This DATSETNAMEreadme.txt file was generated on [2023-05-09] by [Davis Carter]


-------------------
GENERAL INFORMATION
-------------------


1. Title of Dataset 


2. Author Information


Principal Investigator Contact Information
        Name: Matthew J Gray
           Institution: University of Tennessee Institute of Agriculture, Knoxville
           Address:
           Email: mgray11@utk.edu
  Associate or Co-investigator Contact Information
        Name: E. Davis Carter
           Institution: University of Tennessee Institute of Agriculture, Knoxville 
           Address:
           Email: ecarte27@utk.edu
   Associate or Co-investigator Contact Information
           Name: Jonah Piovia-Scott
           Institution: Washington State University, Pullman
           Address:
           Email: jonah.piovia-scott@wsu.edu
  Associate or Co-investigator Contact Information
        Name: J. Patrick W. Cusaac
           Institution: University of Tennessee Institute of Agriculture, Knoxville 
           Address:
           Email:jcusaac@utk.edu
  Associate or Co-investigator Contact Information
           Name: Anna C. Peterson
           Institution: University of Tennessee Institute of Agriculture, Knoxville
           Address:
           Email: apeter53@utk.edu
  Associate or Co-investigator Contact Information
           Name: Ross D. Whetstone 
           Institution: University of Massachusetts, Boston
           Address:
           Email: rosswhetstone@gmail.com
  Associate or Co-investigator Contact Information
           Name: Andreas Hertz
           Institution: University of Massachusetts, Boston
           Address:
           Email: Andreas.Hertz@umb.edu
  Associate or Co-investigator Contact Information
           Name: Anura Y. Muniz-Torres
           Institution: University of Massachusetts, Boston
           Address:
           Email: Aura.MunizTorres001@umb.edu
  Associate or Co-investigator Contact Information
           Name: Molly C Bletz
           Institution: University of Massachusetts, Boston
           Address:
           Email: molly.bletz@umb.edu
  Associate or Co-investigator Contact Information
           Name: Douglas C. Woodhams
           Institution: University of Massachusetts, Boston; Smithsonian Tropical Research Institute
           Address:
           Email: Douglas.Woodhams@umb.edu
  Associate or Co-investigator Contact Information
           Name: John M. Romansic
           Institution: Washington State University, Pullman
           Address:
           Email: john.romansic@wsu.edu
   Associate or Co-investigator Contact Information
           Name: William B. Sutton
           Institution: Tennessee State University, Nashville
           Address:
           Email: wsutton@tnstate.edu
   Associate or Co-investigator Contact Information
           Name: Wesley Sheley
           Institution: University of Tennessee College of Veterinary Medicine,Knoxville
           Address:
           Email: wsiniard@utk.edu
  Associate or Co-investigator Contact Information
           Name: Allan Pessier 
           Institution: Washington State University, Pullman
           Address:
           Email: apessier@wsu.edu
  Associate or Co-investigator Contact Information
           Name: Catherine D. McCusker
           Institution: University of Massachusetts, Boston
           Address:
           Email: mccusker.catherine@gmail.com
  Associate or Co-investigator Contact Information
           Name: Mark Q. Wilber
           Institution:University of Tennessee Institute of Agriculture,Knoxville
           Address:
           Email: mqwilber@gmail.com
  Associate or Co-investigator Contact Information
           Name: Debra L. Miller
           Institution:University of Tennessee College of Veterinary Medicine,Knoxville
           Address:
           Email: dmille42@utk.edu

3. Date of data collection (single date, range, approximate date) <suggested format YYYY-MM-DD>
2016-2021

4. Geographic location of data collection (where was data collected?): 
Knoxville, Tennessee
Boston, Massachusetts
Pullman, Washington



5. Information about funding sources that supported the collection of the data:
BAND Foundation,
Association of Fish and Wildlife Agencies (#2016-01),
Tennessee Wildlife Resource Agency (#5237),
North Carolina Wildlife Resource Commission (#WM-0309),
U.S. Fish and Wildlife Services (#TN-U2-F19AP00047),
The Wildlife Without Borders-Amphibians in Decline program (#F15AP00968),
Amphibian Survival Alliance, 
Liquid Spark,
Nancy Goranson Endowment Fund at the University of Massachusetts Boston, 
National Institute of Health (#R15 HD092180/HD/NICHD and #R25 Bridges to the Baccalaureate NIH/NIGMS 2R25GM075306),
National Science Foundation (EEID #1814520 and IOS #1845634),
U.S. Department of Agriculture National Institute of Food and Agriculture (Hatch Project #1012932),
David H. Smith Postdoc Conservation Fellowship Program, and the
German Science Foundation (#HE 7562/1-1)

6. Abstract/description of the dataset:
Batrachochytrium salamandrivorans (Bsal) is a fungal pathogen of amphibians that is emerging in Europe and could be introduced to North America through international trade or other pathways. To evaluate the risk of Bsal invasion to amphibian biodiversity, we performed dose-response experiments on 36 North American species from 10 families, including larvae from six species. We discovered that Bsal caused infection in 72% and mortality in 36% of species tested. Both salamanders and frogs became infected and developed Bsal chytridiomycosis. In the United States, predicted biodiversity loss is expected to be greatest in the Appalachian Region and along the West Coast. Indices of infection and disease susceptibility suggest that North American amphibian species span a spectrum of vulnerability to Bsal chytridiomycosis and most amphibian communities will include carrier, amplification, and high-risk species. Given the high diversity and abundance of salamanders in North America, we recommend a trilateral agreement among the United States, Canada, and Mexico to prevent introduction of Bsal and substantial biodiversity loss.  

7: Keywords for the dataset (provide 3 - 5):

Wildlife Disease, Batrachochytrium salamandrivorans, Fungal Pathogen, Emerging Infectious Disease


--------------------------
SHARING/ACCESS INFORMATION
-------------------------- 


1. Licenses/restrictions placed on the data:


2. Links to publications that cite or use the data:


3. Links to other publicly accessible locations of the data:


4. Links/relationships to ancillary data sets:


5. Was data derived from another source?
           If yes, list source(s): 
IUCN.  Vol. Version 2019-3   (2020).
Hedges, S. B., Dudley, J. & Kumar, S. TimeTree: a public knowledge-base of divergence times among organisms. Bioinformatics 22, 2971-2972 (2006).
PRISM Climate Group. 201530-year normals, annual and monthly mean temperature, 800 m resolution. Corvallis, OR: Oregon State University. (http://prism.oregonstate.edu)



6. Recommended citation for the data:




---------------------
DATA & FILE OVERVIEW
---------------------


1. File List
   A. Filename: Kcalc_phylosignal.R       
      Short description: The Kcalc phylosignal R script is used to perform the Blomberg's K analysis for phylogenetic signal in mortality and infection for the species tested. This code is also used to create Figure 1. 
   B. Filename: Species_Names.nwk       
      Short description: This is phylogenetic tree created on the timetree.org website which contains all the species challenged in this study.
   C. Filename: Kcalc_Table.csv       
      Short description: This csv contains the mortality and infection for each species challenged with 10^6 Bsal zoospores.
   D. Filename: Nature_Survival_Figure.R       
      Short description: This R script contains the code necessary to produce the figure shown in the Extended Data Figure 1. 
   E. Filename: AllSpeciesSurvival.csv       
      Short description: This csv file has the survival time for each species and animal that experienced mortality due to Bsal chytridiomycosis.
   F. Filename: GIS_Code.R       
      Short description: This R script is used to create the data frame necessary for creating the risk maps found in Figure 2 and Figure S1 in the supplemental file. 
   G. Filename: SalamanderSpecies.nwk       
      Short description: This file conains the phylogenetic relatedness of all salamander species present in the United States downloaded from the TimeTree.org website.
   H. Filename: Nature_Paper_Infection_Mortality_Perc.csv       
      Short description: This csv contains the infection and mortality data from all 10^6 exposed species found in the paper. This csv is used to predict infection and mortality for all salamander species present in the United States that were not challenged. 
   I. Filename: CombinedData.xls       
      Short description: This excel file is the output from the predicted infection and mortality percentages for all salamander species found within the United States. 
   J. Filename: GIS_Data_Creation.xlsx       
      Short description: This excel sheet contains the information needed to create risk estimates for each county FIPS code in the United States. 
   K. Filename: BsalRiskData.csv       
      Short description: This csv file contains the information for each US FIPS code that is present in the GIS_Data_Creation.xlsx. The csv file is used to then create final risk scales using code found in the GIS_Code.R script. 
   L. Filename: SalamanderRiskMod_GIS_Dataframe.csv        
      Short description: This file is the final data frame needed to be imported into GIS. Once connected to the United States map using the FIPS code the maps shown throughout the paper can be recreated.    
   M. Filename:ID50_LD50_Estimation.R       
      Short description: This R.script is used to create the ID50 and LD50 estimates for all the species that experienced infection and mortality. 
   N. Filename:Mort_Inf_NATURE_ID50_LD50.csv      
      Short description:
   O. Filename:ID50_LD50_Ordination_Data.csv      
      Short description:
   P. Filename: Species_qPCR_NATURE_r2.csv       
      Short description:  Bsal load and survival data used in analyses of 
      load growth across specie exposed at various exposure doses.        
   Q. Filename:  BsalSusceptibilityTrials_LoadAnalysis_Final.r      
      Short description: R script used for analyses of load growth across species at various exposure levels.
   R. Filename: SpeciesCategories.csv  


2. Relationship between files:        

Files A-C are the code and data files necessary to perform the Bloomberg's K analysis presented in the paper. Files D and E pertain the survival analysis presented in the paper. Files F-K are the datafiles and code necessary to create a data frame that can be used with ArcMap to recreate all the risk maps displayed in the paper. Files L-N represent the data and code necessary to estimate all the LD50 and ID50 values presented in the paper, as well as recreate the ordination of LD50 and ID50 estimates presented in the paper. Files P-Q contain the data and code necessary to perform all the analysis pertaining to Bsal infection loads present in the supplemental file of the paper. 


3. Additional related data collected that was not included in the current data package:




4. Are there multiple versions of the dataset? No
   If yes, list versions:
           Name of file that was updated:
                     i. Why was the file updated? 
                ii. When was the file updated?
           Name of file that was updated:
                      i. Why was the file updated?
                    ii. When was the file updated?






--------------------------
METHODOLOGICAL INFORMATION
--------------------------


1. Description of methods used for collection/generation of data: 
See methods included in paper and supplemental methods provided to text. 

2. Methods for processing the data: <describe how the submitted data were generated from the raw or collected data>
See methods included in paper and supplemental methods provided to text. 

3. Instrument- or software-specific information needed to interpret the data:

R version 4.0.2 (2020-06-22) -- "Taking Off Again"
ArcMap 10.7

4. Standards and calibration information, if appropriate:


5. Environmental/experimental conditions:
See methods included in paper and supplemental methods provided to text. 

6. Describe any quality-assurance procedures performed on the data:


7. People involved with sample collection, processing, analysis and/or submission:
Matthew J. Gray, Edward Davis Carter, J. Patrick W. Cusaac, Anna C. Peterson, Ross D. Whetstone, Andreas Hertz, Aura Y. Muniz-Torres, Molly C. Bletz, Douglas C. Woodhams, Jonah Piovia-Scott, John M. Romansic, Gabriela Parra Olea, Rebecca H. Hardman, William B. Sutton, Catherine D. McCusker, and Debra L. Miller





-----------------------------------------
DATA-SPECIFIC INFORMATION FOR: [Kcalc_Table.csv]
-----------------------------------------
<create sections for each dataset (or file if appropriate) included>


1. Number of variables:
8

2. Number of cases/rows: 
36

3. Variable List
    A. Name: [Species]
       Description: [Species names which becomes row names]
                    Value labels if appropriate
    B. Name: [SpeciesNames]
       Description: [Species names which become tip labels]
                    Value labels if appropriate
    C. Name: [AbrevSpecies]
       Description: [Abbreviated species names which are used as the labels for the circular phylogeny figure]
                    Value labels if appropriate
    D. Name: [Order]
       Description: [The amphibian order each species belongs to]
                    Value labels if appropriate
    E. Name: [Family]
       Description: [The amphibian family each species belongs to]
                    Value labels if appropriate
    F. Name: [%Infection]
       Description: [The percentage infection observed for each species]
                    Value labels if appropriate
    G. Name: [%Mortality]
       Description: [The percentage mortality observed for each species]
                    Value labels if appropriate
    H. Name: [OrderNumber]
        Description: [The ordering number given to each species used to sort the species into the correct order]
                    Value labels if appropriate

4. Missing data codes:
        Code/symbol        Definition
        Code/symbol        Definition


5. Specialized formats of other abbreviations used

-----------------------------------------
DATA-SPECIFIC INFORMATION FOR: [AllSpeciesSurvival.csv]
-----------------------------------------
<create sections for each dataset (or file if appropriate) included>


1. Number of variables:
5

2. Number of cases/rows: 
519

3. Variable List
    A. Name: [ID]
       Description: [This variable identifies each individual animal used in each challenge experiment.]
                    Value labels if appropriate
    B. Name: [Treatment]
       Description: [This variable identifies the treatment each animal was assigned to in the experiment]
                    Value labels if appropriate
    C. Name: [Species]
       Description: [This variable identifies the species being challenged. The first two letters identify the first to letters of the genus and        the last two letters identify the first two letters of the species name. ]
                    Value labels if appropriate
    D. Name: [Days Survival]
       Description: [The number of days each animal survived after exposure]
                    Value labels if appropriate
    D. Name: [Dead]
       Description: [Whether the animals died (1) or survived the duration of the experiment (0)]
                    Value labels if appropriate
4. Missing data codes:
        Code/symbol        Definition
        Code/symbol        Definition


5. Specialized formats of other abbreviations used
-----------------------------------------
DATA-SPECIFIC INFORMATION FOR: [Nature_Paper_Infection_Mortality_Perc.csv]
-----------------------------------------
<create sections for each dataset (or file if appropriate) included>


1. Number of variables:
6

2. Number of cases/rows: 
34

3. Variable List
    A. Name: [Species]
       Description: [Abbreviated species name which becomes the row name when loaded into R.]
                    Value labels if appropriate
    B. Name: [Species.1]
       Description: [This variable is used to identify the species ]
                    Value labels if appropriate
    C. Name: [Species_Code]
       Description: [This variable identifies the species using the four-digit codes for each species explained in variable C of the        AllSpeciesSurvival.csv]
                    Value labels if appropriate
    D. Name: [Order]
       Description: [This variable identifies the amphibian order each species belongs to.]
                    Value labels if appropriate
    E. Name: [Infection]
       Description: [The percentage of animals infected in the 10^6 exposure group for each species]
                    Value labels if appropriate
    F. Name: [Mortality]
       Description: [The percentage of animals which died in the 10^6 exposure group for each species]
                    Value labels if appropriate
4. Missing data codes:
        Code/symbol        Definition
        Code/symbol        Definition


5. Specialized formats of other abbreviations used
-----------------------------------------
DATA-SPECIFIC INFORMATION FOR: [CombinedData.xls]
-----------------------------------------
<create sections for each dataset (or file if appropriate) included>


1. Number of variables:
3

2. Number of cases/rows: 
177

3. Variable List
    A. Name: [Species.1]
       Description: [This variable identifies the species name.]
                    Value labels if appropriate
    B. Name: [Infection]
       Description: [The predicted or measured infection percentage for each species.]
                    Value labels if appropriate
    C. Name: [Mortality]
       Description: [The predicted or measured mortality percentage for each species.]
                    Value labels if appropriate
4. Missing data codes:
        Code/symbol        Definition
        Code/symbol        Definition


5. Specialized formats of other abbreviations used
-----------------------------------------
DATA-SPECIFIC INFORMATION FOR: [GIS_Data_Creation.xlsx]
-----------------------------------------
<create sections for each dataset (or file if appropriate) included>

GIS_Output (pg1)
1. Number of variables:
6

2. Number of cases/rows: 
209097

3. Variable List
    A. Name: [NAME]
       Description: [The county name]
                    Value labels if appropriate
    B. Name: [STATE_NAME]
       Description: [The state name]
                    Value labels if appropriate
    C. Name: [STATE_FIP]
       Description: [The state FIP code]
                    Value labels if appropriate
    D. Name: [FIPS]
       Description: [Each county FIP code]
                    Value labels if appropriate
    E. Name: [BINOMIAL]
       Description: [The species present in each county]
                    Value labels if appropriate
    F. Name: [PRESENCE]
       Description: [A variable indicating the species present in the BINOMIAL column is present in the county]
                    Value labels if appropriate
4. Missing data codes:
        Code/symbol        Definition
        Code/symbol        Definition


5. Specialized formats of other abbreviations used

Urodele_Presence_by_CountyFIP (pg2)
1. Number of variables:
1 (All columns other than CountyFIP correspond to species names)

2. Number of cases/rows: 
3107

3. Variable List
    A. Name: [CountyFIP]
       Description: [The county FIP code]
                    Value labels if appropriate
    B. Name: [All other columns represent species names. Cells with a 1 indicate the species was present in the corresponding row. Empty cells indicate the species was not present.]
       Description: [The state name]

4. Missing data codes:
        Code/symbol        Definition
        Code/symbol        Definition


5. Specialized formats of other abbreviations used
CombinedData (pg3)
1. Number of variables:
4

2. Number of cases/rows: 
171

3. Variable List
   3. Variable List
    A. Name: [Species.1]
       Description: [This variable identifies the species name.]
                    Value labels if appropriate
    B. Name: [Infection]
       Description: [The predicted or measured infection percentage for each species.]
                    Value labels if appropriate
    C. Name: [Mortality]
       Description: [The predicted or measured mortality percentage for each species.]
                    Value labels if appropriate
    D. Name: [Resistant Species]
       Description: [A binary variable indicating whether the species was resistant (0) or capable of becoming infected (1) based on the        challenge experiments.]
                    Value labels if appropriate
4. Missing data codes:
        Code/symbol        Definition
        Code/symbol        Definition


5. Specialized formats of other abbreviations used

BsalRiskData.csv (pg4)
1. Number of variables:
7

2. Number of cases/rows: 
3104

3. Variable List
    A. Name: [Row Labels]
       Description: [The FIPS county code]
                    Value labels if appropriate
    B. Name: [Richness]
       Description: [The total number of species present in each county]
                    Value labels if appropriate
    C. Name: [InfectionPerc]
       Description: [The predicted average infection percentage for all the species present at a specific FIP]
                    Value labels if appropriate
    D. Name: [AverageMort]
       Description: [The predicted average mortality percentage for all the species present at a specific FIP]
                    Value labels if appropriate
    E. Name: [ResistantSpeciesCount]
       Description: [The percentage of species in a county that are predicted to be resistant to Bsal *-1 for scaling preferences.]
                    Value labels if appropriate
    F. Name: [MeanAtemp]
       Description: [Average annual temperature for each FIP]
                    Value labels if appropriate
    G. Name: [MeanTempWarmestMonth]
       Description: [Average temperature of the warmest month for each FIP]
                    Value labels if appropriate
4. Missing data codes:
        Code/symbol        Definition
        Code/symbol        Definition


5. Specialized formats of other abbreviations used
-----------------------------------------
DATA-SPECIFIC INFORMATION FOR: [BsalRiskData.csv]
-----------------------------------------
<create sections for each dataset (or file if appropriate) included>


1. Number of variables:
7

2. Number of cases/rows: 
3104

3. Variable List
    A. Name: [Row Labels]
       Description: [The FIPS county code]
                    Value labels if appropriate
    B. Name: [Richness]
       Description: [The total number of species present in each county]
                    Value labels if appropriate
    C. Name: [InfectionPerc]
       Description: [The predicted average infection percentage for all the species present at a specific FIP]
                    Value labels if appropriate
    D. Name: [AverageMort]
       Description: [The predicted average mortality percentage for all the species present at a specific FIP]
                    Value labels if appropriate
    E. Name: [ResistantSpeciesCount]
       Description: [The percentage of species in a county that are predicted to be resistant to Bsal *-1 for scaling preferences.]
                    Value labels if appropriate
    F. Name: [MeanAtemp]
       Description: [Average annual temperature for each FIP]
                    Value labels if appropriate
    G. Name: [MeanTempWarmestMonth]
       Description: [Average temperature of the warmest month for each FIP]
                    Value labels if appropriate
4. Missing data codes:
        Code/symbol        Definition
        Code/symbol        Definition


5. Specialized formats of other abbreviations used
-----------------------------------------
DATA-SPECIFIC INFORMATION FOR: [SalamanderRiskMod_GIS_Dataframe]
-----------------------------------------
<create sections for each dataset (or file if appropriate) included>


1. Number of variables:
17

2. Number of cases/rows: 
3104

3. Variable List
    A. Name: [Row Labels]
       Description: [The FIPS county code]
                    Value labels if appropriate
    B. Name: [Richness]
       Description: [The total number of species present in each county]
                    Value labels if appropriate
    C. Name: [InfectionPerc]
       Description: [The predicted average infection percentage for all the species present at a specific FIP]
                    Value labels if appropriate
    D. Name: [AverageMort]
       Description: [The predicted average mortality percentage for all the species present at a specific FIP]
                    Value labels if appropriate
    E. Name: [ResistantSpeciesCount]
       Description: [The percentage of species in a county that are predicted to be resistant to Bsal *-1 for scaling preferences.]
                    Value labels if appropriate
    F. Name: [MeanAtemp]
       Description: [Average annual temperature for each FIP]
                    Value labels if appropriate
    G. Name: [MeanTempWarmestMonth]
       Description: [Average temperature of the warmest month for each FIP]
                    Value labels if appropriate
    H. Name: [MortScale]
       Description: [Average mortality for each FIP scaled 1-4]
                    Value labels if appropriate
    I. Name: [InfScale]
       Description: [Average infection for each FIP scaled 1-4]
                    Value labels if appropriate
    K. Name: [RichnessScale]
       Description: [Species richness for each county scaled 1-4]
                    Value labels if appropriate
    L. Name: [ResistantSpeciesCountScale]
       Description: [Resistant species count scaled 1-4]
                    Value labels if appropriate
    M. Name: [MeanTempScale]
       Description: [Average annual temperature scaled 1-4]
                    Value labels if appropriate
    N. Name: [MeanTempWarmestMonthScale]
       Description: [Average temperature of the warmest month scaled 1-4]
                    Value labels if appropriate
    O. Name: [Temperature_Suitability_score]
       Description: [The average of the MeanTempScale and MeanTempWarmestMonthScale]
                    Value labels if appropriate
    P. Name: [Invasion_Risk_score]
       Description: [See paper for description]
                    Value labels if appropriate
    Q. Name: [Extinction_Risk_score]
       Description: [See paper for description]
                    Value labels if appropriate
    R. Name: [Biodiversity_Risk_score]
       Description: [See paper for description]
                    Value labels if appropriate
4. Missing data codes:
        Code/symbol        Definition
        Code/symbol        Definition


5. Specialized formats of other abbreviations used
-----------------------------------------
DATA-SPECIFIC INFORMATION FOR: [Mort_Inf_NATURE_ID50_LD50.csv]
-----------------------------------------
<create sections for each dataset (or file if appropriate) included>


1. Number of variables:
10

2. Number of cases/rows: 
96

3. Variable List
    A. Name: [Treatment]
       Description: [This variable identifies the treatment or number of Bsal zoospores each group was exposed to.]
                    Value labels if appropriate
    B. Name: [Species]
       Description: [This variable identifies the species using the first two letters of the genus and the first two letters of the species.]
                    Value labels if appropriate
    C. Name: [Infected]
       Description: [The number of animals infected]
                    Value labels if appropriate
    D. Name: [Negative]
       Description: [The number of animals that were negative]
                    Value labels if appropriate
    E. Name: [Total]
       Description: [The total number of animals in each treatment]
                    Value labels if appropriate
    F. Name: [Dead]
       Description: [The total number of animals that died in each treatment]
                    Value labels if appropriate
    G. Name: [Perc_Infected]
       Description: [The percentage of animals in each treatment which became infected]
                    Value labels if appropriate
    H. Name: [Perc_Negative]
       Description: [The percentage of animals in each treatment which were negative]
                    Value labels if appropriate
    I. Name: [Perc_Dead]
       Description: [The percentage of animals in each treatment which died]
                    Value labels if appropriate
    J. Name: [Perc_Survived]
       Description: [The percentage of animals in each treatment which survived]
                    Value labels if appropriate
4. Missing data codes:
        Code/symbol        Definition
        Code/symbol        Definition


5. Specialized formats of other abbreviations used
-----------------------------------------
DATA-SPECIFIC INFORMATION FOR: [ID50_LD50_Ordination_Data.csv]
-----------------------------------------
<create sections for each dataset (or file if appropriate) included>


1. Number of variables:
8

2. Number of cases/rows: 
25

3. Variable List
    A. Name: [Species]
       Description: [This variable identifies the species using the first two letters of the genus and the first two letters of the species.]
                    Value labels if appropriate
    B. Name: [ID50]
       Description: [Estimated ID50 value for each species]
                    Value labels if appropriate
    C. Name: [LD50]
       Description: [Estimated ID50 value for each species. A value of 2415953 was used for the LD50 value for each species which had an estimable ID50 but no mortality]
                    Value labels if appropriate
    D. Name: [Product(Risk)]
       Description: [The  product of the ID50 and LD50.]
                    Value labels if appropriate
    E. Name: [Quotient]
       Description: [The LD50/ID50]
                    Value labels if appropriate
    F. Name: [AverageLoad]
       Description: [The average infection load for each species challenged with 10^6 zoospores]
                    Value labels if appropriate
    G. Name: [Amplification_Potential]
       Description: [The quotient value multiplied by the average load for each species.]
                    Value labels if appropriate
    H. Name: [ConservationRisk]
       Description: [The conservation risk category each species was assigned.]
                    Value labels if appropriate
4. Missing data codes:
        Code/symbol        Definition
        Code/symbol        Definition


5. Specialized formats of other abbreviations used
-----------------------------------------
DATA-SPECIFIC INFORMATION FOR: [ Species_qPCR_NATURE_r2.csv ]
-----------------------------------------
<create sections for each dataset (or file if appropriate) included>


1. Number of variables:
10

2. Number of cases/rows: 
7152

3. Variable List
    A. Name: [ID]
       Description: [The individual ID assigned to each animal.]
                    Value labels if appropriate
    B. Name: [Species]
       Description: [This variable identifies the species using the first two letters of the genus and the first two letters of the species.]
                    Value labels if appropriate
    C. Name: [Treatment]
       Description: [This variable identifies the treatment or number of Bsal zoospores each group was exposed to.]
                    Value labels if appropriate
    D. Name: [Sample]
       Description: [The swab each sample corresponds to.]
                    Value labels if appropriate
    E. Name: [Day_of_Swab]
       Description: [The number of days post exposure each swab was collected.]
                    Value labels if appropriate
    F. Name: [Days_Survival]
       Description: [The number of days post exposure each animal survived.]
                    Value labels if appropriate
    G. Name: [CT_Average]
       Description: [The average CT value for each qPCR run.]
                    Value labels if appropriate
    H. Name: [Copies.uL]
       Description: [The average number of copies/uL estimated for each qPCR sample]
                    Value labels if appropriate
    I. Name: [Days_Survival]
       Description: [A character variable for whether each animal survived or died during the experiment.]
                    Value labels if appropriate
    J. Name: [Test]
       Description: [The qPCR test performed on the sample.]
                    Value labels if appropriate
4. Missing data codes:
        Code/symbol        Definition
        Code/symbol        Definition


5. Specialized formats of other abbreviations used

