Data and code from: Frequent use of empty Parasa lepida cocoons by diverse invertebrates
Data files
Sep 22, 2026 version files 22.62 KB
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cocoons.csv
2.64 KB
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descriptive_summaries.R
1.63 KB
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figure2_reproduce.R
4.12 KB
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occupancy_glmm.R
710 B
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occupants.csv
9.26 KB
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README.md
2.69 KB
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trees.csv
1.56 KB
Abstract
Empty Limacodidae cocoons can remain intact on tree trunks after adult emergence and may be reused by other organisms. This dataset documents secondary occupancy of empty Parasa lepida cocoons on Hachijojima, Japan. On 21-22 January 2026, 95 empty cocoons were collected from 19 trees and dissected; 65 contained at least one secondary occupant. The archived files include tree and cocoon metadata, 112 cocoon-level occupant records, and R code to reproduce the Figure 2 summary.
Data and R code documenting secondary occupancy of empty Parasa lepida cocoons by invertebrates on Hachijojima, Japan. The dataset comprises 95 empty cocoons collected from 19 trees on 21–22 January 2026.
Files
trees.csv: sampled trees; one row per tree.cocoons.csv: sampled cocoons; one row per cocoon.occupants.csv: secondary occupants; one row per cocoon-level morphotaxon record.figure2_reproduce.R: regenerates Figure 2.occupancy_glmm.R: reproduces the binomial occupancy GLMM.descriptive_summaries.R: reproduces morphotaxon-richness and pairwise
co-occurrence summaries.
Data conventions
Files are linked by tree_id and cocoon_id; record_no uniquely identifies each occupant record. Empty cells in the taxonomic columns of occupants.csv indicate unresolved identification at those ranks, not absence of organisms. Dates use ISO 8601 (YYYY-MM-DD), coordinates use WGS84 decimal degrees, cocoon dimensions are in millimetres, and elevation is in metres.
In cocoons.csv, occupied and has_operculum use yes/no. For has_operculum, yes indicates that the original field notes recorded an operculum or white-silk seal; this variable is retained for reuse but is not used in the archived analyses.
A cocoon was scored as occupied when an invertebrate exited it during field handling or was found inside its silk chamber during dissection; organisms found only on the outer surface were excluded. Occupancy indicates presence at collection, not duration of use.
In occupants.csv, id_level gives the lowest taxonomic rank resolved and n_individuals gives the count for that morphotaxon record. For spider and cockroach egg-stage records, n_individuals denotes the number of egg sacs and oothecae, respectively, rather than individual eggs.
In C070, two clausiliid records identified only to family were morphologically distinct and are therefore treated as separate morphotaxa.
Taxonomic notes: Cinnamomum yabunikkei follows Japanese regional-flora usage, although POWO/WCVP treats it as a synonym of C. chekiangense. Diplopods are retained at Eudigraphis sp.
Reproduction
Run from the archive root:
Rscript figure2_reproduce.R
Rscript occupancy_glmm.R
Rscript descriptive_summaries.R
Required packages are dplyr, ggplot2, and lme4 (version 1.1-37 used).
descriptive_summaries.R Uses base R.
Access/contact
License: CC0. Associated article DOI to be added when available.
Contact: Hiroki Akimoto (autumnorigin@akane.waseda.jp).