😐 LDA in R (capitulation)

Author: TanyaS08

code/Topology.R

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+# libraries
+library(ggpubr)
+library(here)
+library(effectsize)
+library(ggrepel)
+library(ggtext)
+library(MASS)
+library(patchwork)
+library(rstatix)
+library(tidyverse)
+library(vegan)
+
+# set path to code sub dir
+setwd(here())
+
+# import data
+
+df <- read_csv("data/outputs/topology.csv") %>%
+  dplyr::select(-c(richness))
+
+dep_vars <- as.matrix(df[2:ncol(df)])
+
+
+fit <- manova(dep_vars ~ model, data = df)
+summary(fit)
+
+#get effect size
+effectsize::eta_squared(fit)
+
+post_hoc <- lda(model~., df)
+post_hoc
+
+# plot 
+plot_lda <- data.frame(model = df$model,
+                       lda = predict(post_hoc)$x)
+
+plot_arrow <- as.data.frame(post_hoc[["scaling"]]) %>%
+  mutate(var = str_replace(row.names(.), "dep_vars", ""),
+         lda.LD1 = scale(LD1),
+         lda.LD2 = scale(LD2))
+
+ggplot(plot_lda) + 
+  geom_point(aes(x = lda.LD1, 
+                 y = lda.LD2, 
+                 colour = model), 
+             size = 3,
+             alpha = 0.3) +
+  #=  geom_segment(data = plot_arrow,
+  #=               aes(x = 0,
+  #=                   y = 0,
+  #=                   xend = lda.LD1,
+  #=                   yend = lda.LD2)) +
+  #=  geom_text_repel(data = plot_arrow,
+  #=                  aes(label = var,
+  #=                      x = lda.LD1,
+  #=                      y = lda.LD2),
+  #=                  max.overlaps = getOption("ggrepel.max.overlaps", default = 100)) +
+  coord_cartesian(clip = "off") +
+  guides(color = guide_legend(override.aes = list(alpha = 1))) +
+  labs(x = "LDA 1",
+       y = "LDA 2") +
+  theme_classic() +
+  theme(panel.border = element_rect(colour = 'black',
+                                    fill = "#ffffff00"),
+        panel.grid.minor = element_blank(),
+        panel.grid.major.x = element_blank(),
+        axis.line = element_blank(),
+        axis.ticks = element_line(colour = colorspace::darken("#dddddd", 0.1),
+                                  linewidth = 0.3),
+        plot.background = element_rect(fill = "white", colour = NA),
+        panel.background = element_rect(fill = "white", colour = NA),
+        legend.background = element_rect(fill = "white", colour = NA),
+        legend.key = element_blank(),
+        text = element_text(color = "#5e5e5e"),
+        plot.margin = margin(10, 5, 5, 10),
+        legend.margin = margin(1, 2, 1, 2)
+  )
+
+ggsave("../figures/lda.png",
+       width = 5000,
+       height = 4000,
+       units = "px",
+       dpi = 700)

code/code.Rproj

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+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX