DOI: 10.5061/dryad.6q573n60j
title: King Rail and Common Moorhen egg pattern matching data

description: This dataset is a combination of egg images and processed output on
 pattern matching of eggshell surfaces from the images using
 NaturePatternMatch (NPM), additional data extracted from NPM, and field
 data. The data are separated into four folders based on species and
 analyses performed. There are two folders of scaled single egg images, one
 for King Rails, Rallus elegans, and one for Common Moorhens, Gallinula
 chloropus chloropus. Each photograph is identified by year, clutch and egg
 identity. Most of the Common Moorhen eggs are numbered in the order of
 their laying sequence, and they are further identified by laying hen. The
 NMDS folder includes NPM matching output and clutch identities needed to
 perform NMDS and PERMANOVA analyses. It includes consolidated and
 organized output from NPM for each species as well as files with clutch
 names needed to create merged datasets for graphing. These data were used
 to perform non-metric multidimensional scaling (NMDS) and permutational
 analysis of variance (PERMANOVA). The Linear Discriminant Analyses folder
 includes field data (egg length, width, and identity), pattern data
 extracted from NPM, as well as the estimated proportion of pigment
 measured within a scaled oval on binary images of eggs. This was used as a
 proxy for the relative amount of pigmentation on each egg. These data were
 used to conduct linear discriminant analyses for each species.
description: 1. Scaled individual egg images can be found in two folders:
 KingRailScaledIndividualEggPhotos and
 CommonMoorhenScaledIndividualEggPhotos<br> A. King Rail egg files
 are labeled in the following format: YYC##E## where YY is the last two
 digits of the year in which an egg was found, C signifies clutch, ## is
 the number of the clutch, E signifies egg, and ## signifies egg
 identification number within a clutch. For example, a file labeled 19C21E2
 would indicate that the year of laying was 2019, the assigned clutch ID
 was 21 and the egg identification number was 2. In most cases, the laying
 sequence of the eggs was not known.<br> B. Common Moorhen egg files
 are labeled in the following format: YYC##H##E## where YY is the last two
 digits of the year in which an egg was found, C signifies clutch, ## is
 the number of the clutch, H stands for hen and ## is the hen's
 identification number, E signifies egg, and ## stands for egg
 identification number. In many cases, the egg identification number
 signified also the laying sequence because laying order was known at many
 nests. For example, a file labeled 92C13H3E4 would indicate that the year
 of laying was 1992, the assigned clutch ID was 13, the egg was laid by hen
 3, and the egg sequence number in the clutch was 4. 2.
 NMDS files: Two file types are used for the NMDS and PERMANOVA analyses.
 The first files contain the pairwise NPM output. The second set of files
 are lists of clutches needed to create merged datasets for graphing in R.
 Numbers in a file name indicate a year, such as 2014, and files are
 delineated as “by clutch” or “indivfolders” standing for individual
 folders to indicate how the data were run through NPM. A file with “all”,
 “NS”, or “SS” indicate the following respectively: all data for a species
 from all years grouped in one file, all data from the North side of the
 refuge, and all data from the South side of the refuge. The date is also
 added to the end of all file names in the day month year format. Column
 titles of “Var1” and “Var2” correspond to the query egg and the best match
 respectively. “Value” refers to the matching coefficient generated by NPM
 for the quality of the match. Clutches in the files are named as follows:
 YYC#, where YY indicates the last two digits of the year the nest was
 found in, C indicates that it is referring to a clutch, and # is the
 number assigned to the clutch when found. Moorhen nests are named slightly
 differently with the following convention: YY-###-H where YY is the last
 two digits of the year the nest was found in, ### indicates the number
 assigned to the clutch when found, and H indicates the number assigned to
 the hen that laid the clutch. 3. LDA files: Files for
 linear discriminant analyses are named following this convention:
 shortened species name_lda_DDMMYYYY, where the shortened species name is
 KIRA for King Rail or MOOR for Common Moorhens. The date is also added in
 the day month year format. Columns within the files: Clutch_wHen indicates
 the a clutch ID where there is first a two letter code for the year then a
 two or three number code for the clutch and finally a one to three number
 code for the hen. Egg_Num refers to the individual egg sequence within a
 given clutch. Number black refers to the number of black pixels counted. %
 Black is the percentage of the measured area of the eggshell that had
 black pixels. Mass is the fresh weight of the egg in grams. Length and
 width are the measurements of each egg in mm. Volume is the volume of each
 egg in mL. Diameter is the calculated diameter of each egg.
 Number_Features refers to the number of features NPM detected on each
 eggshell’s surface. Scale_largest_feature refers to the size in arbitrary
 units of the largest feature detected on the eggshell’s surface by NPM.
 Dominant_orientation refers to the main direction in which the largest
 feature detected was oriented on the eggshell as measured by
 NPM.