DOI: 10.5061/dryad.1pk42
title: Data from: Experimental investigation of alternative transmission functions: quantitative evidence for the importance of non-linear transmission dynamics in host-parasite systems

description: 1. Understanding pathogen transmission is crucial for predicting and
 managing disease. Nonetheless, experimental comparisons of alternative
 functional forms of transmission remain rare, and those experiments that
 are conducted are often not designed to test the full range of possible
 forms. 2. To differentiate among ten candidate transmission functions, we
 used a novel experimental design in which we independently varied four
 factors—duration of exposure, numbers of parasites, numbers of hosts, and
 parasite density—in laboratory infection experiments. 3. We used
 interactions between amphibian hosts and trematode parasites as a model
 system and all candidate models incorporated parasite depletion. An
 additional manipulation involving anesthesia addressed the effects of host
 behaviour on transmission form. 4. Across all experiments, non-linear
 transmission forms involving either a power law or a negative binomial
 function were the best-fitting models and consistently outperformed the
 linear density-dependent and density-independent functions. By testing
 previously published data for two other host-macroparasite systems, we
 also found support for the same non-linear transmission forms. 5. Although
 manipulations of parasite density are common in transmission studies, the
 comprehensive set of variables tested in our experiments revealed that
 variation in density alone was least likely to differentiate among
 competing transmission functions. Across host-pathogen systems, non-linear
 functions may often more accurately represent transmission dynamics and
 thus provide more realistic predictions for infection.
description: DensityRaw data from the varying parasite density (constant volume, variable parasite number) experiment. Cerc_Density is the number of R. ondatrae cercariae added. ID is the unique tadpole number. Stage is Gosner stage of the tadpole. Meta is number of metacercariae recovered. Mass is final wet mass of tadpole. SVL is snout vent length of the tadpole at the end of the experiment. TL is total length of the tadpole at the end of the experiment.Host_Density_CombinedRaw data from the varying host density (constant volume, variable host number) experiment. Cerc_Number is the number of R. ondatrae cercariae added. Meta _Number is the number of metacercariae recovered. Mass is final wet mass of tadpole. Host_Number is the number of tadpoles in the experimental replicate.Karvonen1Raw data from Karvonen et al. 2003 using rainbow trout Oncorhynchus mykiss and Diplostomum spathaceum varying parasite density. Cerc is number of parasites added. Meta is the number of metacercariae. Time is the duration of exposure in minutes. Volume is the size of the experimental area in liters.Karvonen2Raw data from Karvonen et al. 2003 using rainbow trout Oncorhynchus mykiss and Diplostomum spathaceum varying parasite number. Cerc is number of parasites added. Metacerc is the number of metacercariae. Time is the duration of exposure in minutes. Volume is the size of the experimental area in liters.Paller1Raw data from Paller et al. 2003 using minnows Zacco temmincki and Centrocestus armatus varying parasite density. Cerc is number of parasites added. Metacerc is the number of metacercariae. Time is the duration of exposure in minutes. Volume is the size of the experimental area in liters.Paller2Raw data from Paller et al. 2003 using minnows Zacco temmincki and Centrocestus armatus varying parasite number.Cerc is number of parasites added. Metacerc is the number of metacercariae. Time is the duration of exposure in minutes. Volume is the size of the experimental area in liters.Behavior Volume2Raw data from the host behavior experiment. Number is the number of R. ondatrae cercariae added. Meta is number of metacercariae recovered. Mass is final wet mass of tadpole. SVL is snout vent length of the tadpole at the end of the experiment. Total Length is total length of the tadpole at the end of the experiment. Volume is the size of the arena in liters.Time_dataRaw data from the experiment varying duration of exposure. Trt is the number of R. ondatrae cercariae added. ID is the unique tadpole number. Stage is Gosner stage of the tadpole. Meta is number of metacercariae recovered. Mass is final wet mass of tadpole. SVL is snout vent length of the tadpole at the end of the experiment. TL is total length of the tadpole at the end of the experiment.VolumeRaw data from the experiment varying parasite number (constant parasite density, variable volume). Cerc_Number is the number of R. ondatrae cercariae added. ID is the unique tadpole number. Stage is Gosner stage of the tadpole. Meta is number of metacercariae recovered. Mass is final wet mass of tadpole. SVL is snout vent length of the tadpole at the end of the experiment. TL is total length of the tadpole at the end of the experiment. Volume is the size of the arena in liters.MakefileFile that allows all the R-code to be run together to create figures, tables, and generate all results.READMEGeneral description of how to use the makefile to recreate the analysis using R code.mainMain R script to run the analysismechanistic_modsThis script defines a suite of useful functions that will be used often adapted from Sarah Orlofske & Brett Melbourne's code by Max Joseph 6/8/14 Biological models for trematode Ribeiroia ondatrae transmission of cercariae to tadpole second intermediate hosts. Each model contains a separate 'biological model' which is then combined with the stochastic component in the negative log likelihood.likelihoodsNegative log likelihood functions for evaluating the biological models with data and incorporating stochasticity in the distribution generally, parameters to be estimated are packed into the object p fixed parameters are named and need not be unrolled our expected values (meta) are calculated with the mechanistic model observed numbers of metacercariae are called metacerc.helpersHelper functions for use with the other R code files. Contains the library information and other code needed to generate AICc results, AIC tables, and plots.fit_modelR code file for taking the data from each experiment and fitting them across the different transmission functions.fig2R code file for creating figure 2 (Figure 1 in the final manuscript).fig3R code file for creating figure 3 (Figure 2 in the final manuscript).fig4R code file for creating figure 4 (Figure 3 in the final manuscript).behavior_volume2R code that takes the data from the Host Behavior experiment and integrates with the other R code files to fit the models, make the AIC table, and make the parameter table.densityR code that takes the data from the varying parasite density experiment and integrates with the other R code files to fit the models, make the AIC table, and make the parameter table.host_numberR code that takes the data from the varying host density (constant volume, variable host number) experiment and integrates with the other R code files to fit the models, make the AIC table, and make the parameter table.karvonen1R code that takes the data from Karvonen et al. 2003 using rainbow trout Oncorhynchus mykiss and Diplostomum spathaceum varying parasite density experiment and integrates with the other R code files to fit the models, make the AIC table, and make the parameter table.karvonen2R code that takes the data from Karvonen et al. 2003 using rainbow trout Oncorhynchus mykiss and Diplostomum spathaceum varying parasite number experiment and integrates with the other R code files to fit the models, make the AIC table, and make the parameter table.paller1R code that takes the data from Paller et al. 2003 using minnows Zacco temmincki and Centrocestus armatus varying parasite density experiment and integrates with the other R code files to fit the models, make the AIC table, and make the parameter table.paller2R code that takes the data from Paller et al. 2003 using minnows Zacco temmincki and Centrocestus armatus varying parasite number experiment and integrates with the other R code files to fit the models, make the AIC table, and make the parameter table.timeR code that takes the data from the varying duration of exposure experiment and integrates with the other R code files to fit the models, make the AIC table, and make the parameter table.volumeR code that takes the data from the varying parasite number (constant parasite density, variable volume) experiment and integrates with the other R code files to fit the models, make the AIC table, and make the parameter table.behavior_tableTable 2f: Results of the varying parasite number, with tadpoles anaesthesized experiment including the AICc and deltaAIC of each of the transmission functions.host_den_tableTable 2b: Results of the varying host density experiment including the AICc and deltaAIC of each of the transmission functions.karvonen1_tableKarvonen1: Results of the varying parasite density experiment including the AICc and deltaAIC of each of the transmission functions.karvonen2_tableKarvonen2: Results of the varying parasite number experiment including the AICc and deltaAIC of each of the transmission functions.paller1_tablePaller1: Results of the varying parasite density experiment including the AICc and deltaAIC of each of the transmission functions.paller2_tablePaller2: Results of the varying parasite number experiment including the AICc and deltaAIC of each of the transmission functions.paras_density_tableTable 2d: Results of the varying parasite density experiment including the AICc and deltaAIC of each of the transmission functions.time_tableTable 2c: Results of the varying exposure duration experiment including the AICc and deltaAIC of each of the transmission functions.volume_tableTable 2a: Results of the varying parasite number (constant density) experiment including the AICc and deltaAIC of each of the transmission functions.table2Model selection statistics for macroparasite transmission functional forms (table 1 in main text of manuscript) according to different experimental conditions (a-e) of Pseudacris regilla tadpole hosts and cercariae of Ribeiroia ondatrae. Functional forms with identical AICc values are mathematically equivalent under the experimental condition tested.tableSIModel selection statistics for macroparasite transmission functional forms (table 1 in main text of manuscript) according to different experimental conditions (a-b) of rainbow trout Oncorhynchus mykiss hosts and cercariae of Diplostomum spathaceum (Karvonen et al. 2003) and (c-d) of minnow Zacco temmincki and cercariae of Centrocestus armatus (Paller et al.2007). Functional forms with identical AICc values are mathematically equivalent under the experimental condition tested.behaviorTable of parameter estimates of the host behavior (varying parasite number, with tadpoles anaesthesized experiment). Experiment gives the experimental condition. Model gives the specific form of the transmission function tested, the parameter column gives the specific parameter from the function estimated and the MLE column gives the maximum likelihood estimate.host_denTable of parameter estimates of the host density experiment. Experiment gives the experimental condition. Model gives the specific form of the transmission function tested, the parameter column gives the specific parameter from the function estimated and the MLE column gives the maximum likelihood estimate.karvonen1Table of parameter estimates of the varying parasite density experiment from Karvonen et al. 2003. Experiment gives the experimental condition. Model gives the specific form of the transmission function tested, the parameter column gives the specific parameter from the function estimated and the MLE column gives the maximum likelihood estimate.karvonen2Table of parameter estimates of the varying parasite number experiment from Karvonen et al. 2003. Experiment gives the experimental condition. Model gives the specific form of the transmission function tested, the parameter column gives the specific parameter from the function estimated and the MLE column gives the maximum likelihood estimate.paller1Table of parameter estimates of the varying parasite density experiment from Paller et al. 2007. Experiment gives the experimental condition. Model gives the specific form of the transmission function tested, the parameter column gives the specific parameter from the function estimated and the MLE column gives the maximum likelihood estimate.paller2Table of parameter estimates of the varying parasite number experiment from Paller et al. 2007. Experiment gives the experimental condition. Model gives the specific form of the transmission function tested, the parameter column gives the specific parameter from the function estimated and the MLE column gives the maximum likelihood estimate.paras_densityTable of parameter estimates of the parasite density experiment. Experiment gives the experimental condition. Model gives the specific form of the transmission function tested, the parameter column gives the specific parameter from the function estimated and the MLE column gives the maximum likelihood estimate.timeTable of parameter estimates of the varying exposure duration experiment. Experiment gives the experimental condition. Model gives the specific form of the transmission function tested, the parameter column gives the specific parameter from the function estimated and the MLE column gives the maximum likelihood estimate.volumeTable of parameter estimates of the varying parasite number (constant density) experiment. Experiment gives the experimental condition. Model gives the specific form of the transmission function tested, the parameter column gives the specific parameter from the function estimated and the MLE column gives the maximum likelihood estimate.