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”.
rm(list = ls()) #remove past stored objects
options(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.org
library(tidyverse) #package that makes it easier to work with data
library(plotly) #for interactive plotting
library(htmlwidgets) #for saving plots at html files
#### Get data from MERMAID for creating aggregate visualizations ####
allMermaidSampEventsTBL <- mermaidr::mermaid_get_summary_sampleevents()Barplot - number of 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.
### Consolidating the bleaching severity data from the summary sample events
bleachTotalColoniesSummTBL <- 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 categories
bleachLabels <- 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) %>%
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 black
linewidth = 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 plot
bleachingAggBarplot
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).
### Get the relevant data for bleaching severity
bleachPercColoniesYearSummTBL <- 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) %>%
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 values
ticktext = seq(0, 100, by = 10),
linewidth = 2),
xaxis = list(title = "Year",
linecolor = "black", # Set the x-axis line color to black
linewidth = 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(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 plot
bleachingTimeSeriesBarplot
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.
### 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',
name = paste0("Normal (",
bleachSurveySingleSeTBL$
colonies_bleached_percent_normal_avg[1],
"%)"),
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], "%)"),
marker = list(color = "#6288ad")) %>%
add_trace(y = ~colonies_bleached_percent_20_avg,
name = paste0("0-20% bleached (",
bleachSurveySingleSeTBL$
colonies_bleached_percent_20_avg[1], "%)"),
marker = list(color = "#85a3c1")) %>%
add_trace(y = ~colonies_bleached_percent_50_avg,
name = paste0("20-50% bleached (",
bleachSurveySingleSeTBL$
colonies_bleached_percent_50_avg[1], "%)"),
marker = list(color = "#a8bed5")) %>%
add_trace(y = ~colonies_bleached_percent_80_avg,
name = paste0("50-80% bleached (",
bleachSurveySingleSeTBL$
colonies_bleached_percent_80_avg[1], "%)"),
marker = list(color = "#cbdaea")) %>%
add_trace(y = ~colonies_bleached_percent_100_avg,
name = paste0("80-100% bleached (",
bleachSurveySingleSeTBL$
colonies_bleached_percent_100_avg[1], "%)"),
marker = list(color = "#eff7ff")) %>%
add_trace(y = ~colonies_bleached_percent_dead_avg,
name = paste0("Recently dead (",
bleachSurveySingleSeTBL$
colonies_bleached_percent_dead_avg[1], "%)"),
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 = "% Colonies",
linecolor = "black",
linewidth = 2,
range = c(0,100.2),
tickvals = seq(0, 100, by = 10), # Set y-axis tick values
ticksuffix = "%"),
xaxis = list(title = "",
linecolor = "black", # Set the x-axis line color to black
linewidth = 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 plot
bleachingSeveritySingleSeBarplot