EdwardsEtal_JWM2023_abundancedatawithcovariates.csv heading explanations:

Site: Defines individual sites with UPS, DS2, DS1 sites for all 11 streams used in our surveys (site 11 has two UPS sites due to a beaver dam placement).

Transect: Indicates the location of the survey, UPS= upstream from direct application liming, DS sites are downstream from the direct applicaiton liming DS2= sites are fartherest downstream location to the site, DS1= sites are the 
closest to the direct applicaiton liming sites.

TransectNuM: Indicates the number transect within a single site, UPS were designated as 1s, DS1 were designated as 2s, and DS2 were designated as transect number 3, indcating the number transect
from upstream to downstream within a single site. 

SiteNum: Unique site ID.

S1-S5: Sampling occasions 1 through 5 presence (1) absence (0) records of spring salamanders.

Ab1-Ab5: Sampling occasions 1 through 5 counts of spring salamanders.

C1-C5: Conductivity measurements for each sampling occasion not used in our anaysis due to equipment error.

WT1-WT5: Standardized water temperature measuremets for each sampling occasion in °C.

AT1-AT5: Standardized air temperature measurements for each sampling occasion in  °C.

PH1-PH5: pH measurements for each sampling occasion.

RH1-RH5: Relative humidity for each sampling occasion expressed as a % out of 1.

W1-W5: Width in meters, measured to the nearest 0.1 m at the beginning, middle, and end of each transect, then averaged.

Max1-Max5:Maximum water depth measured to the nearest cm at three locations in the stream: the left bank, middle, and right bank (facing upstream), then averaged. 

DO1-DO5: Dissolved oxygen measurement for each sampling occasion, not used in our analysis due to equipment error.

Sand1-Sand5: The amount of sand covering each transect, observed and recorded as % sand coverage out of 100%.

Depth1-Depth5: Water depth measured to the nearest cm within the stream this was correlated with the stream depth average, so maximum depth was not included in the models.  

TimesLimed: Number of times each stream was limed, liming only occured at DS1 and DS2 locations, UPS sites were above the liming application sites and thus have 0 TimesLimed in the data. This is treated as a site covariate. 

DaysPast1-DaysPast5: Number of calendar days after the last liming event that the survey was conducted. 

CC: Canopy cover measured in early August using a Geographic Resource Solutions Densitometer by walking the middle of each transect and recording measurements every three meters (10 measurements per site), expressed as % out of 1.

Dist: Distance to the direct application liming site measured in meters. The first treatment site was 20-50 meters downstream from lime site using random number assignment; the second treatment site was located 100 meters downstream from the first.
The control site was located 100 meters Upstream of the DAL site indicated by -100. 

Distcat: Categorical grouping of the distance category, distance of -100 recieved a value of -100, distances between 20-50 were DS1 sites and distances between 152-178 were DS2 sites

EMB: Total embeddednesss of the stream, Measured using EPA habitat rapid assessment forma for high gradient streams. We ranked each transect according to the rapid assessment protocol during every 
sampling period and then averaged each rank to obtain an average for each site.

Years: Number of years that particular site has been limed.