setna.pt: Set values to 'NA' for potato data.

In reyzaguirre/st4gi: Statistical tools for genetic improvement

Set values to NA for potato data.

Description

Detect impossible values for potato data and set them to missing value (NA) according to some rules.

Usage

setna.pt(dfr, f = 10)

Arguments

dfr	The name of the data frame.
f	Factor for extreme values detection. See details.

Details

The data frame must use the labels (lower or upper case) listed in function check.names.pt. Consider the following groups of traits:

• pre (traits evaluated pre-harvest): ppe, plant_unif, plant_vigor and se.

• cnn (continuos non-negative traits): tntpl, nmtpl, ttwp, ttwpl, mtwp, mtwpl, nomtwp, mtwci, mtwcii, ttya, ttyna, mtya, and mtyna.

• cpo (continuous positive traits): atw, atmw, fwts1, fwts2, dwts1, and dwts2.

• pnn (percentage non-negative traits): ppe, pph, fruc, gluc, sucr, and malt.

• ppo (percentage positive traits): dm, pro, star, and fiber.

• dnn (discrete non-negative traits): ntp, npe, nph, tntp, nmtp, nnomtp, nmtci, and nmtcii.

• ctg (categorical 1 to 9 traits): plant_unif, plant_vigor, se, tuber_apper, tub_unif, tub_size, num_stolon, and leng_stolon.

Values are set to NA with the following rules:

• cnn traits with negative values are set to NA.

• cpo traits with non-positive values are set to NA.

• pnn traits with values out of the [0, 100] interval are set to NA.

• ppo with values out of the (0, 100] interval are set to NA.

• dnn traits with negative and non-integer values are set to NA.

• ctg traits with out of scale values are set to NA.

• Extreme low and high values are detected using the interquartile range. The rule is to detect any value out of the interval [Q_1 - f \times (m/3 + IQR); Q_3 + f \times (m/3 + IQR)] where m is the mean. By default f = 10 and if less than 10 a warning is shown. Values out of this range are set to NA.

• If npe == 0 and there is some data for any trait, then npe is set to NA.

• If nph == 0 and there is some data for any non-pre-harvest trait, then nph is set to NA.

• If nmtp == 0 and mtwp > 0, then nmtp is set to NA.

• If nmtp > 0 and mtwp == 0, then mtwp is set to NA.

• If nnomtp == 0 and nomtwp > 0, then nnomtp is set to NA.

• If nnomtp > 0 and nomtwp == 0, then nomtwp is set to NA.

Value

It returns the data frame with all impossible values set to NA and a list of warnings with all the rows that have been modified.

Author(s)

Raul Eyzaguirre.

Examples

dfr <- data.frame(mtwp = c(2.2, 5.0, 3.6, 12, 1600, -4, 0),
                  dm = c(21, 23, 105, 24, -3, 30, NA),
                  nmtp = c(1.3, 10, 11, NA, 2, 5, NA))
setna.pt(dfr)

reyzaguirre/st4gi documentation built on April 30, 2024, 5:45 a.m.