In efcaguab/pasgear: Analysis of fisheries data

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

```r library(magrittr) library(ggplot2)

cambodia_structure <- suppressMessages( # read data readr::read_csv("data-raw/iri_cambodia.csv")) %>% # make column names R friendly janitor::clean_names() %>% dplyr::mutate(type = dplyr::if_else(type == "N/A", NA_character_, type)) %>% dplyr::rename(percent_n = percent_no, percent_freq = percent_frq) %>% # make percentages percentages (between 0 and 1) dplyr::mutate_at(dplyr::vars(dplyr::contains("percent")), ~ ./100)

cambodia_iri <- cambodia_structure %>% # make sure "types" are ordered by iri dplyr::mutate(type = forcats::fct_reorder(type, iri, .desc = T)) %>% # remove types with zero freq dplyr::filter(percent_freq > 0)

Calculate some variables for the plot

cambodia_iri_plot_df <- cambodia_iri %>% dplyr::mutate(ymax = percent_weight, ymin = -percent_n, xmax = cumsum(percent_freq), xmin = dplyr::lag(xmax, default = 0), xbreaks = (xmin + xmax)/2)

Number of types to show

n_sp <- 6 cambodia_iri_plot_df %>% ggplot() + geom_rect(aes(xmin = xmin, xmax = xmax, ymin = ymin, ymax = ymax, fill = iri), colour = "black") + # a dashed horizontal line on zero geom_hline(yintercept = 0, linetype = 2) + # Set x axis scale_x_continuous(breaks = cambodia_iri_plot_df$xbreaks[1:n_sp], labels = scales::percent(cambodia_iri_plot_df$percent_freq[1:n_sp]), minor_breaks = cambodia_iri_plot_df$xmax, sec.axis = sec_axis(trans = ~., breaks = cambodia_iri_plot_df$xbreaks[1:n_sp], labels = cambodia_iri_plot_df$type[1:n_sp])) + # Set y axis scale_y_continuous(labels = scales::label_percent()) + theme_minimal() + theme(axis.text.x.top = element_text(angle = 90), legend.position = "none", panel.grid.major.x = element_line(linetype = 2)) +

labs(title = "IRI plot of a Cambodian fish community", x = "% frequency", y = "← % number ← | → % weight →")

efcaguab/pasgear documentation built on Oct. 13, 2020, 8:37 p.m.