inst/TEMP-make.R

In pbs-assess/gfsynopsis: Data Synopsis Reports for PBS Groundfish

# Run this from gfsynopsis/
# library(INLA) # FIXME: could not find function "inla.models" on Windows? #31
# devtools::load_all("../gfplot") # for development
# devtools::load_all(".")  # for development
library(gfplot)
library(gfsynopsis)
library(dplyr)
library(doParallel)  # needed in 'optimize png files', even for Windows
# ------------------------------------------------------------------------------
# Settings:
ext <- "png" # PDF vs. PNG figs; PNG for CSAS, PDF for fast LaTeX
example_spp <- "petrale sole" # a species used as an example in the Res Doc
parallel <- FALSE
if (parallel) library(doParallel)

# ------------------------------------------------------------------------------
# Read in fresh data or load cached data if available:
dc <- here::here("report", "data-cache")
gfsynopsis::get_data(type = c("A", "B"), path = dc, force = FALSE)
d_cpue <- readRDS(file.path(dc, "cpue-index-dat.rds"))
spp <- gfsynopsis::get_spp_names() %>%
  select(species_common_name, species_code, species_science_name, spp_w_hyphens, type)

# ------------------------------------------------------------------------------
# This section is used for hacked parallel processing from the command line.
# Unecessary, but speeds up rebuilding.
# e.g. from root project folder in macOS or Linux:
# open new Terminal
# make one
# open new Terminal
# make two
# open new Terminal
# make three
# if (exists("N")) spp <- spp[N, , drop = FALSE]

# ------------------------------------------------------------------------------
# Parse metadata that will be used at the top of each species page:
# spp <- filter(spp, species_common_name != "pacific hake")

make_meta <- function() {
  refs <- readr::read_csv(here::here("report/spp-refs.csv"))
  spp <- left_join(spp, refs, by = "species_common_name")
  spp$species_science_name <- gfplot:::firstup(spp$species_science_name)
  spp$species_science_name <- gsub(" complex", "", spp$species_science_name)
  spp$resdoc <- gsub(", ", ", @", spp$resdoc)
  spp$resdoc <- ifelse(is.na(spp$resdoc), "", paste0("@", spp$resdoc, ""))
  spp$sar <- gsub(", ", ", @", spp$sar)
  spp$sar <- ifelse(is.na(spp$sar), "", paste0("@", spp$sar, ""))
  spp$other_ref_cite <- ifelse(is.na(spp$other_ref), "",
    paste0(spp$type_other_ref, ": @", spp$other_ref, ""))
  spp$other_ref_cite <- gsub(", ", ", @", spp$other_ref_cite)
  spp <- arrange(spp, type, species_code)
}

make_all_pages <- function(spp, N = NULL, parallel = FALSE) {
  if (!is.null(N)) spp <- spp[N, , drop = FALSE]

  # ------------------------------------------------------------------------------
  # This is the guts of where the figure pages get made:
  # i <- which(spp$species_common_name  ==  'kelp greenling')
  if (parallel) registerDoParallel(cores = floor(parallel::detectCores()/2))
  plyr::l_ply(seq_along(spp$species_common_name), function(i) {
    # for (i in seq_along(spp$species_common_name)) {
    fig_check <- paste0(file.path("report", "figure-pages"), "/",
      gfsynopsis:::clean_name(spp$species_common_name[i]))
    fig_check1 <- paste0(fig_check, "-1.", ext)
    fig_check2 <- paste0(fig_check, "-2.", ext)
    if (!file.exists(fig_check1) || !file.exists(fig_check2)) {
      cat(crayon::red(clisymbols::symbol$cross),
        "Building figure pages for", spp$species_common_name[i], "\n")
      dat <- readRDS(paste0(file.path(dc, spp$spp_w_hyphens[i]), ".rds"))
      dat$cpue_index <- d_cpue
      gfsynopsis::make_pages(dat, spp$species_common_name[i],
        include_map_square = FALSE,
        resolution = 160, # balance size with resolution
        png_format = if (ext == "png") TRUE else FALSE,
        parallel = FALSE,

        save_gg_objects = spp$species_common_name[i] %in% example_spp,
        survey_cols = c(RColorBrewer::brewer.pal(5L, "Set1"),
          RColorBrewer::brewer.pal(8L, "Set1")[7:8],
          "#303030", "#a8a8a8", "#a8a8a8", "#a8a8a8")
      )
    } else {
      cat(crayon::green(clisymbols::symbol$tick),
        "Figure pages for", spp$species_common_name[i], "already exist\n")
    }
  }, .parallel = parallel)
}

make_figure_page_rmd <- function() {
  # ------------------------------------------------------------------------------
  # This is the guts of where the .tex / .Rmd figure page code gets made
  spp$b_section <- c(FALSE, diff(as.numeric(as.factor(spp$type))) == 1)
  temp <- lapply(spp$species_common_name, function(x) {
    spp_file <- gfsynopsis:::clean_name(x)
    spp_title <- gfsynopsis:::all_cap(x)
    spp_hyphen <- spp$spp_w_hyphens[spp$species_common_name == x]
    out <- list()
    latin_name <- spp$species_science_name[spp$species_common_name == x]
    sar <- spp$sar[spp$species_common_name == x]
    resdoc <- spp$resdoc[spp$species_common_name == x]
    species_code <- spp$species_code[spp$species_common_name == x]
    other_ref <- spp$other_ref_cite[spp$species_common_name == x]
    .b_section <- spp$b_section[spp$species_common_name == x]

    resdoc_text <- if (grepl(",", resdoc)) "Last Research Documents: " else "Last Research Document: "
    sar_text <- if (grepl(",", sar)) "Last Science Advisory Reports: " else "Last Science Advisory Report: "

    i <- 1
    out[[i]] <- "\\clearpage\n"
    if (.b_section) {
      i <- i + 1
      out[[i]] <- "# SYNOPSIS PLOTS: TYPE B SPECIES {#sec:synopsis-plots-B}\n"
    }
    i <- i + 1
    out[[i]] <- paste0("## ", spp_title, " {#sec:", spp_hyphen, "}\n")
    i <- i + 1
    out[[i]] <- paste0(gfsynopsis:::emph(latin_name),
      ", DFO species code: ", species_code, "\n")
    i <- i + 1
    out[[i]] <- paste0(resdoc_text, resdoc, "\n")
    i <- i + 1
    out[[i]] <- paste0(sar_text, sar, "\n")
    i <- i + 1
    if (!is.na(other_ref)) {
      if (other_ref != "") {
        out[[i]] <- paste0(other_ref)
        i <- i + 1
      }
    }
    out[[i]] <- "\\begin{figure}[b!]"
    i <- i + 1
    out[[i]] <- paste0("\\includegraphics[width=6.4in]{../figure-pages/", spp_file, "-1.", ext, "}")
    i <- i + 1
    out[[i]] <- "\\end{figure}"
    i <- i + 1
    out[[i]] <- "\\clearpage"
    i <- i + 1
    out[[i]] <- "\\begin{figure}[b!]"
    i <- i + 1
    out[[i]] <- paste0("\\includegraphics[width=6.4in]{../figure-pages/", spp_file, "-2.", ext, "}")
    i <- i + 1
    out[[i]] <- "\\end{figure}\n"
    i <- i + 1
    out[[i]] <- "\n"
    out
  })

  temp <- lapply(temp, function(x) paste(x, collapse = "\n"))
  temp <- paste(temp, collapse = "\n")
  if (!exists("N")) writeLines(temp, con = "report/report-rmd/plot-pages.Rmd")
}

optimize_pngs <- function()  {
  # ------------------------------------------------------------------------------
  # Optimize png files for TeX

  if (!exists("N")) {
    cores <- parallel::detectCores()
    files_per_core <- ceiling(length(spp$species_common_name)*2/cores)
    setwd(here::here("report/figure-pages"))
    if (!gfplot:::is_windows()) {
      system(paste0("find -X . -name '*.png' -print0 | xargs -0 -n ",
        files_per_core, " -P ", cores, " optipng -strip all"))
    } else {
      registerDoParallel(cores = cores)
      fi <- list.files(".", "*.png")
      plyr::l_ply(fi, function(i) system(paste0("optipng -strip all ", i)),
        .parallel = TRUE)
    }
    setwd(here::here("."))
  }
}