Read in plantCV csv from bellwether phenotyper style experiments analyzed with plantCV versions <4.

Usage

read.pcv.3(
  file = NULL,
  snapshotFile = NULL,
  designFile = NULL,
  metaCol = "meta",
  metaForm = "vis_view_angle_zoom_horizontal_gain_exposure_v_new_n_rep",
  joinSnapshot = "id",
  conversions = NULL,
  mode = "long",
  ...
)

Arguments

file: Path to the version 3 plantCV output containing phenotypes.
snapshotFile: path to the snapshot info metadata file, typically called SnapshotInfo.csv. This needs to have a column name corresponding to `joinSnapshot` (defaults to "id") which can be used to join the snapshot data to the phenotype data. Generally this joining will happen through a parsed section of the file path to each image present in the phenotype data. This means that including a duplicate name in `metaForm` will be overwritten by parsing image paths, so `metaForm` and `joinSnapshot` should not have duplicated names. If there is a timestamp column in the snapshot data then it will be converted to datetime (assuming a "Y-m-d H:M:S" format) and used to calculate days after starting (DAS) and hours.
designFile: path to a csv file which contains experimental design information (treatments, genotypes, etc) and which will be joined to phenotype and snapshot data through all shared columns.
metaCol: a column name from the phenotype data read in with the `file` argument. Generally for bellwether experiments this will correspond to an image path. The name is split on "/" characters with the last segment being taken and parsed into some number of sections based on `metaForm`.
metaForm: A character string or character vector of column names to parse `metaCol` into. The number of names needs to match with length of `metaCol` when parsed. If a character string is provided then it is assumed to be underscore delimited, so do if you need underscores in a column name then use `c("column_one", "column_two",...)` instead of `column_one_column_two_...`.
joinSnapshot: Column name create in phenotype data to use in joining snapshot data. By default this will attempt to make an "id" column, which is parsed from a snapshot folder in `metaCol` ("/shares/sinc/data/Phenotyper/SINC1/ImagesNew/**snapshot1403**/"). An error will be raised if this column is not present in the snapshot data.
conversions: A named list of phenotypes that should be rescaled by the value in the list. For instance, at zoom 1 `list(area = 13.2 * 3.7/46856)` will convert from pixels to square cm in the 5MP bellwether camera.
mode: The mode to read data in with through read.pcv. The default is "long" because this function is built for pcv3 output, which was generally a wider format to start with than pcv4 output.
...: Other arguments passed to read.pcv.

Value

Returns a dataframe potentially with several files merged into it.

Examples

# \donttest{
base_url <- "https://raw.githubusercontent.com/joshqsumner/pcvrTestData/main/"
bw <- read.pcv.3(
  file = paste0(base_url, "pcv3Phenos.csv"),
  metaCol = NULL,
  reader = "fread"
)
bw <- read.pcv.3(
  file = paste0(base_url, "pcv3Phenos.csv"),
  metaCol = "meta", metaForm = "vis_view_angle_zoom_horizontal_gain_exposure_v_new_n_rep",
  joinSnapshot = "id",
  reader = "fread"
)
bw <- read.pcv.3(
  file = paste0(base_url, "pcv3Phenos.csv"),
  snapshotFile = paste0(base_url, "pcv3Snapshot.csv"),
  designFile = paste0(base_url, "pcv3Design.csv"),
  metaCol = "meta", metaForm = "vis_view_angle_zoom_horizontal_gain_exposure_v_new_n_rep",
  joinSnapshot = "id", conversions = list(area = 13.2 * 3.7 / 46856),
  reader = "fread"
)
# }