pcvr (version 1.2.0)

pwue: Calculate pseudo water use efficiency from phenotype and watering data

Description

Rate based water use efficiency (WUE) is the change in biomass per unit of water metabolized. Using image based phenotypes and watering data we can calculate pseudo-WUE (pwue) over time. Here area_pixels is used as a proxy for biomass and transpiration is approximated using watering data. The equation is then \( \frac{P_{t} - P_{t-1}}{W_{t_{end-1}}-W_{t_{start}} }\), where P is the phenotype and W is the weight before watering.

Absolute value based WUE is the amount of water used to sustain a plants biomass over a given period. The equation is then \(\frac{P_{t}}{W_{t_{end-1}}-W_{t_{start}} }\)

Usage

pwue(
  df,
  w = NULL,
  pheno = "area_pixels",
  time = "timestamp",
  id = "barcode",
  offset = 0,
  pre_watering = "weight_before",
  post_watering = "weight_after",
  method = "rate"
)

Value

A data frame containing the watering data and to phenotype data with new columns for change in the phenotype (pheno_diff), amount of water used (total_water) over the interval between phenotype measurements (water added post to pre phenotype measurement), start and end times for the interval as well as their difference (timeLengthSeconds), and pseudo water use efficiency (pWUE).

Arguments

df

Dataframe containing wide single-value phenotype data. This should already be aggregated to one row per plant per day (angles/rotations combined).

w

Watering data as returned from bw.water.

pheno

Phenotype column name, defaults to "area_pixels"

time

Variable(s) that identify a plant on a given day. Defaults to c("barcode", "DAS").

id

Variable(s) that identify a plant over time. Defaults to "barcode".

offset

Optionally you can specify how long before imaging a watering should not be taken into account. This defaults to 0, meaning that if a plant were watered directly before being imaged then that water would be counted towards WUE between the current image and the prior one. This argument is taken to be in seconds.

pre_watering

Column containing weight before watering in w, defaults to "weight_before".

post_watering

Column containing weight after watering in w, defaults to "weight_after".

method

Which method to use, options are "rate", "abs", and "ndt". The "rate" method considers WUE as the change in a phenotype divided by the amount of water added. The "abs" method considers WUE as the amount of water used by a plant given its absolute size. The "ndt" method calculates normalized daily transpiration, which is the reciprocal of the "abs" method. The "rate" method is for questions more related to efficiency in using water to grow while "abs"/"ndt" are more suited to questions about how efficient a plant is at maintaining size given some amount of water or how much water it uses at a given size.

Examples

set.seed(123)
weight_before <- sort(round(rnorm(20, 100, 10), 0))
weight_after <- sort(round(rnorm(20, 120, 10), 0))
df <- data.frame(
  time = seq_along(weight_before),
  area_pixels = round(130 / (1 + exp( (12 - seq_along(weight_before))/3) ), 0),
  weight_before,
  weight_after,
  barcode = 1,
  other = "x"
)
ex <- pwue(df, time = "time", method = "rate", id = c("barcode", "other"))
w <- df[, c("time", "weight_before", "weight_after", "barcode")]
ex2 <- pwue(df, w, time = c("time", "time"), method = "abs")
ex3 <- pwue(df, w, time = c("time", "time"), method = "ndt")