README This file describes the R scripts and datasets associated with, “Zooplankton recovery from a whole-lake disturbance: Examining roles of abiotic factors, biotic interactions, and traits.” ############################################################################## lme.models.R conducts mixed effects models on water quality, zooplankton, and nutrient parameters with the files described below. The files with water quality and zooplankton parameters follow the convention “years after treatment.year of treatment” in either the prefix or suffix. For example, y1.14 refers to the first year following the 2014 rotenone treatment, y2.14 refers to the second year following the 2014 rotenone treatment, and y1.15 refers to the first year following the 2015 rotenone treatment. ----------------------------------------------------------------- Water quality files include: - phys,chem_y1.14.csv - phys,chem_y1.15.csv - phys,chem_y2.14.csv Headers: Type: categorical, Reference or Treatment, where treatment could be in either 2014 or 2015 (Treatment 2014, Treatment 2015) Period: categorical, before or after treatment occurred Lake: categorical, lake name Month: discrete, calendar month of sample event Day: discrete, calendar day of sample event Year: discrete, calendar year of sample event temp: continuous, water temperature at surface in degrees Celsius do: continuous, dissolved oxygen at surface in mg/L spc: continuous, specific conductance at surface in microSiemens/cm secchi: continuous, Secchi transparency in meters ----------------------------------------------------------------- Zooplankton files include: - y1.14.tab.all.csv - y1.15.tab.all.csv - y2.14.tab.all.csv Headers: Year: discrete, calendar year of sample Month: discrete, calendar month of sample (eg. June 2014 = 7) Month2: discrete, continuous month of sample (eg. June 2014 = 1) Type: categorical, Reference or Treatment, where treatment could be in either 2014 or 2015 (Treatment 2014, Treatment 2015) Period: categorical, Before or after treatment occurred, where after could be either one or two years after treatment (Y1.Post, Y2. Post) Lake: categorical, lake name Total: continuous, crustacean zooplankton abundance in individuals/m^3 Calanoids: continuous, adult calanoid copepod abundance in individuals/m^3 Cladocerans: continuous, adult cladoceran zooplankton abundance in individuals/m^3 Cyclopoids: continuous, adult cyclopoid copepod zooplankton abundance in individuals/m^3 Log.Total: continuous, log10 crustacean zooplankton abundance in individuals/m^3 Log.Cal: continuous, log10 adult calanoid copepod abundance in individuals/m^3 Log.Clad: continuous, log10 adult cladoceran zooplankton abundance in individuals/m^3 Log.Cycl: continuous, log10 adult cyclopoid copepod zooplankton abundance in individuals/m^3 shann: continuous, Shannon-Wiener diversity ----------------------------------------------------------------- Nutrient files include: - nutrients.csv Headers: treatment: categorical, reference or treatment year: discrete, calendar year of sample event period: categorical, before or after treatment occurred lake: categorical, lake name TP: continuous, July total phosphorus concentration in micrograms/L TN: continuous, July total nitrogen concentration in micrograms/L ############################################################################## P1.traits.R analyzes species traits in lakes before and after rotenone treatment (Prediction 1) with the files described below. ----------------------------------------------------------------- The relative abundance of species on each sampling date for treatment lakes is included in: - spp.rel.abun.trt.csv Headers: trt: categorical, treatment year in either 2014 or 2015 (trt 2014, trt 2015) period: categorical, before or after treatment occurred lake: categorical, lake name month: discrete, calendar month of sample (eg. June 2014 = 7) month2: discrete, continuous month of sample (eg. June 2014 = 1) months.post: continuous, number of months after rotenone (0 = before rotenone, partial months were for the month of treatment, which typically included >1 sampling date, 1…23) day: discrete, calendar day of sample event year: discrete, calendar year of sample event [species names in columns I to AG]: continuous, relative abundance of each taxa (between 0-1) ----------------------------------------------------------------- Species traits are included in: - trait.table.csv Headers: species: categorical, species names pelagic: binary, 0 = littoral, 1 = pelagic raptorial: binary, 0 = not raptorial feeder, 1 = raptorial feeder suspension: binary, 0 = not suspension feeder, 1 = suspension feeder filter: binary, 0 = not filter feeder, 1 = filter feeder current.cruiser: binary, 0 = not current cruiser, 1 = current cruiser herbivore: binary, 0 = not herbivore, 1 = herbivore omnivore: binary, 0=not omnivore, 1 = omnivore omni.carn = binary, 0 = not omnivore-carnivore or carnivore, 1 = omnivore-carnivore or carnivore size.cat = ordinal, 1 = smallest size category, 5 = largest size category egg.development: continuous, egg development time in days at 14 degrees Celsius dry.mass: individual zooplankter dry mass in mg ############################################################################## P2.abiotic.R analyzes the role of Secchi depth and water temperature in zooplankton recovery (Prediction 2) with the file described below. ----------------------------------------------------------------- The percent change in zooplankton abundance in relation to abiotic variables is included in: - temp,prod.csv. Headers: trt2: categorical, treatment year in either 2014 or 2015 (rotenone-2014, rotenone-2015) lake: categorical, lake name year: discrete, calendar year of sample event secchi: continuous, average Secchi depth in meters in July and August of respective year water.temp: continuous, average water column temperature in degrees Celsius in July and August of respective year pct.ref.total: continuous, percent change in total zooplankton between reference and rotenone lakes in respective year pct.ref.cal: continuous, percent change in calanoid copepods between reference and rotenone lakes in respective year pct.ref.clad: continuous, percent change in cladocerans between reference and rotenone lakes in respective year pct.ref.cyc: continuous, percent change in cyclopoid copepods between reference and rotenone lakes in respective year pct.prev.total: continuous, percent change in total zooplankton between the year before and after rotenone treatment pct.prev.cal: continuous, percent change in calanoid copepods between the year before and after rotenone treatment pct.prev.clad: continuous, percent change in cladocerans between the year before and after rotenone treatment pct.prev.cyc: continuous, percent change in cyclopoid copepods between the year before and after rotenone treatment ############################################################################## P3.fish.diversity.R analyzes the potential effects of fish stocking on zooplankton diversity (Prediction 3) with the file described below. ----------------------------------------------------------------- Fish stocking density and the change in zooplankton diversity are included in: - fish_div.csv. Headers: treatment: categorical, reference or rotenone lake: categorical, lake name year: discrete, calendar year of sample event date: calendar date of sample event day.of.year: discrete, day of year that sample event occurred deltaSW: continuous, change in Shannon-Wiener diversity in the two months after fish stocking compared to the two months prior to fish stocking log10.deltaSW: continuous, log10 of delta Shannon-Wiener fish.dens: continuous, fish stocking density in # fish/ha ############################################################################## P4.synchrony.R examines synchrony of taxonomic groups within each lake (Prediction 4) with the files described below. Zooplankton files include: y1.14.tab.all.csv, y1.15.tab.all.csv File contents are described above. ############################################################################## spatial.synchrony.R examines synchrony of taxonomic groups across all lakes with the files described below. Zooplankton files include: y1.14.tab.all.csv, y1.15.tab.all.csv File contents are described above.