Theory, R functions & Examples
Section: Ordination analysis
In this example, we will apply constrained ordination (tb-RDA) on Vltava river valley dataset. We will ask how much variance in species composition can be explained by two variables, soil pH and soil depth. Both are important factors for plant growth, and moreover, in the study area, they are somewhat correlated (shallower soils have lower pH since the prevailing geological substrate is acid).
First, upload the Vltava river valley data:
vltava.spe <- read.delim ('https://raw.githubusercontent.com/zdealveindy/anadat-r/master/data/vltava-spe.txt', row.names = 1) vltava.env <- read.delim ('https://raw.githubusercontent.com/zdealveindy/anadat-r/master/data/vltava-env.txt') spe <- vltava.spe # rename variables to make them shorter env <- vltava.env[, c('pH', 'SOILDPT')] # select only two explanatory variables
vegan and calculate tb-RDA based on Hellinger pre-transformed species composition data. Note that since the original data represent estimates of percentage cover, it is better to log transform these values first before Hellinger transformation is done (using function
log1p, which calculates log (x+1) to avoid log (0)):
library (vegan) spe.log <- log1p (spe) # species data are in percentage scale which is strongly rightskewed, better to transform them spe.hell <- decostand (spe.log, 'hell') # we are planning to do tb-RDA, this is Hellinger pre-transformation tbRDA <- rda (spe.hell ~ pH + SOILDPT, data = env) # calculate tb-RDA with two explanatory variables tbRDA
The result printed by
rda function is the following:
Call: rda(formula = spe.hell ~ pH + SOILDPT, data = env) Inertia Proportion Rank Total 0.70476 1.00000 Constrained 0.06250 0.08869 2 Unconstrained 0.64226 0.91131 94 Inertia is variance Eigenvalues for constrained axes: RDA1 RDA2 0.04023 0.02227 Eigenvalues for unconstrained axes: PC1 PC2 PC3 PC4 PC5 PC6 PC7 PC8 0.07321 0.04857 0.04074 0.03144 0.02604 0.02152 0.01917 0.01715 (Showed only 8 of all 94 unconstrained eigenvalues)
and, the same with comments:
The two variables explain 8.9% of the variance (the row
Constrained and column
Proportion in the table above, can be calculated also as the sum of eigenvalues for the constrained axes divided by total variance (inertia): (0.04023+0.02227) /0.70476=0.08869. The first constrained axis (RDA1) explains 0.04023/0.70476=5.7% of the variance, while the second (RDA2) explains 0.02227/0.70476=3.2%. Note that the first unconstrained axis (PC1) represents 0.07321/0.70476=10.4% of the total variance, which is more than the variance explained by both explanatory variables together; the first two unconstrained explain (0.07321+0.04857)/0.70476=17.3%. This means that the dataset may be structured by some strong environmental variable(s) different from pH and soil depth (we will check this below).
The relationship between the variation represented by individual (constrained and unconstrained) ordination axes can be displayed using the barplot of percentage variance explained by individual axes (ie their eigenvalue divided by total inertia):
constrained_eig <- tbRDA$CCA$eig/tbRDA$tot.chi*100 unconstrained_eig <- tbRDA$CA$eig/tbRDA$tot.chi*100 expl_var <- c(constrained_eig, unconstrained_eig) barplot (expl_var[1:20], col = c(rep ('red', length (constrained_eig)), rep ('black', length (unconstrained_eig))), las = 2, ylab = '% variation')
(note that all information about the eigenvalues and total inertia is in the object calculated by
vegan's ordination function (
rda in this case, stored in the list
tbRDA), you just need to search a bit inside to find it - consider using the function
str to check the structure of tbRDA first).
Let's see the ordination diagram:
This example is a direct continuation of Example 1 above.
When checking results of tb-RDA on Vltava data, calculated in Example 1 using tb-RDA, one may notice that the first and second unconstrained ordination axes represent considerably more variation than the two constrained axes:
vltava.spe <- read.delim ('https://raw.githubusercontent.com/zdealveindy/anadat-r/master/data/vltava-spe.txt', row.names = 1) vltava.env <- read.delim ('https://raw.githubusercontent.com/zdealveindy/anadat-r/master/data/vltava-env.txt') spe <- vltava.spe # rename variables to make them shorter env <- vltava.env[, c('pH', 'SOILDPT')] # select only two explanatory variables library (vegan) spe.log <- log1p (spe) spe.log.hell <- decostand (spe.log, 'hell') tbRDA <- rda (spe.log.hell ~ pH + SOILDPT, data = env) head (summary (tbRDA)) # prints first lines of the summary of tbRDA
Call: rda(formula = spe.log.hell ~ pH + SOILDPT, data = env) Partitioning of variance: Inertia Proportion Total 0.7048 1.00000 Constrained 0.0625 0.08869 Unconstrained 0.6423 0.91131 Eigenvalues, and their contribution to the variance Importance of components: RDA1 RDA2 PC1 PC2 PC3 PC4 PC5 PC6 Eigenvalue 0.04023 0.02227 0.07321 0.04857 0.04074 0.03144 0.02604 0.02152 Proportion Explained 0.05709 0.03160 0.10388 0.06891 0.05781 0.04461 0.03695 0.03054 Cumulative Proportion 0.05709 0.08869 0.19257 0.26149 0.31929 0.36391 0.40086 0.43139 ...
From the output above, you can see (rows “Proportion Explained” that the first and the second constrained axes (RDA1, RDA2), explain 5.7 and 3.1% of the variation, respectively, while the first and second unconstrained axes (PC1, PC2) represent 10.4 and 6.9% of the variation, respectively. This indicates that after accounting for soil pH and soil depth (the two variables used as explanatory), there is still quite a considerable variation in species composition left, possibly calling for interpretation.
One thing we can do is to create an ordination diagram with the first and second unconstrained ordination axis (PC1, PC2), and project species into it, and hope that they can help us to understand what environmental variables may be behind these gradients. Of course, this expects that you have at least marginal knowledge about the ecological behaviour of these species (I think I do, since I spent several years working on the vegetation of these valleys, so let's try).
ordiplot (tbRDA, display = 'species', choices = c(3,4), type = 'n') orditorp (tbRDA, display = 'species', choices = c(3,4), pcol = 'grey', pch = '+')
There is 274 species in the Vltava dataset, so I used
orditorp function to draw only some of them (see Ordination diagrams > Examples for details on how to use this function). Also, since RDA is a linear function, the species should be displayed by vectors, not as centroids, but if we want to display only some of the species, this option in R is not so simple (you may need to use
envfit function to project vectors of species onto the ordination diagram). Species are displayed by their abbreviation, where the first four letters are from the genus name, the last four letters from species name, and the numbers indicate the layer (1 for herb layer, 23 for merged shrub and tree layer; for example,
Tilicor23 is an abbreviation of Tilia cordata in shrub and tree layer).
When interpreting the first (horizontal) unconstrained axis (PC1), we can see that the left part (negative scores) is related to high abundances of Quercus petraea (
Querpet23) and Pinus sylvestris (
Pinusyl23) in the shrub and tree layer, and Avenella flexuosa in the herb layer (
Avefle1), while the right part (positive scores) is related to high abundances of Abies alba in shrub and tree layer (
Abiealb23), and Dryopteris filix-mas (
Dryofil1), Galeobdolon montanum (
Galemon1) and Lunaria rediviva (
Lunared1) in the herb layer. These species seem to indicate opposite ends of the gradient of light (light-demanding species on the left, shade-tolerant on the right) and nutrient availability (nutrient demanding species on the right, and species of oligotrophic site on the right). When interpreting the second (vertical) unconstrained axis (PC2), the lower part (negative scores) is related to high abundances of Impatiens glandulifera (
Impagla1), Lycopus europaeus (
Lycoeur1) and Aegopodium podagrarium (
Aegopod1) in the herb layer, while the upper part (positive scores) are related to high abundances of Tilia cordata (
Tilicor23) and Fagus sylvatica (
Fagusyl23) in the shrub and tree layer, and Poa nemoralis (
Poa.nem1), Luzula luzuloides (
Luzuluz1) and Convalaria majalis (
Convmaj1) in the herb layer; this axis seem to negatively correlate with the gradient of moisture, with species indicating wet soil of the alluvial forest at the lower part of the axis and mesic species in the upper part.
If we are not familiar with ecological requirements of the species, but have their tabulated Ellenberg-type indicator values in hand (usually for soil pH, moisture, nutrients, air temperature, light availability and continentality), we can use them to calculate mean indicator values for each plot, representing their estimated ecological conditions. Vltava dataset (
vltava.env) includes such calculated mEIV (mean Ellenberg indicator values), and these can be used as supplementary in the ordination diagram of the first and second unconstrained ordination axes:
ordiplot (tbRDA, choices = c(3,4), type = 'n') points (tbRDA, choices = c(3,4), display = 'sites', pch = as.character (vltava.env$GROUP), col = vltava.env$GROUP) ef <- envfit (tbRDA, vltava.env[,23:28], choices = c(3,4), permutations = 0) plot (ef)
***VECTORS PC1 PC2 r2 LIGHT -0.93135 -0.36411 0.6282 TEMP -0.97246 -0.23305 0.2352 CONT -0.86643 -0.49929 0.0885 MOIST 0.44495 -0.89556 0.4706 REACT 0.95614 -0.29291 0.1166 NUTR 0.94383 -0.33044 0.4519
The highest R2 of the regression with the first two axes have light, moisture and nutrients, with light and nutrients associated mostly with the first unconstrained axis and the moisture mostly with the second. It seems that these ecological factors, not related to soil pH and soil depth, are important for the studied vegetation, but were not measured. This interpretation fits well with the interpretation based on the relationship between axes and abundances of species listed above.
Note one more thing: when applying the function
envfit on mean Ellenberg indicator values, I did not test for the significance (I set the argument
permutation = 0). This has a meaning: both mean Ellenberg indicator values and sample scores on ordination axes are calculated from the same matrix of species composition, and to directly test their relationship would be wrong (since they are not independent, it is easy to reject the null hypothesis stating that these variables are independent). Check the section Analysis of species attributes for a detailed explanation on how to solve this.
This example is using Difference between cookies, pastries and pizzas dataset, which I found on reddit.com, posted by author everest4ever. As the post on reddit.com goes, the author attended the Christmas party at his office with “Christmas cookie competition”, which sparked a “huge debate about what are eligible entries for the cookie competition (e.g. are mini-pizzas cookies?)”. The author decided to approach the discussion rigorously and did the following: “I scraped 1931 recipes from the Food Network that contain the keywords cookies (my group of interest), pastry, or pizza (two control groups). Next, I extracted the ingredient list and pooled similar ingredients together (e.g. salt, seasalt, Kosher salt), coming up with a total of 133 unique ingredients. I ended up with a 1931×133 matrix, where each row is one recipe, and each column is whether this recipe contains a certain ingredient (0 or 1)”. The author did PCA analysis on the data accompanied by some clustering and predictions, just to prove that “NO IAN AND JOSEPH YOUR FUCKING EGG TARTS AREN'T COOKIES, NO MATTER HOW GOOD THEY WERE!!”. I think we can also use this dataset for a simple constrained ordination exercise. First import the data:
recipes.ingr <- read.delim ('https://raw.githubusercontent.com/zdealveindy/anadat-r/master/data/cookie_dataset_everest4ever_composition.txt', row.names = 1) recipes.type <- read.delim ('https://raw.githubusercontent.com/zdealveindy/anadat-r/master/data/cookie_dataset_everest4ever_type.txt', row.names = 1)
Data represent a matrix of presence/absence of different ingredients in individual recipes (each row of
recipes.ingr matrix is a recipe, each column one ingredients). To know which recipe is classified how, we need a variable
type_of_food in the data frame
To get familiar with data, let's first calculate DCA:
library (vegan) DCA <- decorana (recipes.ingr) DCA
Call: decorana(veg = recipes.ingr) Detrended correspondence analysis with 26 segments. Rescaling of axes with 4 iterations. DCA1 DCA2 DCA3 DCA4 Eigenvalues 0.5633 0.2598 0.2224 0.2185 Decorana values 0.5918 0.2622 0.2352 0.2138 Axis lengths 6.2276 4.1302 5.6396 3.5449
The output shows that the length of the first axis is 6.2 S.D. units, so unimodal ordination methods is advisable. The ordination diagram which displays recipes of cookies, pastries and pizzas by different symbols and colours, is more informative:
type_num <- as.numeric (recipes.type$type_of_food) ordiplot (DCA, type = 'n') points (DCA, display = 'sites', col = type_num, pch = type_num) legend ('topright', col = 1:3, pch = 1:3, legend = levels (recipes.type$type_of_food))
type_num contains numerical values 1, 2 and 3 in place of Cookies, Pastries and Pizzas from the original
type_of_food variable in
recipes.type data frame, so as we can use these values as colors and symbols in ordination diagram).
It seems that pizzas are somewhat different from the rest (although part of pastries is close), while pastries and cookies form a cloud with big overlap. Let's try to ask the following question: can the classification of a recipe into cookies/pastries/pizzas (done largely subjectively by authors of that recipes based on their opinion how each category item should look like) explain the difference in “ingredients composition” of individual recipes? This is task for constrained ordination. Since the first DCA axis is long, we use CCA for it, with recipes dependent variable and assignment into the type as explanatory. Note that explanatory variable is categorical with three levels (
type <- recipes.type$type_of_food CCA <- cca (recipes.ingr ~ type) CCA
Call: cca(formula = recipes.ingr ~ type) Inertia Proportion Rank Total 14.28961 1.00000 Constrained 0.60311 0.04221 2 Unconstrained 13.68650 0.95779 132 Inertia is scaled Chi-square Eigenvalues for constrained axes: CCA1 CCA2 0.4649 0.1382 Eigenvalues for unconstrained axes: CA1 CA2 CA3 CA4 CA5 CA6 CA7 CA8 0.30447 0.28409 0.26249 0.25278 0.23942 0.21521 0.21069 0.20674 (Showed only 8 of all 132 unconstrained eigenvalues)
(note that I saved the column
type_of_food from the data frame
recipes.type into a variable
type, not really because I want to simplify the
cca (it would need to be
CCA <- cca (recipes.ingr ~ type_of_food, data = recipes.type), but that is still fine), but because this will make it simple to display individual factor levels onto ordination diagram (the levels are displayed as the Name_of_variableName_of_category, which would be too long with the original names).
We got two constrained axes (explanatory variable is qualitative with three factor levels -> number of contrained axes = number of levels - 1), the first exlaining more than 3 time more than the second (eigCCA1 = 0.4649, eigCCA2 = 0.1382, which means that the first axis represents 0.4649/14.28961 = 3.3 % of variance (eigenvalue/total inertia), while the second 0.1382/14.28961 = 1.0%. Ordination diagram shows that the first axis is mostly separating pizzas (right) and cookies+pastries (left), while the second axis is mostly separating cookies (up) from pastries (bottom):
ordiplot (CCA, display = c('si', 'cn'), type = 'n') points (CCA, display = 'si', col = type_num, pch = type_num) text (CCA, display = 'cn', col = 'navy', cex = 1.5) legend ('topright', col = 1:3, pch = 1:3, legend = levels (recipes.type$type_of_food))
Few more things. First, we should ask whether the CCA ordination is significant and whether it is worth to interpret it:
Permutation test for cca under reduced model Permutation: free Number of permutations: 999 Model: cca(formula = recipes.ingr ~ type) Df ChiSquare F Pr(>F) Model 2 0.6031 42.479 0.001 *** Residual 1928 13.6865 --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Indeed, it is. And how about individual axes, are they both significant? We will use the argument
by = “axis” in the function
anova - see this explanation what it means:
Permutation test for cca under reduced model Forward tests for axes Permutation: free Number of permutations: 999 Model: cca(formula = recipes.ingr ~ type) Df ChiSquare F Pr(>F) CCA1 1 0.4649 65.493 0.001 *** CCA2 1 0.1382 19.465 0.001 *** Residual 1928 13.6865 --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Both axes are significant, which means that even the distinction between cookies and pastries along the second axis is important. So I would say, without further testing, that not only pizza is (quite obviously) different from cookies, but also much more ambiguous category pastries are different regarding ingredients they use. Btw, let's see these ingredients (display species in CCA ordination diagram):
ordiplot (CCA, display = c('sp', 'cn'), type = 'n') orditorp (CCA, display = 'sp', priority = colSums (recipes.ingr))
Note that I did not display all 133 ingredients (“species”); otherwise the diagram gets too cluttered. I used the low-level graphical function
orditorp which is adding only some labels and draws others as symbols. It has argument
priority (the species with the highest priority will be more likely plotted as text, with lower as symbols, if there is not enough space); the priority here is the overall frequency of ingredence in the dataset (
colSums applied on the
recipes.ingr data frame). The diagram shows clear triangle, with each corner representing one type of food. There is a gradient of ingredients connecting pizzas with pastries and pastries with cookies, but almost no ingredients connecting pizzas and cookies (except
pine nuts, which can perhaps make it in both pizzas and cookies - but I have no idea). Some ingredients are shared among all three (obviously water and seems that also honey), some are only for that type of food (basil for pizza, puff pastry for pastries and cookies(??) and ice cream for cookies. Please, see the diagram and guess which item in your opinion should be where (carrots in pastry? not sure...).