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Sep 17 00:00:00 2001 From: jcaracappa1 <57966543+jcaracappa1@users.noreply.github.com> Date: Thu, 30 Sep 2021 17:54:22 -0400 Subject: [PATCH 2/5] Script to pull seasonal movement parameters from biology.prm --- R/get_param_seasonal_migration.R | 63 ++++++++++++++++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 R/get_param_seasonal_migration.R diff --git a/R/get_param_seasonal_migration.R b/R/get_param_seasonal_migration.R new file mode 100644 index 00000000..da3855fc --- /dev/null +++ b/R/get_param_seasonal_migration.R @@ -0,0 +1,63 @@ +#script to get seasonal migration parameters FXXX_SY + +get.move = function(bio.file,fgs,nbox = 30){ + library(dplyr) + + fgs = read.csv(fgs) + + #Get groups and age class + groups = fgs$Code + is.age = fgs$NumCohorts > 1 + + seasons = 1:4 + + #read in lines + bio.lines = readLines(bio.file) + + find.line = function(x){ + line.match = grep(paste0('^',x,'\\b'),bio.lines,ignore.case = T) + if(length(line.match) == 0){ + return(NULL) + }else{ + line.vals = as.numeric(strsplit(bio.lines[line.match + 1],'\t| ')[[1]])[1:nbox] + } + return(line.vals) + } + + #loop over species + spp.ls = list() + for(i in 1:length(groups)){ + + #construct parameters + if(is.age[i] == 1){ + param.names = c(c(sapply(seasons, function(x) paste0('F',groups[i],'_S',x))), + c(sapply(seasons, function(x) paste0('F',groups[i],'_S',x,'juv')))) + season.id = rep(1:4,2) + }else{ + param.names = c(sapply(seasons, function(x) paste0('F',groups[i],'_S',x))) + season.id = rep(1:4) + } + + spp.vals = sapply(param.names,find.line) + + if(all(sapply(spp.vals,is.null))){ + spp.ls[[i]] = NULL + }else{ + spp.ls[[i]] = spp.vals %>% + as.data.frame() %>% + mutate(box = 0:(nbox-1))%>% + reshape2::melt(id.vars = 'box')%>% + mutate(group = groups[i], + phase = ifelse(grepl('juv$',variable)&is.age[i]==1,'juv','adult'), + season = rep(season.id,each = nbox)) + } + # print(groups[i]) + } + return(dplyr::bind_rows(spp.ls)) +} + +move.params = get.move(fgs = here::here('currentVersion','neus_groups.csv'), + bio.file = here::here('currentVersion','at_biology.prm') + ) +write.csv(move.params, here::here('data-raw','seasonal_movements.csv'),row.names = F) + From c72f3f9660a07b0ef4d354e30eae0744ba06215b Mon Sep 17 00:00:00 2001 From: jcaracappa1 <57966543+jcaracappa1@users.noreply.github.com> Date: Thu, 30 Sep 2021 18:31:29 -0400 Subject: [PATCH 3/5] Functions to generate types of spatial biomass plots without maps --- R/plot_biomass_box_summary.R | 230 +++++++++++++++++++++++++++++++++++ 1 file changed, 230 insertions(+) create mode 100644 R/plot_biomass_box_summary.R diff --git a/R/plot_biomass_box_summary.R b/R/plot_biomass_box_summary.R new file mode 100644 index 00000000..3903515f --- /dev/null +++ b/R/plot_biomass_box_summary.R @@ -0,0 +1,230 @@ +#Functions to make box/epu species biomass presence/absence + +# Box Gradient ------------------------------------------------------------ + +plot_biomass_box_season = function(bio.box, + bio.box.invert, + plot.presence=F, + species.list = NULL, + save.fig = T, + fig.dir, + tolerance = 0.1){ + library(dplyr) + library(ggplot2) + + box2epu = read.csv(here::here('Geometry','box2epu.csv')) + month2season = read.csv(here::here('data-raw','month2season.csv')) + season2name = data.frame(season = 1:4, season.name = unique(month2season$season.name)) + fgs = read.csv(here::here('currentVersion','neus_groups.csv')) + + move.param = read.csv(here::here('data-raw','seasonal_movements.csv'))%>% + group_by(group,box,season)%>% + summarise(orig = mean(value,na.rm=T))%>% + left_join(season2name)%>% + left_join(fgs,by = c('group' = 'Code'))%>% + rename(polygon = 'box',species = "LongName")%>% + ungroup()%>% + left_join(box2epu,by = c('polygon' = 'box'))%>% + select(species,polygon,epu,season.name,orig)%>% + mutate(orig.presence = ifelse(orig == 0,0,1))%>% + filter(!is.na(epu)) + + + bio.all = rbind(bio.box,bio.box.invert)%>% + mutate(day = time * 365) + + bio.all = bio.all %>% + mutate(date = as.POSIXct(day * 86400, origin = '1964-01-01 00:00:00',tz = 'UTC'), + month = as.numeric(format(date,format = '%m')))%>% + left_join(month2season)%>% + group_by(species,polygon,season.name)%>% + summarise(atoutput = mean(atoutput,na.rm=T)) + + if(!is.null(species.list)){ + bio.all = bio.all %>% + filter(species %in% species.list) + } + + bio.all = bio.all %>% + group_by(species,polygon,season.name)%>% + summarise(atoutput = mean(atoutput,na.rm=T)) + + bio.max = bio.all %>% + group_by(species,season.name)%>% + summarise(atoutput.max = sum(atoutput,na.rm=T)) + + box.combs = expand.grid(species = unique(bio.all$species), + polygon = sort(unique(bio.all$polygon)), + season.name = unique(month2season$season.name)) + + bio.presence = box.combs %>% + left_join(bio.all)%>% + left_join(box2epu,by = c('polygon' = 'box'))%>% + mutate(presence = ifelse(atoutput == 0 | is.na(atoutput),0,1))%>% + left_join(bio.max)%>% + mutate(atoutput.scaled = atoutput/atoutput.max, + atoutput.scaled = ifelse(is.na(atoutput.scaled),0,atoutput.scaled))%>% + left_join(move.param)%>% + tidyr::replace_na(list(atoutput = 0))%>% + mutate( + presence.match = ifelse(orig.presence == presence,1,0), + prop.match = ifelse(orig >= (atoutput.scaled-tolerance) & orig <= (atoutput.scaled+tolerance), 1,0)) + + bio.presence$polygon = factor(bio.presence$polygon, + levels = c(1:7,9,8,12:15,10:11,16:22)) + + if(plot.presence){ + + # plot.ls = list() + plot.name = paste0(fig.dir,'Box_EPU_season_presence.png') + p = ggplot(bio.presence,aes(x=polygon,y=season.name,alpha = presence.match,fill = epu))+ + geom_tile(color = 'black')+ + facet_wrap(~species,ncol = 8)+ + xlab('Box')+ + guides(alpha = F)+ + ylab('')+ + theme_minimal()+ + theme(panel.grid = element_blank(), + legend.position = 'bottom', + plot.title = element_text(hjust = 0.5)) + + }else{ + plot.name = paste0(fig.dir,'Box_EPU_Season_scaled.png') + p = ggplot(bio.presence,aes(x=polygon,y=season.name,alpha = atoutput.scaled,fill = epu))+ + geom_tile(color = 'black')+ + facet_wrap(~species,ncol = 8)+ + xlab('Box')+ + guides(alpha = F)+ + ylab('')+ + theme_minimal()+ + theme(panel.grid = element_blank(), + legend.position = 'bottom', + plot.title = element_text(hjust = 0.5)) + + } + + if(save.fig){ + p + theme(axis.text.x = element_text(size = 6))+ ggsave(plot.name,width = 24, height = 10, units = 'in',dpi = 350) + }else{ + return(p) + } + +} + +# Box Time Range ------------------------------------------------------------ + +plot_biomass_box_range = function(bio.box, + bio.box.invert, + day.min=NA, + day.max=NA, + plot.presence = T, + species.list = NULL, + save.fig = T, + fig.dir){ + + library(dplyr) + library(ggplot2) + + box2epu = read.csv(here::here('Geometry','box2epu.csv')) + + bio.all = rbind(bio.box,bio.box.invert)%>% + mutate(day = time * 365) + + bio.all = bio.all %>% + filter(day >= day.min & day <= day.max) + + if(!is.null(species.list)){ + bio.all = bio.all %>% + filter(species %in% species.list) + } + + bio.all = bio.all %>% + group_by(species,polygon)%>% + summarise(atoutput = mean(atoutput,na.rm=T)) + + bio.max = bio.all %>% + group_by(species)%>% + summarise(atoutput.max = max(atoutput,na.rm=T)) + + box.combs = expand.grid(species = unique(bio.all$species), + polygon = sort(unique(bio.all$polygon))) + + bio.presence = box.combs %>% + left_join(bio.all)%>% + left_join(box2epu,by = c('polygon' = 'box'))%>% + mutate(presence = ifelse(atoutput == 0 | is.na(atoutput),0,1))%>% + left_join(bio.max)%>% + mutate(atoutput.scaled = atoutput/atoutput.max, + atoutput.scaled = ifelse(is.na(atoutput.scaled),0,atoutput.scaled)) + + bio.presence$polygon = factor(bio.presence$polygon, + levels = c(1:7,9,8,12:15,10:11,16:22)) + + spp.order = bio.presence %>% + group_by(species)%>% + summarise(presence.freq = mean(atoutput.scaled))%>% + arrange(desc(presence.freq)) + + bio.presence$species = factor(bio.presence$species, + levels = rev(spp.order$species)) + + if(plot.presence){ + p = ggplot(bio.presence,aes(x=polygon,y=species,alpha = presence,fill= epu))+ + geom_tile(color = 'black')+ + guides(alpha = F)+ + xlab('Box')+ + ylab('')+ + scale_fill_manual(name = 'EPU', values = RColorBrewer::brewer.pal(3,'Set2'))+ + theme_minimal()+ + theme(panel.grid = element_blank(), + legend.position = 'bottom') + + plot.name = paste0(fig.dir,'Box_EPU_summary.png') + }else{ + + p = ggplot(bio.presence,aes(x=polygon,y=species,alpha = atoutput.scaled,fill= epu))+ + geom_tile(color = 'black')+ + guides(alpha = F)+ + xlab('Box')+ + ylab('')+ + scale_fill_manual(name = 'EPU', values = RColorBrewer::brewer.pal(3,'Set2'))+ + theme_minimal()+ + theme(panel.grid = element_blank(), + legend.position = 'bottom') + + plot.name = paste0(fig.dir,'Box_EPU_summary.png') + } + + if(save.fig){ + p + ggsave(plot.name,width = 12, height = 12, units = 'in') + }else{ + return(p) + } +} + + +# Example ----------------------------------------------------------------- + +# plot_biomass_box_range(bio.box = readRDS('C:/Users/joseph.caracappa/Documents/Atlantis/Obs_Hindcast/Atlantis_Runs/ZM_Spatial_Final/Post_Processed/Data/biomass_box.rds'), +# bio.box.invert = readRDS('C:/Users/joseph.caracappa/Documents/Atlantis/Obs_Hindcast/Atlantis_Runs/ZM_Spatial_Final/Post_Processed/Data/biomass_box_invert.rds'), +# fig.dir = 'C:/Users/joseph.caracappa/Documents/Atlantis/Obs_Hindcast/Atlantis_Runs/ZM_Spatial_Final/Post_Processed/' , +# day.min = 366, +# day.max = 730, +# # species.list = c('Carnivorous zooplankton','Mesozooplankton','Microzooplankton','Gelatinous zooplankton'), +# species.list = NULL, +# plot.presence = F, +# save.fig = T +# +# ) +# +plot_biomass_box_season(bio.box = readRDS('C:/Users/joseph.caracappa/Documents/Atlantis/Obs_Hindcast/Atlantis_Runs/ZM_Spatial_Final/Post_Processed/Data/biomass_box.rds'), + bio.box.invert = readRDS('C:/Users/joseph.caracappa/Documents/Atlantis/Obs_Hindcast/Atlantis_Runs/ZM_Spatial_Final/Post_Processed/Data/biomass_box_invert.rds'), + fig.dir = 'C:/Users/joseph.caracappa/Documents/Atlantis/Obs_Hindcast/Atlantis_Runs/ZM_Spatial_Final/Post_Processed/' , + # species.list = c('Carnivorous zooplankton','Mesozooplankton','Microzooplankton','Gelatinous zooplankton'), + species.list = NULL, + plot.presence = T, + save.fig = T + +) + + From 49acf071c5dfbc81d73698f3407a3d3c42fb58bf Mon Sep 17 00:00:00 2001 From: jcaracappa1 <57966543+jcaracappa1@users.noreply.github.com> Date: Thu, 30 Sep 2021 18:31:55 -0400 Subject: [PATCH 4/5] Added spatial biomass seasonal plots - cleaned up too --- R/make_atlantis_diagnostic_figures.R | 73 +++++----------------------- R/test post-processing.R | 19 ++++---- 2 files changed, 21 insertions(+), 71 deletions(-) diff --git a/R/make_atlantis_diagnostic_figures.R b/R/make_atlantis_diagnostic_figures.R index cb093149..69d6e009 100644 --- a/R/make_atlantis_diagnostic_figures.R +++ b/R/make_atlantis_diagnostic_figures.R @@ -40,67 +40,6 @@ #' Author: Ryan Morse, modified by J. Caracappa #' -# atl.dir = 'C:/Users/joseph.caracappa/Documents/Atlantis/ROMS_COBALT/Atlantis_Output_NutrientForcing/' -# out.dir = 'C:/Users/joseph.caracappa/Documents/Atlantis/ROMS_COBALT/Atlantis_Output_NutrientForcing/Post_Processed/' -# param.dir = here::here('CurrentVersion') -# run.prefix = 'neus_output_test' -# run.name = 'NutrientForcing' -# -# -# source(here::here('R','get_atl_paramfiles.R')) -# source(here::here('R','process_atl_output.R')) -# param.ls= get_atl_paramfiles(param.dir,atl.dir,include_catch=T) -# -# # process_atl_output( param.dir = here::here('CurrentVersion'), -# # atl.dir = 'C:/Users/joseph.caracappa/Documents/Atlantis/ROMS_COBALT/Atlantis_Output_NutrientForcing/', -# # out.dir = 'C:/Users/joseph.caracappa/Documents/Atlantis/ROMS_COBALT/Atlantis_Output_NutrientForcing/Post_Processed/', -# # run.prefix = 'neus_output_test', -# # include_catch = T, -# # save.out = T, -# # bgm.file = param.ls$bgm, -# # groups.file = param.ls$func.groups, -# # init.file = param.ls$init.nofill, -# # param.ls$biol.prm = param.ls$param.ls$biol.prm, -# # run.prm = param.ls$run.prm, -# # main.nc = param.ls$main.nc, -# # prod.nc = param.ls$prod.nc, -# # dietcheck = param.ls$dietcheck, -# # ssb = param.ls$ssb, -# # yoy = param.ls$yoy, -# # catch.file = param.ls$catch, -# # totcatch.file = param.ls$catchtot, -# # spatial.overlap = F -# # ) -# -# load(paste0(out.dir,'neus_output_test_postprocessed.rdata')) -# -# fig.width = 10 -# fig.height = 8 -# benthic.box = 10 -# benthic.level = 4 -# -# bgm.file = param.ls$bgm -# param.ls$func.groups = param.ls$func.groups -# run.prm = param.ls$run.prm -# param.ls$biol.prm = param.ls$biol.prm -# phytopl.history = here::here('R','phytoplankton_timeseries_biomass_tonnes_1998_2016.csv') -# zoopl.history = here::here('R','Zooplankton_total_biomass_tonnes_N_20yrs.csv') -# -# plot.benthic = T -# plot.overall.biomass = T -# plot.biomass.timeseries = T -# plot.length.age=T -# plot.biomass.box=T -# plot.c.mum=T -# plot.sn.rn=T -# plot.recruits=T -# plot.numbers.timeseries=T -# plot.physics=T -# plot.growth.cons=T -# plot.cohort=T -# plot.diet=T -# plot.spatial.biomass=T -# plot.LTL=T make_atlantis_diagnostic_figures = function( out.dir, @@ -135,6 +74,7 @@ make_atlantis_diagnostic_figures = function( plot.diet, plot.consumption, plot.spatial.biomass, + plot.spatial.biomass.seasonal, plot.LTL, plot.catch ){ @@ -1008,4 +948,15 @@ make_atlantis_diagnostic_figures = function( dev.off() } + + if(plot.spatial.biomass.seasonal){ + source(here::here('R','plot_biomass_box_summary.R')) + + plot_biomass_box_season(bio.box = readRDS(paste0(out.dir,'biomass_box.rds')), + bio.box.invert = readRDS(paste0(out.dir,'biomass_box_invert.rds')), + fig.dir = fig.dir, + species.list = NULL, + plot.presence = T, + save.fig = T) + } } diff --git a/R/test post-processing.R b/R/test post-processing.R index 5555832f..7b5ae592 100644 --- a/R/test post-processing.R +++ b/R/test post-processing.R @@ -13,19 +13,17 @@ source(here::here('R','make_atlantis_diagnostic_figures.R')) run.name = 'ZM_Spatial_Final' - atl.dir = paste0('C:/Users/joseph.caracappa/Documents/Atlantis/Obs_Hindcast/Atlantis_Runs/',run.name,'/') -dir.create(paste0(atl.dir,'Post_Processed2/')) -dir.create(paste0(atl.dir,'Post_Processed2/Data/')) +dir.create(paste0(atl.dir,'Post_Processed/')) +dir.create(paste0(atl.dir,'Post_Processed/Data/')) param.dir = here::here ('currentVersion') -out.dir = paste0(atl.dir,'Post_Processed2/Data/') -fig.dir = paste0(atl.dir,'Post_Processed2/') +out.dir = paste0(atl.dir,'Post_Processed/Data/') +fig.dir = paste0(atl.dir,'Post_Processed/') #Run prefix is the filename prefix in the atlantis output (specified in run.bat) run.prefix = 'neus_output' - #Run function that retreives parameter files param.ls= get_atl_paramfiles(param.dir = param.dir, atl.dir=atl.dir, @@ -43,7 +41,7 @@ process_atl_output( diet.agg.time = 'month', spatial.overlap = F, large.file = F - ) +) #If result object saved to file or already exists load it into env. # load(paste0(out.dir,'neus_output_postprocessed.rdata')) @@ -69,7 +67,7 @@ make_atlantis_diagnostic_figures( phytopl.history = here::here('R','phytoplankton_timeseries_biomass_tonnes_1998_2016.csv'), zoopl.history = here::here('R','Zooplankton_total_biomass_tonnes_N_20yrs.csv'), - plot.all = T, + plot.all = F, #Turn these on/off for desired output plot.benthic =F, plot.overall.biomass = F, @@ -86,7 +84,8 @@ make_atlantis_diagnostic_figures( plot.diet=F, plot.consumption= F, plot.spatial.biomass=F, - plot.LTL=T, - plot.catch =T + plot.spatial.biomass.seasonal = T, + plot.LTL=F, + plot.catch =F ) From b3c28ff7a66f037e26b864267bf00e18c2ba9d11 Mon Sep 17 00:00:00 2001 From: andybeet <22455149+andybeet@users.noreply.github.com> Date: Fri, 1 Oct 2021 10:32:20 -0400 Subject: [PATCH 5/5] put ggsave command on separate line (causing an error using +) - commented out example (would be sourced otherwise) --- R/plot_biomass_box_summary.R | 21 +++++++++++---------- 1 file changed, 11 insertions(+), 10 deletions(-) diff --git a/R/plot_biomass_box_summary.R b/R/plot_biomass_box_summary.R index 3903515f..b5b54c62 100644 --- a/R/plot_biomass_box_summary.R +++ b/R/plot_biomass_box_summary.R @@ -104,7 +104,8 @@ plot_biomass_box_season = function(bio.box, } if(save.fig){ - p + theme(axis.text.x = element_text(size = 6))+ ggsave(plot.name,width = 24, height = 10, units = 'in',dpi = 350) + p + theme(axis.text.x = element_text(size = 6)) + ggsave(plot.name,plot = p,width = 24, height = 10, units = 'in',dpi = 350) }else{ return(p) } @@ -217,14 +218,14 @@ plot_biomass_box_range = function(bio.box, # # ) # -plot_biomass_box_season(bio.box = readRDS('C:/Users/joseph.caracappa/Documents/Atlantis/Obs_Hindcast/Atlantis_Runs/ZM_Spatial_Final/Post_Processed/Data/biomass_box.rds'), - bio.box.invert = readRDS('C:/Users/joseph.caracappa/Documents/Atlantis/Obs_Hindcast/Atlantis_Runs/ZM_Spatial_Final/Post_Processed/Data/biomass_box_invert.rds'), - fig.dir = 'C:/Users/joseph.caracappa/Documents/Atlantis/Obs_Hindcast/Atlantis_Runs/ZM_Spatial_Final/Post_Processed/' , - # species.list = c('Carnivorous zooplankton','Mesozooplankton','Microzooplankton','Gelatinous zooplankton'), - species.list = NULL, - plot.presence = T, - save.fig = T - -) +# plot_biomass_box_season(bio.box = readRDS('C:/Users/joseph.caracappa/Documents/Atlantis/Obs_Hindcast/Atlantis_Runs/ZM_Spatial_Final/Post_Processed/Data/biomass_box.rds'), +# bio.box.invert = readRDS('C:/Users/joseph.caracappa/Documents/Atlantis/Obs_Hindcast/Atlantis_Runs/ZM_Spatial_Final/Post_Processed/Data/biomass_box_invert.rds'), +# fig.dir = 'C:/Users/joseph.caracappa/Documents/Atlantis/Obs_Hindcast/Atlantis_Runs/ZM_Spatial_Final/Post_Processed/' , +# # species.list = c('Carnivorous zooplankton','Mesozooplankton','Microzooplankton','Gelatinous zooplankton'), +# species.list = NULL, +# plot.presence = T, +# save.fig = T +# +# )