Create new rmd for reporting

Author: EmmaCartuyvels1

source/reports/standardisation/standardisation.Rmd

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+---
+title: "Standardisation"
+author: "Emma Cartuyvels, Ward Langeraert, Toon Van Daele"
+date: "`r Sys.Date()`" 
+output:
+  html_document:
+    code_folding: hide
+    toc: true
+    toc_float: true
+    toc_collapsed: true
+editor_options: 
+  chunk_output_type: console
+---
+
+```{r setup, include = FALSE}
+library(knitr)
+opts_chunk$set(collapse = TRUE, comment = "#>")
+
+library(targets)
+Sys.setenv(TAR_PROJECT = "standardisation")
+
+library(ggplot2)
+library(ggpubr)
+library(dplyr)
+library(ggforce)
+library(crosstalk)
+library(DT)
+library(plotly)
+```
+
+```{r consistent colors}
+# Create a custom color scale
+library(RColorBrewer)
+my_colors <- brewer.pal(5, "Dark2")
+names(my_colors) <- c("Very rare", "Rare", "Common",
+                      "Very common", "Extremely common")
+col_scale <- scale_color_manual(name = "Category",
+                                values = my_colors)
+fill_scale <- scale_fill_manual(name = "Category",
+                                values = my_colors)
+```
+
+## Trend comparison {.tabset}
+
+### No filter
+```{r}
+selected_species <- c("Spinus spinus", "Dendrocoptes medius",
+                      "Pyrrhula pyrrhula")
+
+tar_read(trend_comp_0) |>
+  mutate(selected_species = ifelse(species %in% selected_species,
+                                   "yes", "no")) |> 
+  filter(id_spat_res == "1km",
+         time_period == "cyclus") |>
+  ggplot(aes(x = correlation, fill = category)) +
+  geom_histogram() +
+  xlim(-1, 1) +
+  fill_scale +
+  labs(x = "Correlation",
+       y = "Number of species")
+```
+
+
+### Standardized for total observations per cycle
+```{r}
+tar_read(trend_comp_3) |>
+  filter(id_spat_res == "1km",
+         time_period == "cyclus",
+         id_filter_per == "cyclus") |>
+  ggplot(aes(x = correlation, fill = category)) +
+  geom_histogram() +
+  xlim(-1, 1) +
+  fill_scale +
+  labs(x = "Correlation",
+       y = "Number of species")
+
+```
+
+### Standardized for order
+```{r}
+tar_read(trend_comp_order) |>
+  filter(id_spat_res == "1km",
+         time_period == "cyclus") |>
+  ggplot(aes(x = correlation, fill = category)) +
+  geom_histogram() +
+  xlim(-1, 1) +
+  fill_scale +
+  labs(x = "Correlation",
+       y = "Number of species")
+```
+
+### Standardized for family
+```{r}
+tar_read(trend_comp_family) |>
+  filter(id_spat_res == "1km",
+         time_period == "cyclus") |>
+  ggplot(aes(x = correlation, fill = category)) +
+  geom_histogram() +
+  xlim(-1, 1) +
+  fill_scale +
+  labs(x = "Correlation",
+       y = "Number of species")
+```
+
+### Standardized for genus
+```{r}
+tar_read(trend_comp_genus) |>
+  filter(id_spat_res == "1km",
+         time_period == "cyclus") |>
+  ggplot(aes(x = correlation, fill = category)) +
+  geom_histogram() +
+  xlim(-1, 1) +
+  fill_scale +
+  labs(x = "Correlation",
+       y = "Number of species")
+```
+
+
+
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