Final_code_analysis.R: This file contains the code necessary to plot and run the statistics for shell length, density, von bertalanffy growth function, and distance-to-dock analysis. The code was run in R 4.0.2. hst_bgyalgae3.1.csv: This file contains all data used to calculate size and species distribution. Photo is the filename/photonumber. Transect is the transect number for each site. Site is the abbreviated site name where the measurement was taken. Site is the abbreviated species name for each measurement. Reef is the reef type where the measurement was taken. length_mm is the shell length in mm. maturity is the designation of whether the clam was a recruit, juvenile, or adult. conservation is the classification of whether the measurement was inside an MPA, yes; or outside, no. dockdist_km is the distance each site was from the nearest dock in km. hst_bgyalgae3.1_depth.csv: This file contains the depth data for the study. depth is the final depth measurement used to analyze the depth, in meters, at which a clam was measured. transect is the transect number for each site. site is the abbreviated site name where the measurement was taken. species is the abbreviated species name for each measurement. reef is the reef type where the measurement was taken. Length_mm is the shell length in mm. depth_og is the original depth data from the HydroLight model before the data was converted to meters. density_clams.csv: this file contains the pivot table used to analyze depth within and between sites/reefs. reef is the reef type of each site. site is the abbreviated site names. conservation is the classification of whether the measurement was inside an MPA, yes; or outside, no. transect is the transect number for each site. species is the abbreviated species name for each measurement. count is the number of clams per species and within each transect per site. distancetodock.xlsx: This file contains the data for how far each site was to their nearest state dock. site is the site name. disttodockkm is the distance (km), measured in google earth, from the site to their state’s dock. alb_cc_1_14_19.csv: This file contains data used to calculate the depth each photo was taken at. filename is the name of file and photonumber. Ra is the red channel albedo of the masked clam in the image (Ra = Rclam/(Rwhite+Gwhite+Bwhite)). Ba is the blue channel albedo of the masked clam. Ga is the green channel albedo of the masked clam. Rs is the standard deviation of the red channel albedo of the masked clam. Bs is the standard deviation of the blue channel albedo of the masked clam. Gs is the standard deviation of the green channel albedo of the masked clam. white_B_mean is the mean value of the camera’s blue channel of the white swatch. white_B_std is the standard deviation of the camera’s blue channel of the white swatch. black_B_mean is the mean value of the camera’s blue channel of the black swatch. black_B_std is the standard deviation of the camera’s blue channel of the black swatch. white_R_mean is the standard deviation of the camera’s red channel of the white swatch. white_R_std is the standard deviation of the camera’s red channel of the white swatch. white_G_mean is the standard deviation of the camera’s green channel of the white swatch. white_G_std is the standard deviation of the camera’s green channel of the white swatch. black_R_mean is the mean value of the camera’s red channel of the black swatch. black_R_std is the standard deviation of the camera’s red channel of the black swatch. black_G_mean is the mean value of the camera’s green channel of the black swatch. black_G_std is the standard deviation of the camera’s green channel of the black swatch. gray_R_mean is the mean value of the camera’s red channel of the neutral35 swatch. gray_R_std is the standard deviation of the camera’s red channel of the neutral35 swatch.gray_G_mean is the mean value of the camera’s green channel of the neutral35 swatch. gray_G_std is the standard deviation of the camera’s green channel of the neutral35 swatch.gray_B_mean is the mean value of the camera’s blue channel of the neutral35 swatch. gray_B_std is the standard deviation of the camera’s blue channel of the neutral35 swatch. clam_pix_num is the total number of pixels in the masked clam. flux is the sum of white_R_mean, white_B_mean and white_G_mean. For determining depth, only white_R_mean, white_G_mean and white_B_mean and the subsequent standard deviation columns were used. CameraRGBCalib1.txt: This file contains the sensitivity curves for the NikonD4S used for all photos. The first column is wavelength, the second column is the response of the red channel in intensity, the third column is the response of the green channel and the last column is the response of the blue channel. depth_only.csv: This file contains the names of only the photos used in the “Population structure of giant clams (Sub-family: Tridacninae) across Palau: implications for conservation”. This is a subset of photos in the alb_cc_1_14_19.csv file. The first column is the filename and the second column is depth determined by the natural log of the Red channel of the white swatch divided by the atural log of the blue channel of the white swatch (-ln(R)/ln(B)). This column was not ultimately used in the data analysis. KinkoColorCard.mat: This file is a matlab structure that contains the text names of each swatch on the color standard used throughout this project, the measured reflectance (chart.reflectance) and the calcuated tristimulus values (xyz). PTester4Ramanabsprse3a.txt: This file contains the wavelength dependent absorption coefficient for the hydrolight model we used to model the depth at each photo (type-1 water, infinite bottom, Chl content: 0.03 mg/m^3). The first column is the wavelength (nm) and the subsequent columns are the absorption coefficient (1/m) with depth from 0 - 10 m (11 columns). PTester4Ramanabsprse3b.txt: This file contains the wavelength dependent scattering coefficient for the hydrolight model we used to model the depth at each photo (type-1 water, infinite bottom, Chl content: 0.03 mg/m^3). The first column is the wavelength (nm) and the subsequent columns are the scattering coefficient (1/m) with depth from 0 - 10 m (11 columns). WvwithIr0_10msci.txt: This file contains the downwelling radiance in the ocean modeled by hydrolight with depth. The first column is the wavelength (nm) and the subsequent columns are the downwelling irradiance (W/m^2) with depth for depths 0-10 m (11 columns).