EVR628_Portfolio

This is Aidan O’Brien’s repository for EVR 628.

This project deals with the federally endangered Santa Cruz Long-toed salamander (SCLTS). The intent is to assess if there is any relationship between prey abundance or larval salamander density and SCLTS larval body condition.

Link to final report.

Repository Folders:

data

Contains subfolders for raw, processed, and output datasets.

results

Contains figure images

scripts

Contains three subfolders for scripts that process, analyze, or visualize data

Metadata:

morphometric_variables

Raw dataset containing data on each individual salamander larva captured during the duration of the study. This is necessary to calculate body conditions.

pond: Pond where individual was captured

date: Date of the survey

method: Method by which larva was captured. Meaning of most of these codes is defined in the html document attached to this file.

effort: Total effort conducted in the survey. Please note that this is NOT the effort required to capture the single individual but rather the total effort exerted for that survey.

species: Species of salamander captured.

mass: Mass in grams

svl: Snout to vent length of the larva in mm

tl: Total length of the larva in mm

age/sex: Life stage of the individual

development: Only for larvae. Can be 1, 2, 3, or 4 to signify how close an individual is to metamorphosis. 1 indicates no metamorphosis is occurring. 2 indicates some dorsal fin absorption. 3 indicates dorsal fin absorption past halfway down the back. 4 Indicates individual is essentially fully metamorphosed and could leave pond at any time.

genetic: Were tail clips taken from the individual (1 indicates yes; 0 indicates no)

year: Year in which larva was sampled.

coordinates

Contains localities of all sampled ponds

lat: Latitude

lon: Longitude

pond: Pond name

breeding_pond: Whether or not SCLTS larvae were detected in the pond at any point between 2021 and 2024. 1 indicates yes. 0 indicates no.

distance_to_nearest_breeding_pond: Distance in meters to the nearest other pond with SCLTS detected in it between 2021 and 2024.

aquatic_variables

This is the raw dataset of aquatic habitat parameters that are half of the data used to create the tidy dataset for analysis.

pond: The pond where measurements were obtained

year: Year of survey

larv_density: The density of SCLTS larvae in larvae/m\^2

med_prey: Total number of chironomids, ghost midges, and amphipods found in 4 plankton tows

large_prey: Combined density of chorus frog tadpoles, planorbid snails, physid snails, backswimmers, and waterboatmen (#/m\^2)

vert_pred: Combined density of newt larvae, newt adults, sticklebacks, sculpins, gambusia, and CTS (vertebrate predators/m\^2)

invert_pred: Combined density of crawfish, dytiscids, anisoptera, belostomatids, and damselfly larvae (invertebrates/m\^2)

plankton: Total number of plankton from 4 tow hauls

water_temp: Temperature of the pond (Celsius)

DO: Dissolved oxygen concentration (mg/L)

nitrates: Nitrate concentration

pH: pH of the pond

salinity: Salinity of the pond (parts per thousand)

chlorophyll: Chlorophyll concentration in the pond (parts per billion)

turbidity: Turbidity of the pond (NTU)

emergent_veg: Percent of pond surface with emergent vegetation

conductivity: Pond conductivity

depth: Pond depth at sampling (cm)

dist_to_breed: Distance to the nearest pond with larvae

per_suitable_hab: Percent of terrestrial habitat within 598m of a pond that is viable for juvenile and adult SCLTS

suitable_598_split: Amount of upland habitat that is viable for SCLTS within 598m after accounting for barrier roads (m\^2)

suitable_598: Amount of upland habitat that is viable for SCLTS within 598m (m\^2; does not account for roads)

tidy_data

This is the processed dataset used to conduct most visualizations and analyses.

pond_year: The year and pond where measurements were obtained

body_condition: Mean body condition of SCLTS larvae at the site. Calculated as the average residuals of log(mass) vs. log(SVL)