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- .Rprofile
  
  115 Bytes
- Data
  - ICTV Master Species List 2018b.v1.xlsx
    
    466.4 kB
  - Internal
    - VirusReservoirs.csv
      
      82.7 kB
    - VirusReservoirs_Citations.bib
      
      497.1 kB
    - ZoonoticStatus_Merged.rds
      
      18.1 kB
  - NameMatchesNEW.csv
    
    117.4 kB
  - PublicationCounts_Reservoir.csv
    
    413 Bytes
  - PublicationCounts_ReservoirByFamily.csv
    
    23.3 kB
  - PublicationCounts_VirusFamily.csv
    
    784 Bytes
  - PublicationCounts_VirusSpp.csv
    
    19.6 kB
  - ReservoirTaxonomyRaw.rds
    
    124.8 kB
  - ReservoirTrees
    - Reservoir_Timetree_Clean.rds
      
      637 Bytes
    - Timetree_ReservoirMapping.csv
      
      481 Bytes
    - Timetree_ReservoirRepresentatives.nwk
      
      644 Bytes
    - Timetree_ReservoirRepresentatives.txt
      
      263 Bytes
  - VirusDistances_gravity
    - III_dsRNAviruses_CompositeGeneralisedJaccard.csv
      
      356.5 kB
    - II_ssDNAviruses_CompositeGeneralisedJaccard.csv
      
      16.0 MB
    - IV_+ssRNAviruses_CompositeGeneralisedJaccard.csv
      
      17.2 MB
    - I_dsDNAviruses_CompositeGeneralisedJaccard.csv
      
      2.4 MB
    - VI_VII_RTviruses_CompositeGeneralisedJaccard.csv
      
      397.6 kB
    - V_-ssRNAviruses_CompositeGeneralisedJaccard.csv
      
      3.3 MB
  - VirusFamilyFeatures.csv
    
    902 Bytes
- DataOverview.html
  
  919.5 kB
- MainScripts
  - .Rhistory
    
    0 Bytes
  - CalculateDerivedVars.R
    
    6.1 kB
  - CleanData.R
    
    3.1 kB
  - Database_overview_stats.R
    
    5.7 kB
  - InfluenceOfAddingBirds.R
    
    7.6 kB
  - InfluenceOfDetectionHosts.R
    
    10.0 kB
  - InitialPlots.R
    
    20.6 kB
  - MergeData.R
    
    10.1 kB
  - ModelChecks_Main.Rmd
    
    4.3 kB
  - ModelFits.R
    
    8.1 kB
  - ModelFits_2_NumberOfZoonoses.R
    
    5.9 kB
  - Plot_InfluenceOfAddingBirds.R
    
    14.2 kB
  - Plot_InfluenceOfDetectionHosts.R
    
    15.6 kB
  - Plot_MainFits.R
    
    23.9 kB
  - Plot_NumberOfZoonosesModels.R
    
    19.6 kB
- Makefile
  
  15.5 kB
- Misc
  - DownloadReservoirTaxonomy.R
    
    1.6 kB
  - ExtractGravitySimilarityMatrixes.py
    
    1.6 kB
  - Plot_PubBias.R
    
    7.9 kB
  - PublicationCounts.py
    
    9.8 kB
  - RawData_FamilyByReservoir-ZoonoticOnly_TikzAnnotations.txt
    
    2.3 kB
  - RawData_FamilyByReservoir_TikzAnnotations.txt
    
    2.5 kB
  - ReservoirData-Citations.Rmd
    
    1.3 kB
  - ReservoirPhylo_DownloadSeqs.py
    
    1.9 kB
- Plots
  - Figure1_RawData.tex
    
    1.0 kB
  - Figure2_TopModel.tex
    
    5.2 kB
  - Figure4_Nzoonoses.tex
    
    1.7 kB
  - Supplement-DetectionHosts
    - SupplementaryVersionOfFigure2_PCRDetectionHostsAdded.tex
      
      3.3 kB
  - Supplement-MammalsOnly
    - SupplementaryVersionOfFigure2_MammalsOnly.tex
      
      3.6 kB
  - Supplement_SeparateEffects.tex
    
    2.0 kB
  - SupplementaryFig4_TotalCountModels.tex
    
    1.7 kB
  - SupplementaryFig5.tex
    
    776 Bytes
- README.md
  
  5.8 kB
- SourcesOfZoonoses.Rproj
  
  225 Bytes
- Utils
  - gam_fit_utils.R
    
    4.4 kB
  - gam_plot_utils.R
    
    11.8 kB
  - gam_summary_utils.R
    
    3.3 kB
  - reservoir_plot_utils.R
    
    4.3 kB
- packrat
  - init.R
    
    8.4 kB
  - packrat.lock
    
    21.4 kB
  - packrat.opts
    
    398 Bytes
  - src
    - BH
    - DBI
    - DHARMa
    - DT
    - EnvStats
    - Formula
    - Hmisc
    - MASS
    - Matrix
    - R6
    - RColorBrewer
    - Rcpp
    - RcppEigen
    - TMB
    - WikidataR
    - WikipediR
    - XML
    - acepack
    - animation
    - ape
    - assertthat
    - backports
    - base64enc
    - binom
    - bold
    - boot
    - broom
    - callr
    - cellranger
    - checkmate
    - cli
    - clipr
    - cluster
    - clusterGeneration
    - coda
    - codetools
    - colorspace
    - combinat
    - cowplot
    - crayon
    - crosstalk
    - crul
    - curl
    - data.table
    - dbplyr
    - digest
    - doParallel
    - dplyr
    - ellipsis
    - evaluate
    - expm
    - fansi
    - fastmatch
    - filehash
    - forcats
    - foreach
    - foreign
    - fs
    - gap
    - ggfittext
    - ggimage
    - ggplot2
    - ggplotify
    - ggstance
    - ggthemes
    - ggtree
      - ggtree_1.4.20.tar.gz
        
        14.5 MB
      - ggtree_1.8.2.tar.gz
        
        7.3 MB
    - glmmTMB
    - glue
    - gridBase
    - gridExtra
    - gridGraphics
    - gtable
    - haven
    - highr
    - hms
    - htmlTable
    - htmltools
    - htmlwidgets
    - httpcode
    - httpuv
    - httr
    - igraph
    - iterators
    - jsonlite
    - knitr
    - labeling
    - langcog
      - 947511e68759386d3a55d43f0721326abca123d3.tar.gz
        
        8.9 kB
    - later
    - lattice
    - latticeExtra
    - lazyeval
    - lme4
    - lmtest
    - lubridate
    - magick
    - magrittr
    - maps
    - markdown
    - mgcv
    - mime
    - minqa
    - mnormt
    - modelr
    - msm
    - munsell
    - mvtnorm
    - natserv
    - nlme
    - nloptr
    - nnet
    - nortest
    - numDeriv
    - openssl
    - packrat
    - pbapply
    - phangorn
    - phytools
    - pillar
    - pkgconfig
    - plogr
    - plotrix
    - plyr
    - png
    - prettyunits
    - processx
    - progress
    - promises
    - proxy
    - ps
    - psych
    - purrr
    - qrnn
    - quadprog
    - rdiversity
    - readr
    - readxl
    - rematch
    - rentrez
    - reprex
    - reshape
    - reshape2
    - ritis
    - rlang
    - rmarkdown
    - rncl
    - rotl
    - rpart
    - rphylopic
    - rprojroot
    - rredlist
    - rstudioapi
    - rvcheck
    - rvest
    - scales
    - scatterplot3d
    - selectr
    - sfsmisc
    - shiny
    - solrium
    - sourcetools
    - spaMM
    - stringi
    - stringr
    - survival
    - taxize
    - tibble
    - tidyr
    - tidyselect
    - tidyverse
    - tikzDevice
    - tinytex
    - treeio
      - treeio_1.0.2.tar.gz
        
        404.5 kB
    - treemapify
    - triebeard
    - urltools
    - utf8
    - vctrs
    - viridis
    - viridisLite
    - visreg
    - whisker
    - wikitaxa
    - withr
    - worrms
    - xml2
    - xtable
    - yaml
    - zeallot
    - zoo

Mollentze_Streicker_2020_Zoonotic_Reservoirs.zip