Initial commit.

phyto-final/.gitignore

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+# History files
+.Rhistory
+.Rapp.history
+
+# Session Data files
+.RData
+
+# User-specific files
+.Ruserdata
+
+# Example code in package build process
+*-Ex.R
+
+# Output files from R CMD build
+/*.tar.gz
+
+# Output files from R CMD check
+/*.Rcheck/
+
+# RStudio files
+.Rproj.user/
+
+# produced vignettes
+vignettes/*.html
+vignettes/*.pdf
+
+# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+.httr-oauth
+
+# knitr and R markdown default cache directories
+*_cache/
+/cache/
+
+# Temporary files created by R markdown
+*.utf8.md
+*.knit.md
+
+# R Environment Variables
+.Renviron
+
+# Image files
+*.png
+*.jpg
+*.ai
+*.pdf
+
+# Folders 
+plots/
+Primer/

phyto-final/Aulacoseira.BV.Analyses.R

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+# Load Libraries and Data Files ------------------------------------------------
+## Script just to look at Aulacoseira
+
+library("tidyverse");packageVersion("tidyverse")
+
+# Set working directory
+setwd("./phyto_code/")
+getwd()
+
+# Set visual theme in ggplot
+theme_set(theme_bw())
+
+# Clean workspace
+rm(list=ls()) 
+
+# Set folder name to output graphs into
+output <- "plots"
+
+# Import combined EMP & AEU data files 
+load("RData/df_phyto.RData")
+
+# Filter out non-Aulacoseira taxa and years outside of FASTR study
+df_Aul <- df_phyto %>% 
+  filter(Genus == "Aulacoseira") %>%
+  filter(Year %in% c(2014,2015,2016,2017,2018,2019))
+
+# Plot GALD by year
+plot_GALD <- ggplot(df_Aul, aes(x = Year, y = GALD)) +
+  geom_jitter(width = 0.1)
+
+plot_GALD +
+  facet_wrap(Study ~ ., ncol = 1)
+
+# Plot Cell Biovolume by Year
+plot_Cell_BV <- ggplot(df_Aul, aes(x = Year, y = BV.Avg)) +
+  geom_jitter(width = 0.1)
+
+plot_Cell_BV +
+  facet_wrap(Study ~ ., ncol = 1)
+
+# Plot EMP and FASTR samples by year, facet by study
+ggplot(df_Aul, aes(x = Year, y = BV.um3.per.L)) +
+  geom_jitter(width = 0.1,
+              size = 2,
+              pch = 21, 
+              color = "black",
+              fill = "darkgreen") +
+  labs(x = "Year",
+       y = "Biovolume (um^3 per L)") +
+  facet_wrap(Study ~ ., ncol = 1)
+
+ggsave(path = output,
+       filename = "Fig 4.13 - Aulacoseira_abundance_FASTR_EMP_yearly_all.pdf", 
+       device = "pdf",
+       scale=1.0, 
+       units="in",
+       height=4,
+       width=4, 
+       dpi="print")
+
+## Plot EMP and FASTR samples by month, facet by study
+ggplot(df_Aul, aes(x = Month, y = BV.um3.per.L)) +
+  geom_jitter(data = subset(df_Aul, Year == "2016"),
+              width = 0.1,
+              size = 2,
+              pch = 21, 
+              color = "black",
+              fill = "darkgreen") +
+  labs(x = "Year",
+       y = "Biovolume (um^3 per L)") +
+  facet_wrap(Study ~ ., ncol = 1)
+
+ggsave(path = output,
+       filename = "Fig 4.14 - Aulacoseira_abundance_FASTR_EMP_month_2016.pdf", 
+       device = "pdf",
+       scale=1.0, 
+       units="in",
+       height=4,
+       width=4, 
+       dpi="print")

phyto-final/CSVs/EMP_Stations_All.csv

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+Station ID,Location,Latitude,Longitude,StationType
+ANH,San Joaquin River at Antioch,38.017854,-121.802939,Continuous
+C10A,San Joaquin River near Vernalis @ SJR Club,37.67934,-121.2647,Continuous
+C10A,San Joaquin River near Vernalis @ SJR Club,37.67934,-121.2647,Discrete
+C10A,San Joaquin River near Vernalis @ SJR Club,37.67934,-121.2647,Phytoplankton
+C3A,Sacramento River @ Hood,38.36771,-121.5205,Continuous
+C3A,Sacramento River @ Hood,38.36771,-121.5205,Discrete
+C3A,Sacramento River @ Hood,38.36771,-121.5205,Phytoplankton
+C9,West Canal @ Clifton Court Intake,37.83095,-121.554,Discrete
+C9,West Canal @ Clifton Court Intake,37.83095,-121.554,Phytoplankton
+D10,Sacramento River @ Chipps Island,38.04631,-121.9183,Discrete
+D10,Sacramento River @ Chipps Island,38.04631,-121.9183,Phytoplankton
+D10,Sacramento River @ Chipps Island,38.04631,-121.9183,Zooplankton
+D12,San Joaquin River @ Antioch Ship Channel,38.02161,-121.8063,Benthic
+D12,San Joaquin River @ Antioch Ship Channel,38.02161,-121.8063,Discrete
+D12,San Joaquin River @ Antioch Ship Channel,38.02161,-121.8063,Phytoplankton
+D12,San Joaquin River @ Antioch Ship Channel,38.02161,-121.8063,Zooplankton
+D16,San Joaquin River @ Twitchell Island,38.0969,-121.6691,Discrete
+D16,San Joaquin River @ Twitchell Island,38.0969,-121.6691,Phytoplankton
+D16,San Joaquin River @ Twitchell Island,38.0969,-121.6691,Zooplankton
+D19,Frank's Tract near Russo's Landing,38.04376,-121.6148,Discrete
+D19,Frank's Tract near Russo's Landing,38.04376,-121.6148,Phytoplankton
+D22,Sacramento River @ Emmaton,38.08453,-121.7391,Benthic
+D22,Sacramento River @ Emmaton,38.08453,-121.7391,Discrete
+D22,Sacramento River @ Emmaton,38.08453,-121.7391,Phytoplankton
+D22,Sacramento River @ Emmaton,38.08453,-121.7391,Zooplankton
+D24,Sacramento River below Rio Vista Bridge,38.15778,-121.6847,Continuous
+D26,San Joaquin River @ Potato Slough,38.07664,-121.5669,Benthic
+D26,San Joaquin River @ Potato Slough,38.07664,-121.5669,Discrete
+D26,San Joaquin River @ Potato Slough,38.07664,-121.5669,Phytoplankton
+D26,San Joaquin River @ Potato Slough,38.07664,-121.5669,Zooplankton
+D28A,Old River @ Rancho Del Rio,37.97048,-121.573,Benthic
+D28A,Old River @ Rancho Del Rio,37.97048,-121.573,Discrete
+D28A,Old River @ Rancho Del Rio,37.97048,-121.573,Phytoplankton
+D28A,Old River @ Rancho Del Rio,37.97048,-121.573,Zooplankton
+D4,Sacramento River above Point Sacramento,38.06248,-121.8205,Benthic
+D4,Sacramento River above Point Sacramento,38.06248,-121.8205,Discrete
+D4,Sacramento River above Point Sacramento,38.06248,-121.8205,Phytoplankton
+D4,Sacramento River above Point Sacramento,38.06248,-121.8205,Zooplankton
+D41 ,San Pablo Bay near Pinole Point,38.03022,-122.3729,Benthic
+D41 ,San Pablo Bay near Pinole Point,38.03022,-122.3729,Discrete
+D41 ,San Pablo Bay near Pinole Point,38.03022,-122.3729,Phytoplankton
+D41 ,San Pablo Bay near Pinole Point,38.03022,-122.3729,Zooplankton
+D41A,San Pablo Bay near Mouth of Petaluma River,38.08472,-122.3907,Benthic
+D41A,San Pablo Bay near Mouth of Petaluma River,38.08472,-122.3907,Discrete
+D41A,San Pablo Bay near Mouth of Petaluma River,38.08472,-122.3907,Phytoplankton
+D41A,San Pablo Bay near Mouth of Petaluma River,38.08472,-122.3907,Zooplankton
+D6,Suisun Bay @ Bulls Head nr. Martinez,38.04436,-122.1177,Benthic
+D6,Suisun Bay @ Bulls Head nr. Martinez,38.04436,-122.1177,Discrete
+D6,Suisun Bay @ Bulls Head nr. Martinez,38.04436,-122.1177,Phytoplankton
+D6,Suisun Bay @ Bulls Head nr. Martinez,38.04436,-122.1177,Zooplankton
+D7,Grizzly Bay @ Dolphin nr. Suisun Slough,38.11714,-122.0397,Discrete
+D7,Grizzly Bay @ Dolphin nr. Suisun Slough,38.11714,-122.0397,Phytoplankton
+D7,Grizzly Bay @ Dolphin nr. Suisun Slough,38.11714,-122.0397,Zooplankton
+D8,Suisun Bay off Middle Point nr. Nichols,38.05992,-121.99,Discrete
+D8,Suisun Bay off Middle Point nr. Nichols,38.05992,-121.99,Phytoplankton
+D8,Suisun Bay off Middle Point nr. Nichols,38.05992,-121.99,Zooplankton
+FRK,Frank's Tract Mid Tract,38.046499,-121.598063,Continuous
+GZL,Grizzly Bay,38.124281,-122.037962,Continuous
+HON,Honker Bay,38.072229,-121.93718,Continuous
+MAL,Sacramento River at Mallard Island,38.042799,-121.92013,Continuous
+MD10A,Disappointment Slough @ Bishop Cut,38.04226,-121.4199,Discrete
+MD10A,Disappointment Slough @ Bishop Cut,38.04226,-121.4199,Phytoplankton
+MD10A,Disappointment Slough @ Bishop Cut,38.04226,-121.4199,Zooplankton
+MRZ,Suisun Bay - Martinez,38.02762,-122.14052,Continuous
+MSD,San Joaquin River at Mossdale Bridge,37.786144,-121.306474,Continuous
+NZ002,Carquinez Strait near Glencove Harbor,38.06529,-122.2152,Discrete
+NZ002,Carquinez Strait near Glencove Harbor,38.06529,-122.2152,Phytoplankton
+NZ002,Carquinez Strait near Glencove Harbor,38.06529,-122.2152,Zooplankton
+NZ004,Carquinez Strait near Ozol Pier,38.03576,-122.1616,Discrete
+NZ004,Carquinez Strait near Ozol Pier,38.03576,-122.1616,Phytoplankton
+NZ004,Carquinez Strait near Ozol Pier,38.03576,-122.1616,Zooplankton
+NZ032,"Montezuma Slough, 2nd bend from mouth",38.16991,-122.0211,Discrete
+NZ032,"Montezuma Slough, 2nd bend from mouth",38.16991,-122.0211,Phytoplankton
+NZ032,"Montezuma Slough, 2nd bend from mouth",38.16991,-122.0211,Zooplankton
+NZ068,Sacramento River below Rio Vista Bridge,38.14272,-121.6895,Benthic
+NZ068,Sacramento River below Rio Vista Bridge,38.14272,-121.6895,Discrete
+NZ068,Sacramento River below Rio Vista Bridge,38.14272,-121.6895,Phytoplankton
+NZ068,Sacramento River below Rio Vista Bridge,38.14272,-121.6895,Zooplankton
+NZ325,San Pablo Bay near Rock Wall and Light 15,38.05798,-122.2919,Discrete
+NZ325,San Pablo Bay near Rock Wall and Light 15,38.05798,-122.2919,Phytoplankton
+NZ325,San Pablo Bay near Rock Wall and Light 15,38.05798,-122.2919,Zooplankton
+NZS42,Suisun Slough @ Volanti Slough,38.18045,-122.0476,Benthic
+NZS42,Suisun Slough @ Volanti Slough,38.18045,-122.0476,Discrete
+NZS42,Suisun Slough @ Volanti Slough,38.18045,-122.0476,Phytoplankton
+NZS42,Suisun Slough @ Volanti Slough,38.18045,-122.0476,Zooplankton
+P8,San Joaquin River @ Buckley Cove,37.97817,-121.3823,Discrete
+P8,San Joaquin River @ Buckley Cove,37.97817,-121.3823,Phytoplankton
+P8,San Joaquin River @ Buckley Cove,37.97817,-121.3823,Zooplankton
+PPT,SJR - Prisoner's Point,38.056296,-121.549973,Continuous
+RRI,SJR - Prisoner-Rough & Ready,37.962726,-121.365603,Continuous
+RYC,Suisun Bay - Cutoff Near Ryer,38.083961,-121.995641,Continuous
+SSI,Sacramento R Nr Sherman Island,38.074153,-121.761764,Continuous
+TWI,San Joaquin River at Twitchell Island,38.097455,-121.668718,Continuous

phyto-final/CSVs/FlowDatesDesignations_45days.csv

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+Year,PreFlowStart,PreFlowEnd,PostFlowStart,PostFlowEnd,WYType,FlowPulseType,NetFlowDays
+2011,7/8/2011,8/22/2011,10/25/2011,12/9/2011,W,NF,63
+2012,7/11/2012,8/25/2012,10/3/2012,11/17/2012,BN,CA,38
+2013,7/7/2013,8/21/2013,10/3/2013,11/17/2013,D,NF,42
+2014,7/25/2014,9/8/2014,9/24/2014,11/8/2014,C,NF,15
+2015,7/6/2015,8/20/2015,10/2/2015,11/16/2015,C,NF,42
+2016,5/29/2016,7/13/2016,8/2/2016,9/16/2016,BN,MA-SR,19
+2017,7/14/2017,8/28/2017,9/19/2017,11/3/2017,W,CA,12
+2018,7/13/2018,8/27/2018,9/27/2018,11/11/2018,BN,MA-Ag,30
+2019,7/11/2019,8/25/2019,9/22/2019,11/6/2019,W,MA-Ag,26

phyto-final/CSVs/FlowPulseType.csv

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+Year,FlowPulseType
+2011,High
+2012,High
+2013,Low
+2014,Low
+2015,High
+2016,High
+2017,Low
+2018,High
+2019,High