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.

#### Density

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.

#### Host_Density_Combined

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.

#### Karvonen1

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.

#### Karvonen2

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.

#### Paller1

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.

#### Paller2

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.

#### Behavior Volume2

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.

#### Time_data

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.

#### Volume

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.

#### Makefile

File that allows all the R-code to be run together to create figures, tables, and generate all results.

#### README

General description of how to use the makefile to recreate the analysis using R code.

#### main

Main R script to run the analysis

#### mechanistic_mods

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.

#### likelihoods

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.

#### helpers

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.

#### fit_model

R code file for taking the data from each experiment and fitting them across the different transmission functions.

#### fig2

R code file for creating figure 2 (Figure 1 in the final manuscript).

#### fig3

R code file for creating figure 3 (Figure 2 in the final manuscript).

#### fig4

R code file for creating figure 4 (Figure 3 in the final manuscript).

#### behavior_volume2

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.

#### density

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.

#### host_number

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.

#### karvonen1

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.

#### karvonen2

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.

#### paller1

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.

#### paller2

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.

#### time

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.

#### volume

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.

#### behavior_table

Table 2f: Results of the varying parasite number, with tadpoles anaesthesized experiment including the AICc and deltaAIC of each of the transmission functions.

#### host_den_table

Table 2b: Results of the varying host density experiment including the AICc and deltaAIC of each of the transmission functions.

#### karvonen1_table

Karvonen1: Results of the varying parasite density experiment including the AICc and deltaAIC of each of the transmission functions.

#### karvonen2_table

Karvonen2: Results of the varying parasite number experiment including the AICc and deltaAIC of each of the transmission functions.

#### paller1_table

Paller1: Results of the varying parasite density experiment including the AICc and deltaAIC of each of the transmission functions.

#### paller2_table

Paller2: Results of the varying parasite number experiment including the AICc and deltaAIC of each of the transmission functions.

#### paras_density_table

Table 2d: Results of the varying parasite density experiment including the AICc and deltaAIC of each of the transmission functions.

#### time_table

Table 2c: Results of the varying exposure duration experiment including the AICc and deltaAIC of each of the transmission functions.

#### volume_table

Table 2a: Results of the varying parasite number (constant density) experiment including the AICc and deltaAIC of each of the transmission functions.

#### table2

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.

#### tableSI

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.

#### behavior

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.

#### host_den

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.

#### karvonen1

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.

#### karvonen2

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.

#### paller1

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.

#### paller2

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.

#### paras_density

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.

#### time

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.

#### volume

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.