Website last updated 2020-09-24 11:09:32 by Benjamin Meyer ()


Introduction

This document will outline preliminary results from exploratory data analysis from UAF/SFR’s ongoing Chena Fire/Drift 2020 research


People

Principal Investigator
Co-Principal Investigators
Other Personnel

Methods

Study Area


Field Sampling Effort

When and where did in-situ aquatic ecology data collection occur, and by whom?

  • Main stem drift (SFR 2019-2020, UAF 2020)
# Will import from J. Neuswanger Python output results.  B Meyer will use to create/display summary table of sampling efforts here
  • Headwaters drift (UAF 2020)
# Will import from J. Neuswanger Python output results.  B Meyer will use to create/display summary table of sampling efforts here
  • Juvenile Chinook fishing effort (SFR 2019-2020, UAF 2020)
# Import Excel sheet from Dropbox, "Fishing Data 2020.xlsx".  
# a.) Create simple bar chart of catch by site faceted by week
# b.) Create plot of CPUE vs time for MT and dipnets, faceted by Upper vs. Lower river
  • Juvenile Chinook weight/length (UAF/SFR 2019, 2020)
# Import  Excel sheet from dropbox, "Fish Datasheet 2020.xlsx".  Create plot(s) of mean FL vs time, a.) all sites combined and b.) by lower vs. upper river c.) by year
  • Water temperature logger data, (UAF/SFR 2019 & 2020)
# Import Excel sheet from dropbox, "/Users/bmeyer/Dropbox_auxiliary/Dropbox/Chena_Data_2020/UAF_Data/2020_Logger_Downloads/HOBO_Final_Data".  Create summary figure displaying temporal extent of various loggers and their parameters.
  • Hydrolab Sonde turbidity, DO, conductivity, and water temperature data, (UAF 2008, 2009, 2020)
# Import Excel sheet from dropbox, "/Users/bmeyer/Dropbox_auxiliary/Dropbox/Chena_Data_2020/UAF_Data/2020_Logger_Downloads/Hydrolab_Final_Data"
# read in 2020 Hydrolab data in progress


Remote Sensing Data collection

When and where did remote sensing data collection occur, and by whom?

# Summary table of dates & extent of aerial imagery data collected
  • Remote sensing of watershed vegetation composition and % of watershed burned (UAF 2020)
# Currently in discussion with potential collaborator(s) Dr. Alison York and Dr. Santosh Pandya


Laboratory Data Collection Effort

How many samples were processed, and what type?

  • Coarse fraction
# share in-text result from J. Neuswangers Python output table
  • Fine Fraction
# share in-text result from J. Neuswangers Python output table


Results

Headwaters Tributaries

  • Were habitat conditions distinct in recent burn vs. old burn tributaries?

    • Parameters
      • Drift debris density
      • Invertebrate density
      • Prey energy density
      • Water temperature
      • Turbidity
      • Others
Chena Mainstem

  • Were habitat conditions distinct in the main stem upstream vs. downstream of the 2019 Nugget Creek fire?

    • Parameters
      • Drift debris density
      • Invertebrate density
      • Prey energy density
      • Water temperature
      • Turbidity
      • Juvenile Chinook salmon growth rate
      • Others
# import mile28 site data

## from 7/10/20 - 7/28/20
mile28 <- read.csv("/Users/bmeyer/Dropbox_auxiliary/Dropbox/Chena_Data_2020/UAF_Data/2020_Logger_Downloads/Hydrolab _Raw_Downloads/Excel_Hydrolab_Downloads_2020/Mile28/Sonde46712_20200710_20200728.csv", head = F, skip = 12) %>% 
  slice(-2) %>%
    row_to_names(row_number = 1) %>%
    # remove hydrolab model and brand name
    #mutate_all(funs(str_replace(., "Hydrolab MS5 ", ""))) %>%
    slice(-1) %>%
    # convert columns to desired formats
    transform(Date = mdy(Date),
            LoggerID = as.character(LoggerID)) %>%
    filter(!is.na(Date)) %>%
    transform(Time = as.character(Time)) %>%
    transform(Time = as_hms(Time))  



# import first bridge site data

## from 7/10/20 - 7/28/20 
firstbridge <- read.csv("/Users/bmeyer/Dropbox_auxiliary/Dropbox/Chena_Data_2020/UAF_Data/2020_Logger_Downloads/Hydrolab _Raw_Downloads/Excel_Hydrolab_Downloads_2020/FirstBridge/Sonde45497_20200710_20200728.csv", head = F, skip = 12) %>%
  slice(-2) %>%
    row_to_names(row_number = 1) %>%
    # remove hydrolab model and brand name
    #mutate_all(funs(str_replace(., "Hydrolab MS5 ", ""))) %>%
    slice(-1) %>%
    # convert columns to desired formats
    transform(Date = mdy(Date),
            LoggerID = as.character(LoggerID)) %>%
    filter(!is.na(Date)) %>%
    transform(Time = as.character(Time)) %>%
    transform(Time = as_hms(Time)) 



# bind together dataframes & prep for plotting
hydrolabs <- bind_rows(mile28,firstbridge) %>%
  mutate(DateTime = as.POSIXct(paste(Date,Time))) %>%
  transform(DateTime = round_date(DateTime, "minute")) %>%
  arrange(DateTime) %>%
  separate(LoggerID, sep = " ", into = c("a","b","LoggerID")) %>%
  select(-a,-b,-Circ,-Date,-Time,-IBatt,-LoggerID) %>%
  gather(key = "Parameter", value = "value",Temp,SpCond,TurbSC,LDO.) %>%
  filter(!is.na(value)) %>%
  transform(value = as.numeric(value))

# rename hydrolab sites
HydrolabSites <- c("First Bridge" = "Upstream of Fire (Mile 37.7)", "Mile28" = "Downstram of Fire (Mile 37.7)")
# plot turbidity data
hydrolabs %>%
  filter(Parameter == "TurbSC") %>%
  ggplot(aes(DateTime,value)) +
  geom_point() +
  facet_grid(SiteID ~ ., labeller = labeller(SiteID = HydrolabSites)) +
  theme_bw() +
  ggtitle("") +
  xlab("") +
  ylab("Turbidity (NTU)") +
  ggtitle("Preliminary Turbidity Data, Summer 2020\nChena River Mainstem\nAbove vs. Below Nugget Creek Fire")

# note to self: attempt to follow cleaner coding example from KWF hydrolabs later

Note: the above data is preliminary and has not been checked for quality assurance.