1claude "I need to prepare my dataset for BCO-DMO submission.
2 
3Read data/coral_survey_final.csv and create a complete submission package:
4 
51. DATA DICTIONARY
6   - All column names, types, units
7   - Allowed values/ranges
8   - Missing value codes used
9   - Link each variable to collection method (I'll fill details)
10 
112. ABSTRACT (250 words)
12   - What data this is
13   - How it was collected
14   - Geographic/temporal scope
15   - Potential uses
16 
173. METHODS DOCUMENT
18   - Sampling design
19   - Collection protocols
20   - Quality control procedures
21   - Processing steps applied
22   - Known limitations
23 
244. METADATA FILE (ISO 19115 format)
25   - Following BCO-DMO template structure
26 
275. README.txt
28   - File inventory
29   - How to cite
30   - Contact information
31   - Related publications
32 
33Export each as separate files matching BCO-DMO naming conventions."

1claude "Create documentation for archiving this analysis on Zenodo:
2 
31. README.md covering:
4   - Project description
5   - File inventory with descriptions
6   - How to reproduce the analysis
7   - Citation instructions
8   - License information (suggest appropriate one)
9 
102. CITATION.cff file for proper citation tracking
11 
123. Suggested keywords and description for the Zenodo upload form
13 
14Match the style of highly-cited data repositories in ecology."

1claude "Based on our main analysis, create a supplementary materials document:
2 
3STRUCTURE NEEDED:
4- Table S1: Full model results (not truncated like Table 2)
5- Table S2: Sensitivity analysis results
6- Table S3: Site characteristics
7- Figure S1: Diagnostic plots for main model
8- Figure S2: Map of study sites
9- Methods S1: Detailed statistical methodology
10 
11For each item:
121. Generate the content from our analysis results
132. Add appropriate captions
143. Cross-reference to main text
15 
16Format for Nature Ecology & Evolution style.
17Export as both Word (.docx) and LaTeX (.tex)."

1claude "Convert this supplementary material:
2- FROM: supplementary.tex (LaTeX)
3- TO: supplementary.docx (Word)
4 
5Preserve:
6- Table formatting
7- Figure references
8- Equation numbering
9- Citation style
10 
11My co-author needs Word and won't learn LaTeX."

1claude "Parse this reviewer response document and create a structured response template:
2 
3REVIEWER COMMENTS:
4[paste the full reviewer letter]
5 
6CREATE:
71. A numbered list of every distinct comment/request
82. Categorize each as:
9   - Minor: Quick fix
10   - Moderate: Some work needed
11   - Major: Significant revision
12   - Disagree: We should push back
13 
143. For each comment, create response skeleton:
15   - Our response: [to fill]
16   - Changes made: [to fill]
17   - Location in manuscript: [to fill]
18 
194. Track which analyses/figures need updating
20 
21Export as Word table I can fill in with co-authors."

1claude "Draft a response to this reviewer comment:
2 
3COMMENT: 'The authors should justify their choice of mixed-effects
4model over a simpler repeated-measures ANOVA. The sample size
5(n=47) may be insufficient for the complexity of their model.'
6 
7CONTEXT:
8- We chose mixed-effects because we have unbalanced data
9- Random slopes are needed due to site-specific variation
10- We did run power analysis during design phase
11 
12Draft a response that:
131. Acknowledges the valid concern
142. Explains our rationale clearly
153. Cites methodological literature supporting our choice
164. Describes any additional analyses we'll add to address this
175. Is diplomatic but defends our approach
18 
19Tone: Respectful but confident. Don't be obsequious."

1claude "Compile our individual responses into a formatted response letter:
2 
3Include:
41. Cover letter to editor (brief, professional)
52. Point-by-point responses organized by reviewer
63. Summary of major changes
74. Track changes reference guide
8 
9Format conventions:
10- Reviewer comments in italic
11- Our responses in regular text
12- Changed manuscript text in quotes with line numbers
13- New analyses/figures highlighted
14 
15Generate both Word and PDF versions."

1claude "Based on my analysis code in analysis/main.R, draft a Methods section:
2 
3REQUIREMENTS:
4- Sufficient detail for reproducibility
5- Statistical terminology appropriate for [journal]
6- Report all test statistics, effect sizes, confidence intervals
7- Explain any non-standard approaches
8- Reference software versions
9 
10STRUCTURE:
111. Study design and sampling
122. Data collection procedures
133. Statistical analysis
14   - Data cleaning and preparation
15   - Primary analysis approach
16   - Secondary/sensitivity analyses
174. Software and packages used
18 
19LENGTH: ~500 words for PLOS ONE format
20 
21I'll add the domain-specific details; you handle the statistical reporting."

1claude "Generate a Results section skeleton from my analysis outputs:
2 
3For each significant finding:
41. State the finding in plain language
52. Report statistics properly: F(df1, df2) = X.XX, p = .XXX, η² = .XX
63. Reference the appropriate table/figure
74. Note effect size interpretation
8 
9For non-significant findings:
101. Report the statistics
112. Note the power/sample size considerations
12 
13DO NOT interpret—just report. I'll add the interpretation."

1claude "Write publication-ready figure captions for these figures:
2 
3Figure 1: [describe what it shows]
4Figure 2: [describe what it shows]
5Figure 3: [describe what it shows]
6 
7Each caption should:
81. Start with a single-sentence summary
92. Describe what is being plotted (axes, colors, symbols)
103. Explain any statistical annotations
114. Define abbreviations on first use
125. Note sample sizes
13 
14Style: Nature Ecology & Evolution
15Maximum: 350 words per caption"

1claude "I'm writing an NSF proposal. Here are my three specific aims:
2 
3[paste current aims]
4 
5Help me strengthen them:
61. Are they logically connected?
72. Is each aim achievable in the timeline?
83. Do they build on each other or are they independent?
94. Suggest how to make the impact statement stronger
105. Flag any red flags a reviewer might raise
11 
12Be critical—I'd rather fix problems now than get triaged."

1claude "Generate a Data Management Plan for my NSF proposal:
2 
3PROJECT: [brief description]
4DATA TYPES:
5- Field observations (CSV, ~10GB)
6- Photographs (JPEG, ~50GB)
7- Derived data products (NetCDF, ~5GB)
8- Analysis code (R scripts)
9 
10REQUIREMENTS TO ADDRESS:
111. What data will be generated
122. Data formats and standards
133. Data storage during project
144. Data sharing and access
155. Long-term preservation
166. Roles and responsibilities
17 
18Follow NSF BIO requirements.
19Include specific repository names (BCO-DMO, Zenodo, GitHub).
20Keep to 2 pages."

1claude "Draft budget justification text for these line items:
2 
31. Graduate student (2 years, 50% time): $XX,XXX
42. Undergraduate assistants (3 students, summer): $X,XXX
53. Field equipment (list attached): $XX,XXX
64. Travel (2 field seasons + 1 conference/year): $XX,XXX
75. Publication costs: $X,XXX
8 
9For each item:
10- Explain what they'll do
11- Why this amount/duration is appropriate
12- How it connects to the proposed work
13 
14Tone: Clear, justified, not defensive."

1claude "Help me set up a collaborative LaTeX project:
2 
3CREATE:
41. Main.tex (master document that includes chapters)
52. Chapters/ directory structure for sections
63. A preamble.tex with common packages and commands
74. A Makefile for easy compilation
85. .gitignore for LaTeX projects
9 
10INCLUDE:
11- Natbib setup for [citation style]
12- Cross-referencing with cleveref
13- Draft mode with line numbers
14- Clean compilation without warnings
15 
16My co-authors will edit separate chapter files."

1claude "Convert this regression output to a publication-ready LaTeX table:
2 
3[paste R/Python output or CSV]
4 
5REQUIREMENTS:
6- Three-line table style (no vertical lines)
7- Proper alignment (left for text, right for numbers)
8- Significance stars with footnote explaining
9- Standard errors in parentheses
10- Model fit statistics at bottom
11- Booktabs package formatting
12 
13Match the style of tables in Journal of Ecology."

1claude "Clean up my BibTeX file:
2 
3Read references.bib and:
41. Fix inconsistent formatting
52. Fill in missing fields where you can infer them
63. Flag entries that seem incomplete
74. Remove duplicate entries (keep most complete version)
85. Standardize journal name abbreviations
96. Check DOIs are properly formatted
10 
11Also create a 'needed_refs.txt' listing any citations in my .tex files
12that aren't in the .bib file."

1claude "From this analysis, generate outputs for different audiences:
2 
31. TECHNICAL (for co-authors):
4   - Full statistical output
5   - All diagnostics
6   - Code and data references
7 
82. MANUSCRIPT (for submission):
9   - Cleaned tables (Tables 1-3)
10   - Publication figures (Figures 1-4)
11   - Results text snippets
12 
133. PRESENTATION (for conference):
14   - Key findings as bullet points
15   - Simplified figures (higher contrast, bigger fonts)
16   - Talking points for each slide
17 
184. SUMMARY (for stakeholders):
19   - Plain language summary (1 paragraph)
20   - Key numbers without statistics
21   - Implications for practice
22 
23Export each to appropriate formats."

1claude "Create a submission checklist for [journal]:
2 
3PRE-SUBMISSION:
4- [ ] All co-authors have approved final version
5- [ ] All figures meet journal specifications
6- [ ] References formatted correctly
7- [ ] Word/page count within limits
8- [ ] Cover letter drafted
9- [ ] Suggested reviewers identified
10- [ ] Competing interests declared
11 
12REQUIRED FILES:
13- [ ] Main manuscript (format: ___)
14- [ ] Figures (format: ___, resolution: ___)
15- [ ] Tables (format: ___)
16- [ ] Supplementary materials
17- [ ] Data availability statement
18- [ ] Author contributions (CRediT format)
19 
20METADATA NEEDED:
21- [ ] All author ORCIDs
22- [ ] Keywords (n = ___)
23- [ ] Running title (max ___ characters)
24- [ ] Corresponding author details
25 
26Pull specific requirements from [journal] guidelines."

1claude "Compare these two manuscript versions and create a clean summary:
2- v2_from_advisor.docx
3- v2_from_coauthor.docx
4 
5Show me:
61. Changes they both made (keep these)
72. Conflicting changes (I need to decide)
83. Changes only one person made (review needed)
9 
10Don't generate a merged file—just help me see what needs reconciling."

1claude "My figure/table numbers changed during revision.
2Search the manuscript and update all references:
3 
4OLD -> NEW mapping:
5- Figure 2 -> Figure 3
6- Figure 3 -> Figure 2
7- Table 1 -> Table 2
8- Table S1 -> Table S2
9 
10Find and update all occurrences in main text and supplementary materials."

1claude "Regenerate all figures at these specifications:
2- Single column: 89mm wide
3- Double column: 183mm wide
4- Full page: 183mm x 247mm
5- Resolution: 300 DPI for photos, 600 DPI for line art
6- Format: TIFF with LZW compression
7- Fonts: Arial, minimum 8pt
8 
9Current figures are in figures/. Match content exactly, just resize."