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.
data(RicePrepped.dat)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) |
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 tools:::Rd_expr_doi("10.1038/ncomms13342").