utils_data_org {metan}

Utilities for data organization

Description

Useful function for data organization before statistical analysis

• add_seq_block(): Add a column with sequential block numeration in multi-environment data sets.

• recode_factor(): Recode a factor column. A sequential numbering (with possible prefix) is used to identify each level.

• df_to_selegen_54(): Given a multi-environment data with environment, genotype, and replication, format the data to be used in the Selegen software (model 54).

Usage

add_seq_block(data, env, rep, new_factor = BLOCK, prefix = "", verbose = TRUE)

recode_factor(data, factor, new_factor = CODE, prefix = "", verbose = TRUE)

df_to_selegen_54(data, env, gen, rep, verbose = TRUE)

Arguments

data

A data frame.

env

The name of the column that contains the levels of the environments.

rep

The name of the column that contains the levels of the replications/blocks.

new_factor

The name of the new column created.

prefix

An optional prefix to bind with the new factor.

verbose

Logical argument. If verbose = FALSE the code will run silently.

factor

A column to recode.

gen

The name of the column that contains the levels of the genotypes, that will be treated as random effect.

Author(s)

Tiago Olivoto [e-mail]

References

Resende, M.D. V. 2016. Software Selegen-REML/BLUP: a useful tool for plant breeding. Crop Breed. Appl. Biotechnol. 16(4): 330–339. doi:10.1590/1984-70332016v16n4a49.

Examples

library(metan)
df_ge <- ge_simula(ngen = 2,
                   nenv = 3,
                   nrep = 2) %>%
         add_cols(ENV = c(rep("CACIQUE", 4),
                          rep("FREDERICO", 4),
                          rep("SANTA_MARIA", 4)))
df_ge

# Add sequential block numbering over environments
add_seq_block(df_ge, ENV, REP, prefix = "B")

# Recode the 'ENV' column to "ENV1", "ENV2", and so on.
recode_factor(df_ge,
              factor = ENV,
              prefix = "ENV",
              new_factor = ENV_CODE)

# Format the data to be used in the Selegen software (model 54)
df <- df_to_selegen_54(df_ge, ENV, GEN, REP) %>%
recode_factor(ENV, prefix = "E", new_factor = ENV)