Functions for extracting and adding metadata for objects of class TD.getMeta extracts a data.frame with location, date, design, latitude,
longitude, plot width and plot length for all trials in TD.setMeta adds metadata from a data.frame to an object of class TD. See
details for the specifications of the data.frame.
The most common use case is extracting metadata from a TD object, modifying
the content and then adding it back to the TD object.
Information in the metadata of a TD object is used in plotting functions
(e.g. latitude and longitude for a map plot) and when fitting models on the
data (the trial design).
Details
When setting metadata, metadata has to be a data.frame with rownames
corresponding to the trials in TD. The data.frame should contain one
or more of the following columns:
- trLocation
The location of the trial. Used as default name when creating plots and summaries.
- trDate
The date of the trial.
- trDesign
The design of the trial. One of "none" (no (known) design), "ibd" (incomplete-block design), "res.ibd" (resolvable incomplete-block design), "rcbd" (randomized complete block design), "rowcol" (row-column design) or "res.rowcol" (resolvable row-column design). Used when fitting models.
- trLat
The latitude of the trial on a scale of -90 to 90. Used when plotting the trials on a map.
- trLong
The longitude of the trial on a scale of -180 to 180. Used when plotting the trials on a map.
- trPlWidth
The width of the plot. Used in combination with trPlLength to determine the size of the plots in a layout plot of a trial.
- trPlLength
The length of the plot. Used in combination with trPlWidth to determine the size of the plots in a layout plot of a trial.
The values of the metadata of TD will be set to the values in the
corresponding column in meta. Existing values will be overwritten,
but NA will be ignored so setting a value to NA won't result
in accidentally removing it.
See also
Other functions for TD objects:
TD,
plot.TD(),
summary.TD()
Examples
data("dropsRaw")
## Create a TD object.
dropsTD <- createTD(data = dropsRaw[dropsRaw$year == 2012, ],
genotype = "Variety_ID",
trial = "Experiment",
loc = "Site",
repId = "Replicate",
subBlock = "block",
rowCoord = "Row",
colCoord = "Column",
trLat = "Lat",
trLong = "Long")
## Get meta data from dropsTD.
(dropsMeta <- getMeta(dropsTD))
#> trLocation trDate trDesign trLat trLong trPlWidth trPlLength
#> Cam12R Campagnola <NA> NA 45.171 9.532 NA NA
#> Cra12R Craiova <NA> NA 44.116 24.348 NA NA
#> Gai12W Gaillac <NA> NA 43.910 1.890 NA NA
#> Kar12W Karlsruhe <NA> NA 49.100 8.320 NA NA
#> Ner12R Nerac <NA> NA 44.170 0.307 NA NA
## Add trial date to meta data.
dropsMeta$trDate <- as.Date(rep("010112", times = 5), "%d%m%y")
## Add back meta data to wheatTD.
dropsTD <- setMeta(dropsTD,
dropsMeta)