Carvalho-Bd-Virulence

Data sets and code for Carvalho et al. Amphibian Hymenochirus boettgeri as an experimental model for infection studies with the chytrid fungus Batrachochytrium dendrobatidis

This readme file was generated on 2023-06-01 by Tamilie Carvalho

GENERAL INFORMATION

Title of Dataset: Amphibian Hymenochirus boettgeri as an experimental model for infection studies with the chytrid fungus Batrachochytrium dendrobatidis.

Author Information Name: Tamilie Carvalho ORCID: https://orcid.org/0000-0001-7300-2777 Institution: University of Michigan Address: 2220 Biological Science Building, 1105 North University, Ann Arbor, MI 48109-1085, USA. Email: tamiliec@gmail.com; tamilie@umich.edu

Date of data collection: 2022-03-01 to 2022-09-01

Geographic location of data collection: Ann Arbor, USA.

Information about funding sources that supported the collection of the data: This work was supported by the Gordon and Betty Moore Foundation Award #9337 (10.37807/GBMF9337). TYJ is a Fellow in the CIFAR program Fungal Kingdom: Threats and Opportunities. The work was partially supported by a catalyst grant from CIFAR and CIFAR fellowship funds.

Recommended citation for this dataset: Carvalho, T; Si, C.; Clemons, A.R; Faust, E; James, T.Y. 2023. Amphibian Hymenochirus boettgeri as an experimental model for infection studies with the chytrid fungus Batrachochytrium dendrobatidis.

DATA & FILE OVERVIEW

File List: 1. Bddosageresponse.csv 2. Modelgeneralizability.csv 3. Validation.csv 4. Statistical_analyses.Rmd

Relationship between files: Use files number 1, 2 and 3 to run R code number 4.

DATA-SPECIFIC INFORMATION FOR: Bddosageresponse.csv

Number of variables: 3

Number of rows: 36

Variable List: 1. Treatment: Treatments reflect the combination of genotypes (JEL423 or CLFT073) and Bd dose (HD - high dose and LD - low dose), and a control group.

1. Mortality_day: Values reflect the number of days until death after exposure to the pathogen.

2. Censor: 1 when the frog died, and 0 when it survived until the end of the experiment.

DATA-SPECIFIC INFORMATION FOR: Modelgeneralizability.csv

Number of variables: 4

Number of rows: 70

Variable List: 1. Censor: 1 when the frog died, and 0 when it survived until the end of the experiment.

1. Mortality_day: Values reflect the number of days until death after exposure to the pathogen.

2. Genotype: Genotype name used in the exposure treatment and a Control group.

3. Lineage: Name of the lineages to which the genotypes used in the exposure experiment belong. Control (No lineages/genotypes used).

DATA-SPECIFIC INFORMATION FOR: Validation.csv

Number of variables: 6

Number of rows: 40

Variable List: 1. ID: Frog identification number.

1. Bd_Load: Bd pathogen load.

2. Genotype_experiment: Combinations of genotypes (CLFLT150 or CLFT039) and experiments (MG - model generalizability or V - validation) of each treatment and control groups.

3. Censor: 1 when the frog died, and 0 when it survived until the end of the experiment.

4. Mortality_day: Values reflect the number of days until death after exposure to the pathogen.

5. Lineage: Name of the lineages to which the genotypes used in the exposure experiment belong. Control (No lineages/genotypes used).