Data from: Experimental investigation of alternative transmission functions: quantitative evidence for the importance of non-linear transmission dynamics in host-parasite systems

Orlofske SA, Flaxman SM, Joseph MB, Fenton A, Melbourne BA, Johnson PTJ

Date Published: November 8, 2017

DOI: https://doi.org/10.5061/dryad.1pk42

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Title Density
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Description Raw 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.
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Title Host_Density_Combined
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Description Raw 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.
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Title Karvonen1
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Description Raw 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.
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Title Karvonen2
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Description Raw 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.
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Title Paller1
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Description Raw 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.
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Title Paller2
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Description Raw 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.
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Title Behavior Volume2
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Description Raw 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.
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Title Time_data
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Description Raw 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.
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Title Volume
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Description Raw 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.
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Title Makefile
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Description File that allows all the R-code to be run together to create figures, tables, and generate all results.
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Title README
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Description General description of how to use the makefile to recreate the analysis using R code.
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Title main
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Description Main R script to run the analysis
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Title mechanistic_mods
Description This 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.
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Title likelihoods
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Description Negative 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.
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Title helpers
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Description Helper 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.
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Title fit_model
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Description R code file for taking the data from each experiment and fitting them across the different transmission functions.
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Title fig2
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Description R code file for creating figure 2 (Figure 1 in the final manuscript).
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Title fig3
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Description R code file for creating figure 3 (Figure 2 in the final manuscript).
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Title fig4
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Description R code file for creating figure 4 (Figure 3 in the final manuscript).
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Title behavior_volume2
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Description R 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.
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Title density
Description R 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.
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Title host_number
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Description R 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.
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Title karvonen1
Description R 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.
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Title karvonen2
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Description R 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.
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Title paller1
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Description R 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.
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Title paller2
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Description R 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.
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Title time
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Description R 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.
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Title volume
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Description R 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.
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Title behavior_table
Description Table 2f: Results of the varying parasite number, with tadpoles anaesthesized experiment including the AICc and deltaAIC of each of the transmission functions.
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Title host_den_table
Description Table 2b: Results of the varying host density experiment including the AICc and deltaAIC of each of the transmission functions.
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Title karvonen1_table
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Description Karvonen1: Results of the varying parasite density experiment including the AICc and deltaAIC of each of the transmission functions.
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Title karvonen2_table
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Description Karvonen2: Results of the varying parasite number experiment including the AICc and deltaAIC of each of the transmission functions.
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Title paller1_table
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Description Paller1: Results of the varying parasite density experiment including the AICc and deltaAIC of each of the transmission functions.
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Title paller2_table
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Description Paller2: Results of the varying parasite number experiment including the AICc and deltaAIC of each of the transmission functions.
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Title paras_density_table
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Description Table 2d: Results of the varying parasite density experiment including the AICc and deltaAIC of each of the transmission functions.
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Title time_table
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Description Table 2c: Results of the varying exposure duration experiment including the AICc and deltaAIC of each of the transmission functions.
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Title volume_table
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Description Table 2a: Results of the varying parasite number (constant density) experiment including the AICc and deltaAIC of each of the transmission functions.
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Title table2
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Description Model 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.
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Title tableSI
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Description Model 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.
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Title behavior
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Description Table 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.
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Title host_den
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Description Table 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.
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Title karvonen1
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Description Table 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.
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Title karvonen2
Description Table 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.
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Title paller1
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Description Table 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.
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Title paller2
Description Table 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.
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Title paras_density
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Description Table 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.
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Title time
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Description Table 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.
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Title volume
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Description Table 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.
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When using this data, please cite the original publication:

Orlofske SA, Flaxman SM, Joseph MB, Fenton A, Melbourne BA, Johnson PTJ (2017) Experimental investigation of alternative transmission functions: quantitative evidence for the importance of non-linear transmission dynamics in host-parasite systems. Journal of Animal Ecology, online in advance of print. https://doi.org/10.1111/1365-2656.12783

Additionally, please cite the Dryad data package:

Orlofske SA, Flaxman SM, Joseph MB, Fenton A, Melbourne BA, Johnson PTJ (2017) Data from: Experimental investigation of alternative transmission functions: quantitative evidence for the importance of non-linear transmission dynamics in host-parasite systems. Dryad Digital Repository. https://doi.org/10.5061/dryad.1pk42
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