This page runs a non-metric multidimensional scaling (NMDS) ordination on coral-genera percent cover across the 2007 to 2017 recovery period. It builds a site-by-genera community matrix, fits the NMDS with a Bray-Curtis distance, and produces biplots that trace how coral community composition shifted over time at each site. The interactive dashboard and the derived percent-cover table let you explore the underlying data directly.
This page uses annual coral-genera percent cover derived from the benthic-cover surveys of the Territorial Coral Reef Monitoring Program (tcrmp), the Virgin Islands National Park Service reef monitoring (vinps), and the California State University Northridge surveys (csun). The genera-level percent-cover product read here is available in the Downloads section below.
Here we import cover of coral genera into data as well as associated metadata and sitedat.
benthicCoverCoralGeneraFile <- latest_output("s2pt4_benthicCoverCoralGenera")
data <- read.csv(paste("../../outputs/",benthicCoverCoralGeneraFile,".csv",sep=""))
metadata <- readLines(paste("../../outputs/",benthicCoverCoralGeneraFile,".txt",sep=""))
sitedat <- read.csv("../../../RRSdata/00_RRS_dataCatalogStatus/00_RRS_siteMaster_allSites_data.csv")Explore the complete coral-genera percent-cover dataset behind this section. The plot shows mean percent cover through time for the most abundant genera; the table is the entire dataset, searchable and filterable by any column.
Table shows a random sample of 15,000 of 219,964 rows. The plot above uses every row.
###############################
filename: s2pt4_benthicCoverCoralGenera_49sites_1987_2023.csv
date: 2026-07-06 01:33:05.158472
description: aggregated surveyed coral species by genera and annual percent cover at 35 sites. The idea to use coral genera is based on coral genera groupings in `csun_random_benthicDat` , resilience of coral genera scored by @vanwoesik2012 , and analyses of coral genera frequency by @longterm_moritz_2021
###############################
column names:
year program date site period replicate replicatetype coralGenera perccover pres
column: year
description: survey year
Data Type: numeric
Mean: 2012.58813260352
Min: 1987
Max: 2023
column: program
description: monitoring program
Data Type: character
Unique Values: (showing all 3 entries)
TCRMP
VINPS
CSUN
column: date
description: date of survey
Data Type: Date
Date Range: 1987-06-01 to 2023-12-07
column: site
description: survey site
Data Type: character
Unique Values: (showing all 49 entries)
Cane Bay
Eagle Ray
Lang Bank Red Hind FSA
Jacks Bay
Buck Island STX
Salt River West
Coculus Rock
Magens Bay
Sprat Hole
Fish Bay
Brewers Bay
Botany Bay
Hind Bank East FSA
Castle
Grammanik Tiger FSA
College Shoal East
Mutton Snapper FSA
Flat Cay
Seahorse Cottage Shoal
Great Pond
Black Point
Savana
South Capella
Buck Island STT
South Water
St James
Meri Shoal
Kings Corner
Salt River Deep
Lang Bank EEMP
Cane Bay Deep
Ginsburg Fringe
Coral Bay
Buck Island STX Deep
VIIS-Newfound
VIIS-Yawzi
VIIS-Mennebeck
VIIS-Haulover
VIIS-Tektite
BUIS-Western Spur and Groove
BUIS-South Fore Reef
Cabritte Horn
East Tektite
Europa Bay
West Little Lameshur
West Tektite
White Point
Yawzi
Tektite
column: period
description: monitoring period
Data Type: character
Unique Values: (showing all 6 entries)
Annual
PeakBL
WS
SCTLD
PostBL
NA
column: replicate
description: replicate number/identifier
Data Type: character
Unique Values: (showing all 20 entries)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
column: replicatetype
description: type of replicate
Data Type: character
Unique Values: (showing all 2 entries)
transect
site
column: coralGenera
description: coral genus
Data Type: character
Unique Values: (showing all 29 entries)
Millepora
Dendrogyra
Acropora
Orbicella
Scolymia
Porites
Mycetophyllia
Mussa
Madracis
Isopyhyllastrea
unknown
unknown juv.
Helioseris
Oculina
Solenastrea
Tubastraea
Stephanocoenia
Siderastrea
Montastraea
Meandrina
Favia
Eusmilia
Diploria
Dichocoenia
Colpophyllia
Pseudodiploria
Manicina
Agaricia
Isophyllia
column: perccover
description: percentage cover of that coral genus
Data Type: numeric
Mean: 0.414024306680286
Min: 0
Max: 74.23
column: pres
description: presence/absence of that coral genus
Data Type: numeric
Mean: 0.160589914713281
Min: 0
Max: 1
siteres : get summary of site/year replication Creating a summary table siteres that joins the main dataset with site-specific data. This table provides a breakdown of replication by site and year.
siteres <-
data |>
full_join(sitedat |> select(site), by = "site") |>
group_by(site, year) |>
summarise(nreplicate = length(unique(replicate))) |> pivot_wider(names_from = year, values_from = nreplicate) |>
select(-"NA")
kbl(siteres) |>
kable_paper(full_width = F) |>
kable_styling(
fixed_thead = T,
bootstrap_options = c("hover", "condensed"),
font_size = 8
) |>
scroll_box(width = "200%", height = "250px")| site | 2002 | 2003 | 2004 | 2005 | 2006 | 2007 | 2008 | 2009 | 2010 | 2011 | 2012 | 2013 | 2014 | 2015 | 2016 | 2017 | 2018 | 2019 | 2020 | 2021 | 2022 | 2023 | 2000 | 2001 | 1992 | 1993 | 1994 | 1995 | 1996 | 1997 | 1998 | 1999 | 1987 | 1988 | 1989 | 1990 | 1991 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| BUIS-South Fore Reef | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| BUIS-Western Spur and Groove | 19 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | NA | NA | NA | NA | NA | NA | NA | NA | NA | 19 | 19 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Black Point | NA | 6 | NA | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Botany Bay | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 5 | NA | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Brewers Bay | 6 | 6 | NA | NA | NA | NA | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Buck Island STT | NA | NA | NA | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Buck Island STX | 3 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | NA | 6 | 6 | NA | 6 | 6 | 6 | NA | 3 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Buck Island STX Deep | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | 6 | 6 | 6 | NA | 6 | 6 | 6 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Cabritte Horn | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | NA | NA | NA | NA | NA |
| Cane Bay | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | NA | 6 | 6 | NA | 6 | 6 | 6 | NA | 6 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Cane Bay Deep | NA | NA | NA | NA | NA | NA | NA | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | NA | 6 | 6 | NA | 6 | 6 | 6 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Castle | NA | 6 | NA | NA | NA | NA | NA | NA | 6 | 6 | 6 | 6 | 6 | 6 | 6 | NA | 6 | 6 | NA | 6 | 6 | 6 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Coculus Rock | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | NA | 6 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| College Shoal East | NA | 6 | NA | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | NA | 6 | 6 | 6 | 6 | 5 | 5 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Coral Bay | NA | NA | NA | NA | NA | NA | NA | NA | NA | 6 | 6 | NA | 6 | 6 | 6 | NA | 6 | 6 | 6 | 6 | 6 | 6 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Eagle Ray | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | NA | 6 | 6 | NA | 6 | 6 | 6 | NA | 6 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| East Tektite | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | NA | NA | NA | NA | NA |
| Europa Bay | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | NA | NA | NA | NA | NA |
| Fish Bay | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | NA | 6 | 6 | 6 | NA | 6 | 6 | 6 | 6 | 6 | 6 | NA | 6 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Flat Cay | NA | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Ginsburg Fringe | NA | NA | NA | NA | NA | NA | NA | NA | NA | 6 | NA | 6 | 6 | 6 | NA | 6 | 6 | NA | 6 | 6 | 6 | 6 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Grammanik Tiger FSA | NA | 6 | 10 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | NA | 6 | 6 | 6 | 6 | 6 | 6 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Great Pond | NA | 6 | 6 | 6 | 6 | 6 | 6 | NA | 6 | 6 | 6 | 6 | 6 | 6 | 6 | NA | 6 | 6 | NA | 6 | 6 | 6 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Hind Bank East FSA | NA | 6 | 10 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | NA | 6 | 6 | 6 | 6 | 6 | 6 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Jacks Bay | 6 | 6 | 6 | 6 | 6 | 6 | 6 | NA | 6 | 6 | 6 | 6 | 6 | 6 | 6 | NA | 6 | 6 | NA | 6 | 6 | 6 | NA | 6 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Kings Corner | NA | NA | NA | NA | NA | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | NA | 6 | 6 | NA | 6 | 6 | 6 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Lang Bank EEMP | NA | NA | NA | NA | NA | NA | NA | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | NA | 6 | 6 | NA | 6 | 6 | 6 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Lang Bank Red Hind FSA | 5 | NA | 6 | 4 | 6 | NA | NA | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | NA | 6 | 6 | NA | 6 | 6 | 6 | NA | 6 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Magens Bay | 6 | 6 | 6 | 6 | 5 | 6 | 6 | 6 | 6 | 6 | NA | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | NA | 6 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Meri Shoal | NA | NA | NA | 6 | 6 | 6 | 5 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | NA | 6 | 6 | 6 | 6 | 6 | 6 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Mutton Snapper FSA | NA | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 5 | 6 | 6 | 6 | 6 | 6 | NA | 6 | 6 | NA | 6 | 6 | 6 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Neptunes Table | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| SARI-Salt River | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Salt River Deep | NA | NA | NA | NA | NA | NA | NA | 6 | 6 | 5 | 6 | 6 | 6 | 6 | 6 | NA | 6 | 6 | NA | 6 | 6 | 6 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Salt River West | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | NA | 6 | 6 | NA | 6 | 6 | 6 | NA | 6 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Savana | NA | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | NA | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Seahorse Cottage Shoal | NA | 6 | 10 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| South Capella | NA | 6 | 10 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | NA | 6 | 6 | 6 | 6 | 6 | 6 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| South Water | NA | NA | NA | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | NA | 6 | 6 | 6 | 6 | 6 | 6 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Sprat Hole | 5 | 6 | 6 | 6 | NA | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | NA | 6 | 6 | NA | 6 | 6 | 6 | NA | 6 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| St James | NA | NA | NA | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | 6 | NA | 6 | 6 | 6 | 6 | 6 | 6 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Tektite | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| VIIS-Haulover | NA | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| VIIS-Mennebeck | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 19 | 20 | 20 | 20 | 20 | NA | 20 | 20 | 20 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| VIIS-Newfound | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | NA | NA | NA | NA | NA | NA | NA | 20 | NA | NA | NA | NA | NA |
| VIIS-Tektite | NA | NA | NA | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| VIIS-Yawzi | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 20 | NA | 20 | 20 | 20 | NA | NA | NA | NA | NA | NA | NA | 20 | NA | NA | NA | NA | NA |
| West Little Lameshur | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | NA | NA | NA | NA | NA |
| West Tektite | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | NA | NA | NA | NA | NA |
| White Point | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | NA | NA | NA | NA | NA |
| Yawzi | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
Generating a summarized dataset datasum that averages percent cover across transects for each coral genera. This dataset is then reshaped to a wider format and missing values are replaced with zeros.
make community_matrix Filtering the data to focus on the years between 2007 and 2017, extracting only the data-containing columns from datasum to get community_matrix, and then removing columns representing genera with <75%ile of total abundance across sites.
datasum <- datasum |>
filter(year>2006 & year<2018)
#make matrix of data
community_matrix <-
datasum[, 3:ncol(datasum)] # Adjust columns as needed
#removing 75% of species with lowest occurrences so metamds will converge
coltorm <- which(as.logical(colSums(community_matrix) <
quantile(colSums(community_matrix))[[4]]))
community_matrix <- community_matrix[, -coltorm]Conducting a Non-metric multidimensional scaling (NMDS) analysis on the community matrix using the Bray-Curtis distance measure, allowing for multiple tries to ensure convergence.
nmds <- metaMDS(community_matrix,
dist = "bray",
trymax = 40,
k = 3)display the basic statistics and results derived from the NMDS analysis.
nmds
Call:
metaMDS(comm = community_matrix, distance = "bray", k = 3, trymax = 40)
global Multidimensional Scaling using monoMDS
Data: wisconsin(community_matrix)
Distance: bray
Dimensions: 3
Stress: 0.129092
Stress type 1, weak ties
Best solution was repeated 1 time in 20 tries
The best solution was from try 13 (random start)
Scaling: centring, PC rotation, halfchange scaling
Species: expanded scores based on 'wisconsin(community_matrix)' preparing for plot Extracting the coordinates from the NMDS results to prepare for visualization. The coordinates are enriched with additional metadata such as site depth. The data is then arranged for sequential plotting.
# Extract NMDS coordinates
nmds_coordinates <- as.data.frame(scores(nmds, display = "sites"))
#continuous grouping var
nmds_coordinates$site <- as.factor(datasum$site)
nmds_coordinates$year <- as.factor(datasum$year)
#join with depth for reordering
nmds_coordinates <- nmds_coordinates |>
left_join(sitedat|> select(site,depth), by = "site")
nmds_coordinates <-
nmds_coordinates[order(nmds_coordinates$depth), ]
nmds_coordinates$site <-
factor(nmds_coordinates$site, levels = unique(nmds_coordinates$site))
nmds_coordinates <- nmds_coordinates |>
arrange(site, year)plot the NMDS biplot with lines connecting data from each year, representing the shift in coral genera composition over time at different sites.
p <- ggplot(nmds_coordinates,
aes(
x = NMDS1,
y = NMDS2,
color = as.factor(site),
# group = year
# shape = site
)) +
geom_point(aes(alpha = year)) +
geom_path(aes(group = site, alpha=year)) +
# scale_color_gradient(low = "red", high = "blue") + # Define color scale from blue to
# scale_shape_manual(values=c(16,1))+
xlab("NMDS Axis 1") +
ylab("NMDS Axis 2") +
theme_minimal() +
labs(
color = "depth",
shape = "protection status",
size = "relief"
)
p
#ggplotly(p)
another NMDS biplot with added arrows indicating the direction and magnitude of change in coral genera composition over the years at each site.
# Build one arrow per site from its earliest to its latest recovery-period year.
# Selecting by each site's own min/max year keeps this correct for any year set
# (the earlier factor-index split assumed a fixed 2007-2017 window).
yr <- function(x) as.numeric(as.character(x))
starts <- nmds_coordinates |>
group_by(site) |>
slice_min(yr(year), n = 1, with_ties = FALSE) |>
ungroup() |>
transmute(site, x = NMDS1, y = NMDS2)
ends <- nmds_coordinates |>
group_by(site) |>
slice_max(yr(year), n = 1, with_ties = FALSE) |>
ungroup() |>
transmute(site, xend = NMDS1, yend = NMDS2)
arrow_segments <- dplyr::inner_join(starts, ends, by = "site")
p <- ggplot(arrow_segments,
aes(
x = x,
xend = xend,
y = y,
yend = yend,
group = site,
color = site
)) +
# geom_point(aes(alpha = year)) +
geom_segment(arrow = arrow(type = "closed", length = unit(0.1, "inches"))) +
theme_minimal()+
xlab("NMDS Axis 1") +
ylab("NMDS Axis 2")
p
This page reads the derived coral-genera percent-cover product that underlies the ordination. Download the data and its metadata sidecar directly from the repository: