RicePrepped.dat: Prepped data from an experiment to investigate a rice...

In growthPheno: Functional Analysis of Phenotypic Growth Data to Smooth and Extract Traits

Prepped data from an experiment to investigate a rice germplasm panel.

Description

The data is the full set of Lanes and Positions from an experiment in a Smarthouse at the Plant Accelerator in Adelaide. It is used in the growthPheno-package as an executable example to illustrate the use of growthPheno. The experiment and data collection are described in Al-Tamimi et al. (2016) and the data is derived from the data.frame in the file 00-raw.0254.dat.rda that is available from Al-Tamimi et al. (2017); halpf od the unprred data is in RiceRaw.dat.

Usage

data(RicePrepped.dat)

Format

A data.frame containing 14784 observations on 32 variables. The names of the columns in the data.frame are:

Column	Name	Class	Description
1	Smarthouse	factor	the Smarthouse in which a individual occurs.
2	Snapshot.ID.Tag	character	a unique identifier for each individual in the experiment.
3	xDAP	numeric	the numbers of days after planting on which the current
			data was observed.
4	DAST	factor	the numbers of days after the salting treatment on which
			the current data was observed.
5	xDAST	numeric	the numbers of days after the salting treatment on which
			the current data was observed.
6	cDAST	numeric	a centered numeric covariate for DAST.
7	DAST.diffs	numeric	the number of days between this and the previous
			observations (all one for this experiment).
8	Lane	factor	the Lane in the 24 Lane x 24 Positions grid.
9	Position	factor	the Position in the 24 Lane x 24 Positions grid.
10	cPosn	numeric	a centered numeric covaariate for Positions.
11	cMainPosn	numeric	a centered numeric covaariate for Main plots.
12	Zone	factor	the Zone of 4 Lanes to which the current individual belonged.
13	cZone	numeric	a centered numeric covariate for Zone.
14	SHZone	factor	the Zone numbered across the two Smarthouses.
15	ZLane	factor	the number of the Lane within a Zone.
16	ZMainunit	factor	the number of the Main plot within a Zone.
17	Subunit	factor	the number of an Individual within a Main plot.
18	Reps	numeric	the replicate number of each Genotype-Salinity combination.
19	Genotype	factor	the number assigned to the 298 Genotypes in the experiment.
20	Salinity	factor	the Salinity treatment (Control, Salt) allocated to a Individual.
21	PSA	numeric	the Projected shoot area (kpixels).
22	PSA.AGR	numeric	the Absolute Growth Rate for the Projected shoot area (kpixels/day).
23	PSA.RGR	numeric	the Relative Growth Rate for the Projected shoot area (per day).
24	Tr	numeric	the amount of water (g) transpired by a plant.
25	TrR	numeric	the rate of water transpireation (g/day) for a plant.
26	PSA.TUE	numeric	the Transpiration Use Efficiency for PSA (kpixels / day)
			for a plant.
27	sPSA	numeric	the smoothed Projected shoot area (kpixels).
29	sPSA.AGR	numeric	the smoothed Absolute Growth Rate for the Projected shoot
			area (kpixels/day).
29	sPSA.RGR	numeric	the smoothed Relative Growth Rate for the Projected shoot
			area (per day).
30	sTr	numeric	the smoothed amount of water (g) transpired by a plant.
31	sTrR	numeric	the smoothed rate of water transpireation (g/day) for a plant.
32	sPSA.TUE	numeric	the smoothed Transpiration Use Efficiency for PSA (kpixels / day)
			for a plant.

Source

Al-Tamimi N, Brien C, Oakey H, Berger B, Saade S, Ho YS, Schmockel SM, Tester M, Negrao S. (2017) Data from: Salinity tolerance loci revealed in rice using high-throughput non-invasive phenotyping. Retrieved from: \Sexpr[results=rd]{tools:::Rd_expr_doi("10.5061/dryad.3118j")}.

References

Al-Tamimi, N, Brien, C.J., Oakey, H., Berger, B., Saade, S., Ho, Y. S., Schmockel, S. M., Tester, M. and Negrao, S. (2016) New salinity tolerance loci revealed in rice using high-throughput non-invasive phenotyping. Nature Communications, 7, 13342. Retrieved from \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1038/ncomms13342")}.

growthPheno documentation built on June 8, 2025, 12:51 p.m.