:bomb: Task manager

:pick: Data collection

• [x] Body mass (5400 spp)
  • [x] EltonTraits 1.0 (will only use this for now)
    • [x] collected
    • [x] cleaned
      - [ ] ADW
      - [x] scraped
      - [ ] cleaned
      - [ ] AnAge
      - [x] collected
      - [ ] cleaned
      - [ ] PanTheria
      - [x] collected
      - [ ] cleaned
      - [ ] Smith et al.
      - [x] collected
      - [ ] cleaned
• [x] GBIF geographical location (4721 spp)
• [x] Phylogeny (6952 spp)
• [x] Human use (1472 spp)
  • [x] collected from IUCN
  • [x] try pivot_wider()
• [x] IUCN status (5934 spp)
  • [x] collected
  • [x] cleaned

:abacus: Pre-analysis

• [x] Combine datasets (8308 spp)
• [x] More cleaning up
  • [x] remove species with only genus or species name (8305 spp)
• [x] Add classification levels (taxize)
  • will have to come back to do this after itis is working again
• [x] Synonym matching (rotl)
  • [x] create a species list in long form with the ID
• [x] h-index (specieshindex)
  • [x] put quotation marks around synonyms
  • [x] fix weird NA dataframe (putting synonyms around the synonyms seems to have fixed the problem)
  • [x] divide species list into 2 to fix timeout issue
  • [x] run the 2nd list next week since I’ve reached the limit of 20,000 requests this week
• [x] Missing data (mice)
• [x] Google Trends (gtrendsR)

:art: Making graphs

• [x] h vs mass
• [ ] h vs phylogeny :round_pushpin:
  • something wrong with the new artificial tree, need to find out why
• [x] h vs location
• [x] h-index map
• [x] h vs human use
• [x] h vs domestication
• [x] h vs iucn
• [x] h with vs without conservation keyword
  • [x] check for patterns
• [x] Google Trends sum
• For all plots
  • [x] change font
  • [x] change h-index axis scale to true values
  • [ ] add p-values / other stats on the plots

:rocket: Statistical analysis :gem::round_pushpin:

• [x] correlation matrix of complete entries
• [x] Phylogenetic signals (phytools)
• MCMCglmm
  • [x] impute 10 datasets
  • [x] trim all trees + pick 50 randomly
  • [x] write nested loop + TESTING
  • [x] katana
  • [ ] extract data from models :round_pushpin:
  • [ ] Pagel’s λ (calculated from MCMCglmm results) :round_pushpin:

:jigsaw: Other materials :gem::round_pushpin:

• [ ] data summary table for thesis
• [ ] supplementary material

Legend
What I’m working on now :round_pushpin:
Priority :gem: