This readme file was generated on 2024-10-22 by Sarah Risley



GENERAL INFORMATION

Title of Dataset: 2021-2022 Damariscotta Community Science Program 

Author/Principal Investigator Information
Name: Heather M. Leslie
ORCID: https://orcid.org/0000-0003-4512-9417
Institution: University of Maine Darling Marine Center
Address: 193 Clarks Cove Rd, Walpole, ME 04573
Email: heather.leslie@maine.edu

Author/Associate or Co-investigator Information
Name: Sarah C. Risley
ORCID: https://orcid.org/0009-0007-6013-0287
Institution: University of Maine Darling Marine Center
Address: 193 Clarks Cove Rd, Walpole, ME 04573
Email: Sarah.rilsey1@maine.edu

Date of data collection: 2021-07-20 - 2022-08-01 

Geographic location of data collection: Surveys (Ecological and Green Crab) occurred at 3 long-term monitoring sites in the towns of Damariscotta and Newcastle, ME, USA. 

Site Name	Waypoint	                  Access Address 	
Days Cove 	N 44° 01.618' W 069° 32.023'	  35 Schooner St, Damariscotta, ME 04543	
Westview	N 44° 00.816' W 069° 12.356'	  97 W View Rd, Damariscotta, ME 04543	
Chadbourne	N 44° 01.391' W 069° 32.348'	  3 Pleasant St, Newcastle, ME 04553	


Geographic location of data collection: Soft-shell clam recruitment studies occurred at 3 long-term monitoring sites in the towns of Damariscotta, Newcastle, and Walpole ME, USA. 

Site Name	Waypoint	                  Access Address 	
Days Cove 	N 44° 01.618' W 069° 32.023'	  35 Schooner St, Damariscotta, ME 04543	
Chadbourne	N 44° 01.391' W 069° 32.348'	  3 Pleasant St, Newcastle, ME 04553
Lowes Cove	N 43° 56'10"  W 69°34'30"	  193 Clarks Cove Rd, Walpole, ME 04573


Information about funding sources that supported the collection of the data: Broad Reach-Maine Shellfish Restoration and Resilience Fund, The University of Maine Mitchell Center for Sustainability Solutions, local donors of the UMaine Darling Marine Center 



SHARING/ACCESS INFORMATION

Licenses/restrictions placed on the data: NA

Links to publications that cite or use the data: https://digitalcommons.library.umaine.edu/cgi/viewcontent.cgi?article=1952&context=mpr

Links to other publicly accessible locations of the data: : https://umaine.edu/leslie-lab/research-2/damariscotta-community-science-project/

Links/relationships to ancillary data sets:
Downeast Institute - Clam Recruitment Monitoring Network = https://downeastinstitute.org/research/soft-shell-clams/shellfish-recruitment-monitoring-network/

Manomet Conservation Sciences - Green Crab Research = https://www.manomet.org/project/green-crab-research/?gad_source=1&gclid=Cj0KCQjw4Oe4BhCcARIsADQ0csmeJgiHvjW25DglrrfwNK44HTNuyNf5WSFrYs_do5VPnXhKdb1kAaUaAr4AEALw_wcB


Was data derived from another source? No 
If yes, list source(s): NA

Recommended citation for this dataset: Leslie, H. M., Risley, S. C. "2021-2022 Ecological Shellfish Survey" (Walpole, ME: University of Maine Darling Marine Center, 2024), https://umaine.edu/leslie-lab/research-2/damariscotta-community-science-project/



DATA & FILE OVERVIEW

File List: 
21-22_EcolSurvey_AnalysisMaster.csv = Survey results for the Shellfish Ecological Survey (cleaned for analysis)
22-21_GCSurvey_AnalysisMaster.csv = Survey results for the Green Crab Intertidal Survey (cleaned for analysis)
21-22_SSRecruitment_AnalysisMaster = Results from soft-shell clam recruitment box study (cleaned for analysis) 


METHODOLOGICAL INFORMATION

Description of methods used for collection/generation of data: Details on each of the protocol methods and materials for the community science program can be found here: https://drive.google.com/drive/folders/1fW7fHyXNnpshxz_i_C_y0JDtSR8V2Abd?usp=sharing

Specific methodology information for the Green Crab Intertidal Survey efforts through Manomet Conservation Sciences = https://www.manomet.org/project/green-crab-research/?gad_source=1&gclid=Cj0KCQjw4Oe4BhCcARIsADQ0csmeJgiHvjW25DglrrfwNK44HTNuyNf5WSFrYs_do5VPnXhKdb1kAaUaAr4AEALw_wcB

Specific methodology information for the soft-shell clam recruitment boxes through the Downeast Institute's Clam Recruitment Monitoring Network: https://downeastinstitute.org/research/soft-shell-clams/shellfish-recruitment-monitoring-network/

Methods for processing the data: Data from field surveys are recorded on standardized data sheets in the field. All data sheets are photographed prior to entry and the images are uploaded onto a shared Google Drive. 


Instrument- or software-specific information needed to interpret the data: RStudio Version 2023.06.1+524 (2023.06.1+524)

library(dplyr)
library(tidyr)
library(tidyverse)
library(here)
library(skimr) 
library(kableExtra) 



Describe any quality-assurance procedures performed on the data: Scientist Advisors enter all data collected into a shared Google spreadsheet, separate from the analysis (raw data only). Scientist Advisors will review data entered into the spreadsheet and compare every 5-10 lines with the uploaded photos of the data sheets.

Upon completion of data entry and data checks, the raw data Google spreadsheet will be downloaded as a CSV for analysis in R Studio. CSVs are then processed by prewritten code to calculate: species average abundance per m2 and species size structure. A series of statistical tests will be used to determine significant trends related to environmental and/or habitat variables.

People involved with sample collection, processing, analysis and/or submission: Sarah Risley, Heather Leslie, Amelia Papi, Caroline Rolfe, Jacob O'Neal, Brandon Mirra, Audrey Hufnagel, and multiple graduate, undergraduate, and high school student volunteers. 




DATA-SPECIFIC INFORMATION FOR: 21-22_EcolSurvey_AnalysisMaster.CSV


Number of variables: 18

Number of cases/rows: 904


Variable List: 

Year = Year survey was completed (2021 or 2022). 

Town = Name of town where survey was completed, Damariscotta/Newcastle.

Site = Name of site where survey was completed, Westview/Days Cove/ Chadbourne, see above for site information. 

Date = Date when survey was completed, YYYY-MM-DD.

Trans_Num = Survey transect number, Format: First three letters of site name + number in series, e.g., Wes3 is 3 transect completed at the Westview Site. 

Plot_Size_m2 = Size of area to be sampled, m2, 0.25 m2 sample plots were used for this survey.

Tidal_Zone = Location in the intertidal zone, Low/Mid/High. 

Survey_Habitat = Habitat area surveyed, the survey targeted two habitat types 1) Mudflat or 2) Rocky intertidal areas, Mudflat/Rocky.
 
Sample_Plot = Number of plot in series for each transect (#1-5), five plots total were sampled for each transect.

Algae_Percent = Estimated percent algal cover within each 0.25 m2 sample plot, rounded to the nearest 25%, 0%/25%/50%/100%.

Algae_Species = Species names of algae found within each sample plot, Fucus=F/ Ascophyllum=A/ General green algae (e.g., Ulva)=G/ General red algae (e.g., Chondrus)=R. 

Sediment = Characterization of the different sediment types found within each sample plot, Clay=C/ Mud=M/ Sand=S/ Gravel=G/, R=Rock. 

Percent_Rock = Estimated percent rock surface within each 0.25 m2 sample plot, rounded to the nearest 25%, 0%/25%/50%/100%. 

Num_Siphon = Number of visible siphon holes (for soft-shell clams) within each 0.25 m2 plot. 

Species = Name of species found within each 0.25 m2 plot. 

Shell_Length_or_Crab_CW_mm = Shell length measurement recorded for bivalve shellfish and carapace width (CW) recorded for each crab, measurements in millimeters, no measurements taken for worms beyond count and are entered as NA.  

Shell_height_or_qua_hingewidth_mm = Shell height recorded for all bivalve shellfish (hinge width captured for quahogs/hard shell clams), measurements in millimeters, no measurements taken for worms beyond count and are entered as NA. 

Other_Species = List of other species (outside of commercially important bivalve shellfish/worms and crabs) found within each 0.25 m2 plot.

Notes = Additional notes captured in the field. Notes often include descriptions of the plot itself that are notable (e.g., lots of organic material) or other observations. 


Missing data codes: 

F = Fucus family, includes Fucus vesiculosus (bladderwrack)
A = Ascophyllum family, includes Ascophyllum nodosum (rockweed) 
R = Red algae general, includes Palmaria palmata (Dulse) 
G = Green algae general, includes Ulva lactic (sea lettuce) 
SS = Soft-shell clam, Mya arenaria
Q = Quahog/ hard clam, Mercenary mercenaria
R = Razor clam, Ensis directus
SC = Atlantic surf clam, Spisula solidissima
AO = American oyster/eastern oyster, Crassostrea virginica
EO = European oyster/belon, Ostrea edulis
BW = Bloodworm, Glycera dibranchiata
SW = Sandworm, Nereis virens
MW = Marine worm, not identified to species level
GC = Green crab, Carninus maenas
RC = Atlantic rock crab, Cancer irroratus
JC = Jonah crab, Cancer borealis 
CW = Carapace width (mm)

Specialized formats or other abbreviations used: NA





DATA-SPECIFIC INFORMATION FOR: 22-21_GCSurvey_AnalysisMaster.csv 


Number of variables: 22

Number of cases/rows: 408


Variable List: 

Site = Name of site where survey was completed, Westview/Days Cove/ Chadbourne, see above for site information. 

Gps = GPS coordinates taken at header of survey transect, Lat/ Lon. 

Data = Date when survey was completed, YYYY-MM-DD.

Participants = Names of individuals who completed the survey.

Low_tide_time_24hr = Time of low tide on day that survey was completed, 24 hour time.

Low_tide_height = Low tide height, meters.

Lunar_phase_percent = Percent of full moon exposure.

Water_temp_c = Water temperature at site on day of survey, degrees celsius.

Salinity_ppt = Water salinity at site on day of survey, parts per thousand (ppt).

Survey_start_time = Time when survey began, 24 hour time.

Survey_end_time = Time when survey ended, 24 hour time.

Quad_num = Number sample quadrat in series for each transect, (#1-5).

Perc_moveable_rock = Estimated percent moveable rock (able to be lifted) within each sample plot, rounded to the nearest 25%, 0%/25%/50%/100%. 

Perc_algal_canopy = Estimated percent algal cover within each sample plot, rounded to the nearest 25%, 0%/25%/50%/100%.

Species_code = Name of species found within each plot. 

Cw_mm = Carapace width of crabs found within each plot, millimeters. 

Sex = Sex of crabs found within each plot, male (M) or female (F).

Num_claws = Number of claws counted on each crab, 0-2.

Num_legs = Number of legs counted on each crab, 0-8.

Shell_cond = Characterization of crab shell condition based on feel, hard shell/ soft shell/ pre-molt. 

Ovigerous = Crab holding a clutch of eggs, yes/no. 

Color = Color characterization of crab shell based on A.M. Young et al., Green Crab Color Index, 1-12. 
https://academic.oup.com/jcb/article/37/5/556/4158081

Notes = Additional notes captured in the field. Notes may include information about the specific green crab animals being sampled (e.g., copulating) or other observations about the crab conditions. 


Missing data codes: 
Cm = Carcinus maenas (green crab)
Cb = Cancer borealis (Jonah crab)
Ci = Cancer irroratus (rock crab)
Hs = Hemigrapsus sanguineus (Asian shore crab)
H = Hard shell 
S = Soft shell 
+P = Pre molt 
C = Celcius 
PPT = Parts per thousand 
Y/N = Yes/No 

Specialized formats or other abbreviations used: Species codes for crabs in the Ecological Survey differ from the Green Crab Survey. We chose to use codes for the Ecological survey that are derived from common names and are therefore easier to remember by our high school student volunteers. We maintained the abbreviations for the Green Crab Survey so that our survey results align with regional data collected as part of Manomet's Green Crab Research.  




DATA-SPECIFIC INFORMATION FOR: 21-22_SSRecruitment_AnalysisMaster


Number of variables: 12

Number of cases/rows: 292 


Variable List: 

Year = Year survey was completed (2021 or 2022). 

Town = Name of town where study was completed, Damariscotta/Newcastle/Walpole.

Site = Name of site where survey was completed, Westview/Days Cove/ Chadbourne, see above for site information. 

Date = Date when recruitment boxes were pulled from the mudflats for analysis, YYYY-MM-DD. 

Participants = Names of individuals who completed recruitment box extraction and processing.

Sample_Plot = Number of each sample plot in the study, C/G/P + series number.

Treatment = Distinguishes the different treatment types of the study, including recruitment boxes with groundcloth bottoms, recruitment boxes with PetScreen bottoms, and core samples collected adjacent to the recruitment boxes in the field.

Protected_Unprotected = General categorization of whether the treatment represented protected  

Depth_mm = Depth of sediment within each recruitment box, taken at the average depth in the box, millimeters.

Species = Name of species found within each recruitment box/ core sample.

Length_mm = Length in mm of the bivalve shellfish species shells and of the crab carapace widths.

Other_species = List of other species found within each recruitment box/ core sample.

Notes =  Additional notes captured in the field. Notes often include descriptions of the contents of the recruitment box itself that are notable (e.g., many bloodworms present) or other observations. 


Missing data codes:
C = Core sample, these represent the ambient/unprotected study conditions
G = Ground cloth, recruitment boxes with ground cloth bottoms (only in 2021)
P = PetScreen, recruitment boxes with PetScreen bottoms 
UN = Unprotected, core sample taken adjacent to recruitment boxes to represent the ambient/unprotected study conditions
PR = Protected, recruitment box sample (PetScreen or groundcloth)
SS = Soft-shell clam, Mya arenaria
Q = Quahog/ hard clam, Mercenary mercenaria
R = Razor clam, Ensis directus
SC = Atlantic surf clam, Spisula solidissima
AO = American oyster/eastern oyster, Crassostrea virginica
EO = European oyster/belon, Ostrea edulis
BW = Bloodworm, Glycera dibranchiata
SW = Sandworm, Nereis virens
MW = Marine worm, not identified to species level
GC = Green crab, Carninus maenas
RC = Atlantic rock crab, Cancer irroratus
JC = Jonah crab, Cancer borealis 


Specialized formats or other abbreviations used: NA 


