--- title: "Body Size Changes in Northeast Shelf Finfish Community" author: name: "Adam A. Kemberling" title: "Quantitative Research Associate" url: https://github.com/adamkemberling affiliation: Gulf of Maine Research Institute description: | Changes in Mean/Median Length and Weight of 68 Finfish Species date: "`r Sys.Date()`" format: html: self-contained: true code-fold: true code-tools: true df-print: kable toc: true toc-depth: 2 editor: source execute: echo: false warning: false message: false fig-height: 8 fig-width: 7 fig.align: center comment: "" --- # Foundational Understanding Check: Has Body Size Changed ## Changes to Median body-size # Use Crosstalk instead of tab nesting ```{r} library (crosstalk)library (plotly)library (targets)library (gmRi)library (tidyverse)library (patchwork)library (showtext)# levels for faceting areas <- c ("Northeast Shelf" , "GoM" , "GB" , "SNE" , "MAB" )<- c ("Northeast Shelf" , "Gulf of Maine" , "Georges Bank" , "Southern New England" , "Mid-Atlantic Bight" )# table to join for swapping shorthand for long-hand names <- data.frame (area = c ("Scotian Shelf" , "Gulf of Maine" , "Georges Bank" , "Southern New England" , "Mid-Atlantic Bight" , "All" ),survey_area = c ("SS" , "GoM" , "GB" , "SNE" , "MAB" , "Northeast Shelf" ),area_titles = c ("Scotian Shelf" , "Gulf of Maine" , "Georges Bank" , "Southern New England" , "Mid-Atlantic Bight" , "Northeast Shelf" ))# Load the average body size data :: with_dir (rprojroot:: find_root ('_targets.R' ), tar_load (mean_sizes_ss_groups)) # 1. Overall Body Sizes Across all regions <- mean_sizes_ss_groups %>% filter (` group ID ` == "single years" ) %>% mutate (Year = as.numeric (Year),survey_area = "Northeast Shelf" )# 2. Grouped on year and region <- mean_sizes_ss_groups %>% filter (` group ID ` == "single years * region" ) %>% mutate (Year = as.numeric (Year),survey_area = as.character (survey_area)) %>% left_join (area_df) %>% mutate (area_titles = factor (area_titles, levels = area_levels_long),area_copy = survey_area)# 3. Grouped on year region and functional group sizes <- mean_sizes_ss_groups %>% filter (` group ID ` == "single years * region * functional group" ) %>% mutate (Year = as.numeric (Year)) %>% left_join (area_df) %>% mutate (survey_area = factor (survey_area, levels = area_levels),area_titles = factor (area_titles, levels = area_levels_long),area_copy = survey_area)# GGplot theme theme_set (theme_gmri () + theme (panel.grid.major = element_line (linewidth = 0.5 , linetype = 1 , color = "gray" ),panel.grid.major.x = element_line (linewidth = 0.5 , linetype = 3 , color = "gray" ),panel.grid.minor = element_line (linewidth = 0.5 , linetype = 3 , color = "gray90" ),axis.line = element_line (color = "black" ),axis.line.y = element_line (color = "black" ), strip.background = element_rect (colour = gmri_cols ("teal" )),legend.position = "bottom" ))``` ```{r} #| label: style-sheet #| results: asis # Use GMRI style use_gmri_style_rmd ()``` ```{r} #| label: fonts-config #| echo: false # # Using Raleway Font because it works # sysfonts::font_add_google("Raleway") # Path to the directory containing the font file (replace with your actual path) <- paste0 (system.file ("stylesheets" , package = "gmRi" ), "/GMRI_fonts/Avenir/" )# Register the font font_add (family = "Avenir" ,file.path (font_dir, "LTe50342.ttf" ),bold = file.path (font_dir, "LTe50340.ttf" ),italic = file.path (font_dir, "LTe50343.ttf" ),bolditalic = file.path (font_dir, "LTe50347.ttf" ))# Why is the gt package able to add it wtf!! # google_font(name = "Avenir") # Load the font :: showtext_auto ()``` # Examining Body Size Changes ## Overall Body Size Changes ### Shelf-Wide ```{r} #| label: shelf-body-size-change <- shelf_size<- size_df %>% ggplot (aes (Year, mean_len_cm)) + geom_line (color = "gray60" , alpha = 0.3 , linewidth = 1 ) + geom_point (size = 1.2 ) + facet_wrap (~ survey_area) + labs (x = "Year" , y = "Average Length (cm)" , title = "Average Length" )<- size_df %>% ggplot (aes (Year, med_wt_kg)) + geom_line (color = "gray60" , alpha = 0.3 , linewidth = 1 ) + geom_point (size = 1.2 ) + facet_wrap (~ survey_area) + labs (x = "Year" , y = "Average Weight (kg)" , title = "Average Weight" )<- size_df %>% ggplot (aes (Year, mean_len_cm)) + geom_line (color = "gray60" , alpha = 0.3 , linewidth = 1 ) + geom_point (size = 1.2 ) + facet_wrap (~ survey_area) + labs (x = "Year" , y = "Median Length (cm)" , title = "Median Length" )<- size_df %>% ggplot (aes (Year, med_wt_kg)) + geom_line (color = "gray60" , alpha = 0.3 , linewidth = 1 ) + geom_point (size = 1.2 ) + facet_wrap (~ survey_area) + labs (x = "Year" , y = "Median Weight (kg)" , title = "Median Weight" )| w1) / (l2 | w2)``` ### Regional Lengths ```{r} #| label: regional-body-length-change <- regional_size<- size_df %>% ggplot (aes (Year, mean_len_cm)) + geom_line (color = "gray60" , alpha = 0.3 , linewidth = 1 ) + geom_point (size = 1.2 ) + facet_wrap (~ survey_area) + labs (x = "Year" , y = "Average Length (cm)" , title = "Average Length" )<- size_df %>% ggplot (aes (Year, med_len_cm)) + geom_line (color = "gray60" , alpha = 0.3 , linewidth = 1 ) + geom_point (size = 1.2 ) + facet_wrap (~ survey_area) + labs (x = "Year" , y = "Median Length (cm)" , title = "Median Length" )/ l2 ``` ### Regional Weights ```{r} #| label: regional-body-weight-change <- regional_size<- size_df %>% ggplot (aes (Year, mean_wt_kg)) + geom_line (color = "gray60" , alpha = 0.3 , linewidth = 1 ) + geom_point (size = 1.2 ) + facet_wrap (~ survey_area) + labs (x = "Year" , y = "Average Weight (kg)" , title = "Average Weight" )<- size_df %>% ggplot (aes (Year, med_wt_kg)) + geom_line (color = "gray60" , alpha = 0.3 , linewidth = 1 ) + geom_point (size = 1.2 ) + facet_wrap (~ survey_area) + labs (x = "Year" , y = "Median Weight (kg)" , title = "Median Weight" )/ w2``` ### Functional Group Lengths ```{r} <- fgroup_size# l1 <- size_df %>% # ggplot(aes(Year, mean_len_cm)) + # geom_line(color = "gray60", alpha = 0.3, linewidth = 1) + # geom_point(size = 1.2, alpha = 0.8) + # facet_grid(hare_group~survey_area, scales = "free") + # labs(x = "Year", y = "Average Length (cm)", title = "Average Length") <- size_df %>% ggplot (aes (Year, med_len_cm)) + geom_line (color = "gray60" , alpha = 0.3 , linewidth = 1 ) + geom_point (size = 1.2 , alpha = 0.8 ) + facet_grid (hare_group~ survey_area, scales = "free" ) + labs (x = "Year" , y = "Median Length (cm)" , title = "Median Length" )# l1 | l2 ``` ### Functional Group Weights ```{r} #| fig-height: 8 <- fgroup_size# w1 <- size_df %>% # ggplot(aes(Year, mean_wt_kg)) + # geom_line(color = "gray60", alpha = 0.3, linewidth = 1) + # geom_point(size = 1.2, alpha = 0.8) + # facet_grid(hare_group~survey_area, scales = "free") + # labs(x = "Year", y = "Average Weight (kg)", # title = "Average Weight") <- size_df %>% ggplot (aes (Year, med_wt_kg)) + geom_line (color = "gray60" , alpha = 0.3 , linewidth = 1 ) + geom_point (size = 1.2 , alpha = 0.8 ) + facet_grid (hare_group~ survey_area, scales = "free" ) + labs (x = "Year" , y = "Median Weight (kg)" , title = "Median Weight" )# w1 | w2 ``` # Examining Body Size Changes ## Average Length ```{r} #| label: crosstalk-test <- crosstalk:: SharedData$ new (bind_rows (select (shelf_size, survey_area, Year, med_len_cm, med_wt_kg, mean_len_cm, mean_wt_kg),select (regional_size, survey_area, Year, med_len_cm, med_wt_kg, mean_len_cm, mean_wt_kg)# Make Median Length Plot <- shared_data %>% :: plot_ly (y = ~ mean_len_cm, x = ~ Year, color = ~ survey_area) %>% add_lines () %>% layout (title = 'Mean Length Change' , plot_bgcolor = "#e5ecf6" , xaxis = list (title = 'Year' ), yaxis = list (title = 'Mean Length (cm)' ), legend = list (title= list (text= '<b> Survey Area </b>' )))# Set up checkbox <- crosstalk:: filter_checkbox (id = "Survey_Area" ,label = "Survey Area" ,sharedData = shared_data,group = ~ survey_area# Use them bscols (checkbox_area, plot, widths = c (4 ,8 ))``` ## Average Weight ```{r} # Make Median Length Plot <- shared_data %>% :: plot_ly (y = ~ mean_wt_kg, x = ~ Year, color = ~ survey_area) %>% add_lines () %>% layout (title = 'Mean Weight Change' , plot_bgcolor = "#e5ecf6" , xaxis = list (title = 'Year' ), yaxis = list (title = 'Mean Weight (kg)' ), legend = list (title= list (text= '<b> Survey Area </b>' )))# Set up checkbox <- crosstalk:: filter_checkbox (id = "Survey_Area" ,label = "Survey Area" ,sharedData = shared_data,group = ~ survey_area, # Use them bscols (checkbox_area, plot, widths = c (4 ,8 ))``` ### Functional Group Changes ```{r} <- crosstalk:: SharedData$ new (%>% filter (survey_area == "GoM" ) %>% select (survey_area, hare_group, Year, mean_len_cm, mean_wt_kg), #%>% #pivot_longer(cols = starts_with("mean"), names_to = "variable", values_to = "measure"), key = ~ hare_group# Make Median Length Plot <- shared_data %>% :: plot_ly (y = ~ mean_len_cm, x = ~ Year, color = ~ hare_group) %>% add_lines () %>% layout (title = 'Gulf of Maine - Mean Length Change' , plot_bgcolor = "#e5ecf6" , xaxis = list (title = 'Year' ), yaxis = list (title = 'Mean Length (cm)' ), legend = list (title= list (text= '<b> Functional Group </b>' )))<- shared_data %>% :: plot_ly (y = ~ mean_wt_kg, x = ~ Year, color = ~ hare_group) %>% add_lines (showlegend = F) %>% layout (title = 'Gulf of Maine - Mean Weight Change' , plot_bgcolor = "#e5ecf6" , xaxis = list (title = 'Year' ), yaxis = list (title = 'Mean Weight (kg)' ), legend = list (title= list (text= '<b> Functional Group </b>' )))# subplot (plot1, plot2, nrows = 2 ) %>% :: highlight (persistent = F, on = "plotly_click" , off = "plotly_doubleclick" )``` ```{r} #| results: asis insert_gmri_footer ()``` 
