This is a read me file describing the contents of data and code used in Shelton et al. Environmental DNA provides quantitative estimates of a threatened salmon species. 2019. This data repository contains 6 files with raw data, scripts for modifying the data, and statistical models for estimating parameters of interest from the data. Data: Chinook_seine_dat.csv - is observed catches of Chinook salmon from beach seine surveys in 2017 qPCR_data_Shelton_2018.Rdata - is data from quantitative PCR (qPCR) detecting Chinook salmon from water samples in 2017 R scripts to modify data, generate plots, and call the statistical models: qPCR_analysis_Dryad.R Seine_analysis_Dryad.R Bayesian statistical model in files the stan language: qPCR_Dryad_Shelton.stan - statistical model for quantitative PCR data Seine_chinook_Dryad_Shelton.stan - statistical model for beach seine data. ### Detailed descriptions of the data files. Chinook_seine_dat.csv: This data file has six columns: Site - A character vector indicating the sampling site (there are 8 unique sites) year - A numeric value indicating the year (2017) month - A numeric value indicating the calendar month (range 2 to 6) julian - The numeric value indicating the Julian day of the year on which sampling occurred species.comb - A character value indicating the species code ("CK" indicates Chinook salmon) qPCR_data_Shelton_2018.Rdata: contains a list called "QPCR.DAT" containing three separate data frames: 1) QPCR.DAT$dat.stand.chin is a data frame containing information about qPCR using known DNA concentrations to create a standard curve against which to compare samples taken from the field. It has the following columns of data. qpcr_date - numeric value noting which day the standard was performed (format four number year, two number month two number day:YYYYMMDD) Position - position on 96 well plate. The data is not used explicity in the analysis Detector - the name of the primer used for the qPCR assay Task - an Ct - the estimated PCR cycle at which the fluorescence exceeded the threshold level. This is the raw data that goes into the various statistical models Quantity - this is an extra column that can be ignored density - this is the known concentration of Chinook salmon DNA Flag - this is output from the PCR machine software and is not used in the analysis lab_label - the laboratory label number for each field sample (blank for this data frame) comments - a character column with occasional notes on specific samples species - a character column indicating the sapecies of interest ("chinook") pres - a binary data column indicating whether the Ct column is NA (pres=0) or numeric (pres=1) 2) QPCR.DAT$dat.samp is a data frame containing information about qPCR results from field collected samples. It has the following columns of data: qpcr_date - numeric value noting which day the standard was performed (format four number year, two number month two number day:YYYYMMDD) Position - position on 96 well plate. The data is not used explicity in the analysis Detector - the name of the primer used for the qPCR assay Task - an Ct - the estimated PCR cycle at which the fluorescence exceeded the threshold level. This is the raw data that goes into the various statistical models Quantity - this is an extra column that can be ignored density - this is the known concentration of Chinook salmon DNA Flag - this is output from the PCR machine software and is not used in the analysis lab_label - the laboratory label number for each field sample comments - a character column with occasional notes on specific samples species - a character column indicating the sapecies of interest ("chinook") year - numeric calendar year of sample (2017) month - numeric month of sample day - numeric day of sample site_name - character string indicating the site name. pres - a binary data column indicating whether the Ct column is NA (pres=0) or numeric (pres=1) 3) QPCR.DAT$dat.pcr.control.chin is a data frame containing information about qPCR results from control samples (samples which should have no DNA and exist to look for contamination during the laboratory processing). It has the following columns. qpcr_date - numeric value noting which day the standard was performed (format four number year, two number month two number day:YYYYMMDD) Position - position on 96 well plate. The data is not used explicity in the analysis Detector - the name of the primer used for the qPCR assay Task - an Ct - the estimated PCR cycle at which the fluorescence exceeded the threshold level. This is the raw data that goes into the various statistical models Quantity - this is an extra column that can be ignored density - this is the known concentration of Chinook salmon DNA Flag - this is output from the PCR machine software and is not used in the analysis lab_label - the laboratory label number for each field sample (blank for this data frame) comments - a character column with occasional notes on specific samples species - a character column indicating the sapecies of interest ("chinook") pres - a binary data column indicating whether the Ct column is NA (pres=0) or numeric (pres=1)