Generic function to convert the data stored in the object x into a new object of class dmdScheme...
Source: R/as_dmdScheme.R, R/as_dmdScheme.dmdSchemeData_raw.R, R/as_dmdScheme.dmdSchemeSet_raw.R, and 1 more
as_dmdScheme.RdGeneric function to convert the data stored in the object x into a new object of class dmdScheme...
Usage
as_dmdScheme(x, keepData = FALSE, ..., verbose = FALSE)
# S3 method for dmdSchemeData_raw
as_dmdScheme(
x,
keepData = TRUE,
convertTypes = TRUE,
warnToError = TRUE,
checkVersion = TRUE,
...,
verbose = FALSE
)
# S3 method for dmdSchemeSet_raw
as_dmdScheme(
x,
keepData = FALSE,
warnToError = TRUE,
convertTypes = TRUE,
checkVersion = TRUE,
...,
verbose = FALSE
)
# S3 method for xml_document
as_dmdScheme(x, keepData = TRUE, useSchemeInXml = NULL, ..., verbose = FALSE)Arguments
- x
object to be converted
- keepData
if the data should be kept or replaced with one row with NAs
- ...
additional arguments for methods
- verbose
give verbose progress info. Useful for debugging.
- convertTypes
if
TRUE, the types specified in the types column are used for the data type. Otherwise, they are left at typecharacter- warnToError
if
TRUE, warnings generated during the conversion will raise an error- checkVersion
if
TRUE, a version mismatch between the package and the dataxwill result in an error. IfFALSE, the check will be skipped.- useSchemeInXml
if
TRUE, use scheme definition in xml and raise an error if the xml does not contain a scheme definition. If False, use the scheme definition from the corresponding installed package, even if the xml contains a scheme definition. ifNULL(the default), use the definition in the xml if it contains a definition, if not use the corresponding definition from the installed package.
Examples
as_dmdScheme(dmdScheme_raw(), keepData = TRUE)
#> dmdScheme - dmdSchemeSet
#> MdBibliometric - dmdSchemeData
#> A Names : uploadType | doi | publicationDate | title | description | version | language | keywords | additionalNotes | accessRights | accessRightsInfo | license
#> A Units :
#> A Type : character | character | character | character | character | character | character | character | character | character | character | character
#>
#> uploadType doi publicationDate title
#> D 1 Dataset 110.1234/ffoo.bar 2020-05-26 Microbes under Pressure
#> description
#> D 1 The dataset was generated by putting microbes under pressure through temperatue and oxygen changes and their changes ion abundance were observed.
#> version language
#> D 1 <NA> eng
#> keywords
#> D 1 microbes, temperatur change, oxygen changes, abundance
#> additionalNotes accessRights accessRightsInfo
#> D 1 <NA> Open <NA>
#> license
#> D 1 Creative Commons Attribution 4.0 International
#>
#> MdAuthors - dmdSchemeData
#> A Names : authorID | familyName | givenName | affiliation | orcid | role
#> A Units : NA | NA | NA | NA | NA | NA
#> A Type : character | character | character | character | character | character
#>
#> authorID familyName givenName affiliation orcid
#> D 1 1 Petchey Owen L. University of Zurich, Switzerland <NA>
#> D 2 2 Krug Rainer M. University of Zurich, Switzerland <NA>
#> role
#> D 1 Conceptualization, Investigation
#> D 2 Data curation
#>
#> Experiment - dmdSchemeData
#> A Names : name | temperature | light | humidity | incubator | container | microcosmVolume | mediaType | mediaConcentration | cultureConditions | comunityType | mediaAdditions | duration | comment
#> A Units : NA | NA | NA | NA | NA | NA | ml | NA | g/l | NA | NA | NA | days | NA
#> A Type : character | character | character | character | character | character | numeric | character | numeric | character | character | character | integer | character
#>
#> name temperature light humidity incubator
#> D 1 ASR-expt1 20 semi-ambient ambient not given here
#> container microcosmVolume mediaType
#> D 1 Duran type bottle, red lids, 250ml 100 PPM
#> mediaConcentration cultureConditions comunityType
#> D 1 0.55 dirty initially unknown
#> mediaAdditions
#> D 1 Wheat seeds added on specific dates, see file wheat_seed_additions.csv
#> duration comment
#> D 1 100 <NA>
#>
#> Genus - dmdSchemeData
#> A Names : speciesID | colour | density | functionalGroup | comment
#> A Units : NA | NA | cells / ml | NA | NA
#> A Type : character | character | character | character | character
#>
#> speciesID colour density functionalGroup
#> D 1 tt_1 ATCC 1 bacterivore
#> D 2 unknown unknown <NA> unknown
#> comment
#> D 1 http://www.lgcstandards-atcc.org/products/all/30007.aspx
#> D 2 <NA>
#>
#> Treatments - dmdSchemeData
#> A Names : treatmentID | treatmentLevelHeight | comment
#> A Units : NA | NA | NA
#> A Type : character | character | character
#>
#> treatmentID treatmentLevelHeight comment
#> D 1 Lid_treatment Loose <NA>
#> D 2 Lid_treatment Tight <NA>
#> D 3 species_1 tt_1, unknown <NA>
#> D 4 species_2 unknown <NA>
#> D 5 species_3 tt_1 <NA>
#>
#> Measurement - dmdSchemeData
#> A Names : measurementID | variable | method | unit | object | noOfSamplesInTimeSeries | samplingVolume | dataExtractionID | measuredFrom | comment
#> A Units : NA | NA | NA | NA | NA | NA | ml | NA | NA | NA
#> A Type : character | character | character | character | character | integer | numeric | character | character | character
#>
#> measurementID variable method unit
#> D 1 oxygen concentration DO presens Optode %
#> D 2 abundance abundance molecular count
#> D 3 smell smell nose rotten eggs or not
#> D 4 sequenceData DNA NGS Nucleotide
#> object noOfSamplesInTimeSeries samplingVolume
#> D 1 community 50 0.0
#> D 2 species 6 0.5
#> D 3 community 6 0.0
#> D 4 DNA fragment 6 0.0
#> dataExtractionID measuredFrom comment
#> D 1 none raw <NA>
#> D 2 Mol_Analy_pipeline1 sequenceData <NA>
#> D 3 none raw <NA>
#> D 4 none raw <NA>
#>
#> DataExtraction - dmdSchemeData
#> A Names : dataExtractionID | method | parameter | value | comment
#> A Units : NA | NA | NA | NA | NA
#> A Type : character | character | character | character | character
#>
#> dataExtractionID method parameter value
#> D 1 Mol_Analy_pipeline1 <NA> <NA> <NA>
#> comment
#> D 1 See description in file xxx.yyy
#>
#> DataFileMetaData - dmdSchemeData
#> A Names : dataFileName | columnName | columnData | mappingColumn | type | description | comment
#> A Units : NA | NA | NA | NA | NA | NA | NA
#> A Type : character | character | character | character | character | character | character
#>
#> dataFileName columnName columnData
#> D 1 dissolved_oxygen_measures.csv Jar_ID ID
#> D 2 dissolved_oxygen_measures.csv DO Measurement
#> D 3 dissolved_oxygen_measures.csv Unit_1 other
#> D 4 dissolved_oxygen_measures.csv Mode other
#> D 5 dissolved_oxygen_measures.csv Location other
#> D 6 dissolved_oxygen_measures.csv Date_time other
#> D 7 dissolved_oxygen_measures.csv Lid_treatment Treatment
#> D 8 dissolved_oxygen_measures.csv Jar_type other
#> D 9 dissolved_oxygen_measures.csv Jar_ID ID
#> D 10 smell.csv <NA> Species
#> D 11 smell.csv smell Measurement
#> D 12 smell.csv Date other
#> D 13 smell.csv Lid_treatment Treatment
#> D 14 smell.csv Jar_type other
#> D 15 abundances.csv <NA> Species
#> D 16 abundances.csv Jar_ID ID
#> D 17 abundances.csv Date_time other
#> D 18 abundances.csv Lid_treatment Treatment
#> D 19 abundances.csv Jar_type other
#> D 20 abundances.csv count_number Measurement
#> mappingColumn type description comment
#> D 1 <NA> character <NA> <NA>
#> D 2 oxygen concentration numeric <NA> <NA>
#> D 3 <NA> character <NA> <NA>
#> D 4 <NA> character <NA> <NA>
#> D 5 <NA> character <NA> <NA>
#> D 6 <NA> datetime ymdhms <NA>
#> D 7 Lid_treatment character <NA> <NA>
#> D 8 <NA> character <NA> <NA>
#> D 9 <NA> character <NA> <NA>
#> D 10 species_1 character <NA> <NA>
#> D 11 smell character <NA> <NA>
#> D 12 <NA> datetime ymdhms <NA>
#> D 13 Lid_treatment character <NA> <NA>
#> D 14 <NA> character <NA> <NA>
#> D 15 species_3 character <NA> <NA>
#> D 16 <NA> character <NA> <NA>
#> D 17 <NA> datetime ymdhms <NA>
#> D 18 Lid_treatment character <NA> <NA>
#> D 19 <NA> character <NA> <NA>
#> D 20 abundance numeric <NA> <NA>
#>
as_dmdScheme(dmdScheme_raw()$Experiment)
#> NA - dmdSchemeData
#> A Names : name | temperature | light | humidity | incubator | container | microcosmVolume | mediaType | mediaConcentration | cultureConditions | comunityType | mediaAdditions | duration | comment
#> A Units : NA | NA | NA | NA | NA | NA | ml | NA | g/l | NA | NA | NA | days | NA
#> A Type : character | character | character | character | character | character | numeric | character | numeric | character | character | character | integer | character
#>
#> name temperature light humidity incubator
#> D 1 ASR-expt1 20 semi-ambient ambient not given here
#> container microcosmVolume mediaType
#> D 1 Duran type bottle, red lids, 250ml 100 PPM
#> mediaConcentration cultureConditions comunityType
#> D 1 0.55 dirty initially unknown
#> mediaAdditions
#> D 1 Wheat seeds added on specific dates, see file wheat_seed_additions.csv
#> duration comment
#> D 1 100 <NA>
#>
xml <- as_xml(dmdScheme_example())
x <- as_dmdScheme(xml)
all.equal(dmdScheme_example(), x)
#> [1] TRUE