Data and Code for Meta-analysis of Host Manipulation

Data data_final.csv Effect sizes with information on each observation parasite Parasite species or genus host Host species parasite_stage Parasite developemental stage host_origin Host origin infection Infection procedure behavior_details Details on recorded behavior/ phenotype predator_type Type of predator present if any behavior_type detailed behavioral categoris behavior_type1 broader behavioral categories used for analysis effect_on_predation Expected effect on predation; 1 indcates increased predation in infected individuals, -1 indicates decreased predation in infected individuals; compared to uninfected individuals CN Sample size, uninfected IN Sample size infected Ntot total sample size CMean average value for uninfected Cerr error for uninfected IMean average value for infected Ierr error for infected mean type of mean error type of error effect_size value of effect size type_effect_size effect size meassure used values_remarks remarks on values paper_id unique paper identifier ref_long reference year publication year remarks stage_assumed stage not entirely clear study_excluded 1= yes; 0=no exclusion_reason categorized exclusion reson if study was excluded exclusion_reason_details detailed exclusion reason predator_type1 broader categories for predator type used in the final analysis data_host.csv host Host species genus Host genus family Host family habitat_cat habitat category habitat2 additional information on habitat host_group1 host group based on phylogeny length_cm host length in cm mass host mass life_span_mean average host lifespan in years TL trophic level data_para.csv host Host species parasite Parasite species or genus genus parasite genus family parasite family parasite_group parasite group parathenic 1= yes; 0=no encysted 1= yes; 0=no site infection site dev time (days) developemental time next host length parasite length in mm width parasite width in mm remarks data_host1.csv File produced by add_host_para_data.Rmd; same as data_host, but proportion of trophic interactions as predator added data_out.csv File produced by data_preparation.Rmd; combines data_final with host and parasite data and adds effect sizes and cleans up some factors host_tree.RData & host_tree.tre Host tree generated by phylogenetic_tree.Rmd in .RData format (as used by the scripts) and in Newick format for better compatibility para_tree.RData & para_tree.tre Parasite tree generated by phylogenetic_tree.Rmd in .RData format (as used by the scripts) and in Newick format for better compatibility Workflow and files for data analysis Data preparation add_host_para_data.Rmd prepares host data by adding proportion of trophic interactions; takes data_host.csv and returns data_hos1.csv data_preparation.Rmd Calculates effect sizes and cleans up some factors and comones data on observations with host and parasite data; takes data_final, data_host1.csv and data_para.csv and returns data_out phylogenetic_tree.Rmd takes data_out and creates phylogenetic trees for hosts and parasites used in thsi analysis; returns host_tree.Rdata and para_tree.RData Data analysis All subsequent files take data_out and host_tree.Rdata and para_tree.Rdata as input run_auto_all.Rmd runs the entire analysis for the full data set with all parasite stages run_auto_mat2.Rmd runs the entire analysis for the a data set with only mature parasites run_auto_imat2.Rmd runs the entire analysis for the a data set with only immature parasites run_auto_predation_susceptibility2.Rmd runs the entire analysis for data that directly meassures predation susceptibility only run_auto_no_outl5_all.Rmd runs the entire analysis after the removel of outliers for the full data set with all parasite stages run_auto_no_outl5_mat2.Rmd runs the entire analysis after the removel of outliers for the a data set with only mature parasites run_auto_no_outl5_imat2.Rmd runs the entire analysis after the removel of outliers for the a data set with only immature parasites Custom scripts and functions preparation and functions contain costum code and function required by the scripts mentioned above to prepare the data and run the entire analysis. These scripts expect them to be located in folders called “preparations” and “functions” respectively. preparations: data.R final data preparations and checks prior to analysis libraries.R loads necessary libraries plots.R sets a theme for all plots in ggplot2 tables1.R prepares formating for tables if they are written directly to word functions: calc_I2_brms.R Calculate heterogenetiy (I2) following brms models check_brms_model_v2.R runs some diagnostics on brms models compare_brms_models1_v2.R compares two brms models using loo_compare diagnose.R produces diagnostic plots fro brms models funnel_plot.R, funnel3.R produce a funnel plot get_emmean.R, get_emmean_cor2.R, get_emmean_cor2_extra1.R obtain estimated marginal means using emmeans get_loos.R calculate loo and svae within brms model for later use get_outls.R obtain outliers overall_comparison_to_table.R create a nice looking table from different compairons between brms models plot_forest.R creates a simple forest plot plot_inter_behave_pred.R creates a forest plot for the interaction between behavior and predator plot_single_effect_combi2.R plot the effect of differenc factors within a model and combine plot_single_effect1.R plots the effect of a single effect in the model radnefs1.R obtain estimates for random effects redo_fact_plot4.R Creates final plots for factors in brms model run_brms_model1_v2.R run the actual brms model run_complete_v2.R Combines the entire analysis; i.e. running brms models, comparing them to a less complicated model, obtaining estimated marginal means and basic plots for models of interest