Chapter3_parasites

This is the code for the chapter 3 of my PhD

Sociality

Sociality status is based on flcok observations from Manu only, some particular species have changes in thh status

Lophotriccus pileatus::This species has been obserevd in flocks but those floks were incomplete and therefore not included in the analyses, I changed 0 to 1 in sociality manually

##File names and description ##

Raw data files:

[1]The raw files of bird diversity form Manu diversity

0.flocks_manu_complete_18052022.csv 0.netting_manu_complete_18052022.csv

[2] The tidy files of manu diversity 1.Manu_bird_species_detections_tidy_taxonomy_18052022.csv 1.manu_bird_species_list_flocks.csv 1.Manu_bird_species_list_tidy_18052022.csv

[3] The functional traits of Manu birds 4.df_traits_manu_birds.csv

[4] Files to correct taxonomy

We match the taxonomy with Jetz taxonomy that we aleady curated form manu data( see list of species that were manually matched)

0.species_manual_taxonomy_match.csv 4.list_manu_jetz_tax_missmatches_corrected.csv

These are the raw files of the ectoparasies without taxonomy corrected or any calculation EctoparsiteRawData_All_07.22.2022.xlsx 7.ectoparasite_raw_pres_abs_07222022.csv 7.ectoparsite_raw_lice_abundance_07222022.csv 7.ectoparsite_raw_mites_abundance_07222022 7.ectoparsite_raw_ticks_abundance_07222022.csv

The above files were used to create the datafiles (df) using script 1. 5.ectos_pres_abs_df copy.csv # this includes data from manu only 5.ectos_pres_abs_df.csv # this files includes data from manu and iquitos

5.lice_df_abundance_manu.csv # lice manu only 5.lice_df_abundance_means # lice abundance manu only 5.lice_richness_sp_df_manu.csv # lice richness manu only

These files are the ones used for the analyses it includes the parasite information with traits information, jetz taxonomy and taxonomy corrected to 2022:

7.ectoparasite_df_presence_absence.csv 7.lice_df_abundance_means.csv 7.lice_df_abundance.csv 7.lice_df_diversity_genus.csv 7.lice_df_diversity_species.csv 7.mites_df_abundance_means.csv 7.mites_df_abundance.csv 7.mites_df_diversity_genus.csv 7.mites_df_diversity_group.csv 7.ticks_df_abundance.csv

From those files we generated the datasets for data_analyses, selecting only relevant collumns with the following characeterustics: Script 2

Jetz taxonomy only Manu data, excluded iquitos, included sociality_binomial included and selected some bird traits included elevation of the sample included elevation midpoint ofthe species

The data files used for analyses

this are teh files used for teh thesis draft

data<data_manuscript

3_dff_all_ectos_network_metrics_individuals_FILE_TIDY 3_dff_all_ectos_prevalence_abundance_diversity_individual_elevation_mass_FILE_TIDY 3_dff_ectos_diversity_network_metrics_species_FILE_TIDY 3_dff_ectos_diversity_species_prevalence_abundance_diversity_elevation_mass_FILE_TIDY

7_dff_network_metrics_ectoparasite_samples_FILE_method 7_prevalence_ectoparasite_family_level

files

7.dff_all_ectos_prevalence_abundance_individual.csv # includes Abundance and prevalence

We the included the individual elevation for the samples using teh metadata from samples #0.ectoparasite_samples_elevation_metadata.csv

And for some ( few smples nputed data manually)

#P121006 Rupicola_peruvianus 1362 The correct name of this is SP121006 AND THE ELEVATION 1362 #"P120889" is Leptopogon superciliaris CORRRECT NAME SP120889 AND THE ELEVATION IS 1395 #P120085 Formicarius rufipectus correct name SP120085 elev 1362 #P115912 Leptopogon amaurocephalus elevation 381

Created collumn with extrapolated date

This column take the NA for elevation and use the information about date and station to see which other species were captured the same data in the same station and used that elevation

included degree_general_network (at the species level) included refined degree at the individual level