),showarrow =FALSE, xref ='paper', yref ='paper', xanchor ='left', yanchor ='top',font =list(size =12)) ),legend =list(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 plotfishbeltTimeSeriesBarplot
Barplot - Fish biomass by trophic group (single survey)
Barplot showing fish biomass (y-axis) colored by trophic group (x-axis). This is an example with a single sample event (i.e. survey), but the code could easily be adapted to show averages across surveys or sites.
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## Get a single sample event that has biomass in each of the trophic groups as an examplefishbeltSingleSeTBL <- allMermaidSampEventsTBL %>%filter(beltfish_biomass_kgha_avg >0) %>%select(starts_with("beltfish_biomass_kgha_trophic_group_avg"), beltfish_sample_unit_count) %>%select(-beltfish_biomass_kgha_trophic_group_avg_other) %>%#remove "Other"replace(is.na(.), 0) #replace NA's with zeroes## create fixed label and color mapping for the trophic levelstrophicLabels <-str_to_sentence(gsub(x =colnames(fishbeltSingleSeTBL %>%select(-beltfish_sample_unit_count)),pattern ="beltfish_biomass_kgha_trophic_group_avg_",replacement =""))trophicColorMap <-setNames(object =c("#80cdc1", "#377eb8", "#bebada", "#fcae61", "#fdd92f", "#d9ed8b", "#4d9221", "#b4b4b4"),nm = trophicLabels)fishbeltSingleSeBarplot <-plot_ly(x = trophicLabels,y =as.numeric(fishbeltSingleSeTBL[1,colnames(fishbeltSingleSeTBL %>%select(-beltfish_sample_unit_count))]),type ="bar",color = trophicLabels,colors = trophicColorMap,marker =list(line =list(color ="black", width =1)),hovertemplate =paste('%{x}','<br>%{y:.1f} kg/ha','<extra></extra>'), #Custom hover textheight =450) %>%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 ="Trophic group",linecolor ="black",linewidth =2, tickangle =-45),yaxis =list(title ="Fish biomass (kg/ha)",linecolor ="black", # Set the y-axis line color to blacklinewidth =2),annotations =list(list(x =0, y =1.15, text ="FISH BIOMASS", showarrow =FALSE, xref ='paper', yref ='paper', xanchor ='left', yanchor ='top',font =list(size =20)),list(x =0, y =1.07,text =paste0(fishbeltSingleSeTBL$beltfish_sample_unit_count[1]," sample units"),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 plotfishbeltSingleSeBarplot
