This metadata file describes two datasets collected for the paper, “Systematic review of modeling assumptions and empirical evidence: does parasite transmission increase nonlinearly with host density?”, which we revised and re-submitted in November 2019 to Methods in Ecology and Evolution. 

Authors:  Skylar R. Hopkins1*, Arietta E. Fleming-Davies2,3, Lisa K. Belden1, Jeremy M. Wojdak3 
1.	Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
2.	Biology Department, University of San Diego, San Diego, CA
3.	Department of Biology, Radford University, Radford, VA, USA
Email addresses:  skylar.hopkins@vt.edu, arietta.flemingdavies@gmail.com, belden@vt.edu, jmwojdak@radford.edu

SystematicLitReview_TransmissionFunctions.csv

Overview: This CSV describes a systematic literature review of seven journals that publish ecological research: American Naturalist, Ecology, Ecology Letters, Journal of Animal Ecology, Journal of Applied Ecology, Proceedings of the National Academy of Sciences, and Proceedings of the Royal Society B. We examined the full text of 2,019 papers to find 262 papers containing SIR-type epidemiological models. This dataset contains the bibliographic information for each paper as well as information regarding the transmission function(s) used in the SIR-type model.

Description of columns:
Journal	: the name of one of seven journals that we systematically reviewed for relevant papers

Volume: the volume number of the journal in which the paper was published

Issue: the issue of the journal in which the paper was published

Year: the publication year of the paper

Title: the title of the paper

TransmissionFunction: A numerical code indicating which transmission function or transmission function category was used in the epidemiological model. 1=density-dependent (DD), 2=frequency-dependent(FD), 5=test of multiple functions, 6=negative binomial, 7=Dwyer’s heterogeneity function, and 8=the power function (see Fenton et al. 2002). Note that 6, 7, and 8 are nonlinear functions, and 5 might involve nonlinear options.

SingleNLYN: Whether the epidemiological model used a single nonlinear transmission function, as opposed to testing multiple functions or using linear functions. 1=yes, a single nonlinear function was used and 0=no, a single nonlinear function was not used. 

Justification: A numerical code indicating the method that author’s used to justify their choice of transmission function(s) in the prose of the paper. 1=authors cited a general paper about transmission functions, 2=authors cited a paper from the same biological system or based the decision on their own knowledge of the system, 3=authors cited a general paper about SIR/epidemiological modeling that doesn’t focus on transmission functions specifically, 4=no explanation, and 5=both 1 and 2.

CitationForJustification: If the authors cited a paper when justifying their choice of transmission function(s) in the prose of the paper, the citation was recorded in this column.

DensityConstantYN: Our best attempt to determine whether the host(s) population density was constant in the epidemiological model, using information provided in the model and in the text of the paper. 0=no, the density varied, 1=yes, the density was constant, 2=we assume density varied because the theoretical model included demography, and 3=we could not determine whether host density was constant or not.

PopChangeNotes: Brief notes made when determining whether the host(s) population density was constant in the epidemiological model, using information provided in the model and in the text of the paper. Sometimes these notes are quotes from the paper, and we designate those cases with quotation marks.

Notes: This is a general notes column where we recorded the host–parasite system (or whether it was a purely theoretical/hypothetical system) and any notes regarding the transmission function(s) used in the model and how we made decisions in ambiguous cases. 

PurelyTheoreticalYN: 1=Yes, the study was purely theoretical and 0=No, the study contained empirical data. If a study used data from a previously published paper (e.g., as parameter estimates), we considered it to be 0.

FittoDataYN: 1=Yes, the epidemiological model was fit to data (e.g., nonlinear regression) in this paper and 0=No, the model was analytically described or numerically simulated without fitting it to a dataset.

VectoredYN: 1=Yes, the model describes the transmission of a vectorborne parasite/pathogen and 0=No, the model does not describe the transmission of a vectorborne parasite/pathogen

FreeLivingStageInModelYN: 1=Yes, the model describes the transmission of a free-living or environmentally-transmitted parasite/pathogen stage and 0=No, the model does not describe the transmission of a free-living or environmentally-transmitted parasite/pathogen stage

MacroparasiteYN: 1=Yes, the model describes the transmission of a macroparasite and 0=No, the model does not describe the transmission of a macroparasite

SexuallyTransmittedYN: 1=Yes, the model describes the transmission of a sexually-transmitted parasite/pathogen and 0=No, the model does not describe the transmission of a sexually-transmitted parasite/pathogen

SpatialStructureYN: 1=Yes, the model includes spatial structure in the host and/or parasite population (e.g., nearest neighbor models) and 0=No, the model does not include spatial structure in the host and/or parasite population 

HumanDiseaseYN: 1=Yes, the model describes the transmission of a parasite/pathogen that infects humans as one host species and 0=No, the model does not describe the transmission of a parasite/pathogen that infects humans as one host species 

AreainModelYN: 1=Yes, either area is explicitly included as a variable in the model or the text explains how area was considered in the model, 0=No, area is not explicitly included as a variable in the model or explained in the text 

AreaConstantYN: Our best attempt to determine area occupied by the host(s) population(s) was constant in the epidemiological model, using information provided in the model and in the text of the paper. 0=No, the area was not constant, 1=Yes, the area was constant, 2= we assume area was constant (e.g., just one study location/site, theoretical model), and 3= we could not determine whether area was constant or not.

TallyofEmpiricalTestsofMultipleTransmissionFunctions.csv

Overview: This CSV describes a review of 42 papers that used statistical analyses with contact rate, transmission rate (or force of infection, FOI), and/or time series data to compare multiple transmission functions and decide which was most appropriate for a given host–parasite system. 

Description of columns:
Title: the title of the paper

TypeofTest: A numerical code indicating the response variable(s) used in the statistical analysis. 1=contact rates AND transmission rates (or FOI), 2=contact rates, 3=transmission rates (or FOI) AND host susceptibility, 4=transmission rates (or FOI), 5=prevalence or incidence time series data, 6=host mortality rates (just one paper).

FunctionsTested: A numerical code indicating which collection of transmission functions were compared. 1=compared linear functions only (DD vs. FD), 2=compared at least one linear function to at least one nonlinear function that was not the power function, 3= compared at least one linear function to the power function (a particular nonlinear function), 4=compared a large suite of functions including one linear function, the power function, and one other nonlinear function

BestFunction: A numerical code indicating which transmission function the authors decided was most parsimonious based on their statistical analysis. 1=DD, 2=FD, 3=A nonlinear function that wasn’t the power function, 4=The power function, 5=Other (see notes), 6=NB Nonlinear

VectoredYN: 1=Yes, the model describes the transmission of a vectorborne parasite/pathogen and 0=No, the model does not describe the transmission of a vectorborne parasite/pathogen

FreeLivingStageInModelYN: 1=Yes, the model describes the transmission of a free-living or environmentally-transmitted parasite/pathogen stage and 0=No, the model does not describe the transmission of a free-living or environmentally-transmitted parasite/pathogen stage

MacroparasiteYN: 1=Yes, the model describes the transmission of a macroparasite and 0=No, the model does not describe the transmission of a macroparasite

SexuallyTransmittedYN: 1=Yes, the model describes the transmission of a sexually-transmitted parasite/pathogen and 0=No, the model does not describe the transmission of a sexually-transmitted parasite/pathogen

SpatialStructureYN: 1=Yes, the model includes spatial structure in the host and/or parasite population (e.g., nearest neighbor models) and 0=No, the model does not include spatial structure in the host and/or parasite population 

HumanDiseaseYN: 1=Yes, the model describes the transmission of a parasite/pathogen that infects humans as one host species and 0=No, the model does not describe the transmission of a parasite/pathogen that infects humans as one host species 

FentonYN: 1=Yes, this paper/dataset was re-analyzed by Fenton et al. (2002) or 0=No, this paper/dataset was not re-analyzed by Fenton et al. (2002)

DensityConstantYN: Our best attempt to determine whether the host(s) population density was constant in the epidemiological model, using information provided in the model and in the text of the paper. 0=no, the density varied, 1=yes, the density was constant, or 2=we could not determine whether host density was constant or not.

OnlyInfectedsorFreeLivingVariedYN: 1=Yes, only the number/density of the infected hosts or parasite stages was varied (rather than total host numbers/densities), 0=No, total host numbers/densities varied

AreaConstantYN: Our best attempt to determine area occupied by the host(s) population(s) was constant in the epidemiological model, using information provided in the model and in the text of the paper. 0=No, the area was not constant, 1=Yes, the area was constant, 2=we could not determine whether area was constant or not.

AreaExplictlyIncludedYN: 1=Yes, either area is explicitly included as a variable in the model or the text explains how area was considered in the model, 0=No, area is not explicitly included as a variable in the model or explained in the text 

InSystematicReviewYN: 1=Yes, this paper was included in the systematic literature review of 2,019 papers or 0= No, this paper was not included in the systematic literature review of 2,019 papers

Notes: This is a general notes column where we recorded the host–parasite system and any notes regarding the transmission function(s) compared, experimental details, and how we made decisions in ambiguous cases.