knitr::opts_chunk$set( fig.width = 11, fig.height = 8.5, # fig.path=paste0("figs/", spp, "/"), echo = FALSE, warning = FALSE, message = FALSE ) library(dplyr) library(ggplot2) library(gfplot) library(gfdata) library(sdmTMB) library(gfranges)
species <- params$species region <- params$region covariates <- params$covariates covs <- params$covs priors <- FALSE paste("region =", region) paste("model covariates =", covariates) paste("model label =", covs) paste("priors =", priors)
spp <- gsub(" ", "-", gsub("\\/", "-", tolower(species))) # folder to hold figs for this species dir.create(file.path("figs", spp)) dir.create(file.path("data", spp)) if (region == "Both odd year surveys") { survey <- c("SYN QCS", "SYN HS") model_ssid <- c(1, 3) ssid_string <- paste0(model_ssid, collapse = "n") years <- NULL } if (region == "West Coast Vancouver Island") { survey <- c("SYN WCVI") model_ssid <- c(4) ssid_string <- paste0(model_ssid, collapse = "n") years <- NULL } if (region == "West Coast Haida Gwaii") { survey <- c("SYN WCHG") model_ssid <- c(16) ssid_string <- paste0(model_ssid, collapse = "n") years <- NULL } if (region == "All synoptic surveys") { survey <- c("SYN QCS", "SYN HS", "SYN WCVI", "SYN WCHG") model_ssid <- c(1, 3, 4, 16) ssid_string <- paste0(model_ssid, collapse = "n") years <- NULL }
Check max depth depth?
biomass <- readRDS(paste0( "data/", spp, "/data-by-maturity-", spp, "-", ssid_string, ".rds" )) if(nrow(biomass)<4000) {stop("Need to recalculate split by maturity!")} covars <- readRDS("data/event-covariates.rds") %>% select(-geometry) data <- dplyr::left_join(biomass, covars) # scale predictors before filtering to ensure mean and SD are global data <- data %>% mutate(raw_depth = depth, depth = log(raw_depth)) data <- gfranges::scale_predictors(data, # predictors = c(quo(depth))) predictors = c(quo(depth), quo(mixed), quo(muddy), quo(sandy), quo(rocky), quo(any_rock)) ) data <- data %>% mutate(depth = raw_depth) %>% filter(ssid %in% model_ssid) %>% filter(year < 2019) # max_depth_found <- max(data[data$present == 1, ]$raw_depth, na.rm = TRUE) #max_depth_found <- 800
rm(depth_model_list) rm(adult_biomass) rm(imm_biomass) rm(total_biomass) try({ adult_biomass <- readRDS(paste0( "data/", spp, "/mod-mat-biomass-", spp, covs, "-1n3n4n16-prior-", priors, ".rds" )) adult_biomass <- sdmTMB:::update_model(adult_biomass) }) try({ imm_biomass <- readRDS(paste0( "data/", spp, "/mod-imm-biomass-", spp, covs, "-1n3n4n16.rds" )) imm_biomass <- sdmTMB:::update_model(imm_biomass) # depth_model_list <- list(adult = adult_biomass, imm = imm_biomass) }) if (!exists("adult_biomass")) { try({ total_biomass <- readRDS(paste0( "data/", spp, "/model-total-biomass-", spp, covs, "-1n3n4n16.rds" )) }) } if (!exists("adult_biomass")) adult_biomass <- NULL if (!exists("imm_biomass")) imm_biomass <- NULL if (!exists("total_biomass")) total_biomass <- NULL depth_model_list <- list(adult = adult_biomass, imm = imm_biomass, total = total_biomass) depth_model_list <- depth_model_list[!sapply(depth_model_list, is.null)]
depth_model_list
signif(max(depth_model_list$adult$gradients), digits = 8) signif(max(depth_model_list$imm$gradients), digits = 8) signif(max(depth_model_list$total$gradients), digits = 8)
write_grads <- function(x, macro, ...) { paste0("\\newcommand{\\", macro, "}{", x, "}") %>% readr::write_lines("model-grads.tex", append = TRUE) } write_grads(signif(max(depth_model_list$adult$gradients), digits = 8), paste0("oct2020-", spp, "-mat")) write_grads(signif(max(depth_model_list$imm$gradients), digits = 8), paste0("oct2020-", spp, "-imm")) write_grads(signif(max(depth_model_list$total$gradients), digits = 8), paste0("oct2020-", spp, "-total"))
write_knots <- function(x, macro, ...) { paste0("\\newcommand{\\", macro, "}{", x, "}") %>% readr::write_lines("model-knots.tex", append = TRUE) } write_knots(nrow(depth_model_list$adult$spde$loc_centers), paste0(spp, "-mat")) write_knots(nrow(depth_model_list$imm$spde$loc_centers), paste0(spp, "-imm")) write_knots(nrow(depth_model_list$total$spde$loc_centers), paste0(spp, "-total"))
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