library("EML")One essential role of EML metadata is in precisely defining the units in which data is measured. To make sure these units can be understood by (and thus potentially converted to other units by) a computer, it’s necessary to be rather precise about our choice of units. EML knows about a lot of commonly used units, referred to as “standardUnits,” already. If a unit is in EML’s standardUnit dictionary, we can refer to it without further explanation as long as wer are careful to use the precise id for that unit, as we will see below.
Sometimes data involves a unit that is not in standardUnit dictionary. In this case, the metadata must provide additional information about the unit, including how to convert the unit into the SI system. EML uses an existing standard, stmml, to represent this information, which must be given in the additionalMetadata section of an EML file. The stmml standard is also used to specify EML’s own standardUnit definitions.
Let us start by examining the numeric attributes in an example EML file. First we read in the file:
f <- system.file("xsd/test/eml-datasetWithUnits.xml", package = "EML")
eml <- read_eml(f)We extract the attributeList, and examine the numeric attributes (e.g. those which have units):
attribute_tables <- eml_get(eml, "attributeList")
a <- attribute_tables$attributes
numerics <- a[a$domain == "numericDomain",]
numerics## attributeName domain precision minimum maximum
## 3 sr numericDomain 0.50 0 <NA>
## 4 pctcov numericDomain 0.10 0 1e2
## 5 avesr91 numericDomain 0.10 0 <NA>
## 6 avesr92 numericDomain 0.10 0 <NA>
## 7 avesr93 numericDomain 0.10 0 <NA>
## 8 avesr94 numericDomain 0.10 0 <NA>
## 9 avesr95 numericDomain 0.10 0 <NA>
## 10 avesr96 numericDomain 0.10 0 <NA>
## 11 MeanSR numericDomain 0.10 0 <NA>
## 12 biomass numericDomain 0.01 0 <NA>
## 13 sppm2 numericDomain 0.01 0 <NA>
## unit numberType formatString definition pattern source
## 3 number real <NA> <NA> <NA> <NA>
## 4 dimensionless real <NA> <NA> <NA> <NA>
## 5 second real <NA> <NA> <NA> <NA>
## 6 cubicFeetPerSecond real <NA> <NA> <NA> <NA>
## 7 cubicMeter real <NA> <NA> <NA> <NA>
## 8 radian real <NA> <NA> <NA> <NA>
## 9 meter real <NA> <NA> <NA> <NA>
## 10 inch real <NA> <NA> <NA> <NA>
## 11 nanogram real <NA> <NA> <NA> <NA>
## 12 gramsPerSquareMeter real <NA> <NA> <NA> <NA>
## 13 speciesPerSquareMeter real <NA> <NA> <NA> <NA>
## attributeLabel storageType missingValueCode
## 3 Species Richness float <NA>
## 4 percent cover float <NA>
## 5 Average Species Richness for 1991 float <NA>
## 6 Average Species Richness for 1992 float <NA>
## 7 Average Species Richness for 1993 float <NA>
## 8 Average Species Richness for 1994 float <NA>
## 9 Average Species Richness for 1995 float <NA>
## 10 Average Species Richness for 1996 float <NA>
## 11 mean species richness float <NA>
## 12 Biomass float <NA>
## 13 Species Per Square Meter float <NA>
## missingValueCodeExplanation measurementScale
## 3 <NA> interval
## 4 <NA> ratio
## 5 <NA> ratio
## 6 <NA> ratio
## 7 <NA> ratio
## 8 <NA> ratio
## 9 <NA> ratio
## 10 <NA> ratio
## 11 <NA> ratio
## 12 <NA> ratio
## 13 <NA> ratio
## attributeDefinition
## 3 Species richness for CDR
## 4 The percent ground cover on the field\n
## 5 The average species richness for the field in 1991\n
## 6 The average species richness for the field in 1992\n
## 7 The average species richness for the field in 1993\n
## 8 The average species richness for the field in 1994\n
## 9 The average species richness for the field in 1995\n
## 10 The average species richness for the field in 1996\n
## 11 the mean species richness from 1991 to 1996\n
## 12 The total biomass measured in this field\n
## 13 Calculated species per square meter\nWe see this data contains eleven columns containing numeric data, with metadata for the unit, precision, range, and number type (integer, real complex) given in the resulting table.
EML knows about many standard units already, but a metadata file may occassionally need to define a unit that is not in the StandardUnit dictionary. We can use the function is_standardUnit() to quickly check if the units shown here are in EML’s dictionary:
units <- numerics$unit
units[ !is_standardUnit(units) ]## [1] "speciesPerSquareMeter"This shows us that the unit speciesPerSquareMeter is the only unit not in the Standard Unit Dictionary. We can have a look at the definitions for all units that are in the Standard Unit dictionary using the function get_unitList() with no arguments:
standardUnits <- get_unitList()
standardUnits$units## id
## 1 dimensionless
## 2 second
## 3 meter
## 4 kilogram
## 5 kelvin
## 6 coulomb
## 7 ampere
## 8 mole
## 9 candela
## 10 number
## 11 cubicMeter
## 12 nominalMinute
## 13 nominalHour
## 14 nominalDay
## 15 nominalWeek
## 16 nominalYear
## 17 nominalLeapYear
## 18 nanogram
## 19 microgram
## 20 milligram
## 21 centigram
## 22 decigram
## 23 gram
## 24 dekagram
## 25 hectogram
## 26 megagram
## 27 tonne
## 28 pound
## 29 ton
## 30 celsius
## 31 fahrenheit
## 32 nanometer
## 33 micrometer
## 34 micron
## 35 millimeter
## 36 centimeter
## 37 decimeter
## 38 dekameter
## 39 hectometer
## 40 kilometer
## 41 megameter
## 42 angstrom
## 43 inch
## 44 Foot_US
## 45 foot
## 46 Foot_Gold_Coast
## 47 fathom
## 48 nauticalMile
## 49 yard
## 50 Yard_Indian
## 51 Link_Clarke
## 52 Yard_Sears
## 53 mile
## 54 nanosecond
## 55 microsecond
## 56 millisecond
## 57 centisecond
## 58 decisecond
## 59 dekasecond
## 60 hectosecond
## 61 kilosecond
## 62 megasecond
## 63 minute
## 64 hour
## 65 kiloliter
## 66 microliter
## 67 milliliter
## 68 liter
## 69 gallon
## 70 quart
## 71 bushel
## 72 cubicInch
## 73 pint
## 74 radian
## 75 degree
## 76 grad
## 77 megahertz
## 78 kilohertz
## 79 hertz
## 80 millihertz
## 81 newton
## 82 joule
## 83 calorie
## 84 britishThermalUnit
## 85 footPound
## 86 lumen
## 87 lux
## 88 becquerel
## 89 gray
## 90 sievert
## 91 katal
## 92 henry
## 93 megawatt
## 94 kilowatt
## 95 watt
## 96 milliwatt
## 97 megavolt
## 98 kilovolt
## 99 volt
## 100 millivolt
## 101 farad
## 102 ohm
## 103 ohmMeter
## 104 siemen
## 105 weber
## 106 tesla
## 107 pascal
## 108 megapascal
## 109 kilopascal
## 110 atmosphere
## 111 bar
## 112 millibar
## 113 kilogramsPerSquareMeter
## 114 gramsPerSquareMeter
## 115 milligramsPerSquareMeter
## 116 kilogramsPerHectare
## 117 tonnePerHectare
## 118 poundsPerSquareInch
## 119 kilogramPerCubicMeter
## 120 milliGramsPerMilliLiter
## 121 gramsPerLiter
## 122 milligramsPerCubicMeter
## 123 microgramsPerLiter
## 124 milligramsPerLiter
## 125 gramsPerCubicCentimeter
## 126 gramsPerMilliliter
## 127 gramsPerLiterPerDay
## 128 litersPerSecond
## 129 cubicMetersPerSecond
## 130 cubicFeetPerSecond
## 131 squareMeter
## 132 are
## 133 hectare
## 134 squareKilometers
## 135 squareMillimeters
## 136 squareCentimeters
## 137 acre
## 138 squareFoot
## 139 squareYard
## 140 squareMile
## 141 litersPerSquareMeter
## 142 bushelsPerAcre
## 143 litersPerHectare
## 144 squareMeterPerKilogram
## 145 metersPerSecond
## 146 metersPerDay
## 147 feetPerDay
## 148 feetPerSecond
## 149 feetPerHour
## 150 yardsPerSecond
## 151 milesPerHour
## 152 milesPerSecond
## 153 milesPerMinute
## 154 centimetersPerSecond
## 155 millimetersPerSecond
## 156 centimeterPerYear
## 157 knots
## 158 kilometersPerHour
## 159 metersPerSecondSquared
## 160 waveNumber
## 161 cubicMeterPerKilogram
## 162 cubicMicrometersPerGram
## 163 amperePerSquareMeter
## 164 amperePerMeter
## 165 molePerCubicMeter
## 166 molarity
## 167 molality
## 168 candelaPerSquareMeter
## 169 metersSquaredPerSecond
## 170 metersSquaredPerDay
## 171 feetSquaredPerDay
## 172 kilogramsPerMeterSquaredPerSecond
## 173 gramsPerCentimeterSquaredPerSecond
## 174 gramsPerMeterSquaredPerYear
## 175 gramsPerHectarePerDay
## 176 kilogramsPerHectarePerYear
## 177 kilogramsPerMeterSquaredPerYear
## 178 molesPerKilogram
## 179 molesPerGram
## 180 millimolesPerGram
## 181 molesPerKilogramPerSecond
## 182 nanomolesPerGramPerSecond
## 183 kilogramsPerSecond
## 184 tonnesPerYear
## 185 gramsPerYear
## 186 numberPerMeterSquared
## 187 numberPerKilometerSquared
## 188 numberPerMeterCubed
## 189 numberPerLiter
## 190 numberPerMilliliter
## 191 metersPerGram
## 192 numberPerGram
## 193 gramsPerGram
## 194 microgramsPerGram
## 195 cubicCentimetersPerCubicCentimeters
## name unitType
## 1 dimensionless dimensionless
## 2 second time
## 3 meter length
## 4 kilogram mass
## 5 kelvin temperature
## 6 coulomb charge
## 7 ampere current
## 8 mole amount
## 9 candela luminosity
## 10 number dimensionless
## 11 cubicMeter volume
## 12 nominalMinute time
## 13 nominalHour time
## 14 nominalDay time
## 15 nominalWeek time
## 16 nominalYear time
## 17 nominalLeapYear time
## 18 nanogram mass
## 19 microgram mass
## 20 milligram mass
## 21 centigram mass
## 22 decigram mass
## 23 gram mass
## 24 dekagram mass
## 25 hectogram mass
## 26 megagram mass
## 27 tonne mass
## 28 pound <NA>
## 29 ton <NA>
## 30 celsius <NA>
## 31 fahrenheit <NA>
## 32 nanometer <NA>
## 33 micrometer <NA>
## 34 micron <NA>
## 35 millimeter <NA>
## 36 centimeter <NA>
## 37 decimeter <NA>
## 38 dekameter <NA>
## 39 hectometer <NA>
## 40 kilometer <NA>
## 41 megameter <NA>
## 42 angstrom <NA>
## 43 inch <NA>
## 44 Foot_US <NA>
## 45 foot <NA>
## 46 Foot_Gold_Coast <NA>
## 47 fathom <NA>
## 48 nauticalMile <NA>
## 49 yard <NA>
## 50 Yard_Indian <NA>
## 51 Link_Clarke <NA>
## 52 Yard_Sears <NA>
## 53 mile <NA>
## 54 nanosecond <NA>
## 55 microsecond <NA>
## 56 millisecond <NA>
## 57 centisecond <NA>
## 58 decisecond <NA>
## 59 dekasecond <NA>
## 60 hectosecond <NA>
## 61 kilosecond <NA>
## 62 megasecond <NA>
## 63 minute <NA>
## 64 hour <NA>
## 65 kiloliter volume
## 66 microliter volume
## 67 milliliter volume
## 68 liter volume
## 69 gallon <NA>
## 70 quart <NA>
## 71 bushel volume
## 72 cubicInch volume
## 73 pint <NA>
## 74 radian angle
## 75 degree angle
## 76 grad angle
## 77 megahertz frequency
## 78 kilohertz frequency
## 79 hertz frequency
## 80 millihertz frequency
## 81 newton force
## 82 joule energy
## 83 calorie energy
## 84 britishThermalUnit energy
## 85 footPound energy
## 86 lumen luminosity
## 87 lux illuminance
## 88 becquerel radionucleotideActivity
## 89 gray specificEnergy
## 90 sievert doseEquivalent
## 91 katal catalyticActivity
## 92 henry inductance
## 93 megawatt power
## 94 kilowatt power
## 95 watt power
## 96 milliwatt power
## 97 megavolt potentialDifference
## 98 kilovolt potentialDifference
## 99 volt potentialDifference
## 100 millivolt potentialDifference
## 101 farad capacitance
## 102 ohm resistance
## 103 ohmMeter resistivity
## 104 siemen conductance
## 105 weber magneticFlux
## 106 tesla magneticFluxDensity
## 107 pascal pressure
## 108 megapascal pressure
## 109 kilopascal pressure
## 110 atmosphere pressure
## 111 bar pressure
## 112 millibar pressure
## 113 kilogramsPerSquareMeter arealMassDensity
## 114 gramsPerSquareMeter arealMassDensity
## 115 milligramsPerSquareMeter arealMassDensity
## 116 kilogramsPerHectare arealMassDensity
## 117 tonnePerHectare arealMassDensity
## 118 poundsPerSquareInch arealMassDensity
## 119 kilogramPerCubicMeter massDensity
## 120 milliGramsPerMilliLiter massDensity
## 121 gramsPerLiter massDensity
## 122 milligramsPerCubicMeter massDensity
## 123 microgramsPerLiter massDensity
## 124 milligramsPerLiter massDensity
## 125 gramsPerCubicCentimeter massDensity
## 126 gramsPerMilliliter massDensity
## 127 gramsPerLiterPerDay volumetricMassDensityRate
## 128 litersPerSecond volumetricRate
## 129 cubicMetersPerSecond volumetricRate
## 130 cubicFeetPerSecond volumetricRate
## 131 squareMeter area
## 132 are area
## 133 hectare area
## 134 squareKilometers area
## 135 squareMillimeters area
## 136 squareCentimeters area
## 137 acre area
## 138 squareFoot area
## 139 squareYard area
## 140 squareMile area
## 141 litersPerSquareMeter volumetricArea
## 142 bushelsPerAcre volumetricArea
## 143 litersPerHectare volumetricArea
## 144 squareMeterPerKilogram specificArea
## 145 metersPerSecond speed
## 146 metersPerDay speed
## 147 feetPerDay speed
## 148 feetPerSecond speed
## 149 feetPerHour speed
## 150 yardsPerSecond speed
## 151 milesPerHour speed
## 152 milesPerSecond speed
## 153 milesPerMinute speed
## 154 centimetersPerSecond speed
## 155 millimetersPerSecond speed
## 156 centimeterPerYear speed
## 157 knots speed
## 158 kilometersPerHour speed
## 159 metersPerSecondSquared acceleration
## 160 waveNumber lengthReciprocal
## 161 cubicMeterPerKilogram specificVolume
## 162 cubicMicrometersPerGram specificVolume
## 163 amperePerSquareMeter currentDensity
## 164 amperePerMeter magneticFieldStrength
## 165 molePerCubicMeter amountOfSubstanceConcentration
## 166 molarity amountOfSubstanceConcentration
## 167 molality amountOfSubstanceWeight
## 168 candelaPerSquareMeter luminance
## 169 metersSquaredPerSecond transmissivity
## 170 metersSquaredPerDay transmissivity
## 171 feetSquaredPerDay transmissivity
## 172 kilogramsPerMeterSquaredPerSecond arealMassDensityRate
## 173 gramsPerCentimeterSquaredPerSecond arealMassDensityRate
## 174 gramsPerMeterSquaredPerYear arealMassDensityRate
## 175 gramsPerHectarePerDay arealMassDensityRate
## 176 kilogramsPerHectarePerYear arealMassDensityRate
## 177 kilogramsPerMeterSquaredPerYear arealMassDensityRate
## 178 molesPerKilogram amountOfSubstanceWeight
## 179 molesPerGram amountOfSubstanceWeight
## 180 millimolesPerGram amountOfSubstanceWeight
## 181 molesPerKilogramPerSecond amountOfSubstanceWeightFlux
## 182 nanomolesPerGramPerSecond amountOfSubstanceWeightFlux
## 183 kilogramsPerSecond massFlux
## 184 tonnesPerYear massFlux
## 185 gramsPerYear massFlux
## 186 numberPerMeterSquared arealDensity
## 187 numberPerKilometerSquared arealDensity
## 188 numberPerMeterCubed volumetricDensity
## 189 numberPerLiter volumetricDensity
## 190 numberPerMilliliter volumetricDensity
## 191 metersPerGram massSpecificLength
## 192 numberPerGram massSpecificCount
## 193 gramsPerGram massPerMass
## 194 microgramsPerGram massPerMass
## 195 cubicCentimetersPerCubicCentimeters volumePerVolume
## parentSI multiplierToSI constantToSI
## 1 <NA> <NA> <NA>
## 2 <NA> 1 <NA>
## 3 <NA> 1 <NA>
## 4 <NA> 1 <NA>
## 5 <NA> 1 <NA>
## 6 <NA> 1 <NA>
## 7 <NA> 1 <NA>
## 8 <NA> 1 <NA>
## 9 <NA> 1 <NA>
## 10 <NA> <NA> <NA>
## 11 <NA> 1 <NA>
## 12 second 60 <NA>
## 13 second 3600 <NA>
## 14 second 86400 <NA>
## 15 second 604800 <NA>
## 16 second 31536000 <NA>
## 17 second 31622400 <NA>
## 18 kilogram 0.000000000001 <NA>
## 19 kilogram 0.000000001 <NA>
## 20 kilogram 0.000001 <NA>
## 21 kilogram 0.00001 <NA>
## 22 kilogram 0.0001 <NA>
## 23 kilogram 0.001 <NA>
## 24 kilogram 0.01 <NA>
## 25 kilogram 0.1 <NA>
## 26 kilogram 1000 <NA>
## 27 kilogram 1000 <NA>
## 28 kilogram 0.4536 <NA>
## 29 kilogram 907.1999 <NA>
## 30 kelvin 1 273.18
## 31 kelvin 0.556 255.402
## 32 meter 0.000000001 <NA>
## 33 meter 0.000001 <NA>
## 34 meter 0.000001 <NA>
## 35 meter 0.001 <NA>
## 36 meter 0.01 <NA>
## 37 meter 0.1 <NA>
## 38 meter 10 <NA>
## 39 meter 100 <NA>
## 40 meter 1000 <NA>
## 41 meter 1000000 <NA>
## 42 meter 0.0000000001 <NA>
## 43 meter 0.0254 <NA>
## 44 meter 0.3048 <NA>
## 45 meter 0.3048 <NA>
## 46 meter 0.3047997 <NA>
## 47 meter 1.8288 <NA>
## 48 meter 1852 <NA>
## 49 meter 0.9144 <NA>
## 50 meter 0.914398530744440774 <NA>
## 51 meter 0.2011661949 <NA>
## 52 meter 0.91439841461602867 <NA>
## 53 meter 1609.344 <NA>
## 54 second 0.000000001 <NA>
## 55 second 0.000001 <NA>
## 56 second 0.001 <NA>
## 57 second 0.01 <NA>
## 58 second 0.1 <NA>
## 59 second 10 <NA>
## 60 second 100 <NA>
## 61 second 1000 <NA>
## 62 second 1000000 <NA>
## 63 second 60 <NA>
## 64 second 3600 <NA>
## 65 cubicMeter 1 <NA>
## 66 cubicMeter 0.000000001 <NA>
## 67 cubicMeter 0.000001 <NA>
## 68 cubicMeter 0.001 <NA>
## 69 liter 3.785412 <NA>
## 70 liter 0.946353 <NA>
## 71 liter 0.035239 <NA>
## 72 liter 0.000016387064 <NA>
## 73 liter 0.473176 <NA>
## 74 <NA> 1 <NA>
## 75 radian 0.0174532924 <NA>
## 76 radian 0.015707 <NA>
## 77 hertz 1000000 <NA>
## 78 hertz 1000 <NA>
## 79 <NA> 1 <NA>
## 80 hertz 0.000001 <NA>
## 81 <NA> 1 <NA>
## 82 <NA> 1 <NA>
## 83 joule 4.1868 <NA>
## 84 joule 1055.0559 <NA>
## 85 joule 1.355818 <NA>
## 86 <NA> 1 <NA>
## 87 <NA> 1 <NA>
## 88 <NA> 1 <NA>
## 89 <NA> 1 <NA>
## 90 <NA> 1 <NA>
## 91 <NA> 1 <NA>
## 92 <NA> 1 <NA>
## 93 watt 1000000 <NA>
## 94 watt 1000 <NA>
## 95 <NA> 1 <NA>
## 96 watt 0.001 <NA>
## 97 volt 1000000 <NA>
## 98 volt 1000 <NA>
## 99 <NA> 1 <NA>
## 100 volt 0.001 <NA>
## 101 <NA> 1 <NA>
## 102 <NA> 1 <NA>
## 103 <NA> 1 <NA>
## 104 <NA> 1 <NA>
## 105 <NA> 1 <NA>
## 106 <NA> 1 <NA>
## 107 <NA> 1 <NA>
## 108 pascal 1000000 <NA>
## 109 pascal 1000 <NA>
## 110 pascal 101325 <NA>
## 111 pascal 100000 <NA>
## 112 pascal 100 <NA>
## 113 <NA> 1 <NA>
## 114 kilogramsPerSquareMeter 0.001 <NA>
## 115 kilogramsPerSquareMeter 0.000001 <NA>
## 116 kilogramsPerSquareMeter 0.0001 <NA>
## 117 kilogramsPerSquareMeter 0.1 <NA>
## 118 kilogramsPerSquareMeter 17.85 <NA>
## 119 <NA> 1 <NA>
## 120 kilogramsPerCubicMeter 1 <NA>
## 121 kilogramsPerCubicMeter 1 <NA>
## 122 kilogramsPerCubicMeter 0.000001 <NA>
## 123 kilogramsPerCubicMeter 0.000001 <NA>
## 124 kilogramsPerCubicMeter 0.001 <NA>
## 125 kilogramsPerCubicMeter 1000 <NA>
## 126 kilogramsPerCubicMeter 1000 <NA>
## 127 <NA> 1 <NA>
## 128 <NA> 1 <NA>
## 129 litersPerSecond 1 <NA>
## 130 litersPerSecond 28.316874 <NA>
## 131 <NA> 1 <NA>
## 132 squareMeter 100 <NA>
## 133 squareMeter 10000 <NA>
## 134 squareMeter 1000000 <NA>
## 135 squareMeter 0.000001 <NA>
## 136 squareMeter 0.0001 <NA>
## 137 squareMeter 4046.8564 <NA>
## 138 squareMeter 0.092903 <NA>
## 139 squareMeter 0.836131 <NA>
## 140 squareMeter 2589998.49806 <NA>
## 141 <NA> 1 <NA>
## 142 litersPerSquareMeter 0.00870 <NA>
## 143 litersPerSquareMeter 0.0001 <NA>
## 144 <NA> 1 <NA>
## 145 metersPerSecond 1 <NA>
## 146 <NA> .0000115741 <NA>
## 147 metersPerSecond 0.00000352778 <NA>
## 148 metersPerSecond 0.3048 <NA>
## 149 metersPerSecond 0.000084667 <NA>
## 150 metersPerSecond 0.9144 <NA>
## 151 metersPerSecond 0.44704 <NA>
## 152 metersPerSecond 1609.344 <NA>
## 153 metersPerSecond 26.8224 <NA>
## 154 metersPerSecond 0.01 <NA>
## 155 metersPerSecond 0.001 <NA>
## 156 metersPerSecond 0.000000000317098 <NA>
## 157 metersPerSecond 0.514444 <NA>
## 158 metersPerSecond 0.2778 <NA>
## 159 <NA> 1 <NA>
## 160 <NA> 1 <NA>
## 161 <NA> 1 <NA>
## 162 cubicMeterPerKilogram 0.000000000000001 <NA>
## 163 <NA> 1 <NA>
## 164 <NA> 1 <NA>
## 165 <NA> 1 <NA>
## 166 molesPerCubicMeter 1000 <NA>
## 167 <NA> 1 <NA>
## 168 <NA> 1 <NA>
## 169 <NA> 1 <NA>
## 170 metersSquaredPerSecond 86400 <NA>
## 171 metersSquaredPerSecond 0.000124586 <NA>
## 172 <NA> 1 <NA>
## 173 kilogramsPerMeterSquaredPerSecond 0.1 <NA>
## 174 kilogramsPerMeterSquaredPerSecond 0.0000000000317098 <NA>
## 175 kilogramsPerMeterSquaredPerSecond 0.0000000000011574 <NA>
## 176 kilogramsPerMeterSquaredPerSecond 0.000317 <NA>
## 177 kilogramsPerMeterSquaredPerSecond 0000000317 <NA>
## 178 <NA> 1 <NA>
## 179 molesPerKilogram 1000 <NA>
## 180 molesPerKilogram 1 <NA>
## 181 <NA> 1 <NA>
## 182 molesPerKilogramPerSecond 0.000001 <NA>
## 183 <NA> 1 <NA>
## 184 kilogramsPerSecond 0.0000317 <NA>
## 185 kilogramsPerSecond 0.0000000000317 <NA>
## 186 <NA> 1 <NA>
## 187 numberPerMeterSquared 0.000001 <NA>
## 188 <NA> 1 <NA>
## 189 numberPerMeterCubed 0.001 <NA>
## 190 numberPerMeterCubed 0.000001 <NA>
## 191 <NA> 1 <NA>
## 192 <NA> 1 <NA>
## 193 <NA> 1 <NA>
## 194 gramsPerGram 0.000001 <NA>
## 195 <NA> 1 <NA>
## abbreviation
## 1 <NA>
## 2 sec
## 3 m
## 4 kg
## 5 K
## 6 C
## 7 A
## 8 mol
## 9 cd
## 10 <NA>
## 11 m³
## 12 <NA>
## 13 <NA>
## 14 <NA>
## 15 <NA>
## 16 <NA>
## 17 <NA>
## 18 ng
## 19 μg
## 20 mg
## 21 cg
## 22 dg
## 23 g
## 24 dag
## 25 hg
## 26 Mg
## 27 T
## 28 lbs
## 29 ton
## 30 C
## 31 F
## 32 nm
## 33 μm
## 34 μ
## 35 mm
## 36 cm
## 37 dm
## 38 dam
## 39 hm
## 40 km
## 41 Mm
## 42 Å
## 43 in
## 44 usft
## 45 ft
## 46 gcft
## 47 <NA>
## 48 <NA>
## 49 yard
## 50 <NA>
## 51 <NA>
## 52 <NA>
## 53 mile
## 54 nsec
## 55 μsec
## 56 msec
## 57 csec
## 58 dsec
## 59 dasec
## 60 hsec
## 61 ksec
## 62 Msec
## 63 min
## 64 hr
## 65 kL
## 66 μl
## 67 ml
## 68 L
## 69 gal
## 70 qt
## 71 b
## 72 in³
## 73 pint
## 74 rad
## 75 º
## 76 grad
## 77 MHz
## 78 KHz
## 79 Hz
## 80 mHz
## 81 N
## 82 J
## 83 cal
## 84 btu
## 85 <NA>
## 86 lm
## 87 lx
## 88 Bq
## 89 Gy
## 90 Sv
## 91 kat
## 92 H
## 93 MW
## 94 kW
## 95 W
## 96 mW
## 97 MV
## 98 kV
## 99 V
## 100 mV
## 101 F
## 102 Ω
## 103 Ωm
## 104 S
## 105 Wb
## 106 T
## 107 Pa
## 108 MPa
## 109 kPa
## 110 atm
## 111 bar
## 112 mbar
## 113 kg/m²
## 114 g/m²
## 115 mg/m²
## 116 <NA>
## 117 <NA>
## 118 lbs/in²
## 119 <NA>
## 120 kg/m³
## 121 g/l
## 122 mg/m³
## 123 μg/l
## 124 mg/l
## 125 g/cm³
## 126 g/ml
## 127 <NA>
## 128 l/s
## 129 m³/s
## 130 ft³/sec
## 131 m²
## 132 a
## 133 ha
## 134 <NA>
## 135 <NA>
## 136 <NA>
## 137 a
## 138 ft²
## 139 yd²
## 140 mile²
## 141 l/m²
## 142 <NA>
## 143 <NA>
## 144 m²/kg
## 145 m/s
## 146 m/day
## 147 ft/day
## 148 ft/s
## 149 ft/hr
## 150 yd/s
## 151 mph
## 152 mps
## 153 mpm
## 154 cm/s
## 155 mm/s
## 156 cm/year
## 157 <NA>
## 158 km/hr
## 159 m/s²
## 160 <NA>
## 161 m³/kg
## 162 μm³/kg
## 163 A/m²
## 164 A/m
## 165 <NA>
## 166 M
## 167 m
## 168 cd/m²
## 169 m²/s
## 170 m²/day
## 171 ft²/day
## 172 <NA>
## 173 <NA>
## 174 <NA>
## 175 <NA>
## 176 <NA>
## 177 <NA>
## 178 <NA>
## 179 <NA>
## 180 <NA>
## 181 <NA>
## 182 <NA>
## 183 kg/s
## 184 <NA>
## 185 g/yr
## 186 <NA>
## 187 <NA>
## 188 <NA>
## 189 <NA>
## 190 <NA>
## 191 m/g
## 192 <NA>
## 193 <NA>
## 194 <NA>
## 195 <NA>
## description
## 1 a designation asserting the absence of an associated unit
## 2 SI unit of time
## 3 SI unit of length
## 4 SI unit of mass
## 5 SI unit of temperature
## 6 SI unit of charge
## 7 SI unit of electrical current
## 8 SI unit of substance amount
## 9 SI unit of luminosity
## 10 a number
## 11 cubic meter
## 12 one minute excluding leap seconds, 60 seconds
## 13 one hour excluding leap seconds, 3600 seconds
## 14 one day excluding leap seconds, 86400 seconds
## 15 one day excluding leap seconds, 604800 seconds
## 16 one year excluding leap seconds and leap days, 31536000 seconds
## 17 one 366 day year excluding leap seconds, 31622400 seconds
## 18 0.000000000001 kg
## 19 0.000000001 kg
## 20 0.000001 kg
## 21 0.00001 kg
## 22 0.0001 kg
## 23 0.001 kg
## 24 .01 kg
## 25 .1 kg
## 26 1000 kg
## 27 metric ton or tonne
## 28 1 pound in the Avoirdupois (commerce) scale
## 29 standard US (short) ton = 2000 lbs
## 30 A common unit of temperature
## 31 An obsolescent unit of temperature still used in popular meteorology
## 32 .000000001 meters
## 33 .000001 meters
## 34 .000001 meters
## 35 .001 meters
## 36 .01 meters
## 37 .1 meters
## 38 10 meters
## 39 100 meters
## 40 1000 meters
## 41 1000000 meters
## 42 1/10000000000 meter
## 43 An imperial measure of length
## 44 12 inches
## 45 12 inches
## 46 12 inches
## 47 6 feet
## 48 nautical mile
## 49 3 feet
## 50 This is an ESRI unit and the multiplier comes from ESRI. It\n may not be accurate.
## 51 This is an ESRI unit and the multiplier comes from ESRI. It\n may not be accurate.
## 52 This is an ESRI unit and the multiplier comes from ESRI. It\n may not be accurate.
## 53 5280 ft or 1609.344 meters
## 54 1/1000000 of a second
## 55 1/100000 of a second
## 56 1/1000 of a second
## 57 1/100 of a second
## 58 1/10 of a second
## 59 10 seconds
## 60 100 seconds
## 61 1000 seconds
## 62 1000000 seconds
## 63 60 seconds
## 64 3600 seconds
## 65 1 cubic meter
## 66 1/1000000 of a liter
## 67 1/1000 of a liter
## 68 1000 cm^3
## 69 US liquid gallon
## 70 US liquid quart
## 71 1 bushel = 35.23907 liters
## 72 cubic inch
## 73 US liquid pint
## 74 2 pi radians comprise a unit circle.
## 75 360 degrees comprise a unit circle
## 76 a plane angle equivalent to 1/400 of a full circle
## 77 megahertz
## 78 kilohertz
## 79 hertz
## 80 millihertz
## 81 newton
## 82 joule = N*m
## 83 1 cal = 4.1868 J
## 84 1 btu = 1055.0559 J
## 85 1 ft-lbs = 1.355818 J
## 86 lumen
## 87 lux
## 88 becquerel
## 89 gray
## 90 sievert
## 91 katal
## 92 henry
## 93 megawatt
## 94 kilowatt
## 95 watt = J/s
## 96 milliwatt
## 97 megavolt
## 98 kilovolt
## 99 volt
## 100 millivolt
## 101 farad
## 102 ohm
## 103 ohm meters
## 104 siemen
## 105 weber
## 106 tesla
## 107 pascal
## 108 megapascal
## 109 kilopascal
## 110 1 atmosphere = 101325 pascals
## 111 1 bar = 100000 pascals
## 112 millibar
## 113 kilograms per square meter
## 114 grams per square meter
## 115 milligrams Per Square Meter
## 116 kilograms per hectare
## 117 metric ton or tonne per hectare
## 118 lbs/square inch
## 119 kilogram per cubic meter
## 120 milligrams per milliliter
## 121 grams per liter
## 122 milligrams Per Cubic Meter
## 123 micrograms / liter
## 124 milligrams / liter
## 125 grams per cubic centimeter
## 126 grams per milliliter
## 127 grams Per (Liter Per Day)
## 128 liters per second
## 129 cubic meters per second
## 130 cubic feet per second
## 131 square meters
## 132 100 square meters
## 133 1 hectare is 10^4 square meters
## 134 square kilometers
## 135 square millmeters
## 136 square centimeters
## 137 1 acre = 4046.8564 square meters or 1 hectare = 2.4710 acres
## 138 12 inches squared
## 139 36 inches squared
## 140 1 mile squared
## 141 liters per square meter
## 142 bushels per acre -- 1 bushel = 35.23907 liters/1 acre = 4046.8564 squareMeters
## 143 liters per hectare
## 144 square meters per kilogram
## 145 meters per second
## 146 meters per day
## 147 feet per day
## 148 feet per second
## 149 feet per hour
## 150 yards per second
## 151 miles per hour
## 152 miles per second
## 153 miles per minute
## 154 centimeters per second
## 155 millimeters per second
## 156 centimeter Per Year
## 157 knots
## 158 km/hr
## 159 meters per second squared
## 160 1/meters
## 161 cubic meters per kilogram
## 162 cubic micrometers per gram
## 163 ampere per meter squared
## 164 ampere per meter
## 165 mole per cubic meter
## 166 molarity = moles/liter
## 167 molality = moles/kg
## 168 candela Per Square Meter
## 169 meters squared per second
## 170 meters squared per day
## 171 feet squared per day
## 172 kilograms per meter sqared per second
## 173 grams Per Centimeter Squared Per Second
## 174 grams Per Meter Squared Per Year
## 175 grams Per Hectare Squared Per Day
## 176 kilograms Per Hectare Per Year
## 177 kilograms Per Meter Squared Per Year
## 178 moles per kilogram
## 179 moles per gram
## 180 millimoles per gram
## 181 moles per kilogram per second
## 182 nanomoles Per Gram Per Second
## 183 kilograms per second
## 184 tonnes Per Year
## 185 grams Per Year
## 186 number per meter squared
## 187 number per kilometer squared
## 188 number per meter cubed
## 189 number of entities per liter
## 190 number of entities per milliliter
## 191 meters per gram
## 192 number of entities per gram
## 193 grams per gram
## 194 micrograms per gram
## 195 cubic centimeters per cubic centimeterUse View(standardUnits$units) for a prettier display locally.
The get_unitList() function returns two tables, units and unitType. We will see the importance of the latter in a moment. This table can be useful in identifying the appropriate unit id to use when creating an EML file using set_attributes().
For now, we would like to learn more about the custom unit that isn’t in the standard dictionary. A valid EML file must provide the definitions for any custom unit in the addtionalMetadata section. We can use get_unitList() to extract this information from the EML document:
customUnits <- get_unitList(eml@additionalMetadata[[1]]@metadata)
customUnits## $units
## id name unitType
## 1 gramsPerSquareMeter gramsPerSquareMeter arealMassDensity
## 2 speciesPerSquareMeter speciesPerSquareMeter arealDensity
## parentSI multiplierToSI constantToSI abbreviation
## 1 kilogramsPerSquareMeter .001 <NA> <NA>
## 2 numberPerSquareMeter 1 <NA> <NA>
## description
## 1 a description of the unit Grams per Square Meter
## 2 <NA>
##
## $unitTypes
## NULLWe see that this EML file defines two custom units (though as we’ve seen gramsPerSquareMeter is actually in the standard unit list now, so that one isn’t needed.) We also see that the unitTypes table is empty, since the custom unit speciesPerSquareMeter uses the standard unitType arealDensity, which we can look up in the standards table:
which(standardUnits$unitTypes$id == "arealDensity")## [1] 55 56standardUnits$unitTypes[c(55,56),]## id name dimension power
## 55 arealDensity arealDensity dimensionless <NA>
## 56 arealDensity arealDensity length -2Which tells us that an arealDensity is a dimensionless unit times a length to -2 power.
When writing our own EML files, we must thus take care to define our units.
For tabular data (e.g. csv files), this information is provided in the attributeList element, such as we created using the set_attributes() function in the vignette, “creating EML”. When working with any numeric data, this function takes a data.frame with a column for unit that provides the name of the unit listed.
These units cannot be any free-form text, but should instead be one of the standard units recognized by EML. Since EML knows about lots of units already, this usually just means making sure we use the correct id for the desired unit in the attributes metadata. As we have seen above, the standardUnits list can help us with this. We can just skim the table by eye, or, for instance, we can look up the unit id for a some units by abbreviation:
i <- which(standardUnits$units$abbr == "btu")
j <- which(standardUnits$units$abbr == "μm³/kg")
standardUnits$units[c(i,j),]## id name unitType
## 84 britishThermalUnit britishThermalUnit energy
## 162 cubicMicrometersPerGram cubicMicrometersPerGram specificVolume
## parentSI multiplierToSI constantToSI abbreviation
## 84 joule 1055.0559 <NA> btu
## 162 cubicMeterPerKilogram 0.000000000000001 <NA> μm³/kg
## description
## 84 1 btu = 1055.0559 J
## 162 cubic micrometers per gramnote that EML names units in camelCase, with compound units spelled out. We will need to give the full unit id, not the abbreviation, to the units column when defining attribute metadata, e.g.:
df <- data.frame(attributeName = "energy",
attributeDefinition = "energy absorbed by the surface",
unit = "britishThermalUnit",
numberType = "real",
stringsAsFactors = FALSE)
attributeList <- set_attributes(df, col_classes = "numeric")Sometimes we will want to use a unit that is not avaialble in the standardUnit list, such as the example of species per square meter seen above. To add this information to our EML file, we use set_unitList, using definitions that follow the same data.frame format we saw returned by the get_unitList() function. Here we provide the definition for species per square meter, following the camelCase convention of EML
custom_units <- data.frame(id = "speciesPerSquareMeter", unitType = "arealDensity", parentSI = "numberPerSquareMeter", multiplierToSI = 1, description = "number of species per square meter")
set_unitList(custom_units)## <unitList>
## <unit id="speciesPerSquareMeter" name="speciesPerSquareMeter" parentSI="numberPerSquareMeter" unitType="arealDensity" multiplierToSI="1">
## <description>number of species per square meter</description>
## </unit>
## </unitList>Note that this definition refers to the unitType arealDensity, which, as we have already seen, is defined in the standard unit types. Users should consult the standardUnits$unitType table for the names and defintitions of standard types, e.g.
unique(standardUnits$unitTypes$id)## [1] "length" "time"
## [3] "mass" "current"
## [5] "temperature" "amount"
## [7] "luminosity" "dimensionless"
## [9] "angle" "acceleration"
## [11] "charge" "magneticFieldStrength"
## [13] "currentDensity" "area"
## [15] "lengthReciprocal" "frequency"
## [17] "volume" "volumetricArea"
## [19] "speed" "massDensity"
## [21] "massPerMass" "volumePerVolume"
## [23] "volumetricRate" "volumetricMassDensityRate"
## [25] "arealMassDensityRate" "specificVolume"
## [27] "amountOfSubstanceConcentration" "amountOfSubstanceWeight"
## [29] "amountOfSubstanceWeightFlux" "massFlux"
## [31] "luminance" "volumetricDensity"
## [33] "arealDensity" "arealMassDensity"
## [35] "specificArea" "force"
## [37] "energy" "power"
## [39] "potentialDifference" "capacitance"
## [41] "resistance" "resistivity"
## [43] "conductance" "magneticFlux"
## [45] "magneticFluxDensity" "inductance"
## [47] "illuminance" "radionucleotideActivity"
## [49] "specificEnergy" "doseEquivalent"
## [51] "catalyticActivity" "pressure"
## [53] "transmissivity" "massSpecificLength"
## [55] "massSpecificCount"Likewise, parentSI should refer to a unit already defined in the standard unit dictionary, or otherwise provided by similar custom definition. A multiplierToSI should be provided. If necessary an additive constantToSI can also be provided. An abbreviation and description of the unit is optional.
In even rarer cases, a unitType might not be available in the standard unit list. It is possible to convert between different units that share a common unitType such as length, but not units with different unitTypes. This may be particularly applicable for compound units: for instance, there is no unit type with dimensions of length per time cubed, (equivalently, acceleration per time, also known as a “jerk”). We can define a custom unit type by providing the appropriate data frame, with one row for each base type. Note we have to repeat the id for each row that is shared by the unit. The unit definition follows from the product of the each of the base dimensions raised to the power given (a missing value for power is equivalent to a power of 1), e.g. for our jerk:
unitType <- data.frame(id = c("jerk", "jerk"), dimension = c("length", "time"), power = c(1, -3) )Of course we cannot use a unitType without a unit to measure it in, so we define the SI unit as well (note we do not need a parentSI or multiplier because this is already an SI unit):
unit <- data.frame(id = "meterPerSecondCubed", unitType = "jerk")We can now generate the required unitList:
unitList <- set_unitList(unit, unitType)Note that there are often many equivalent ways to express a unit (our jerk could have been acceleration per time instead). Before defining a new unitType, some dilegence may help you recognize a unitType that has already been defined in a different way.
As we have seen above, the custom unit declearations must be found in the additionalMetadata section of an EML file. To do so, we can simply coerce the unitList into an additionalMetadata element when creating our eml object:
eml <- new("eml", additionalMetadata = as(unitList, "additionalMetadata"))