Paper ID,Citation,Journal,Year,Should the paper be kept or rejected? (The paper should be rejected if it is not a within-between host model that includes data),"If rejected, give reason why",Focal host species type?,Species name,Other species?,Other species name(s),Type of infection?,Infection name(s),How is infection transmission modeled?,Results PRIMARILY tactical or strategic?,PRIMARY focus of main result?,"If Other, state the focus of the main result",Type of within-host model?,"If Other, state the type of model",Type of between-host model?,"If Other, state the type of model",How are the models linked?,Linking method used?,Within-host linking: Pathogen growth rate?,Within-host linking: Pathogen load?,Within-host linking: Pathogen death rate,Within-host linking: Immune response?,Within-host linking: Symptoms?,Other within-host linking traits/states?,Between-host linking: Pathogen transmission rate?,Between-host linking: Host recovery rate?,Between-host linking: Host death rate?,Between-host linking: Pathogen virulence?,Between-host linking: Frequency of strains?,Other between-host linking traits/states?,Is data used at the within-host level?,"If within-host data, top-down or bottom-up?","If within-host data, fitting method?","If Other, state the fitting method",Is data used for the linking mechanism?,"If linking mechanism data, top-down or bottom-up?","If linking mechanism data, fitting method?","If Other, state the fitting method",Is data used at the between-host level?,"If between-host data, top-down or bottom-up?","If between-host data, fitting method?","If Other, state the fitting method"
6,Stephenson,Phil Trans R Soc B,2017,Keep,,Reptile/Amphibian/Fish,Guppy (Poecilia reticulata),No,,Macroparasite (Worms/ticks/etc),,Direct contact,Strategic,Impact of within-host dynamics on between-host dynamics,,Statistical,,Statistical,,Within-host linked to between-host,Both,Yes,Yes,No,No,No,"resistance, stage of infection",Yes,No,No,No,No,"Transmission load, transmitted parasite fitness",Yes,Bottom-up,Maximum likelihood,,Yes,Bottom-up,Maximum likelihood,,Yes,Bottom-up,Maximum likelihood,
8,Volz 2017,Mol Biol Evol,2017,Keep,,Human,,No,,Multiple,HIV/Ebola,Direct contact,Strategic,Impact of within-host dynamics on between-host dynamics,,Statistical,,Deterministic,,Within-host linked to between-host,Traits,No,No,No,No,No,probabilities of different lineages,Yes,No,No,No,No,,Yes,Bottom-up,Maximum likelihood,,No,,,,Yes,Top-down,Other,"Multiple models used, least squares and Bayesian inference"
14,Giardina,Plos Comp Biol,2017,Keep,,Human,,No,,Viral,HIV-1,Direct contact,Strategic,Impact of within-host dynamics on between-host dynamics,,Deterministic,,Individual-based,,Within-host linked to between-host,States,No,Yes,No,No,No,,Yes,No,No,No,Yes,,Yes,Top-down,Bayesian Inference,,No,,,,No,,,
33,Althouse,Phil Trans R Soc B,2015,Keep,,Non-human Mammal,Macaque,No,,Viral,Dengue,Direct contact,Strategic,Impact of within-host dynamics on between-host dynamics,,Deterministic,,Stochastic,,Within-host linked to between-host,States,No,Yes,No,No,No,,Yes,No,No,No,No,,Yes,Top-down,Other,Qualitative,No,,,,No,,,
54,van Dorp,Plos Comp Biol,2014,Keep,,Human,,No,,Viral,HIV,Direct contact,Strategic,Other,Impact on within-host characteristics of virus based on within-host distribution of hosts,Individual-based,,Individual-based,,Both,States,No,Yes,No,No,No,,No,No,No,Yes,No,Virus success in host depends on host immune characteristics,No,,,,No,,,,Yes,Bottom-up,,Not fitted but used for general comparison of trends
59,Handel,Proc R Soc B,2014,Keep,,Birds,Ducks,No,,Viral,Influenza A/Avian Influenza,Indirect contact,Strategic,Impact of between-host dynamics on within-host dynamics,,Deterministic,,Deterministic,,Within-host linked to between-host,States,No,Yes,No,No,No,,No,No,No,No,No,,Yes,Bottom-up,Least squares,,Yes,Bottom-up,Least squares,,Yes,Bottom-up,Other,"mechanistic model, odes and phenomenological model"
64,Vrancken,Plos Comp Biol,2014,Keep,,Human,,No,,Viral,HIV,Direct contact,Both,Impact of within-host dynamics on between-host dynamics,,Statistical,coalescent,Statistical,using BEAST,Both,States,No,No,No,No,No,population proportion,no,No,No,No,no,"Viral Evolution,, transmission timing",Yes,Top-down,Bayesian Inference,Bayesian Genealogical Inference,No,,,,Yes,Top-down,Bayesian Inference,Bayesian Genealogical Inference
66,Leclerc 2014,Plos One,2014,Keep,,Plants,sugar beet,,,Fungal,Rhizoctonia solani,Direct contact,Tactical,Impact of within-host dynamics on between-host dynamics,,Statistical,,Stochastic,,Within-host linked to between-host,Traits,No,No,No,No,No,,Yes,No,No,No,No,,Yes,Bottom-up,Maximum likelihood,,No,,,,No,,,
76,Chen 2013,Prev Vet Med,2013,Keep,,Non-human Mammal,cattle,No,,Bacterial,Ecoli O157,Indirect contact,Strategic,Impact of within-host dynamics on between-host dynamics,,Individual-based,,Deterministic,,Both,States,No,Yes,No,No,No,,Yes,Yes,No,No,No,,Yes,Top-down,Other,Use shedding density data to model individual level of shedding; cubic spline interpolation,Yes,Top-down,Other,cubic spline interpolation,No,,,
78,Handel,Plos Comp Biol,2013,Keep,,Birds,mallards Anas platyrhynchos,No,,Viral,Influenza A,Multiple,Strategic,Other,The impact of both within and between host dynamics on fitness.,Deterministic,,Deterministic,,Both,Both,No,Yes,No,No,Yes,,Yes,Yes,No,No,No,,Yes,Bottom-up,Least squares,,Yes,Bottom-up,Least squares,,No,,,
90,Reperant 2012,Plos One,2012,Keep,,Human,Homo sapien,Yes,Avian,Viral,Influenza A and Avian,Direct contact,Strategic,Impact of within-host dynamics on between-host dynamics,,Stochastic,Also statistical,Deterministic,,Within-host linked to between-host,Both,Yes,No,Yes,Yes,No,Both transmission and recovery rates depend on pathogen traits.,No,No,No,No,No,,Yes,Bottom-up,Least squares,,Yes,Bottom-up,Least squares,,No,,,
93,Fryer,J Virol,2012,Keep,,Human,,No,,Viral,HIV,Direct contact,Strategic,Impact of within-host dynamics on between-host dynamics,,Statistical,,Deterministic,,Within-host linked to between-host,Traits,No,No,No,No,No,escape prevalence,No,No,No,No,No,"reversion rate, escape rate",Yes,Bottom-up,Maximum likelihood,,No,,,,No,,,
103,Day (2-part paper with 105-Mideo),Evolution,2011,Keep,,Non-human Mammal,C57B1/6J Mice,No,,Protozoa (Malaria parasite/etc),"P chabaudi (rodent malaria), multiple genotypes",Direct contact,Strategic,Other,"Interaction between within-host and between-host, how affect evolutionary predictions",Statistical,,Deterministic,,Both,Both,No,Yes,No,No,No,age,Yes,No,Yes,No,No,,Yes,Bottom-up,Maximum likelihood,,Yes,Bottom-up,Maximum likelihood,,No,,,
105,Mideo 2011,Evolution,2011,Keep,,Non-human Mammal,C57B1/6J Mice,No,,Protozoa (Malaria parasite/etc),"P chabaudi (rodent malaria), multiple genotypes",Direct contact,Strategic,Other,"Interaction between within-host and between-host, how affect evolutionary predictions",Statistical,,Deterministic,,Both,Both,No,Yes,No,No,No,age,Yes,No,Yes,No,No,,Yes,Bottom-up,Maximum likelihood,,Yes,Bottom-up,Maximum likelihood,,No,,,
123,Chaves,Ecology,2009,Keep,,Human,homo sapiens,No,NA,Protozoa (Malaria parasite/etc),Malaria,Indirect contact,Strategic,Other,within on between and between on within,Deterministic,,Deterministic,,Both,States,Yes,Yes,Yes,Yes,No,,Yes,No,No,Yes,No,,No,,,,No,,,,Yes,Both,Other,
142,Dennehy,Am Nat,2006,Keep,,Other,P phaseolicola (bacteria),Yes,P pseudoalcaligenes (bacteria),Viral,Phage Phi 6,Direct contact,Tactical,Impact of within-host dynamics on between-host dynamics,,Deterministic,,Statistical,,Within-host linked to between-host,Both,Yes,Yes,No,No,No,,Yes,No,No,No,No,,Yes,Bottom-up,Least squares,,No,,,,Yes,Bottom-up,Other,Qualitative
146,Cooper,Proc R Soc B,2005,Keep,,Other,JHC510/JHC514a (bacteria),,,Other,Plasmid,Multiple,Strategic,Other,within host competition and between host tranmission effects on virulence,Deterministic,,Deterministic,,Both,Both,No,Yes,No,No,No,reproduction,Yes,No,Yes,Yes,Yes,,Yes,Bottom-up,Other,don't say,Yes,Both,Other,don't say,Yes,Both,Other,don't say
147,McKenzie,J Theor Biol,2005,Keep,,Human,,Yes,mosquitoes,Protozoa (Malaria parasite/etc),Plasmodium falciparum,Indirect contact,Strategic,Impact of within-host dynamics on between-host dynamics,,Deterministic,,Individual-based,,Both,States,No,Yes,No,No,No,pathogen load of sexual (transmissable) stage,No,No,No,No,Yes,,Yes,Top-down,Least squares,steepest-descent algorithm,No,,,,No,,,
156,Dwyer,Ecol Monographs,1990,Keep,,Non-human Mammal,Rabbit,No,,Viral,Myxoma virus,Direct contact,Strategic,Impact of within-host dynamics on between-host dynamics,,Deterministic,,Deterministic,,Within-host linked to between-host,States,No,Yes,No,No,No,,Yes,No,No,No,No,,Yes,Top-down,Least squares,,No,,,,No,,,
221,Hall,Philosophical Transactions B,2018,Keep,,Invertebrates (Insects/snails/worms/etc),Daphnia magna,No,,Bacterial,Pasteuria ramosa,Indirect contact,Strategic,Impact of within-host dynamics on between-host dynamics,,Statistical,,Deterministic,,Both,Both,Maybe,Yes,No,No,No,,Yes,No,Yes,Yes,No,,Yes,Top-down,Least squares,doesn't specify - uses slope (least squares?),Yes,Top-down,Other,doesn't specify - fits exponential with single value,No,,,
225,Kennedy,PLOS Biology,2018,Keep,,Invertebrates (Insects/snails/worms/etc),gypsy moth,No,,Viral,baculovirus,Direct contact,Strategic,Impact of between-host dynamics on within-host dynamics,,Stochastic,,Stochastic,,Both,States,No,Yes,No,No,No,,No,No,No,No,Yes,,Yes,Top-down,NA,no direct fitting to data - comparison of predictions to nucleotide sequence diversity,No,,,,No,,,
227,Lindberg,Journal of Theoretical Biology,2018,Keep,,Invertebrates (Insects/snails/worms/etc),Drosophila melanogaster,No,,Bacterial,Pseudomonas aeruginosa,Direct contact,Tactical,Impact of within-host dynamics on between-host dynamics,,Deterministic,,Stochastic,,Within-host linked to between-host,Traits,Yes,No,No,No,No,,No,No,No,No,No,,Yes,Bottom-up,Least squares,,No,,,,No,,,
244,Scholle,The American Naturalist,2013,Keep,,Birds,,No,,Other,,Direct contact,Strategic,Impact of within-host dynamics on between-host dynamics,,Deterministic,,Deterministic,,Within-host linked to between-host,States,No,Yes,No,No,No,,Yes,No,No,No,No,,Yes,Top-down,Least squares,,No,,,,No,,,
246,Takumi ,International Journal for Parasitology,2010,Keep,,Non-human Mammal,rat,No,,Macroparasite (Worms/ticks/etc),Trichinella spiralis,Direct contact,Strategic,Impact of within-host dynamics on between-host dynamics,,Statistical,,Stochastic,,Within-host linked to between-host,Both,No,Yes,No,No,No,,No,No,No,No,No,,Yes,Top-down,Other,Functional form,Yes,Bottom-up,Maximum likelihood,,No,,,
249,Tuncer,Bulletin of Math Biology,2016,Keep,,Non-human Mammal,Livestock,Yes,"Human, mosquitoes",Viral,Rift Valley Fever,Direct contact,Strategic,Other,develop a numerical approach for a structural and practical identifiability analysis of a nested immuno-epidemiological model,Deterministic,,Deterministic,,Both,States,No,Yes,No,No,No,,Yes,Yes,Yes,No,No,,Yes,Top-down,Maximum likelihood,,Yes,Top-down,Least squares,,Yes,Top-down,Least squares,