ms/make-tables.R

In pbs-assess/gfranges: Groundfish Ranges

library(kableExtra)
setwd(here::here())
model_vel <- readRDS(here::here("analysis/VOCC/data/vel-all-95-optimized4-11-28-vel-both-1-600.rds"))
keepspp <- unique(model_vel$data$species_only)
stats <- readRDS(paste0("analysis/VOCC/data/life-history-behav-new-growth3.rds")) %>% mutate(
    age = firstup(age),
    Diet = factor(Diet, levels = c("Zooplankton", "Generalist", "Polychaetes", "Crustaceans", "Fish")),
    `Foraging zone` = factor(BenthoPelagicPelagicDemersal, levels = c("Demersal", "Benthopelagic", "Pelagic")),
    `Range limit` = factor(if_else(NorthMiddleSouth == "North", "N", 
      "S")),
    Sociality = as.factor(Schooling),
    `Trophic level` = factor(if_else(Diet == "Zooplankton", "L", "H")),
    Specialist = factor(if_else(Diet == "Generalist", "Generalist", "Specialist"), levels = c("Generalist", "Specialist"))
  ) 

stats$`Foraging zone`[stats$`Foraging zone` == "Pelagic"] <- "Benthopelagic"

spptab <- stats %>% filter(age == "Mature" & species %in% keepspp) %>% 
  arrange(desc(prop_pos_sets)) %>% 
  mutate( `Scientific name` = paste(firstup(genus), specific),
    family = firstup(family), 
    prop_pos_sets = paste0(round(prop_pos_sets*100),"%")
  ) %>%
  select(species, 
    `Scientific name`, 
    #family, 
    prop_pos_sets, depth, depth_mat_iqr, age_mean, 
    `Range limit`, `Trophic level`, `Foraging zone`, Sociality
    ) %>% 
  rename(
    `Common name` = species,
    # Family = family,
    `Proportion present` = prop_pos_sets,
    `Mature mean` = depth,
    `Mature IQR` = depth_mat_iqr,
    `Mature mean age` =age_mean) 

keepimm <- filter(model_vel$data, age_class == "immature") %>% select(species_only) %>% distinct()
keepimm <- unique(keepimm$species_only)
spptabimm <- stats %>% filter(age == "Immature" & species %in% keepimm) %>% select(species, depth, depth_imm_iqr,
  age_mean, 
  `Trophic level`
  # , `Foraging zone` # only POP diff...
  # , Sociality # only POP diff... imm = solitary
  ) %>%
  rename(
    `Common name` = species,
    `Immature mean` = depth,
    `Immature IQR` = depth_imm_iqr,
    `Immature mean age` = age_mean, 
    `Imm. trophic level` = `Trophic level`
    )

spptab <- left_join(spptab, spptabimm) %>% select(
  `Common name`, `Scientific name`,
  # Family,
  `Proportion present`, 
  `Immature mean`, `Immature IQR`, `Mature mean`, `Mature IQR`, 
  `Immature mean age`, `Mature mean age`, 
  `Range limit`, `Imm. trophic level`, `Trophic level`, `Foraging zone`, Sociality
  )

# library("imputeTS")
spptab <- imputeTS::na_replace(spptab, "-") 

knitr::kable(spptab, "latex", vline = "", 
  booktabs = T) %>%  
  kable_styling(font_size = 9) %>%
  column_spec(2, italic = T) %>%
  row_spec(0, bold = T)