Manuscript

This Dryad package accompanies the manuscript:

Huron, N. A., Hedges, S. B., and Helmus, M. R. Detecting functional diversity loss under directional, stabilizing, and disruptive models of nonrandom anthropogenic extinction of species.

The study analyzes past and predicted-future nonrandom extinction in the Caribbean lizard genus Leiocephalus using body size, morphology, and simulation-based model comparisons.

Source

• Repository: https://github.com/ieco-lab/extinctFD
• Commit used to build this package: 9684ac78afb2d625d7c04efdfa412ded7350904f

Study overview

The manuscript examines functional diversity loss in Leiocephalus under random, directional, stabilizing, and disruptive extinction models.

Relevant data coverage described in the manuscript:

• the genus includes 32 known species
• maximum body size (snout-vent length, SVL) data are available for all 32 species
• an additional suite of 15 morphological traits was measured for 21 extant species and 1 extinct species
• these morphology data were summarized with principal component analysis (PCA)
• the first two PCA axes capture the major dimensions of variation:
  • PC1: primarily body-size-related morphology
  • PC2: primarily appendage/limb-length morphology

According to the manuscript text, PC1 explained 49.43% and PC2 explained 19.87% of total trait variance among the species included in the PCA.

What is included here

This directory contains non-.rda exports of the data objects used to reproduce the analyses in the extinctFD repository. It includes:

• cleaned source and analysis-input datasets
• PCA-ready analysis tables
• simulation outputs used to compare extinction models
• empirical replicate outputs used in the heuristic extinction-order analyses
• metadata and validation files documenting the export

Relationship of files to the manuscript

1. Body-size analyses

These files support analyses of past and predicted-future extinction using maximum SVL:

• maxsvl.csv
• iucn.csv
• empirical_extinct_reps.csv.gz
• rep_emp_svl.csv.gz
• rep_emp_present_svl.csv.gz
• sim_extinction.csv.gz
• sim_extinction_past.csv.gz
• sim_extinction_present.csv.gz

2. Morphology cleaning and species-level summaries

These files support construction of species-level morphology summaries and PCA inputs:

• morph.csv.gz
• morph_means.csv
• trait_key.csv

3. PCA and multivariate morphology analyses

These files support PCA-based analyses of ecomorphological diversity:

• dat_pca_tidy.csv
• dat_pca_tidy_nosvl.csv
• dat_pca_tidy_norescale.csv
• dat_pca_tidy_nosvl_norescale.csv
• empirical_extinct_reps_pca.csv.gz
• rep_emp_pc1.csv.gz
• rep_emp_pc2.csv.gz
• sim_extinction_present_pc1.csv.gz
• sim_extinction_present_pc2.csv.gz

Data files included in this Dryad package

Primary cleaned and analysis-input files

• morph.csv.gz — specimen-level morphology dataset used as the starting point for morphology cleaning and summarization
• maxsvl.csv — species-level maximum snout-vent length data used in body-size and extinction analyses
• morph_means.csv — species-level morphology summaries derived from cleaned specimen-level measurements
• iucn.csv — species metadata including IUCN categories, island grouping, range, and extinction-order fields used in the analyses
• trait_key.csv — trait code lookup table describing morphology variables
• dat_pca_tidy.csv — primary PCA-ready morphology table used in the main PCA analyses

Additional PCA variants

These are alternate analysis-ready PCA tables produced in the repository and retained here for reproducibility:

• dat_pca_tidy_nosvl.csv — PCA-ready table excluding SVL from the PCA
• dat_pca_tidy_norescale.csv — PCA-ready table without SVL correction/rescaling
• dat_pca_tidy_nosvl_norescale.csv — PCA-ready table without SVL in the PCA and without rescaling

Empirical replicate datasets

These files encode replicate extinction-order procedures used in the empirical heuristic analyses:

• empirical_extinct_reps.csv.gz — matrix of heuristic empirical extinction replicate sequences for body-size analyses
• empirical_extinct_reps_pca.csv.gz — matrix of heuristic empirical extinction replicate sequences for PCA analyses
• rep_emp_svl.csv.gz — stepwise empirical replicate summaries for body-size extinction analyses
• rep_emp_present_svl.csv.gz — stepwise empirical replicate summaries for present/future body-size extinction analyses
• rep_emp_pc1.csv.gz — stepwise empirical replicate summaries for PCA axis 1 analyses
• rep_emp_pc2.csv.gz — stepwise empirical replicate summaries for PCA axis 2 analyses

Simulated extinction outputs

These files contain the simulation outputs used to compare observed extinction trajectories to expected trajectories under different extinction models:

• sim_extinction.csv.gz — simulated extinction trajectories across models for the body-size analysis
• sim_extinction_past.csv.gz — simulated trajectories representing past extinction for body-size analyses
• sim_extinction_present.csv.gz — simulated trajectories representing predicted-future/present-threat extinction for body-size analyses
• sim_extinction_present_pc1.csv.gz — simulated trajectories for PCA axis 1 analyses
• sim_extinction_present_pc2.csv.gz — simulated trajectories for PCA axis 2 analyses

Notes on major variables and interpretation

iucn.csv

Contains species-level metadata used to define extinction-order scenarios and grouping variables. Fields include species identity, Red List status, island-bank grouping, and range-related information.

morph.csv.gz

Contains specimen-level morphology measurements used as the basis for cleaning, trait filtering, and downstream species-level summaries.

morph_means.csv

Contains species-level summarized morphology values after cleaning and aggregation.

dat_pca_tidy*.csv

Contain species-level metadata plus PCA scores. These tables are the main inputs for multivariate morphology analyses.

sim_extinction*.csv.gz

Contain model-based simulated extinction trajectories. Core columns are:

• n_spp — number of species remaining at that step
• avg — change in mean trait value
• var — change in trait variance
• type — extinction model
• rep — simulation replicate identifier

rep_emp*.csv.gz

Contain empirical heuristic replicate summaries. Core columns are:

• n_spp — number of species remaining at that step
• avg — change in mean trait value
• var — change in trait variance
• spp_rm — species removed at that step
• rep_num — empirical replicate identifier

empirical_extinct_reps*.csv.gz

Contain wide matrices of replicate extinction-order draws used to propagate uncertainty when multiple species shared overlapping extinction timing.

Metadata files

• manifest.csv — file-by-file inventory with source object names, classes, provenance, export status, and validation results
• validation_report.csv — round-trip export validation summary for each exported dataset

Export conventions

• Smaller tabular objects were exported as .csv
• Larger tables and matrices were exported as .csv.gz
• Missing values are written as empty fields
• Matrix objects were exported in rectangular tabular form preserving their column names

Missing values

Empty fields were intentionally preserved as blank cells in the deposited files. They were not replaced with NA, null, or n/a so that the archived tables remain faithful to the source data structures used in the analysis workflow.

Depending on the file and column, blank cells indicate one of the following:

• information was not recorded in the original source data
• information was unavailable from the source compilation
• field was not applicable for that row
• a summary value was structurally undefined for that analysis step

Validation

Each exported dataset was read back into R and checked for matching row count, column count, and column names relative to the exported in-memory table. See validation_report.csv for file-level validation results.

Excluded non-tabular objects

The following objects were documented in the manifest but not exported as Dryad datasets:

• extinction_pc1_best.rda / object extinction_pc1_best — saved ggplot object for the PCA axis 1 best-fit visualization
• extinction_pc2_best.rda / object extinction_pc2_best — saved ggplot object for the PCA axis 2 best-fit visualization

Files and variables

This section provides a file-by-file description of the Dryad deposit.

• All files ending in .csv.gz are gzipped single-file CSV tables. They do not contain nested folders or additional files.
• Missing values are represented as blank cells in the exported CSV/CSV.GZ files.
• Abbreviations used repeatedly in these files include: SVL = snout-vent length; PC = principal component; IUCN = International Union for Conservation of Nature; EX = extinct; CR = critically endangered; EN = endangered; VU = vulnerable; NT = near threatened; LC = least concern; TH = threatened (grouped category combining currently threatened extant taxa).

File: sim_extinction_present_pc1.csv.gz

Description: Simulated extinction trajectories for PCA axis 1 (PC1) during the present/future-threat analysis. The compressed archive contains one CSV table with five columns.

Variables

• n_spp: number of species remaining at a given extinction step.
• avg: change in the mean PC1 score relative to the starting assemblage mean.
• var: change in the variance of PC1 scores relative to the starting assemblage variance.
• type: simulated extinction model (random, stabilizing, disruptive, directional_l, directional_r). In plotting code these are relabeled as directional loss of smaller- or larger-bodied taxa.
• rep: simulation replicate identifier.

File: sim_extinction.csv.gz

Description: Simulated extinction trajectories across extinction models for the body-size analysis using maximum SVL. The compressed archive contains one CSV table with five columns.

Variables

• n_spp: number of species remaining at a given extinction step.
• avg: change in mean standardized maximum SVL relative to the starting mean.
• var: change in variance of standardized maximum SVL relative to the starting variance.
• type: simulated extinction model (random, stabilizing, disruptive, directional_l, directional_r).
• rep: simulation replicate identifier.

File: sim_extinction_present.csv.gz

Description: Simulated extinction trajectories for the present/future-threat body-size analysis. The compressed archive contains one CSV table with five columns.

Variables

• n_spp: number of species remaining at a given extinction step.
• avg: change in mean standardized maximum SVL relative to the starting mean for the present/future-threat subset.
• var: change in variance of standardized maximum SVL relative to the starting variance for the present/future-threat subset.
• type: simulated extinction model (random, stabilizing, disruptive, directional_l, directional_r).
• rep: simulation replicate identifier.

File: rep_emp_pc1.csv.gz

Description: Stepwise empirical heuristic replicate results for the PCA axis 1 (PC1) extinction analysis. Each row corresponds to one extinction step within one heuristic replicate. The compressed archive contains one CSV table with five columns.

Variables

• n_spp: number of species remaining after the removal step.
• avg: change in mean PC1 score relative to the starting mean.
• var: change in variance of PC1 scores relative to the starting variance.
• spp_rm: species removed at that step. Values are species epithets as used in the PCA tables; blank for the initial no-removal row.
• rep_num: heuristic empirical replicate identifier (r1-r10000).

File: dat_pca_tidy.csv

Description: Primary PCA-ready morphology table used in the main PCA analyses. This table combines species metadata with PCA scores derived from the log-transformed, centered, and scaled morphology matrix.

Variables

• species: species epithet used throughout the analysis tables.
• notes: species status note (extant, extinct, or exotic).
• island_bank: island or island-bank grouping assigned to the species.
• redlist: original IUCN Red List category (EX, CR, EN, VU, NT, LC).
• redlist2: collapsed status category used in the analyses (EX = extinct, TH = threatened extant taxa, LC = non-threatened extant taxa).
• total_island_area: total island area associated with the species occurrence grouping; retained from source metadata (area values in source units, interpreted as square kilometers).
• range: species range-size field retained from the source metadata (interpreted from the source table as area, in square kilometers).
• PC1: principal component 1 score.
• PC2: principal component 2 score.
• PC3: principal component 3 score.
• PC4: principal component 4 score.
• PC5: principal component 5 score.
• PC6: principal component 6 score.
• PC7: principal component 7 score.
• PC8: principal component 8 score.
• PC9: principal component 9 score.
• PC10: principal component 10 score.
• PC11: principal component 11 score.
• PC12: principal component 12 score.
• PC13: principal component 13 score.
• PC14: principal component 14 score.
• PC15: principal component 15 score.

File: sim_extinction_present_pc2.csv.gz

Description: Simulated extinction trajectories for PCA axis 2 (PC2) during the present/future-threat analysis. The compressed archive contains one CSV table with five columns.

Variables

• n_spp: number of species remaining at a given extinction step.
• avg: change in mean PC2 score relative to the starting assemblage mean.
• var: change in variance of PC2 scores relative to the starting assemblage variance.
• type: simulated extinction model (random, stabilizing, disruptive, directional_l, directional_r).
• rep: simulation replicate identifier.

File: dat_pca_tidy_norescale.csv

Description: PCA-ready morphology table variant produced without the SVL correction/rescaling step used in the main table. Species metadata columns are identical to dat_pca_tidy.csv.

Variables

• species: species epithet used throughout the analysis tables.
• notes: species status note (extant, extinct, or exotic).
• island_bank: island or island-bank grouping assigned to the species.
• redlist: original IUCN Red List category (EX, CR, EN, VU, NT, LC).
• redlist2: collapsed status category used in the analyses (EX, TH, LC).
• total_island_area: total island area associated with the species occurrence grouping; retained from source metadata (interpreted as square kilometers).
• range: species range-size field retained from source metadata (interpreted as square kilometers).
• PC1: principal component 1 score.
• PC2: principal component 2 score.
• PC3: principal component 3 score.
• PC4: principal component 4 score.
• PC5: principal component 5 score.
• PC6: principal component 6 score.
• PC7: principal component 7 score.
• PC8: principal component 8 score.
• PC9: principal component 9 score.
• PC10: principal component 10 score.
• PC11: principal component 11 score.
• PC12: principal component 12 score.
• PC13: principal component 13 score.
• PC14: principal component 14 score.
• PC15: principal component 15 score.

File: dat_pca_tidy_nosvl.csv

Description: PCA-ready morphology table variant in which SVL was excluded from the PCA before deriving principal component scores. Species metadata columns are identical to dat_pca_tidy.csv.

Variables

• species: species epithet used throughout the analysis tables.
• notes: species status note (extant, extinct, or exotic).
• island_bank: island or island-bank grouping assigned to the species.
• redlist: original IUCN Red List category (EX, CR, EN, VU, NT, LC).
• redlist2: collapsed status category used in the analyses (EX, TH, LC).
• total_island_area: total island area associated with the species occurrence grouping; retained from source metadata (interpreted as square kilometers).
• range: species range-size field retained from source metadata (interpreted as square kilometers).
• PC1: principal component 1 score.
• PC2: principal component 2 score.
• PC3: principal component 3 score.
• PC4: principal component 4 score.
• PC5: principal component 5 score.
• PC6: principal component 6 score.
• PC7: principal component 7 score.
• PC8: principal component 8 score.
• PC9: principal component 9 score.
• PC10: principal component 10 score.
• PC11: principal component 11 score.
• PC12: principal component 12 score.
• PC13: principal component 13 score.
• PC14: principal component 14 score.

File: empirical_extinct_reps_pca.csv.gz

Description: Matrix of 10,000 heuristic empirical extinction-order replicates used in the PCA extinction analyses. Rows correspond to species rows in the PCA analysis input used to bind these replicate orderings, and columns correspond to replicate extinction-order assignments. The compressed archive contains one CSV table.

Variables

• r1-r10000: heuristic replicate columns. Each column gives the sampled extinction-order value assigned to each row/species in one replicate.

File: rep_emp_present_svl.csv.gz

Description: Stepwise empirical heuristic replicate results for the present/future-threat body-size analysis. Each row corresponds to one extinction step within one heuristic replicate. The compressed archive contains one CSV table with five columns.

Variables

• n_spp: number of species remaining after the removal step.
• avg: change in mean standardized maximum SVL relative to the starting mean.
• var: change in variance of standardized maximum SVL relative to the starting variance.
• spp_rm: species removed at that step; blank for the initial no-removal row.
• rep_num: heuristic empirical replicate identifier (r1-r10000).

File: sim_extinction_past.csv.gz

Description: Simulated extinction trajectories for the past-extinction body-size analysis. The compressed archive contains one CSV table with five columns.

Variables

• n_spp: number of species remaining at a given extinction step.
• avg: change in mean standardized maximum SVL relative to the starting mean for the extinct-species subset.
• var: change in variance of standardized maximum SVL relative to the starting variance for the extinct-species subset.
• type: simulated extinction model (random, stabilizing, disruptive, directional_l, directional_r).
• rep: simulation replicate identifier.

File: empirical_extinct_reps.csv.gz

Description: Matrix of 10,000 heuristic empirical extinction-order replicates used in the body-size extinction analyses. Rows correspond to species rows in the body-size analysis input used to bind these replicate orderings, and columns correspond to replicate extinction-order assignments. The compressed archive contains one CSV table.

Variables

• r1-r10000: heuristic replicate columns. Each column gives the sampled extinction-order value assigned to each row/species in one replicate.

File: dat_pca_tidy_nosvl_norescale.csv

Description: PCA-ready morphology table variant produced both without SVL in the PCA and without the SVL correction/rescaling step. Species metadata columns are identical to dat_pca_tidy.csv.

Variables

• species: species epithet used throughout the analysis tables.
• notes: species status note (extant, extinct, or exotic).
• island_bank: island or island-bank grouping assigned to the species.
• redlist: original IUCN Red List category (EX, CR, EN, VU, NT, LC).
• redlist2: collapsed status category used in the analyses (EX, TH, LC).
• total_island_area: total island area associated with the species occurrence grouping; retained from source metadata (interpreted as square kilometers).
• range: species range-size field retained from source metadata (interpreted as square kilometers).
• PC1: principal component 1 score.
• PC2: principal component 2 score.
• PC3: principal component 3 score.
• PC4: principal component 4 score.
• PC5: principal component 5 score.
• PC6: principal component 6 score.
• PC7: principal component 7 score.
• PC8: principal component 8 score.
• PC9: principal component 9 score.
• PC10: principal component 10 score.
• PC11: principal component 11 score.
• PC12: principal component 12 score.
• PC13: principal component 13 score.
• PC14: principal component 14 score.

File: trait_key.csv

Description: Trait codebook linking numeric trait codes used in morph_means.csv and PCA preprocessing to their human-readable meanings.

Variables

• code: trait code used in the morphology summary tables.
• meaning: descriptive trait name corresponding to that code.

File: rep_emp_pc2.csv.gz

Description: Stepwise empirical heuristic replicate results for the PCA axis 2 (PC2) extinction analysis. Each row corresponds to one extinction step within one heuristic replicate. The compressed archive contains one CSV table with five columns.

Variables

• n_spp: number of species remaining after the removal step.
• avg: change in mean PC2 score relative to the starting mean.
• var: change in variance of PC2 scores relative to the starting variance.
• spp_rm: species removed at that step. Values are species epithets as used in the PCA tables; blank for the initial no-removal row.
• rep_num: heuristic empirical replicate identifier (r1-r10000).

File: morph_means.csv

Description: Species-level morphology summaries generated from the cleaned specimen-level morphology table. Linear measurements are in millimeters (mm) where applicable; count and categorical traits are retained in their native units.

Variables

• species: species name.
• 1: SVL (snout-vent length; mm).
• 1.1: maximum SVL (mm).
• 2: body length (mm).
• 3: fore-hind limb distance (mm).
• 4: midbody width (mm).
• 5: midbody height (mm).
• 6: pelvis width (mm).
• 7: pelvis height (mm).
• 8: tail condition (coded categorical trait).
• 9: tail1 vent-to-break length (mm).
• 9.1: total tail length (mm).
• 10: tail2 regenerated length (mm).
• 11: head length (mm).
• 12: head width (mm).
• 13: head height (mm).
• 14: jaw length (mm).
• 14.1: mental length (mm).
• 15: snout length (mm).
• 15.1: eye-nares distance (mm).
• 15.2: snout width (mm).
• 16.1: hand digit count.
• 16.2: finger IV length (mm).
• 17: finger IV metatarsal length (mm).
• 18: finger IV width (mm).
• 19: finger IV lamella count.
• 19.2: longest finger (coded categorical/identity field retained from source measurements).
• 19.3: longest finger length (mm).
• 19.4: longest finger metatarsal length (mm).
• 20: upperarm length (mm).
• 21: forearm length (mm).
• 22.1: foot digit count.
• 22.2: toe IV length (mm).
• 23: toe IV metatarsal length (mm).
• 24: toe IV width (mm).
• 25: toe IV lamella count.
• 25.2: longest toe (coded categorical/identity field retained from source measurements).
• 26: thigh length (mm).
• 27: shank length (mm).
• 28: ventral scale count midline.
• 29: ventral length of scale count.
• 30: ventral scale overlap.
• 31: ventral scale keeling.
• 32: ventral scale posterior margin.
• 33: dorsal scale count midline.
• 34: dorsal length of scale count.
• 35: dorsal scale overlap.
• 36: dorsal scale keeling.
• 37: dorsal scale posterior margin.

File: manifest.csv

Description: File-by-file inventory of source .rda objects, their Dryad export status, provenance, and validation results.

Variables

• source_repo: source repository URL.
• source_commit: source repository commit SHA used to build the Dryad package.
• source_file: original .rda filename in the source repository.
• object_name: object name loaded from that .rda file.
• object_class: R class or classes of the loaded object.
• nrow: number of rows in the in-memory object before export.
• ncol: number of columns in the in-memory object before export.
• source_file_size_bytes: source .rda file size in bytes.
• include_in_dryad: whether the object was included in the Dryad export (TRUE/FALSE).
• export_status: export outcome (for example exported or excluded).
• export_file: output filename written to the Dryad directory.
• export_format: exported file format (for example .csv or .csv.gz).
• export_size_bytes: exported file size in bytes.
• file_role: curatorial role assigned to the file (for example primary input, derived output, or excluded plot object).
• description: human-readable description of the object.
• created_in: upstream script, vignette, or source location where the object was created.
• used_in: vignette(s) or analysis script(s) where the object was used.
• validation_status: result of round-trip export validation.
• validation_notes: row/column and column-name validation details.

File: iucn.csv

Description: Species metadata table used to define extinction-status groupings and contextual covariates in the body-size and PCA analyses.

Variables

• species: species epithet used throughout the analysis tables.
• notes: species status note (extant, extinct, or exotic).
• island_bank: island or island-bank grouping assigned to the species.
• redlist: original IUCN Red List category (EX, CR, EN, VU, NT, LC).
• redlist2: collapsed status category used in the analyses (EX, TH, LC).
• total_island_area: total island area associated with the species occurrence grouping; retained from source metadata (interpreted as square kilometers).
• range: species range-size field retained from source metadata (interpreted as square kilometers).

File: rep_emp_svl.csv.gz

Description: Stepwise empirical heuristic replicate results for the full body-size extinction analysis. Each row corresponds to one extinction step within one heuristic replicate. The compressed archive contains one CSV table with five columns.

Variables

• n_spp: number of species remaining after the removal step.
• avg: change in mean standardized maximum SVL relative to the starting mean.
• var: change in variance of standardized maximum SVL relative to the starting variance.
• spp_rm: species removed at that step; blank for the initial no-removal row.
• rep_num: heuristic empirical replicate identifier (r1-r10000).

File: maxsvl.csv

Description: Source species-level maximum SVL and extinction-order metadata table retained from the project spreadsheet used to build the body-size analyses. This export preserves original column names, including several legacy spreadsheet labels.

Variables

• X1: legacy row index from the source spreadsheet.
• species: full species name.
• on master: whether the species was retained on the project master list.
• do we have: whether the project team had the needed data for that species at the time of compilation.
• phylo: indicator for phylogenetic-data availability.
• morpho: indicator for morphology-data availability.
• map: indicator for map-data availability.
• network: indicator for network-data availability.
• coords: indicator for coordinate-data availability.
• caribbean: indicator for Caribbean inclusion.
• where: location or island noted for the species.
• in iucn ranges: indicator for whether the species/locality was represented in IUCN ranges.
• other name: alternate taxonomic name or synonym used in source compilation.
• number measured: number of measured specimens summarized for that species where recorded.
• SMITH NOTES: project note field from the source spreadsheet.
• notes: general note field, often summarizing status (for example extinct).
• extinct specimen notes: notes specific to extinct-specimen evidence.
• source for extinct:last seen: literature or source citation for last-seen / extinction dating information.
• extinct: last seen: original last-seen field from the source spreadsheet.
• extinct:last seen CLEAN: cleaned last-seen value retained from source processing.
• extinct_min: minimum bound used for extinction timing.
• extinct_max: maximum bound used for extinction timing.
• extinct_order_cluster: clustered extinction-order grouping used when ties were heuristically sampled.
• extinct_order: sequential extinction-order value used in stepwise analyses.
• island bank: island or island-bank grouping.
• total island area for presence: total island area associated with species presence (interpreted as square kilometers).
• redlist: original IUCN Red List category.
• redlist version: source IUCN version or assessment year where recorded.
• main threats: source threat summary field.
• maxSVL: maximum snout-vent length (mm).
• otherSVL: alternate snout-vent length field retained from source compilation.
• total length: total length (mm), when available.
• head width: head width (mm), when available.
• head length: head length (mm), when available.
• body length: body length (mm), when available.
• fore limb: forelimb length (mm), when available.
• hind limb: hindlimb length (mm), when available.
• tail condition: tail-condition field retained from source compilation.
• total tail: total tail length (mm), when available.
• jaw length: jaw length (mm), when available.
• shank: shank length (mm), when available.
• X41: legacy source-reference text field retained from the source spreadsheet.
• X42: legacy comment / conservation note field retained from the source spreadsheet.
• status: derived status grouping used in the source table.

File: morph.csv.gz

Description: Specimen-level raw/cleaned morphology table used as the starting point for morphology cleaning and species-level summarization. The compressed archive contains one CSV table with 17 variables.

Variables

• X1: legacy row index from the source spreadsheet.
• X: source record identifier / within-file row field retained from the original dataset.
• i: source dataset label or import batch identifier.
• count: measurement occasion or count identifier for a specimen.
• measurer.name: name of the person who took the measurement.
• date.measured: measurement date as recorded in the source file.
• jar.label: container or jar label from specimen curation.
• specimen.id.number: specimen catalog or identifier number.
• archive: archive or collection source.
• species: full species name.
• trait.number: trait code matching trait_key.csv.
• trait: human-readable trait name.
• value: recorded measurement value.
• units: measurement units or category coding for value (for example mm, count, character category, or numeric category 1 full, 2 regen, 3 broke).
• FLAG: source QC/flag field; blank where no flag was recorded.
• NOTES: source note field; blank where no note was recorded.
• SEX: sex field; blank where not recorded.