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.Rbuildignore

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+^\.travis\.yml$

DESCRIPTION

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+Package: InsectDisease
+Title: Ecological Database of the World's Insect Pathogens
+Version: 0.1
+Author: David W. Onstad, Macroecology of Infectious Disease RCN
+Maintainer: Tad Dallas <[email protected]>
+Description: David Onstad from the USDA provided us with this USDA-gathered insect disease database. Files have been converted from SQL to csv, and ported into R for easy exploration and analysis. 
+Depends: R (>= 4.0.0)
+License: GPL-2
+LazyData: true
+RoxygenNote: 7.1.1
+Suggests: knitr, rmarkdown
+

NAMESPACE

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+exportPattern("^[[:alpha:]]+")

R/InsectDisease-package.r

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+#' InsectDisease.
+#' 
+#' @name InsectDisease
+#' @docType package
+#' @description This package provides a `R` workspace with insect disease database data already
+#' present. Data are visible by using the R command ls("package:InsectDisease")`, and individual
+#' data frames can be imported to your local workspace by using the command `data(NAMEOFDATA)`
+#'
+#'
+#' Data frames can be grouped by parasite type, as `nemaref`, `nematode` and `newnema` provide information on nematode infections, as `nvpassoc` provides information on protozoans, and `viraref` and `viruses` provide details of viral infections. `pathogen` provides general taxonomic information on pathogens in the database. Citations are available in a number of places, including but not limited to `assocref`, `citation`, `nemaref`, and `viraref`.
+#'
+#' *When using this database, cite this reference*
+#'
+#' Braxton, S. M., et al. "Description and analysis of two internet-based databases of insect
+#' pathogens: EDWIP and VIDIL." Journal of invertebrate pathology 83.3 (2003): 185-195.
+#' 
+#' Also, this database was originally created by the following people, to whom we are indebted:
+#'
+#' David W. Onstad, EDWIP Director.
+#' Center for Economic Entomology, Illinois Natural History Survey
+#'
+#' Ellen Brewer, Research Programmer
+#' Center for Economic Entomology, Illinois Natural History Survey
+#' 
+#' Susan Braxton, Science & Technology Librarian
+#' Milner Library, Illinois State University
+#'
+#'
+
+
+
+
+
+
+NULL

R/assocref.R

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+#' Insect host-parasite interactions
+#'
+#' Edgelist of known associations between insect host (`Host`) and pathogen (`Pathogen`), and
+#' associated reference and indexing values. The variables are as follows:
+#'
+#' \itemize{
+#'   \item ERNnvp. EDWIP record number 
+#'   \item refCode. Reference code
+#'   \item Reference. Actual citation
+#'   \item Host. Host species
+#'   \item Pathogen. Pathogen species
+#'  }
+#'
+#' @docType data
+#' @keywords datasets
+#' @name assocref
+#' @usage data(assocref)
+#' @format A data.frame with 11005 observations of 5 variables
+
+
+
+"assocref"

R/citation.R

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+#' Citation information for a subset of host-pathogen interactions
+#'
+#' Edgelist of known associations between insect host (`Host`) and pathogen (`Pathogen`), and
+#' associated references and indexing values. These data are smaller than assocref, which provides
+#' more data on host-parasite interactions. CreationDate and ModificationDate are incorrect. The
+#' variables are as follows:
+#'
+#' \itemize{
+#'   \item CitationCode. Citation code
+#'   \item Reference. Actual citation
+#'   \item CreationDate. Record creation date
+#'   \item ModificationDate. Record modification date
+#'   \item ReadBy. 
+#'   \item GetIt. 
+#'   \item nvpCount. 
+#'  }
+#'
+#' @docType data
+#' @keywords datasets
+#' @name citation
+#' @usage data(citation)
+#' @format A data.frame with 1966 observations of 7 variables
+
+
+
+"citation"

R/hosts.R

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+#' Detailed information on insect host species
+#'
+#' 
+#' Data on host species taxonomy, habitat, diet preferences, and distribution (in Canada)
+#' 
+#' 
+#'
+#' \itemize{
+#'   \item RecordNo. Sequence from 1:nrow(hosts)
+#'   \item DateEntered. Date of initial data entry
+#'   \item Habitat. Habitat of host
+#'   \item HostSpecies. Host species
+#'   \item HostOrder. Host order
+#'   \item HostFamily. Host family
+#'   \item Synonyms. Other names for the host species
+#'   \item Food. What does the host eat?
+#'   \item genYr. Number of generations per year. Can be <1, =1, >1, or some combination of these.
+#'   \item CommonName. Host common name
+#'   \item ProvinceI. Canadian provinces where host has been found.
+#'   \item InsectStatus. Is the insect a pest, beneficial, endangered, unknown? Factor variable with
+#'     7 unique values
+#'   \item ModificationDate. Modification date of entry
+#'   \item InCanada. Citations for presence/absence of host in Canada. Numeric indices can be
+#'     related to the citations in the `citations.rda` data file. `Y` and `N` relate to presence and
+#'     absence, respectively.
+#'   \item ChangeSpeciesTo. 
+#'   \item CommonNameOther. Other common names?
+#'   \item Complete. Is this record complete?
+#'   \item AdditionalReferences. Additional reference indices. 
+#'  }
+#'
+#' @docType data
+#' @keywords datasets
+#' @name hosts
+#' @usage data(hosts)
+#' @format A data.frame with 4392 observations of 18 variables
+
+
+
+"hosts"

R/negative.R

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+#' Information on negative host-parasite interactions
+#'
+#' 
+#' Hosts were challenged with pathogen, and did not become infected. These are data on what
+#' pathogens do not infect certain hosts.
+#' 
+#' 
+#' 
+#' \itemize{
+#'   \item ERNntr. EDWIP record number
+#'   \item Pathogen. Pathogen species
+#'   \item DateEntered. Date of initial data entry
+#'   \item DateModified. Modification date of entry
+#'   \item LogMaxDose. Dosage, in many different units
+#'   \item HostStageTested. Host stage exposed to pathogen (e.g. Larvae, Nymph, Adult, or 
+#'      Egg\Larva\Pupa) 
+#'   \item Host. Host species examined
+#'   \item Group. Pathogen group (e.g. viruses) 
+#'   \item HighTaxon. General classification of pathogen (e.g. DNA virus)
+#'   \item LowTaxon. More specific classification of pathogen (e.g. Baculoviridae)
+#'   \item Order. Host taxonomic order.
+#'   \item Family. Host taxonomic family.
+#'  }
+#'
+#' @docType data
+#' @keywords datasets
+#' @name negative
+#' @usage data(negative)
+#' @format A data.frame with 529 observations of 12 variables
+
+"negative"

R/nemaref.R

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+#' Citation information for host-nematode interactions
+#'
+#' Edgelist of known associations between insect host (`Host`) and nematode parasite (`Nematode`),
+#' and associated references and indexing values. These data are smaller than `assocref`, and
+#' `citation`. The variables are as follows:
+#'
+#' \itemize{
+#'   \item ERNnem. EDWIP record number
+#'   \item refCode. Index of reference obtained from `nematode` data frame
+#'   \item Reference. Citation for host-nematode record
+#'   \item Host. Host species
+#'   \item Nematode. Nematode parasite species
+#'  }
+#'
+#' @docType data
+#' @keywords datasets
+#' @name nemaref
+#' @usage data(nemaref)
+#' @format A data.frame with 338 observations of 5 variables
+
+
+
+"nemaref"

R/nematode.R

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+#' Information on nematode parasite occurrences
+#'
+#' Host associations for nematode parasites
+#' 
+#' 
+#' \itemize{
+#'   \item ERNnem
+#'   \item Host. Host species
+#'   \item Nematode. Nematode parasite species
+#'   \item NematodeOrder. Nematode parasite order
+#'   \item NematodeFamily. Nematode parasite family
+#'   \item NematodeStrain. Nematode parasite strain
+#'   \item StageInfected. Host stage infected
+#'   \item TissueInfected. Host tissue infected
+#'   \item FieldOrLab. Was this a field or lab tested association?
+#'   \item Country. What country did the interaction occur in?
+#'   \item SoilType. Type of soil where interaction was observed
+#'   \item AssociatedBacterium. Associated bacterium.
+#'   \item IntermediateHost. Is there an intermediate host present?
+#'   \item CreationDate. Date of initial data entry
+#'   \item ModificationDate. Modification date of entry
+#'  }
+#'
+#' @docType data
+#' @keywords datasets
+#' @name nematode
+#' @usage data(nematode)
+#' @format A data.frame with 234 observations of 15 variables
+
+"nematode"

R/nvpassoc.R

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+#' Information on non-viral pathogens of insect hosts
+#'
+#' 
+#' Non-viral parasite (protozoan, fungi, bacteria) occurrences on host species. The variables are 
+#' as follows: 
+#' 
+#' 
+#' \itemize{
+#'   \item ERNnvp. EDWIP record number
+#'   \item Pathogen. Pathogen species
+#'   \item Group. Pathogen group (e.g. Protozoa)
+#'   \item HighTaxon. General classification of pathogen (e.g. Microspora)
+#'   \item LowTaxon. More specific classification of pathogen (e.g. Microsporea)
+#'   \item Host. Host species examined
+#'   \item Order. Host taxonomic order.
+#'   \item Family. Host taxonomic family.
+#'   \item HostStageTested. Host stage exposed to pathogen (e.g. Larvae, Nymph, Adult, or 
+#'      Egg\Larva\Pupa) 
+#'   \item HostTissueInfected. Host tissue infected
+#'   \item FieldOrLab. Was this a field or lab tested association?
+#'   \item Country. What country did the interaction occur in?
+#'   \item IntermediateHost. Is there an intermediate host present?
+#'   \item DateEntered. Date of initial data entry
+#'   \item DateModified. Modification date of entry
+#'   \item BiogeographicRegion. Biogeographic region (or some combination thereof)
+#'  }
+#'
+#' @docType data
+#' @keywords datasets
+#' @name nvpassoc
+#' @usage data(nvpassoc)
+#' @format A data.frame with 7164 observations of 16 variables
+
+"nvpassoc"

R/pathogen.R

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+#' Information on pathogen species in the database
+#'
+#' Information on taxonomy of parasites present in this database
+#' 
+#' \itemize{
+#'   \item PathogenSpecies. Pathogen species.
+#'   \item Group. Pathogen group (e.g. Protozoa)
+#'   \item HighTaxon. General classification of pathogen (e.g. Microspora)
+#'   \item LowTaxon. More specific classification of pathogen (e.g. Microsporea)
+#'   \item AdditionalNotes. Some additional notes.
+#'  }
+#'
+#' @docType data
+#' @keywords datasets
+#' @name pathogen
+#' @usage data(pathogen)
+#' @format A data.frame with 2041 observations of 5 variables
+
+"pathogen"

R/viraref.R

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+#' Citation information for host-virus interactions
+#'
+#' Edgelist of known associations between insect host (`Host`) and viral pathogen (`Virus`),
+#' and associated references and indexing values. These data are smaller than `assocref`, and
+#' `citation`. The variables are as follows:
+#'
+#' \itemize{
+#'   \item RefCode. Index of reference obtained from `nematode` data frame
+#'   \item Citation. Reference.
+#'   \item ERNv. EDWIP record number
+#'   \item Host. Host species
+#'   \item Virus. Virus name
+#'  }
+#'
+#' @docType data
+#' @keywords datasets
+#' @name viraref
+#' @usage data(viraref)
+#' @format A data.frame with 2124 observations of 5 variables
+
+"viraref"

R/viruses.R

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+#' Information on viral pathogen occurrences
+#'
+#' Host associations for viruses
+#' 
+#' 
+#' \itemize{
+#'   \item ERNv. EDWIP record number
+#'   \item Host. Host species
+#'   \item HighTaxon. General classification of pathogen (e.g. Microspora)
+#'   \item LowTaxon. More specific classification of pathogen (e.g. Microsporea)
+#'   \item Virus. Virus identity
+#'   \item HostStageInfected. Host stage infected
+#'   \item HostTissueInfected. Host tissue infected
+#'   \item FieldOrLab. Was this a field or lab tested association?
+#'   \item Country. What country did the interaction occur in?
+#'   \item IntermediateHost. Is there an intermediate host present?
+#'   \item CreationDate. Date of initial data entry (wrong)
+#'   \item ModificationDate. Modification date of entry (wrong)
+#'   \item ProvinceA. Canadian provinces where host-virus interaction occurs
+#'   \item PathogenValue. Is there value to the pathogen (can it be used as a control agent?)
+#'  }
+#'
+#' @docType data
+#' @keywords datasets
+#' @name viruses
+#' @usage data(viruses)
+#' @format A data.frame with 1659 observations of 14 variables
+
+"viruses"