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T1_1 T1_2 T1_3 T1_4 T1_5 T1_6 T2_1 T2_2 T2_3 T2_4 T2_5 T2_6 T2_7 T2_8 T2_9 T2_10 T2_11 T2_12 T2_13 | |
S01 99 100 100 98 100 100 100 100 100 100 93 100 100 100 100 99 100 97 100 | |
S02 100 100 100 99 100 100 100 100 100 100 100 100 100 100 99 100 100 100 27 | |
S03 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 0 | |
S04 100 100 100 99 100 100 100 100 99 92 100 96 100 100 100 100 100 100 0 | |
S05 100 100 100 98 100 100 100 96 97 93 100 100 98 98 100 90 100 98 0 | |
S06 100 100 100 100 100 100 100 99 99 99 100 97 100 100 99 80 98 96 0 | |
S07 100 100 100 100 100 100 100 100 100 100 100 98 100 100 100 0 100 100 38 | |
S08 100 100 100 98 100 100 99 100 100 57 100 100 100 100 100 62 100 97 0 | |
S09 100 100 99 0 100 100 100 100 100 100 100 100 100 100 100 100 100 100 12 |
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CK_1 CK_2 CK_3 CK_4 CK_5 CK_6 DA_1 DA_2 DA_3 DA_4 DA_5 DA_6 DA_7 DA_8 DA_9 DA_10 DA_11 DA_12 DA_13 | |
b09b01019 99 100 100 98 100 100 100 100 100 100 93 100 100 100 100 99 100 97 100 | |
b07605051 100 100 100 99 100 100 100 100 100 100 100 100 100 100 99 100 100 100 27 | |
b07208023 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 0 | |
b06608068 100 100 100 99 100 100 100 100 99 92 100 96 100 100 100 100 100 100 0 | |
b07b01004 100 100 100 98 100 100 100 96 97 93 100 100 98 98 100 90 100 98 0 | |
b09b01023 100 100 100 100 100 100 100 99 99 99 100 97 100 100 99 80 98 96 0 | |
b09b01013 100 100 100 100 100 100 100 100 100 100 100 98 100 100 100 0 100 100 38 | |
b09b01007 100 100 100 98 100 100 99 100 100 57 100 100 100 100 100 62 100 97 0 | |
b08b01012 100 100 99 0 100 100 100 100 100 100 100 100 100 100 100 100 100 100 12 |
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scale_override <- function(which, scale) { | |
if(!is.numeric(which) || (length(which) != 1) || (which %% 1 != 0)) { | |
stop("which must be an integer of length 1") | |
} | |
if(is.null(scale$aesthetics) || !any(c("x", "y") %in% scale$aesthetics)) { | |
stop("scale must be an x or y position scale") | |
} | |
structure(list(which = which, scale = scale), class = "scale_override") |
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# Individual examples | |
# 1) Both w1 and w2 similarly related to y | |
set.seed (1234) | |
# Generate two random variables N(0,1) | |
x1 <- rnorm (100, 0, 1) | |
x2 <- rnorm (100, 0, 1) | |
X <- cbind (x1, x2) | |
# Generate correlation matrix to make variables correlated at r = 0.8 | |
R <- matrix (c(sqrt (.8), sqrt (.2), sqrt (0.2), sqrt (.8)), ncol = 2) | |
W <- X%*%R |
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# Hellinger distance | |
library (vegan) | |
png (width = 6, height = 6, units = 'in', res = 300) | |
par (mar = c(5,5,2,2)) | |
plot (0:1, 0:1, xlab = list ('Species 1', cex = 1.5), ylab = list ('Species 2', cex = 1.5), axes = F, xlim = c(0, 1.3), ylim = c(0,1.3), type = 'n') | |
par (xpd = NA) | |
arrows (x0 = 0, x1 = 1.3, y0 = 0, y1 = 0) | |
arrows (x0 = 0, x1 = 0, y0 = 0, y1 = 1.3) |
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# Euclidean vs Hellinger vs Bray-Curtis distances and double zero problem | |
library (vegan) | |
library (pals) | |
vltava.spe <- read.delim ('https://raw.githubusercontent.com/zdealveindy/anadat-r/master/data/vltava-spe.txt', row.names = 1) | |
prop_dz <- function (com) | |
(nrow (com)-designdist (x = com, method = "A+B-J", terms = "binary"))/nrow (com) # calculates proportion of double zeros | |
D_eucl <- dist (vltava.spe, method = 'euclidean') | |
D_hell <- dist (decostand (vltava.spe, method = 'hell'), method = 'euclidean') |
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# Diversity along elevation gradient - pseudoreplication issue | |
# Elevation 200-1000 m asl, five elevation zones | |
# Richness (number of species) between 1-100 species | |
seed <- 56654 | |
par (mfrow = c(2,2)) | |
# Scenario 1: 5 replicate at each zone, each replicate at different mountain (random diversity) |
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# Pseudoreplication issue | |
# 1600 quadrats sampled in 8 grids (each grid 200 quadrats) | |
# what happens if we consider quadrats as independent units? | |
DEP <- rnorm (1600) | |
EXP <- rnorm (1600) | |
GRID <- rep (1:8, each = 200) | |
boxplot (DEP ~ GRID) |
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# Mia Momberg - reanalysis of JEcol dataset | |
# importing libraries | |
library (readxl) | |
library (tidyverse) | |
library (modEvA) | |
library (car) | |
# importing data from Dryad repository | |
url <- 'https://datadryad.org/stash/downloads/file_stream/573456' |
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species WSG_obs WSG_data source | |
1 Acacia 0.539 0.9 a | |
2 Adansonia 0.21 0.5 b | |
3 Albizia 0.581 0.69 a | |
4 Azadirachta 0.521 0.7 a | |
5 Bauhinia 0.469 0.619 c | |
6 Bombax 0.335 0.27 d | |
7 Bridelia 0.557 0.62 e | |
8 Butea 0.377 0.465 c | |
9 Cassia 0.665 0.746 c |
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