diff --git a/prep_MHWs.R b/prep_MHWs.R index f64f2b6..df70f02 100644 --- a/prep_MHWs.R +++ b/prep_MHWs.R @@ -420,8 +420,8 @@ survey_summary_cti <- survey_summary %>% ######## # trawl and cti datasets -write_csv(survey_summary_cti, "survey_biomass_with_CTI.csv") -write_csv(survey_spp_summary_cti, "species_biomass_with_CTI.csv") +write_csv(survey_summary_cti, here("processed-data","survey_biomass_with_CTI.csv")) +write_csv(survey_spp_summary_cti, here("processed-data","species_biomass_with_CTI.csv")) write_csv(survey_start_times, here("processed-data","survey_start_times.csv")) # MHWs paired with ref_years diff --git a/prep_survey_extent_nc.R b/prep_survey_extent_nc.R index 15ba1d9..f6c01cb 100644 --- a/prep_survey_extent_nc.R +++ b/prep_survey_extent_nc.R @@ -1,11 +1,10 @@ # code to generate a netcdf file with trawl survey footprints for comparison with MHW data library(ncdf4) # see https://pjbartlein.github.io/REarthSysSci/netCDF.html#create-and-write-a-netcdf-file - +library(here) +library(tidyverse) # pull in data -load(here("processed-data","SurveyCPUEs26102020.Rdata")) # Europe -OApath <- "~/github/pinskylab-OceanAdapt-c913be5" # specify where this directory is stored on your machine -dat_exploded <- readRDS(paste0(OApath, "/data_clean/dat_exploded.rds")) # US +haul_info <- read.csv(here("processed-data","haul_info.csv")) # set up global 0.25x0.25 grid nlon <- 360/0.25 @@ -22,64 +21,29 @@ colnames(worlddf) <- c('lon','lat') worlddf$coords <- paste0(worlddf$lon,",",worlddf$lat) # get survey coordinates -surveycoordsUS <- dat_exploded %>% - select(lat, lon, region) %>% - distinct() %>% - mutate(lat_round = floor(lat*4)/4 + 0.125, - lon_round = floor(lon*4)/4 + 0.125) %>% - select(lon_round, lat_round, region) %>% - distinct() %>% - mutate(coords=paste0(lon_round,",",lat_round)) %>% - select(coords, region) %>% - mutate(regionName = ifelse(region %in% c("Northeast US Spring","Northeast US Fall"), "Northeast", - ifelse(region %in% c("Southeast US Spring", "Southeast US Summer", "Southeast US Fall"), "Southeast", - ifelse(region %in% c('West Coast Triennial','West Coast Annual'), 'West Coast', region)))) %>% # merge seasons of surveys in the same regions - select(-region) %>% - rename(region = regionName) - -surveycoordsUS_save <- dat_exploded %>% - select(lat, lon, region) %>% - distinct() %>% - mutate(regionName = ifelse(region %in% c("Northeast US Spring","Northeast US Fall"), "Northeast", - ifelse(region %in% c("Southeast US Spring", "Southeast US Summer", "Southeast US Fall"), "Southeast", - ifelse(region %in% c('West Coast Triennial','West Coast Annual'), 'West Coast', region)))) %>% # merge seasons of surveys in the same regions - select(-region) %>% - rename(region = regionName) - -# repeat for Europe - note that I think some coordinates are duplicated among surveys -surveycoordsEur <- surveycpue %>% - select(region, lat, long) %>% +surveycoords <- haul_info %>% + select(latitude, longitude, survey) %>% distinct() %>% - mutate(lat_round = floor(lat*4)/4 + 0.125, - lon_round = floor(long*4)/4 + 0.125) %>% - select(lon_round, lat_round, region) %>% + mutate(lat_round = floor(latitude*4)/4 + 0.125, + lon_round = floor(longitude*4)/4 + 0.125) %>% + select(lon_round, lat_round, survey) %>% distinct() %>% mutate(coords=paste0(lon_round,",",lat_round)) %>% - select(coords, region) - -#just for writing out lat/lon -surveycoordsEur_save <- surveycpue %>% - select(region, lat, long) %>% - distinct() %>% - rename(lon=long) - -# combine Europe and US -surveycoords <- rbind(surveycoordsEur, surveycoordsUS)%>% - mutate(survey=as.numeric(factor(region))) - -write_csv(rbind(surveycoordsEur_save, surveycoordsUS_save), file=here("processed-data","survey_coordinates.csv")) + select(coords, survey) %>% + arrange(survey) %>% + mutate(surveyID=as.numeric(factor(survey))) # save which region corresponds to which code surveyIDs <- surveycoords %>% - select(region, survey) %>% + select(surveyID, survey) %>% distinct() # alphabetical ordering -write_csv(surveyIDs, path=here("processed-data","trawl_survey_codes.csv")) +write.csv(surveyIDs,here("processed-data","trawl_survey_codes.csv")) # merge with world coordinates worldsurvey <- worlddf %>% - left_join(surveycoords %>% select(-region),by="coords") %>% + left_join(surveycoords %>% select(-survey),by="coords") %>% select(-coords) %>% - replace_na(list(survey=0)) # replace NAs with FALSE + replace_na(list(surveyID=0)) # replace NAs with FALSE # set up nc file ncfile <- here("processed-data","survey_extent.nc") @@ -106,7 +70,7 @@ for(i in 1:nobs) { k <- which.min(abs(worldlat-tmp_df03$lat[i])) # copy data from the data frame to array - surv_array3[j,k] <- (tmp_df03$survey[i]) + surv_array3[j,k] <- (tmp_df03$surveyID[i]) } # create netCDF file and put arrays - will throw an error if file exists diff --git a/processed-data/survey_extent.nc b/processed-data/survey_extent.nc index aa18e52..e96b137 100644 Binary files a/processed-data/survey_extent.nc and b/processed-data/survey_extent.nc differ diff --git a/processed-data/survey_start_times.csv b/processed-data/survey_start_times.csv index 0aa17e6..eea975e 100644 --- a/processed-data/survey_start_times.csv +++ b/processed-data/survey_start_times.csv @@ -1,457 +1,692 @@ -region,year,month_year,ref_year,survey_date -aleutian_islands,1983,5-1983,aleutian_islands-5-1983,1983-05-01 -aleutian_islands,1997,5-1997,aleutian_islands-5-1997,1997-05-01 -aleutian_islands,2000,5-2000,aleutian_islands-5-2000,2000-05-01 -aleutian_islands,2002,5-2002,aleutian_islands-5-2002,2002-05-01 -aleutian_islands,1986,5-1986,aleutian_islands-5-1986,1986-05-01 -aleutian_islands,1991,5-1991,aleutian_islands-5-1991,1991-05-01 -aleutian_islands,1994,5-1994,aleutian_islands-5-1994,1994-05-01 -aleutian_islands,2004,5-2004,aleutian_islands-5-2004,2004-05-01 -aleutian_islands,2006,5-2006,aleutian_islands-5-2006,2006-05-01 -aleutian_islands,2010,5-2010,aleutian_islands-5-2010,2010-05-01 -aleutian_islands,2012,5-2012,aleutian_islands-5-2012,2012-05-01 -aleutian_islands,2014,5-2014,aleutian_islands-5-2014,2014-05-01 -aleutian_islands,2016,5-2016,aleutian_islands-5-2016,2016-05-01 -aleutian_islands,2018,5-2018,aleutian_islands-5-2018,2018-05-01 -eastern_bering_sea,1982,5-1982,eastern_bering_sea-5-1982,1982-05-01 -eastern_bering_sea,1983,5-1983,eastern_bering_sea-5-1983,1983-05-01 -eastern_bering_sea,1984,5-1984,eastern_bering_sea-5-1984,1984-05-01 -eastern_bering_sea,1987,5-1987,eastern_bering_sea-5-1987,1987-05-01 -eastern_bering_sea,1985,5-1985,eastern_bering_sea-5-1985,1985-05-01 -eastern_bering_sea,1986,5-1986,eastern_bering_sea-5-1986,1986-05-01 -eastern_bering_sea,1988,5-1988,eastern_bering_sea-5-1988,1988-05-01 -eastern_bering_sea,1989,5-1989,eastern_bering_sea-5-1989,1989-05-01 -eastern_bering_sea,1990,5-1990,eastern_bering_sea-5-1990,1990-05-01 -eastern_bering_sea,1991,5-1991,eastern_bering_sea-5-1991,1991-05-01 -eastern_bering_sea,1992,5-1992,eastern_bering_sea-5-1992,1992-05-01 -eastern_bering_sea,1993,5-1993,eastern_bering_sea-5-1993,1993-05-01 -eastern_bering_sea,1994,5-1994,eastern_bering_sea-5-1994,1994-05-01 -eastern_bering_sea,1995,5-1995,eastern_bering_sea-5-1995,1995-05-01 -eastern_bering_sea,1996,5-1996,eastern_bering_sea-5-1996,1996-05-01 -eastern_bering_sea,1997,5-1997,eastern_bering_sea-5-1997,1997-05-01 -eastern_bering_sea,1998,5-1998,eastern_bering_sea-5-1998,1998-05-01 -eastern_bering_sea,1999,5-1999,eastern_bering_sea-5-1999,1999-05-01 -eastern_bering_sea,2000,5-2000,eastern_bering_sea-5-2000,2000-05-01 -eastern_bering_sea,2001,5-2001,eastern_bering_sea-5-2001,2001-05-01 -eastern_bering_sea,2002,5-2002,eastern_bering_sea-5-2002,2002-05-01 -eastern_bering_sea,2003,5-2003,eastern_bering_sea-5-2003,2003-05-01 -eastern_bering_sea,2004,5-2004,eastern_bering_sea-5-2004,2004-05-01 -eastern_bering_sea,2005,5-2005,eastern_bering_sea-5-2005,2005-05-01 -eastern_bering_sea,2006,5-2006,eastern_bering_sea-5-2006,2006-05-01 -eastern_bering_sea,2007,5-2007,eastern_bering_sea-5-2007,2007-05-01 -eastern_bering_sea,2008,5-2008,eastern_bering_sea-5-2008,2008-05-01 -eastern_bering_sea,2009,5-2009,eastern_bering_sea-5-2009,2009-05-01 -eastern_bering_sea,2010,5-2010,eastern_bering_sea-5-2010,2010-05-01 -eastern_bering_sea,2011,5-2011,eastern_bering_sea-5-2011,2011-05-01 -eastern_bering_sea,2012,5-2012,eastern_bering_sea-5-2012,2012-05-01 -eastern_bering_sea,2013,5-2013,eastern_bering_sea-5-2013,2013-05-01 -eastern_bering_sea,2014,5-2014,eastern_bering_sea-5-2014,2014-05-01 -eastern_bering_sea,2015,5-2015,eastern_bering_sea-5-2015,2015-05-01 -eastern_bering_sea,2016,5-2016,eastern_bering_sea-5-2016,2016-05-01 -eastern_bering_sea,2017,5-2017,eastern_bering_sea-5-2017,2017-05-01 -eastern_bering_sea,2018,5-2018,eastern_bering_sea-5-2018,2018-05-01 -gulf_of_alaska,1990,5-1990,gulf_of_alaska-5-1990,1990-05-01 -gulf_of_alaska,1984,5-1984,gulf_of_alaska-5-1984,1984-05-01 -gulf_of_alaska,1993,5-1993,gulf_of_alaska-5-1993,1993-05-01 -gulf_of_alaska,1996,5-1996,gulf_of_alaska-5-1996,1996-05-01 -gulf_of_alaska,1999,5-1999,gulf_of_alaska-5-1999,1999-05-01 -gulf_of_alaska,1987,5-1987,gulf_of_alaska-5-1987,1987-05-01 -gulf_of_alaska,2007,5-2007,gulf_of_alaska-5-2007,2007-05-01 -gulf_of_alaska,2009,5-2009,gulf_of_alaska-5-2009,2009-05-01 -gulf_of_alaska,2003,5-2003,gulf_of_alaska-5-2003,2003-05-01 -gulf_of_alaska,2005,5-2005,gulf_of_alaska-5-2005,2005-05-01 -gulf_of_alaska,2011,5-2011,gulf_of_alaska-5-2011,2011-05-01 -gulf_of_alaska,2013,5-2013,gulf_of_alaska-5-2013,2013-05-01 -gulf_of_alaska,2015,5-2015,gulf_of_alaska-5-2015,2015-05-01 -gulf_of_alaska,2017,5-2017,gulf_of_alaska-5-2017,2017-05-01 -gulf_of_mexico,2008,5-2008,gulf_of_mexico-5-2008,2008-05-01 -gulf_of_mexico,2009,5-2009,gulf_of_mexico-5-2009,2009-05-01 -gulf_of_mexico,2010,5-2010,gulf_of_mexico-5-2010,2010-05-01 -gulf_of_mexico,2011,5-2011,gulf_of_mexico-5-2011,2011-05-01 -gulf_of_mexico,2012,5-2012,gulf_of_mexico-5-2012,2012-05-01 -gulf_of_mexico,2013,5-2013,gulf_of_mexico-5-2013,2013-05-01 -gulf_of_mexico,2014,5-2014,gulf_of_mexico-5-2014,2014-05-01 -gulf_of_mexico,2015,5-2015,gulf_of_mexico-5-2015,2015-05-01 -gulf_of_mexico,2016,5-2016,gulf_of_mexico-5-2016,2016-05-01 -gulf_of_mexico,2017,5-2017,gulf_of_mexico-5-2017,2017-05-01 -gulf_of_mexico,2019,5-2019,gulf_of_mexico-5-2019,2019-05-01 -northeast,1973,2-1973,northeast-2-1973,1973-02-01 -northeast,1974,2-1974,northeast-2-1974,1974-02-01 -northeast,1976,2-1976,northeast-2-1976,1976-02-01 -northeast,1978,2-1978,northeast-2-1978,1978-02-01 -northeast,1979,2-1979,northeast-2-1979,1979-02-01 -northeast,1980,2-1980,northeast-2-1980,1980-02-01 -northeast,1981,2-1981,northeast-2-1981,1981-02-01 -northeast,1982,2-1982,northeast-2-1982,1982-02-01 -northeast,1983,2-1983,northeast-2-1983,1983-02-01 -northeast,1984,2-1984,northeast-2-1984,1984-02-01 -northeast,1985,2-1985,northeast-2-1985,1985-02-01 -northeast,1986,2-1986,northeast-2-1986,1986-02-01 -northeast,1987,2-1987,northeast-2-1987,1987-02-01 -northeast,1988,2-1988,northeast-2-1988,1988-02-01 -northeast,1989,2-1989,northeast-2-1989,1989-02-01 -northeast,1990,2-1990,northeast-2-1990,1990-02-01 -northeast,1991,2-1991,northeast-2-1991,1991-02-01 -northeast,1992,2-1992,northeast-2-1992,1992-02-01 -northeast,1993,2-1993,northeast-2-1993,1993-02-01 -northeast,1994,2-1994,northeast-2-1994,1994-02-01 -northeast,1995,2-1995,northeast-2-1995,1995-02-01 -northeast,1996,2-1996,northeast-2-1996,1996-02-01 -northeast,1997,2-1997,northeast-2-1997,1997-02-01 -northeast,1998,2-1998,northeast-2-1998,1998-02-01 -northeast,1999,2-1999,northeast-2-1999,1999-02-01 -northeast,2000,2-2000,northeast-2-2000,2000-02-01 -northeast,2001,2-2001,northeast-2-2001,2001-02-01 -northeast,2002,2-2002,northeast-2-2002,2002-02-01 -northeast,2003,2-2003,northeast-2-2003,2003-02-01 -northeast,2004,2-2004,northeast-2-2004,2004-02-01 -northeast,2005,2-2005,northeast-2-2005,2005-02-01 -northeast,2006,2-2006,northeast-2-2006,2006-02-01 -northeast,2007,2-2007,northeast-2-2007,2007-02-01 -northeast,2008,2-2008,northeast-2-2008,2008-02-01 -northeast,2009,2-2009,northeast-2-2009,2009-02-01 -northeast,2010,2-2010,northeast-2-2010,2010-02-01 -northeast,2011,2-2011,northeast-2-2011,2011-02-01 -northeast,2012,2-2012,northeast-2-2012,2012-02-01 -northeast,2013,2-2013,northeast-2-2013,2013-02-01 -northeast,2015,2-2015,northeast-2-2015,2015-02-01 -northeast,2016,2-2016,northeast-2-2016,2016-02-01 -northeast,2017,2-2017,northeast-2-2017,2017-02-01 -northeast,2018,2-2018,northeast-2-2018,2018-02-01 -northeast,2019,2-2019,northeast-2-2019,2019-02-01 -northeast,1972,2-1972,northeast-2-1972,1972-02-01 -northeast,1975,2-1975,northeast-2-1975,1975-02-01 -northeast,1977,2-1977,northeast-2-1977,1977-02-01 -northeast,2014,2-2014,northeast-2-2014,2014-02-01 -scotian_shelf,1970,6-1970,scotian_shelf-6-1970,1970-06-01 -scotian_shelf,1971,6-1971,scotian_shelf-6-1971,1971-06-01 -scotian_shelf,1972,6-1972,scotian_shelf-6-1972,1972-06-01 -scotian_shelf,1973,6-1973,scotian_shelf-6-1973,1973-06-01 -scotian_shelf,1974,6-1974,scotian_shelf-6-1974,1974-06-01 -scotian_shelf,1975,6-1975,scotian_shelf-6-1975,1975-06-01 -scotian_shelf,1976,6-1976,scotian_shelf-6-1976,1976-06-01 -scotian_shelf,1977,6-1977,scotian_shelf-6-1977,1977-06-01 -scotian_shelf,1979,6-1979,scotian_shelf-6-1979,1979-06-01 -scotian_shelf,1980,6-1980,scotian_shelf-6-1980,1980-06-01 -scotian_shelf,1981,6-1981,scotian_shelf-6-1981,1981-06-01 -scotian_shelf,1982,6-1982,scotian_shelf-6-1982,1982-06-01 -scotian_shelf,1991,6-1991,scotian_shelf-6-1991,1991-06-01 -scotian_shelf,1983,6-1983,scotian_shelf-6-1983,1983-06-01 -scotian_shelf,1984,6-1984,scotian_shelf-6-1984,1984-06-01 -scotian_shelf,1985,6-1985,scotian_shelf-6-1985,1985-06-01 -scotian_shelf,1987,6-1987,scotian_shelf-6-1987,1987-06-01 -scotian_shelf,1988,6-1988,scotian_shelf-6-1988,1988-06-01 -scotian_shelf,1989,6-1989,scotian_shelf-6-1989,1989-06-01 -scotian_shelf,1990,6-1990,scotian_shelf-6-1990,1990-06-01 -scotian_shelf,1992,6-1992,scotian_shelf-6-1992,1992-06-01 -scotian_shelf,1993,6-1993,scotian_shelf-6-1993,1993-06-01 -scotian_shelf,1994,6-1994,scotian_shelf-6-1994,1994-06-01 -scotian_shelf,1995,6-1995,scotian_shelf-6-1995,1995-06-01 -scotian_shelf,1996,6-1996,scotian_shelf-6-1996,1996-06-01 -scotian_shelf,1997,6-1997,scotian_shelf-6-1997,1997-06-01 -scotian_shelf,1998,6-1998,scotian_shelf-6-1998,1998-06-01 -scotian_shelf,1999,6-1999,scotian_shelf-6-1999,1999-06-01 -scotian_shelf,2000,6-2000,scotian_shelf-6-2000,2000-06-01 -scotian_shelf,2001,6-2001,scotian_shelf-6-2001,2001-06-01 -scotian_shelf,2002,6-2002,scotian_shelf-6-2002,2002-06-01 -scotian_shelf,2003,6-2003,scotian_shelf-6-2003,2003-06-01 -scotian_shelf,2005,6-2005,scotian_shelf-6-2005,2005-06-01 -scotian_shelf,2006,6-2006,scotian_shelf-6-2006,2006-06-01 -scotian_shelf,2009,6-2009,scotian_shelf-6-2009,2009-06-01 -scotian_shelf,2010,6-2010,scotian_shelf-6-2010,2010-06-01 -scotian_shelf,2011,6-2011,scotian_shelf-6-2011,2011-06-01 -scotian_shelf,2012,6-2012,scotian_shelf-6-2012,2012-06-01 -scotian_shelf,2013,6-2013,scotian_shelf-6-2013,2013-06-01 -scotian_shelf,2014,6-2014,scotian_shelf-6-2014,2014-06-01 -scotian_shelf,2015,6-2015,scotian_shelf-6-2015,2015-06-01 -scotian_shelf,2016,6-2016,scotian_shelf-6-2016,2016-06-01 -scotian_shelf,2017,6-2017,scotian_shelf-6-2017,2017-06-01 -scotian_shelf,2004,6-2004,scotian_shelf-6-2004,2004-06-01 -scotian_shelf,2007,6-2007,scotian_shelf-6-2007,2007-06-01 -scotian_shelf,2008,6-2008,scotian_shelf-6-2008,2008-06-01 -southeast,1989,4-1989,southeast-4-1989,1989-04-01 -southeast,1990,4-1990,southeast-4-1990,1990-04-01 -southeast,1991,4-1991,southeast-4-1991,1991-04-01 -southeast,1992,4-1992,southeast-4-1992,1992-04-01 -southeast,1993,4-1993,southeast-4-1993,1993-04-01 -southeast,1994,4-1994,southeast-4-1994,1994-04-01 -southeast,1995,4-1995,southeast-4-1995,1995-04-01 -southeast,1996,4-1996,southeast-4-1996,1996-04-01 -southeast,1997,4-1997,southeast-4-1997,1997-04-01 -southeast,1998,4-1998,southeast-4-1998,1998-04-01 -southeast,1999,4-1999,southeast-4-1999,1999-04-01 -southeast,2000,4-2000,southeast-4-2000,2000-04-01 -southeast,2001,4-2001,southeast-4-2001,2001-04-01 -southeast,2002,4-2002,southeast-4-2002,2002-04-01 -southeast,2003,4-2003,southeast-4-2003,2003-04-01 -southeast,2004,4-2004,southeast-4-2004,2004-04-01 -southeast,2005,4-2005,southeast-4-2005,2005-04-01 -southeast,2006,4-2006,southeast-4-2006,2006-04-01 -southeast,2007,4-2007,southeast-4-2007,2007-04-01 -southeast,2008,4-2008,southeast-4-2008,2008-04-01 -southeast,2009,4-2009,southeast-4-2009,2009-04-01 -southeast,2010,4-2010,southeast-4-2010,2010-04-01 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-EVHOE,4 -FR-CGFS,5 -IE-IGFS,8 -NIGFS,9 -NS-IBTS,12 -PT-IBTS,13 -ROCKALL,14 -SWC-IBTS,17 -Aleutian Islands,1 -Eastern Bering Sea,3 -Gulf of Alaska,6 -Northeast,11 -West Coast,18 -Gulf of Mexico,7 -Southeast,16 -Scotian Shelf,15 +"","surveyID","survey" +"1",1,"AI" +"2",2,"BITS" +"3",3,"DFO-NF" +"4",4,"DFO-QCS" +"5",5,"EBS" +"6",6,"EVHOE" +"7",7,"FR-CGFS" +"8",8,"GMEX" +"9",9,"GOA" +"10",10,"GSL-N" +"11",11,"GSL-S" +"12",12,"ICE-GFS" +"13",13,"IE-IGFS" +"14",14,"NEUS" +"15",15,"NIGFS" +"16",16,"Nor-BTS" +"17",17,"NS-IBTS" +"18",18,"NZ" +"19",19,"PT-IBTS" +"20",20,"ROCKALL" +"21",21,"S-GEORG" +"22",22,"SCS" +"23",23,"SEUS" +"24",24,"SWC-IBTS" +"25",25,"WCANN" +"26",26,"WCTRI"