Description Usage Arguments Details Value Author(s) Examples
Forms the prime traits by selecting a subset of the traits in a data.frame of
imaging data produced by the Lemna Tec Scanalyzer. The imaging traits to be retained
are specified using the traits
and labsCamerasViews
arguments. Some imaging
traits are divided by 1000 to convert them from pixels to kilopixels.
Also added are factors and explanatory variates that might be of use in an analysis.
1 2 3 4 5 6 7 8 9 10 11 12 13 14  longitudinalPrime(data, cartId = "Snapshot.ID.Tag",
imageTimes = "Snapshot.Time.Stamp",
timeAfterStart = "Time.after.Planting..d.",
idcolumns = c("Genotype.ID","Treatment.1"),
traits = list(all = c("Area",
"Boundary.Points.To.Area.Ratio",
"Caliper.Length", "Compactness",
"Convex.Hull.Area"),
side = c("Center.Of.Mass.Y",
"Max.Dist.Above.Horizon.Line")),
labsCamerasViews = list(all = c("SV1", "SV2", "TV"),
side = c("SV1", "SV2")),
smarthouse.lev = NULL,
calcWaterLoss = TRUE, pixelsPERcm)

data 
A Smarthouse, Lane, Position, Weight.Before, Weight.After, Water.Amount, Projected.Shoot.Area..pixels. The defaults for the arguments to Smarthouse, Lane, Position, Weight.Before, Weight.After, Water.Amount, Projected.Shoot.Area..pixels., Area.SV1, Area.SV2, Area.TV, Boundary.Points.To.Area.Ratio.SV1, Boundary.Points.To.Area.Ratio.SV2, Boundary.Points.To.Area.Ratio.TV, Caliper.Length.SV1, Caliper.Length.SV2, Caliper.Length.TV, Compactness.SV1, Compactness.SV2, Compactness.TV, Convex.Hull.Area.SV1, Convex.Hull.Area.SV2, Convex.Hull.Area.TV, Center.Of.Mass.Y.SV1, Center.Of.Mass.Y.SV2, Max.Dist.Above.Horizon.Line.SV1, Max.Dist.Above.Horizon.Line.SV2. 
cartId 
A 
imageTimes 
A 
timeAfterStart 
A 
idcolumns 
A 
traits 
A 
labsCamerasViews 
A 
smarthouse.lev 
A 
calcWaterLoss 
A 
pixelsPERcm 
A 
The columns are copied from data, except for those columns in the list under Value that have ‘(calculated)’ appended.
A data.frame
containing the columns specified by cartId
,
imageTimes
, timeAfterStart
, idcolumns
, traits
and
cameras
. The defaults will result in the following columns:
Smarthouse: factor with levels for the Smarthouse
Lane: factor for lane number in a smarthouse
Position: factor for east/west position in a lane
Days: factor for the number of Days After Planting (DAP)
cartId
: unique code for each cart
imageTimes
: time at which an image was taken in POSIXct format
Reps: factor indexing the replicates for each combination of the factors in idcolumns
(calculated)
xPosn: numeric for the Positions within a Lane (calculated)
Hour: hour of the day, to 2 decimal places, at which the image was taken (calculated)
xDays: numeric for the DAP that is centred by subtracting the mean of the unique days (calculated)
idcolumns
: the columns listed in idcolumns
that have been converted to factors
Weight.Before: weight of the pot before watering (only if calcWaterLoss
is TRUE
)
Weight.After: weight of the pot after watering (only if calcWaterLoss
is TRUE
)
Water.Amount: the weight of the water added (= Water.After  Water.Before) (calculated)
Water.Loss: the difference between Weight.Before for the current imaging and the Weight.After for the previous imaging (calculated unless calcWaterLoss
is FALSE
)
Area: the Projected.Shoot.Area..pixels. divided by 1000 (calculated)
Area.SV1: the Projected.Shoot.Area from Side View 1 divided by 1000 (calculated)
Area.SV2: the Projected.Shoot.Area from Side View 2 divided by 1000 (calculated)
Area.TV: the Projected.Shoot.Area from Top View divided by 1000 (calculated)
Boundary.To.Area.Ratio.SV1
Boundary.To.Area.Ratio.SV2
Boundary.To.Area.Ratio.TV
Caliper.Length.SV1
Caliper.Length.SV2
Caliper.Length.TV
Compactness.SV1 from Side View 1
Compactness.SV2 from Side View 2
Compactness.TV: from Top View
Convex.Hull.Area.SV1: area of Side View 1 Convex Hull divided by 1000 (calculated)
Convex.Hull.Area.SV2: area of Side View 2 Convex Hull divided by 1000 (calculated)
Convex.Hull.TV: Convex.Hull.Area.TV divided by 1000 (calculated)
Center.Of.Mass.Y.SV1: Centre of Mass from Side View 1
Center.Of.Mass.Y.SV2: Centre of Mass from Side View 2
Max.Dist.Above.Horizon.Line.SV1: the Max.Dist.Above.Horizon.Line.SV1 converted to cm using pixelsPERcm
(calculated)
Max.Dist.Above.Horizon.Line.SV2: the Max.Dist.Above.Horizon.Line.SV2 converted to cm using pixelsPERcm
(calculated)
Chris Brien
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20  data(exampleData)
longiPrime.dat < longitudinalPrime(data=raw.dat, smarthouse.lev=1)
longiPrime.dat < longitudinalPrime(data=raw.dat, smarthouse.lev=1,
traits = list(a = "Area", c = "Compactness"),
labsCamerasViews = list(all = c("SV1", "SV2", "TV"),
t = "TV"))
longiPrime.dat < longitudinalPrime(data=raw.dat, smarthouse.lev=1,
traits = c("Area.SV1", "Area.SV2", "Area.TV",
"Compactness.TV"),
labsCamerasViews = NULL)
longiPrime.dat < longitudinalPrime(data=raw.dat, smarthouse.lev=1,
calcWaterLoss = FALSE,
traits = list(img = c("Area", "Compactness"),
H20 = c("Weight.Before","Weight.After",
"Water.Amount")),
labsCamerasViews = list(all = c("SV1", "SV2", "TV"),
H2O = NULL))

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