Last updated: 2020-04-29

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Introduction

The idea laid out in this vignette comes from this publication: https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2018EA000519 . The idea basically is that by taking the mean of the environmental variables during the MHW in a region we are able to create something useful for multivariate analysis. And according to the publication above this works well with environmental variables and K-means clustering to determine primary flavours of the same phenomenon. So my thinking here (actually Young-oh Kwon’s thinking) is that we can do this for MHWs. The anticipated outcome is that we will see groups of MHWs that are clearly due to certain drivers over others. The interesting part will come from seeing if these different flavours of MHWs share some other commonality, like region or season of occurrence.

# All of the libraries and objects used in the project
# Note that this also loads the data we will be using in this vignette
source("code/functions.R")
library(vegan) # For multivariate analyses

Mean values

Before we can run K-means on the mean states during the MHWs, we need to create the mean states themselves. To do this we will take the ALL_anom dataset from the previous vignette and mean those anomaly time series down into single values. We will do this for the full time series’, as well as for the onset and decline portions.

# Create the mean values per event
ALL_mean <- ALL_anom %>% 
  left_join(GLORYS_MHW_clim[c("region", "doy", "t", "event_no")], 
            by = c("region", "doy", "t")) %>% 
  na.omit() %>% 
  select(-t, -doy) %>% 
  group_by(region, event_no, var) %>% 
  summarise_all(mean) %>% 
  ungroup()
saveRDS(ALL_mean, "data/ALL_mean.Rda")

# Create a wide version for only anomaly values
ALL_mean_wide <- ALL_mean %>% 
  select(-val, -seas, -thresh) %>% 
  pivot_wider(names_from = var, values_from = anom)
saveRDS(ALL_mean_wide, "data/ALL_mean_wide.Rda")

Clustering

With a nice wide dataframe of anomalies there is not much more to do than pass ALL_mean_wise to kmeans(). First we need to know what the appropriate number of clusters to use would be. It would be nice if it were six because this matches the number of regions in the study, but let’s let the data take the lead here. Below is the code we use to iterate through the possible results and we end with an elbow plot showing us where the limit of positive returns on model accuracy is. I took this particular code from: https://www.guru99.com/r-k-means-clustering.html.

# Load the wide data
ALL_mean_wide <- readRDS("data/ALL_mean_wide.Rda")

# Then scale the data to a 0 mean 1 SD scale
  # NB: It turns out that scaling the data beforehand
  # causes the model to perform much more poorly
  # I'm not using the dataframe below, but I've left it in for now
ALL_scale <- ALL_mean_wide %>% 
  mutate_if(.predicate = is.double, .funs = scale)

# Base function
kmean_withinss <- function(k) {
    cluster <- kmeans(ALL_mean_wide[,-c(1:2)], k)
    return(cluster$tot.withinss)
}

# sapply() it
wss <- sapply(2:30, kmean_withinss)

# Create a dataframe for plotting
elbow <- data.frame(2:30, wss)

# Plot
ggplot(elbow, aes(x = X2.30, y = wss)) +
    geom_point() +
    geom_line()

Version Author Date
99eda29 robwschlegel 2020-04-16

Where exactly in the above elbow one should focus on is open to some interpretation. Does one take it right at where the curve clearly starts, or one or two steps in? I am going to take it right at the curve as I want to avoid overfitting the model as much as possible. This means we are going with a cluster count of 7. It seems pretty apparent to me that this is a good choice as the gains in model accuracy dramatically slow down after K = 7.

# Performing K-means in R is so easy!
k_res <- kmeans(ALL_mean_wide[,-c(1:2)], 7, iter.max = 10000)
# k_res$betweenss/k_res$totss
k_res
K-means clustering with 7 clusters of sizes 45, 45, 22, 55, 14, 5, 72

Cluster means:
      bottomT        mld         msl     mslhf    msnlwrf     msnswrf
1 0.471574741 -2.2443399  -477.68844  4.177967   5.680558  -5.0115799
2 0.516124796 -1.3044380   257.36320  4.808300   3.764252   1.1349830
3 0.386566719 -1.9107403   522.52090  5.550448   3.281895   1.6940040
4 0.543045116 -0.6390683  -161.76380  2.474876   5.470377  -3.3218037
5 0.629883474 -1.4163425 -1036.10471 -6.002791  13.733660 -12.2098929
6 0.005459932 -0.8848696   824.85607 -3.533757 -18.419867  36.6760660
7 0.673140077 -1.0285660    68.56557  3.510061   4.349774  -0.7638414
       msshf        ssh        sss      t2m     temp            u        u10
1  2.4087017 0.01405337 0.06571314 1.669855 1.600572  0.005533407 -0.8342249
2  2.9757419 0.02166502 0.01510074 2.013063 1.754287  0.012380538 -0.6569050
3  1.7913637 0.01314387 0.08456167 1.807464 1.602244  0.010869651 -0.6904076
4  0.4154442 0.01917429 0.01413808 1.807151 1.708835  0.009187343 -0.3785695
5 -2.2931055 0.02206284 0.16471180 2.100224 1.472360 -0.002747002 -0.5593309
6 -3.0066297 0.00430838 0.05820023 1.101243 1.472727 -0.004518998 -0.3504811
7  1.7170301 0.01789951 0.09585039 1.957934 1.769406  0.007803413 -0.6152098
            v         v10
1 0.016251349  0.29116593
2 0.017520679  0.88400732
3 0.016634591  0.94010401
4 0.010857590  0.28184880
5 0.002993552 -0.46579516
6 0.005990604  0.02350157
7 0.016718279  0.33955102

Clustering vector:
  [1] 7 1 7 6 4 1 2 2 1 7 6 5 7 3 2 7 4 2 1 4 1 1 5 3 2 7 2 7 4 7 2 2 2 1 4 1 3
 [38] 2 1 4 3 1 7 2 7 3 2 7 2 6 1 4 1 4 3 5 4 4 7 7 4 4 1 7 7 4 7 7 2 3 3 1 2 4
 [75] 7 7 3 7 7 1 1 5 7 7 4 2 7 5 4 1 7 2 7 4 7 7 4 2 4 4 7 4 1 4 4 7 4 1 7 1 7
[112] 1 5 5 2 1 3 5 7 7 7 5 3 4 4 2 4 4 7 5 7 2 7 7 2 2 7 4 4 2 4 1 4 4 4 7 1 1
[149] 7 7 4 4 7 1 2 1 1 4 3 3 7 1 4 7 7 4 4 7 4 7 7 5 7 4 7 3 4 2 7 6 1 7 2 2 1
[186] 4 4 2 1 1 3 2 3 4 7 7 7 2 4 2 7 1 3 4 1 3 1 6 2 3 3 2 1 2 1 7 3 1 2 2 2 1
[223] 7 2 7 7 1 1 5 7 2 4 7 7 2 5 2 2 4 4 1 4 7 1 5 7 3 7 7 4 7 7 1 7 4 4 2 2

Within cluster sum of squares by cluster:
[1]  636108.7  181580.3  158182.9  291988.0 2029562.8   51376.7  273470.3
 (between_SS / total_SS =  91.5 %)

Available components:

[1] "cluster"      "centers"      "totss"        "withinss"     "tot.withinss"
[6] "betweenss"    "size"         "iter"         "ifault"

As we may see from the print-out above, the 7 cluster approach explains ~91% of the variance within the dataset. That’s pretty good! So let’s see what these clusters actually look like in relation to one another.

# Cast the K-means results long
k_res_long <- k_res$centers %>% 
  data.frame() %>% 
  mutate(cluster = row.names(.)) %>% 
  pivot_longer(cols = bottomT:v10, names_to = "var", values_to = "val") %>% 
  filter(var != "msl") %>% # These values are so large they make it impossible to see anything else 
  mutate(val = scale(val))

# Create a heatmap of the values per cluster
ggplot(data = k_res_long, aes(x = var, y = as.numeric(cluster), fill = val)) +
  geom_tile() +
  scale_y_continuous(breaks = seq(1, 7, by = 1)) +
  scale_fill_gradient2() +
  coord_equal(expand = F)

Version Author Date
99eda29 robwschlegel 2020-04-16

So that’s not very useful. The scale of the variables are rather different so I think we are going to need to go for scatterplots with ellipses showing the clustering. This may also be a useful application of a shiny app so that one may quickly go through all of the different combinations of Y vs X axes.

# Extract cluster info
ALL_mean_wide <- ALL_mean_wide %>% 
  mutate(cluster = k_res$cluster) 

# A scatterplot showing the assigned clusters
ggplot(data = ALL_mean_wide, aes(x = t2m, y = sss)) +
  geom_smooth(method = "lm") +
  geom_point(aes(colour = as.character(cluster), shape = region)) +
  ggforce::geom_mark_ellipse(aes(group = cluster, colour = as.character(cluster)))

Version Author Date
99eda29 robwschlegel 2020-04-16

In order to efficiently investigate all of these relationships these data should be fed into the shiny app. Regardless, after looking at this for a little bit it appears that there is no clear relationship between the clusters and the regions of occurrence of the MHWs. In fact, there appears to be very little clustering happening at all. I’m not sure how it is that the K-means results claim to explain 90% of the variance between groups when there appears to be no real difference between clusters. I think I need to have more of a think about how to reduce the dimensionality of these data and what exactly this k-means clustering method is doing/saying.

NMDS

Another option open to us is the use of non-metric multidimensional scaling (NMDS) to reduce the dimensionality in the data before performing a clustering. Thinking out loud now though I don’t think this is really necessary as the K-means algorithm above isn’t being pushed too much. But I’ve got the code just lying around so why not just pop it in there and see how it looks.

# The code for an NMDS analysis
ALL_mean_MDS <- metaMDS(vegdist(decostand(ALL_mean_wide[,-c(1:2)], method = "standardize"),
                                method = "euclidean"), try = 100)
Run 0 stress 0.2132493 
Run 1 stress 0.4176571 
Run 2 stress 0.2132428 
... New best solution
... Procrustes: rmse 0.001859736  max resid 0.01875967 
Run 3 stress 0.2132517 
... Procrustes: rmse 0.0006015007  max resid 0.007648459 
... Similar to previous best
Run 4 stress 0.2132583 
... Procrustes: rmse 0.001349996  max resid 0.01505539 
Run 5 stress 0.2138856 
Run 6 stress 0.2157486 
Run 7 stress 0.2151014 
Run 8 stress 0.2132509 
... Procrustes: rmse 0.0005757542  max resid 0.007202895 
... Similar to previous best
Run 9 stress 0.2138627 
Run 10 stress 0.213873 
Run 11 stress 0.2194757 
Run 12 stress 0.2132368 
... New best solution
... Procrustes: rmse 0.001376315  max resid 0.02063375 
Run 13 stress 0.2132458 
... Procrustes: rmse 0.001545518  max resid 0.02350355 
Run 14 stress 0.2151054 
Run 15 stress 0.2394474 
Run 16 stress 0.2196631 
Run 17 stress 0.2138745 
Run 18 stress 0.2156997 
Run 19 stress 0.2491919 
Run 20 stress 0.215084 
Run 21 stress 0.2214643 
Run 22 stress 0.2157033 
Run 23 stress 0.2213485 
Run 24 stress 0.2150825 
Run 25 stress 0.2138667 
Run 26 stress 0.2138929 
Run 27 stress 0.2132434 
... Procrustes: rmse 0.002582142  max resid 0.03487173 
Run 28 stress 0.21571 
Run 29 stress 0.2138832 
Run 30 stress 0.2157632 
Run 31 stress 0.2213175 
Run 32 stress 0.2138726 
Run 33 stress 0.2151527 
Run 34 stress 0.2150993 
Run 35 stress 0.2150867 
Run 36 stress 0.2132491 
... Procrustes: rmse 0.001487244  max resid 0.02099956 
Run 37 stress 0.21325 
... Procrustes: rmse 0.002077323  max resid 0.02583564 
Run 38 stress 0.2132406 
... Procrustes: rmse 0.002489677  max resid 0.03432218 
Run 39 stress 0.2151057 
Run 40 stress 0.2132381 
... Procrustes: rmse 0.0002400459  max resid 0.003355589 
... Similar to previous best
Run 41 stress 0.2369653 
Run 42 stress 0.2209695 
Run 43 stress 0.2202639 
Run 44 stress 0.2157601 
Run 45 stress 0.2132355 
... New best solution
... Procrustes: rmse 0.0004714176  max resid 0.005284649 
... Similar to previous best
Run 46 stress 0.221348 
Run 47 stress 0.2376108 
Run 48 stress 0.2215817 
Run 49 stress 0.2132456 
... Procrustes: rmse 0.001518405  max resid 0.02246817 
Run 50 stress 0.2132405 
... Procrustes: rmse 0.002363793  max resid 0.03269779 
Run 51 stress 0.2132607 
... Procrustes: rmse 0.0007328484  max resid 0.007237298 
... Similar to previous best
Run 52 stress 0.2132589 
... Procrustes: rmse 0.00181695  max resid 0.01810557 
Run 53 stress 0.2213675 
Run 54 stress 0.2157101 
Run 55 stress 0.2138703 
Run 56 stress 0.2146074 
Run 57 stress 0.2214572 
Run 58 stress 0.2151144 
Run 59 stress 0.2132473 
... Procrustes: rmse 0.0015219  max resid 0.02207271 
Run 60 stress 0.2342896 
Run 61 stress 0.2132415 
... Procrustes: rmse 0.002383193  max resid 0.03266069 
Run 62 stress 0.2151081 
Run 63 stress 0.2290111 
Run 64 stress 0.2132373 
... Procrustes: rmse 0.0004750876  max resid 0.004411598 
... Similar to previous best
Run 65 stress 0.2132636 
... Procrustes: rmse 0.002381171  max resid 0.02370774 
Run 66 stress 0.4176901 
Run 67 stress 0.2157103 
Run 68 stress 0.2409388 
Run 69 stress 0.2132449 
... Procrustes: rmse 0.001433844  max resid 0.01989819 
Run 70 stress 0.2138676 
Run 71 stress 0.2157298 
Run 72 stress 0.2150971 
Run 73 stress 0.2151096 
Run 74 stress 0.2213797 
Run 75 stress 0.2353764 
Run 76 stress 0.2198894 
Run 77 stress 0.2194868 
Run 78 stress 0.2138875 
Run 79 stress 0.2138892 
Run 80 stress 0.2221134 
Run 81 stress 0.2156991 
Run 82 stress 0.221347 
Run 83 stress 0.2437205 
Run 84 stress 0.2139238 
Run 85 stress 0.2150864 
Run 86 stress 0.2132433 
... Procrustes: rmse 0.001403583  max resid 0.02017026 
Run 87 stress 0.2157055 
Run 88 stress 0.2132415 
... Procrustes: rmse 0.002378864  max resid 0.03279467 
Run 89 stress 0.2140778 
Run 90 stress 0.2138856 
Run 91 stress 0.213889 
Run 92 stress 0.2394837 
Run 93 stress 0.2157035 
Run 94 stress 0.2150795 
Run 95 stress 0.2150863 
Run 96 stress 0.2322319 
Run 97 stress 0.2413702 
Run 98 stress 0.2191436 
Run 99 stress 0.2213802 
Run 100 stress 0.2417051 
*** Solution reached
# Fit environmental variables
ord_fit <- envfit(ALL_mean_MDS ~ region, data = ALL_mean_wide[,1:2])
ord_fit_df <- as.data.frame(ord_fit$factors$centroids) %>% 
  mutate(region = str_remove(row.names(.), "region"))

# Prep for plotting
mds_df <- data.frame(ALL_mean_MDS$points, ALL_mean_wide)

# The visual
ggplot(data = mds_df, aes(x = MDS1, y = MDS2)) +
  geom_point(aes(colour = region)) +
  geom_segment(data = ord_fit_df, aes(x = 0, y = 0, xend = NMDS1, yend = NMDS2),
               arrow = arrow(angle = 40, length = unit(0.2, "cm"), type = "open"), 
               alpha = 1, colour = "black", size = 0.5)  +
  geom_text(data = ord_fit_df, aes(label = region, x = NMDS1, y = NMDS2), size = 8) +
  theme_grey() +
  theme(strip.background = element_rect(fill = NA),
        panel.border = element_rect(fill = NA, colour = "black", size = 1),
        axis.text = element_text(size = 12, colour = "black"),
        axis.ticks = element_line(colour = "black"))

Version Author Date
99eda29 robwschlegel 2020-04-16

Meh. The analysis works but it shows that there is little difference between the regions. With the exception of the Scotian Shelf being a bit different than the Mid-Atlantic Bight. We could already see in the correlation results that the Scotian Shelf was a bit different, so these underwhelming results are at least consistent with the story thus far.

References


sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.6 LTS

Matrix products: default
BLAS:   /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/libopenblasp-r0.2.18.so

locale:
 [1] LC_CTYPE=en_CA.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_CA.UTF-8        LC_COLLATE=en_CA.UTF-8    
 [5] LC_MONETARY=en_CA.UTF-8    LC_MESSAGES=en_CA.UTF-8   
 [7] LC_PAPER=en_CA.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] vegan_2.5-6          lattice_0.20-35      permute_0.9-5       
 [4] ggraph_1.0.2         correlation_0.2.0    tidync_0.2.3        
 [7] heatwaveR_0.4.2.9001 lubridate_1.7.4      forcats_0.5.0       
[10] stringr_1.4.0        dplyr_0.8.4          purrr_0.3.3         
[13] readr_1.3.1          tidyr_1.0.2          tibble_2.1.3        
[16] ggplot2_3.2.1        tidyverse_1.3.0     

loaded via a namespace (and not attached):
 [1] nlme_3.1-137       fs_1.3.1           doParallel_1.0.15  insight_0.8.3     
 [5] httr_1.4.1         rprojroot_1.3-2    tools_3.6.3        backports_1.1.5   
 [9] R6_2.4.1           mgcv_1.8-24        DBI_1.0.0          lazyeval_0.2.2    
[13] colorspace_1.4-1   withr_2.1.2        tidyselect_1.0.0   gridExtra_2.3     
[17] compiler_3.6.3     git2r_0.26.1       cli_2.0.2          rvest_0.3.5       
[21] RNetCDF_2.1-1      xml2_1.2.2         plotly_4.9.2       labeling_0.3      
[25] bayestestR_0.6.0   scales_1.1.0       digest_0.6.25      rmarkdown_2.1     
[29] pkgconfig_2.0.3    htmltools_0.4.0    dbplyr_1.4.2       htmlwidgets_1.5.1 
[33] rlang_0.4.5        readxl_1.3.1       rstudioapi_0.11    generics_0.0.2    
[37] farver_2.0.3       jsonlite_1.6.1     magrittr_1.5       ncmeta_0.2.0      
[41] Matrix_1.2-14      parameters_0.6.1   Rcpp_1.0.3         munsell_0.5.0     
[45] fansi_0.4.1        viridis_0.5.1      lifecycle_0.1.0    stringi_1.4.6     
[49] whisker_0.4        yaml_2.2.1         MASS_7.3-50        plyr_1.8.5        
[53] grid_3.6.3         parallel_3.6.3     promises_1.1.0     ggrepel_0.8.1     
[57] crayon_1.3.4       haven_2.2.0        hms_0.5.3          knitr_1.28        
[61] pillar_1.4.3       igraph_1.2.2       effectsize_0.3.0   codetools_0.2-15  
[65] reprex_0.3.0       glue_1.3.1         evaluate_0.14      data.table_1.12.8 
[69] modelr_0.1.6       foreach_1.4.4      vctrs_0.2.3        tweenr_1.0.1      
[73] httpuv_1.5.2.9000  cellranger_1.1.0   gtable_0.3.0       polyclip_1.10-0   
[77] assertthat_0.2.1   xfun_0.12          ggforce_0.3.1.9000 broom_0.5.5       
[81] later_1.0.0        ncdf4_1.17         viridisLite_0.3.0  iterators_1.0.10  
[85] cluster_2.0.7-1    workflowr_1.6.0