diff --git a/DESCRIPTION b/DESCRIPTION index 9312885..dcc656a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: esrindex Type: Package Title: Abundance index products for Alaska ESRs Version: 1.0.0 -Date: 2024-11-01 +Date: 2024-11-08 Authors@R: c(person("Sean", "Rohan", email = "sean.rohan@noaa.gov", role = c("aut", "cre")), person("Thaddaeus", "Buser", email = "thaddaeus.buser@noaa.gov", role = "ctb"), person("Christina", "Conrath", email = "christina.conrath@noaa.gov", role = "ctb"), diff --git a/NEWS b/NEWS index 82e5a59..7c9b97b 100644 --- a/NEWS +++ b/NEWS @@ -1,3 +1,12 @@ +esrindex 1.0.0 (November 8, 2024) - First production release +---------------------------------------------------------------- + +NEW FEATURES + +- plot_region_rema() makes individual timeseries plots for each + group. + + esrindex 0.1.4 (October 1, 2024) ---------------------------------------------------------------- diff --git a/R/plot_region_rema.R b/R/plot_region_rema.R index 3850c35..244366a 100644 --- a/R/plot_region_rema.R +++ b/R/plot_region_rema.R @@ -334,6 +334,239 @@ plot_region_rema <- function(x, plot_list[[ii]] <- p1 + # Plots for individual groups + for(kk in 1:length(group_name)) { + + sel_group_fit <- fit_dat[fit_dat$group_name == group_name[kk], ] + + sel_group_obs <- obs_dat[obs_dat$group_name == group_name[kk], ] + + sel_group_ts_summary <- ts_summary[ts_summary$group_name == group_name[kk], ] + + if(error_bar & benchmarks == "none") { + + p1 <- ggplot() + + geom_ribbon(data = sel_group_fit, + mapping = aes(x = year, + ymin = pred_lci, + ymax = pred_uci), + alpha = 0.3, + fill = ribbon_fill) + + geom_errorbar(data = sel_group_obs, + mapping = aes(x = YEAR, + ymin = BIOMASS_PLUS2_SD, + ymax = BIOMASS_MINUS2_SD), + width = 0.5, + color = errorbar_color) + + geom_point(data = sel_group_obs, + mapping = aes(x = YEAR, y = BIOMASS_MT), + color = point_color) + + geom_path(data = sel_group_fit, + mapping = aes(x = year, y = pred), + color = timeseries_color, + size = rel(1.1)) + + scale_y_continuous(name = paste0("Biomass Index (", set_unit, ")"), + expand = expansion(mult = c(0, 0.05)), + labels = lab_fun(trim = lab_trim)) + + scale_x_continuous(name = "Year", + breaks = year_breaks, + labels = year_labels) + + expand_limits(y = y_axis_min) + + facet_wrap(~group_name[kk]) + + theme_blue_strip() + + } + + if(error_bar & benchmarks == "zscore") { + + p1 <- ggplot() + + geom_hline(data = sel_group_ts_summary, + mapping = aes(yintercept = z_mean), + color = hline_color) + + geom_hline(data = sel_group_ts_summary, + mapping = aes(yintercept = plus1), + linetype = 2, + color = hline_color) + + geom_hline(data = sel_group_ts_summary, + mapping = aes(yintercept = minus1), + linetype = 2, + color = hline_color) + + geom_ribbon(data = sel_group_fit, + mapping = aes(x = year, + ymin = pred_lci, + ymax = pred_uci), + alpha = 0.3, + fill = ribbon_fill) + + geom_errorbar(data = sel_group_obs, + mapping = aes(x = YEAR, + ymin = BIOMASS_PLUS2_SD, + ymax = BIOMASS_MINUS2_SD), + width = 0.5, + color = errorbar_color) + + geom_path(data = sel_group_fit, + mapping = aes(x = year, + y = pred), + color = timeseries_color, + size = rel(1.1)) + + geom_point(data = sel_group_obs, + mapping = aes(x = YEAR, y = BIOMASS_MT), + color = point_color) + + scale_y_continuous(name = paste0("Biomass Index (", set_unit, ")"), + expand = expansion(mult = c(0, 0.05)), + labels = lab_fun(trim = lab_trim)) + + scale_x_continuous(name = "Year", + breaks = year_breaks, + labels = year_labels) + + expand_limits(y = y_axis_min) + + facet_wrap(~group_name) + + theme_blue_strip() + + } + + if(!error_bar & benchmarks == "zscore") { + p1 <- ggplot() + + geom_hline(data = sel_group_ts_summary, + mapping = aes(yintercept = z_mean)) + + geom_hline(data = sel_group_ts_summary, + mapping = aes(yintercept = plus1), + linetype = 2, + color = hline_color) + + geom_hline(data = sel_group_ts_summary, + mapping = aes(yintercept = minus1), + linetype = 2, + color = hline_color) + + geom_ribbon(data = sel_group_fit, + mapping = aes(x = year, + ymin = pred_lci, + ymax = pred_uci), + alpha = 0.3, + fill = ribbon_fill) + + geom_path(data = sel_group_fit, + mapping = aes(x = year, y = pred), + color = timeseries_color, + size = rel(1.1)) + + geom_point(data = sel_group_obs, + mapping = aes(x = YEAR, y = BIOMASS_MT), + color = point_color) + + scale_y_continuous(name = paste0("Biomass Index (", set_unit, ")"), + expand = expansion(mult = c(0, 0.05)), + labels = lab_fun(trim = lab_trim)) + + scale_x_continuous(name = "Year", + breaks = year_breaks, + labels = year_labels) + + expand_limits(y = y_axis_min) + + facet_wrap(~group_name) + + theme_blue_strip() + } + + + if(error_bar & benchmarks == "quantile") { + + p1 <- ggplot() + + geom_hline(data = sel_group_ts_summary, + mapping = aes(yintercept = q50)) + + geom_hline(data = sel_group_ts_summary, + mapping = aes(yintercept = q75), + linetype = 2, + color = hline_color) + + geom_hline(data = sel_group_ts_summary, + mapping = aes(yintercept = q100), + linetype = 3, + color = hline_color) + + geom_hline(data = sel_group_ts_summary, + mapping = aes(yintercept = q25), + linetype = 2, + color = hline_color) + + geom_hline(data = sel_group_ts_summary, + mapping = aes(yintercept = q0), + linetype = 3, + color = hline_color) + + geom_ribbon(data = sel_group_fit, + mapping = aes(x = year, + ymin = pred_lci, + ymax = pred_uci), + alpha = 0.3, + fill = ribbon_fill) + + geom_path(data = sel_group_fit, + mapping = aes(x = year, y = pred), + color = timeseries_color, + size = rel(1.1)) + + geom_point(data = sel_group_obs, + mapping = aes(x = YEAR, y = BIOMASS_MT), + color = point_color) + + scale_y_continuous(name = paste0("Biomass Index (", set_unit, ")"), + expand = expansion(mult = c(0, 0.05)), + labels = lab_fun(trim = lab_trim)) + + scale_x_continuous(name = "Year", + breaks = year_breaks, + labels = year_labels) + + expand_limits(y = y_axis_min) + + facet_wrap(~group_name) + + theme_blue_strip() + + } + + if(!error_bar & benchmarks == "quantile") { + p1 <- ggplot() + + geom_hline(data = sel_group_ts_summary, + mapping = aes(yintercept = q50)) + + geom_hline(data = sel_group_ts_summary, + mapping = aes(yintercept = q75), + linetype = 2, + color = hline_color) + + geom_hline(data = sel_group_ts_summary, + mapping = aes(yintercept = q100), + linetype = 3, + color = hline_color) + + geom_hline(data = sel_group_ts_summary, + mapping = aes(yintercept = q25), + linetype = 2, + color = hline_color) + + geom_hline(data = sel_group_ts_summary, + mapping = aes(yintercept = q0), + linetype = 3, + color = hline_color) + + geom_ribbon(data = sel_group_fit, + mapping = aes(x = year, + ymin = pred_lci, + ymax = pred_uci), + alpha = 0.3, + fill = ribbon_fill) + + geom_path(data = sel_group_fit, + mapping = aes(x = year, y = pred), + color = timeseries_color, + size = rel(1.1)) + + geom_point(data = sel_group_obs, + mapping = aes(x = YEAR, y = BIOMASS_MT), + color = point_color) + + scale_y_continuous(name = paste0("Biomass Index (", set_unit, ")"), + expand = expansion(mult = c(0, 0.05)), + labels = lab_fun(trim = lab_trim)) + + scale_x_continuous(name = "Year", + breaks = year_breaks, + labels = year_labels) + + expand_limits(y = y_axis_min) + + facet_wrap(~group_name) + + theme_blue_strip() + } + + suppressWarnings(dir.create(paste0("./plots/", region, "/plots_by_group"), recursive = TRUE)) + + grDevices::png(filename = paste0("./plots/", region, "/", "/plots_by_group/", region, "_rema_", + gsub(x = indicator_name[ii], pattern = " ", replacement = "_"), + "_", + gsub(x = group_name[kk], pattern = " ", replacement = "_"), + "_full_region", append_filename, ".png"), + width = 169, + height = 60, + units = "mm", + res = 300) + print(p1) + grDevices::dev.off() + + + } + } return(plot_list) diff --git a/man/esrindex-package.Rd b/man/esrindex-package.Rd index c0f622e..e9c4afd 100644 --- a/man/esrindex-package.Rd +++ b/man/esrindex-package.Rd @@ -17,6 +17,7 @@ Other contributors: \item Christina Conrath \email{christina.conrath@noaa.gov} [contributor] \item Sarah Friedman \email{sarah.friedman@noaa.gov} [contributor] \item Ned Laman \email{ned.laman@noaa.gov} [contributor] + \item Susanne McDermott \email{susanne.mcdermott@noaa.gov} [contributor] \item Margaret Siple \email{margaret.siple@noaa.gov} [contributor] } diff --git a/plots/AI/AI_rema_forage_fish_full_region_ze.png b/plots/AI/AI_rema_forage_fish_full_region_ze.png index 4cb54f2..9653aa0 100644 Binary files a/plots/AI/AI_rema_forage_fish_full_region_ze.png and b/plots/AI/AI_rema_forage_fish_full_region_ze.png differ diff --git a/plots/AI/AI_rema_misc_species_full_region_ze.png b/plots/AI/AI_rema_misc_species_full_region_ze.png index 4c2433c..fb33c97 100644 Binary files a/plots/AI/AI_rema_misc_species_full_region_ze.png and b/plots/AI/AI_rema_misc_species_full_region_ze.png differ diff --git a/plots/AI/AI_rema_structural_epifauna_full_region_ze.png 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