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The dataset contains example data. It was created by using the code below.

Usage

dmdScheme_example()

Examples

dmdScheme_example()
#>  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>
#>