metan (version 1.19.0)

utils_data_org: 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

Tiago Olivoto

References

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

Examples

# \donttest{
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)
# }