R/check_names_sp.R
In reyzaguirre/st4gi: Statistical tools for genetic improvement
Defines functions
check.names.sp
Documented in
check.names.sp
#' Check fieldbook traits names for sweetpotato
#'
#' Check that fieldbook factors and traits names correspond with the names defined in
#' \url{https://cropontology.org/term/CO_331:ROOT} and in the
#' Procedures for the evaluation and analysis of sweetpotato trials, ISBN 978-92-9060-522-5.
#' @param dfr The name of the data frame.
#' @param add Additional traits.
#' @details The data frame must use the labels (lower or upper case) listed below.
#' Between parentheses are the CO numbers for variables defined in
#' \url{https://cropontology.org/term/CO_331:ROOT}
#' or COMP numbers defined in \url{https://sweetpotatobase.org/}.
#'
#' ----------------------------- Plot identifiers -----------------------------
#' \itemize{
#' \item \code{plot} : Plot number.
#' \item \code{row} : Row number position of the plot (\code{row_number} is also valid).
#' \item \code{col} : Column number position of the plot (\code{col_number} is also valid).
#' }
#' --------------------------- Classification factors--------------------------
#' \itemize{
#' \item \code{loc} : Locations.
#' \item \code{year} : Years.
#' \item \code{season} : Seasons.
#' \item \code{env} : Environments.
#' \item \code{geno} : Genotypes (\code{accession_name} is also valid).
#' \item \code{cipno} : Institutional CIP number.
#' \item \code{type} : Entry type (\code{clon}, \code{check}, \code{progeny}, \code{parent}).
#' \item \code{rep} : Replications (\code{rep_number} is also valid).
#' \item \code{block} : Blocks (\code{block_number} is also valid).
#' \item \code{treat} : Treatment.
#' \item \code{harvest} : Harvest time.
#' }
#' ------------------------------ Roots and vines -----------------------------
#' \itemize{
#' \item \code{nops} : Number of plants planted per plot (CO_331:0000678).
#' \item \code{nope} : Number of plants established per plot (CO_331:0000192).
#' \item \code{noph} : Number of plants harvested per plot (CO_331:0000679).
#' \item \code{vir} : Virus symptoms estimating 1-9 (CO_331:0000193).
#' \item \code{vir1} : Virus symptoms estimating 1-9, first evaluation, 1 month after planting (COMP:0000023).
#' \item \code{vir2} : Virus symptoms estimating 1-9, second evaluation, 1 month before harvest (COMP:0000024).
#' \item \code{alt} : Alternaria symptoms estimating 1-9 (CO_331:0000198).
#' \item \code{alt1} : Alternaria symptoms estimating 1-9, first evaluation, 1 month after planting (COMP:0000026).
#' \item \code{alt2} : Alternaria symptoms estimating 1-9, second evaluation, 1 month before harvest (COMP:0000022).
#' \item \code{vv} : Vine vigor estimating 1-9 (CO_331:0000197).
#' \item \code{vw} : Weight of vines per plot in kg (CO_331:0000227).
#' \item \code{nopr} : Number of plants with storage roots per plot (CO_331:0000211).
#' \item \code{nocr} : Number of commercial storage roots per plot (CO_331:0000214).
#' \item \code{nonc} : Number of non-commercial storage roots per plot (CO_331:0000217).
#' \item \code{crw} : Weight of commercial storage roots per plot in kg (CO_331:0000220).
#' \item \code{ncrw} : Weight of non-commercial storage roots per plot in kg (CO_331:0000223).
#' \item \code{scol} : Storage root predominant skin color estimating 1-9 (CO_331:0000175).
#' \item \code{fcol} : Storage root predominant flesh color estimating 1-9 (CO_331:0000178).
#' \item \code{fcol2} : Storage root secondary flesh color estimating 0-9 (CO_331:0000179).
#' \item \code{fcol.cc} : Root flesh color from RHS color chart, 1-30.
#' \item \code{rs} : Storage root size estimating 1-9 (CO_331:0000184).
#' \item \code{rf} : Storage root appearance estimating 1-9 (CO_331:0000202).
#' \item \code{rtshp} : Storage root shape estimating 1-9 (CO_331:0000181).
#' \item \code{damr} : Storage root damage estimating 1-9 (CO_331:0000206).
#' \item \code{rspr} : Sprouting ability estimating 1-9 (CO_331:0000277).
#' \item \code{alcdam} : Alcidodes sp. damage estimating 1-9 (CO_331:0000806).
#' \item \code{wed} : Reaction to sweet potato weevil estimating 1-9 (CO_331:0000207).
#' \item \code{stspwv} : Reaction to striped sweet potato weevil estimating 1-9 (CO_331:0000720).
#' \item \code{milldam} : Millipede damage estimating 1-9 (CO_331:0000805).
#' }
#' --------------------------- Dry matter assesment ---------------------------
#' \itemize{
#' \item \code{dmf} : Fresh weight of storage root samples for dry matter assessment measuring g (CO_331:0000243).
#' \item \code{dmd} : Dry weight of storage root samples for dry matter assessment measuring g (CO_331:0000247).
#' \item \code{dm} : Storage root dry matter content computing percent (CO_331:0000297).
#' \item \code{dmvf} : Fresh weight of vines samples for dry matter assessment measuring g (CO_331:0000251).
#' \item \code{dmvd} : Dry weight of vines samples for dry matter assessment measuring g (CO_331:0000255).
#' \item \code{dmv} : Vine dry matter content computing percent (CO_331:0001014).
#' }
#' ---------------------- Raw and cooked roots attributes ---------------------
#' \itemize{
#' \item \code{fraw} : Fiber content in raw storage roots estimating 1-9 (CO_331:0001038).
#' \item \code{suraw} : Content of total sugars in raw storage roots estimating 1-9 (CO_331:0000766).
#' \item \code{straw} : Content of starch in raw storage roots estimating 1-9 (CO_331:0001055).
#' \item \code{coof} : Fiber content in boiled storage roots estimating 1-9 (CO_331:0000259).
#' \item \code{coosu} : Storage root sweetness in cooked samples estimating 1-9 (CO_331:0000261).
#' \item \code{coost} : Storage root texture in boiled samples estimating 1-9 (CO_331:0000265).
#' \item \code{coot} : Boiled storage root flesh taste estimating 1-9 (CO_331:0000269).
#' \item \code{cooap} : Boiled storage root overall appearance estimating 1-9 (CO_331:0000273).
#' }
#' --------------------------- Nutrients evaluations --------------------------
#' \itemize{
#' \item \code{prot} : Content of protein in dry weight basis in raw storage roots measuring percentage (CO_331:0000278).
#' \item \code{fe} : Content of iron in dry weight basis measuring mg per 100 g (CO_331:0001016).
#' \item \code{zn} : Content of zinc in dry weight basis measuring mg per 100 g (CO_331:0001017).
#' \item \code{ca} : Content of calcium in dry weight basis measuring mg per 100 g (CO_331:0001029).
#' \item \code{mg} : Content of magnesium in dry weight basis measuring mg per 100 g (CO_331:0001030).
#' \item \code{bc} : Content of beta-carotene in dry weight basis in raw storage roots measuring mg per 100 g (CO_331:0000289).
#' \item \code{bc.cc} : Content of beta-carotene in fresh weight basis in raw storage roots estimating from RHS color chart in mg per 100 g (CO_331:0001023).
#' \item \code{tc} : Content of total carotenoids in dry weight basis in raw storage roots measuring mg per 100 g (CO_331:0000290).
#' \item \code{star} : Content of starch in dry weight basis in raw storage roots measuring percentage (CO_331:0000291).
#' \item \code{star.b} : Content of starch in dry weight basis in boiled storage roots measuring percentage (CO_331:2000027).
#' \item \code{fruc} : Content of fructose in dry weight basis in raw storage roots measuring g per 100 g (CO_331:0001045).
#' \item \code{fruc.b} : Content of fructose in dry weight basis in boiled storage roots measuring g per 100 g (CO_331:0001046).
#' \item \code{gluc} : Content of glucose in dry weight basis in raw storage roots measuring g per 100 g (CO_331:0001047).
#' \item \code{gluc.b} : Content of glucose in dry weight basis in boiled storage roots measuring g per 100 g (CO_331:0001048).
#' \item \code{sucr} : Content of sucrose in dry weight basis in raw storage roots measuring g per 100 g (CO_331:0001049).
#' \item \code{sucr.b} : Content of sucrose in dry weight basis in boiled storage roots measuring g per 100 g (CO_331:0001050).
#' \item \code{malt} : Content of maltose in dry weight basis in raw storage roots measuring g per 100 g (CO_331:0001051).
#' \item \code{malt.b} : Content of maltose in dry weight basis in boiled storage roots measuring g per 100 g (CO_331:0001052).
#' }
#' ----------------------------- Calculated traits ----------------------------
#' \itemize{
#' \item \code{tnr} : Total number of storage roots per plot (CO_331:0000233).
#' \item \code{trw} : Total storage root weight per plot in kg (CO_331:0000237).
#' \item \code{trw.d} : Total storage root weight in dry weight basis per plot in kg (CO_331:0000995).
#' \item \code{biom} : Biomass yield per plot in kg (CO_331:0000683).
#' \item \code{biom.d} : Biomass yield in dry weight basis per plot in kg (CO_331:0000997).
#' \item \code{cytha} : Commercial storage root yield in tons per ha (CO_331:0000809).
#' \item \code{cytha.aj} : Commercial storage root yield adjusted by number of harvested plants per plot in tons per ha (CO_331:0000998).
#' \item \code{rytha} : Total storage roots yield in tons per ha (CO_331:0000296).
#' \item \code{rytha.aj} : Total storage roots yield adjusted by number of harvested plants per plot in tons per ha (CO_331:0000999).
#' \item \code{dmry} : Storage root dry matter yield in tons per ha (CO_331:0001000).
#' \item \code{dmry.aj} : Storage root dry matter yield adjusted by number of harvested plants per plot in tons per ha (CO_331:0001001).
#' \item \code{vw.d} : Dry weight of vines per plot in kg (CO_331:0000996).
#' \item \code{fytha} : Total foliage yield in tons per ha (CO_331:0000684).
#' \item \code{fytha.aj} : Total foliage yield adjusted by number of harvested plants per plot in tons per ha (CO_331:0001002).
#' \item \code{dmvy} : Vine dry matter yield in tons per ha (CO_331:0001005).
#' \item \code{dmvy.aj} : Vine dry matter yield adjusted by number of harvested plants per plot in tons per ha (CO_331:0001006).
#' \item \code{bytha} : Biomass yield in tons per ha (CO_331:0001003).
#' \item \code{bytha.aj} : Biomass yield adjusted by number of harvested plants per plot in tons per ha (CO_331:0001004).
#' \item \code{dmby} : Biomass dry matter yield in tons per ha (CO_331:0001007).
#' \item \code{dmby.aj} : Biomass dry matter yield adjusted by number of harvested plants per plot in tons per ha (CO_331:0001008).
#' \item \code{acrw} : Average commercial storage root weight in kg (CO_331:0000680).
#' \item \code{ancrw} : Average non-commercial storage root weight in kg (CO_331:0002039).
#' \item \code{atrw} : Average total storage root weight in kg (CO_331:0002040).
#' \item \code{nrpp} : Number of storage roots per plant harvested (CO_331:0000230).
#' \item \code{nrpsp} : Number of storage roots per plant planted (CO_331:0000994).
#' \item \code{ncrpp} : Number of commercial storage roots per plant harvested (CO_331:0006024).
#' \item \code{ncrpsp} : Number of commercial storage roots per plant planted (CO_331:0000993).
#' \item \code{ypp} : Storage roots yield per plant harvested in kg (CO_331:0000681).
#' \item \code{ypsp} : Storage roots yield per plant planted in kg (CO_331:0000989).
#' \item \code{vpp} : Vine weight per plant harvested in kg (CO_331:0000990).
#' \item \code{vpsp} : Vine weight per sowed plant in kg (CO_331:0000991).
#' \item \code{rtyldpct} : Yield as percent of check (CO_331:0000792).
#' \item \code{ci} : Commercial index in percentage (CO_331:0000682).
#' \item \code{hi} : Harvest index in percentage (CO_331:0000302).
#' \item \code{shi} : Survival index in percentage (CO_331:0000301).
#' \item \code{rfr} : Root foliage ratio in percentage (CO_331:0001015).
#' }
#' @return It returns a data frame with all traits names in lower case, and a list of the
#' traits with names not included in the list shown above.
#' @author Raul Eyzaguirre.
#' @examples
#' check.names.sp(pjpz09)
#' @export
check.names.sp <- function(dfr, add = NULL) {
# Valid names for factors
plot.id <- c('observationunit_name', "plot", "row", 'row_number', "col", 'col_number')
factors <- c("loc", "year", "season", "env",
"geno", 'accession_name', "cipno", 'type',
"rep", 'rep_number', "block", 'block_number',
"treat", "harvest")
# Valid names for traits
traits <- c("nops", "nope", "noph", "vir", "vir1", "vir2", "alt", "alt1", "alt2",
"vv", "vw", "nopr", "nocr", "nonc", "crw", "ncrw", "scol", "fcol",
"fcol2", "fcol.cc", "rs", "rf", "rtshp", "damr", "rspr", "alcdam",
"wed", "stspwv", "milldam", "dmf", "dmd", "dm", "dmvf", "dmvd",
"dmv", "fraw", "suraw", "straw", "coof", "coosu", "coost", "coot",
"cooap", "prot", "fe", "zn", "ca", "mg", "bc", "bc.cc", "tc", "star",
"star.b", "fruc", "fruc.b", "gluc", "gluc.b", "sucr", "sucr.b",
"malt", "malt.b", "tnr", "trw", "trw.d", "biom",
"biom.d", "cytha", "cytha.aj", "rytha", "rytha.aj", "dmry",
"dmry.aj", "vw.d", "fytha", "fytha.aj", "dmvy", "dmvy.aj", "bytha",
"bytha.aj", "dmby", "dmby.aj", "acrw", "ancrw", "atrw", "nrpp",
"nrpsp", "ncrpp", "ncrpsp", "ypp", "ypsp", "vpp", "vpsp", "rtyldpct",
"ci", "hi", "shi", "rfr")
# Valid names for factors and traits
colnames.valid <- c(plot.id, factors, traits, tolower(add))
# Factors and traits in field book
colnames.fb <- colnames(dfr)
# check.list.1: mark names not valid
check.list.1 <- !(tolower(colnames.fb) %in% colnames.valid)
# check.list.2: mark valid names but upper case to be converted to lower case
colnames.fb.valid <- colnames.fb[!check.list.1]
check.list.2 <- !(colnames.fb.valid %in% colnames.valid)
# Convert all fieldbook names to lower case
colnames(dfr) <- tolower(colnames(dfr))
# Warnings
if (max(check.list.1) == 1)
warning("Some columns with invalid names: ", list(colnames.fb[check.list.1]), call. = FALSE)
if (max(check.list.2) == 1)
warning("Some labels converted to lower case: ", list(colnames.fb.valid[check.list.2]), call. = FALSE)
# Return
dfr
}
reyzaguirre/st4gi documentation built on April 20, 2024, 3:53 a.m.
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Defines functions check.names.sp
Documented in check.names.sp
#' Check fieldbook traits names for sweetpotato
#'
#' Check that fieldbook factors and traits names correspond with the names defined in
#' \url{https://cropontology.org/term/CO_331:ROOT} and in the
#' Procedures for the evaluation and analysis of sweetpotato trials, ISBN 978-92-9060-522-5.
#' @param dfr The name of the data frame.
#' @param add Additional traits.
#' @details The data frame must use the labels (lower or upper case) listed below.
#' Between parentheses are the CO numbers for variables defined in
#' \url{https://cropontology.org/term/CO_331:ROOT}
#' or COMP numbers defined in \url{https://sweetpotatobase.org/}.
#'
#' ----------------------------- Plot identifiers -----------------------------
#' \itemize{
#' \item \code{plot} : Plot number.
#' \item \code{row} : Row number position of the plot (\code{row_number} is also valid).
#' \item \code{col} : Column number position of the plot (\code{col_number} is also valid).
#' }
#' --------------------------- Classification factors--------------------------
#' \itemize{
#' \item \code{loc} : Locations.
#' \item \code{year} : Years.
#' \item \code{season} : Seasons.
#' \item \code{env} : Environments.
#' \item \code{geno} : Genotypes (\code{accession_name} is also valid).
#' \item \code{cipno} : Institutional CIP number.
#' \item \code{type} : Entry type (\code{clon}, \code{check}, \code{progeny}, \code{parent}).
#' \item \code{rep} : Replications (\code{rep_number} is also valid).
#' \item \code{block} : Blocks (\code{block_number} is also valid).
#' \item \code{treat} : Treatment.
#' \item \code{harvest} : Harvest time.
#' }
#' ------------------------------ Roots and vines -----------------------------
#' \itemize{
#' \item \code{nops} : Number of plants planted per plot (CO_331:0000678).
#' \item \code{nope} : Number of plants established per plot (CO_331:0000192).
#' \item \code{noph} : Number of plants harvested per plot (CO_331:0000679).
#' \item \code{vir} : Virus symptoms estimating 1-9 (CO_331:0000193).
#' \item \code{vir1} : Virus symptoms estimating 1-9, first evaluation, 1 month after planting (COMP:0000023).
#' \item \code{vir2} : Virus symptoms estimating 1-9, second evaluation, 1 month before harvest (COMP:0000024).
#' \item \code{alt} : Alternaria symptoms estimating 1-9 (CO_331:0000198).
#' \item \code{alt1} : Alternaria symptoms estimating 1-9, first evaluation, 1 month after planting (COMP:0000026).
#' \item \code{alt2} : Alternaria symptoms estimating 1-9, second evaluation, 1 month before harvest (COMP:0000022).
#' \item \code{vv} : Vine vigor estimating 1-9 (CO_331:0000197).
#' \item \code{vw} : Weight of vines per plot in kg (CO_331:0000227).
#' \item \code{nopr} : Number of plants with storage roots per plot (CO_331:0000211).
#' \item \code{nocr} : Number of commercial storage roots per plot (CO_331:0000214).
#' \item \code{nonc} : Number of non-commercial storage roots per plot (CO_331:0000217).
#' \item \code{crw} : Weight of commercial storage roots per plot in kg (CO_331:0000220).
#' \item \code{ncrw} : Weight of non-commercial storage roots per plot in kg (CO_331:0000223).
#' \item \code{scol} : Storage root predominant skin color estimating 1-9 (CO_331:0000175).
#' \item \code{fcol} : Storage root predominant flesh color estimating 1-9 (CO_331:0000178).
#' \item \code{fcol2} : Storage root secondary flesh color estimating 0-9 (CO_331:0000179).
#' \item \code{fcol.cc} : Root flesh color from RHS color chart, 1-30.
#' \item \code{rs} : Storage root size estimating 1-9 (CO_331:0000184).
#' \item \code{rf} : Storage root appearance estimating 1-9 (CO_331:0000202).
#' \item \code{rtshp} : Storage root shape estimating 1-9 (CO_331:0000181).
#' \item \code{damr} : Storage root damage estimating 1-9 (CO_331:0000206).
#' \item \code{rspr} : Sprouting ability estimating 1-9 (CO_331:0000277).
#' \item \code{alcdam} : Alcidodes sp. damage estimating 1-9 (CO_331:0000806).
#' \item \code{wed} : Reaction to sweet potato weevil estimating 1-9 (CO_331:0000207).
#' \item \code{stspwv} : Reaction to striped sweet potato weevil estimating 1-9 (CO_331:0000720).
#' \item \code{milldam} : Millipede damage estimating 1-9 (CO_331:0000805).
#' }
#' --------------------------- Dry matter assesment ---------------------------
#' \itemize{
#' \item \code{dmf} : Fresh weight of storage root samples for dry matter assessment measuring g (CO_331:0000243).
#' \item \code{dmd} : Dry weight of storage root samples for dry matter assessment measuring g (CO_331:0000247).
#' \item \code{dm} : Storage root dry matter content computing percent (CO_331:0000297).
#' \item \code{dmvf} : Fresh weight of vines samples for dry matter assessment measuring g (CO_331:0000251).
#' \item \code{dmvd} : Dry weight of vines samples for dry matter assessment measuring g (CO_331:0000255).
#' \item \code{dmv} : Vine dry matter content computing percent (CO_331:0001014).
#' }
#' ---------------------- Raw and cooked roots attributes ---------------------
#' \itemize{
#' \item \code{fraw} : Fiber content in raw storage roots estimating 1-9 (CO_331:0001038).
#' \item \code{suraw} : Content of total sugars in raw storage roots estimating 1-9 (CO_331:0000766).
#' \item \code{straw} : Content of starch in raw storage roots estimating 1-9 (CO_331:0001055).
#' \item \code{coof} : Fiber content in boiled storage roots estimating 1-9 (CO_331:0000259).
#' \item \code{coosu} : Storage root sweetness in cooked samples estimating 1-9 (CO_331:0000261).
#' \item \code{coost} : Storage root texture in boiled samples estimating 1-9 (CO_331:0000265).
#' \item \code{coot} : Boiled storage root flesh taste estimating 1-9 (CO_331:0000269).
#' \item \code{cooap} : Boiled storage root overall appearance estimating 1-9 (CO_331:0000273).
#' }
#' --------------------------- Nutrients evaluations --------------------------
#' \itemize{
#' \item \code{prot} : Content of protein in dry weight basis in raw storage roots measuring percentage (CO_331:0000278).
#' \item \code{fe} : Content of iron in dry weight basis measuring mg per 100 g (CO_331:0001016).
#' \item \code{zn} : Content of zinc in dry weight basis measuring mg per 100 g (CO_331:0001017).
#' \item \code{ca} : Content of calcium in dry weight basis measuring mg per 100 g (CO_331:0001029).
#' \item \code{mg} : Content of magnesium in dry weight basis measuring mg per 100 g (CO_331:0001030).
#' \item \code{bc} : Content of beta-carotene in dry weight basis in raw storage roots measuring mg per 100 g (CO_331:0000289).
#' \item \code{bc.cc} : Content of beta-carotene in fresh weight basis in raw storage roots estimating from RHS color chart in mg per 100 g (CO_331:0001023).
#' \item \code{tc} : Content of total carotenoids in dry weight basis in raw storage roots measuring mg per 100 g (CO_331:0000290).
#' \item \code{star} : Content of starch in dry weight basis in raw storage roots measuring percentage (CO_331:0000291).
#' \item \code{star.b} : Content of starch in dry weight basis in boiled storage roots measuring percentage (CO_331:2000027).
#' \item \code{fruc} : Content of fructose in dry weight basis in raw storage roots measuring g per 100 g (CO_331:0001045).
#' \item \code{fruc.b} : Content of fructose in dry weight basis in boiled storage roots measuring g per 100 g (CO_331:0001046).
#' \item \code{gluc} : Content of glucose in dry weight basis in raw storage roots measuring g per 100 g (CO_331:0001047).
#' \item \code{gluc.b} : Content of glucose in dry weight basis in boiled storage roots measuring g per 100 g (CO_331:0001048).
#' \item \code{sucr} : Content of sucrose in dry weight basis in raw storage roots measuring g per 100 g (CO_331:0001049).
#' \item \code{sucr.b} : Content of sucrose in dry weight basis in boiled storage roots measuring g per 100 g (CO_331:0001050).
#' \item \code{malt} : Content of maltose in dry weight basis in raw storage roots measuring g per 100 g (CO_331:0001051).
#' \item \code{malt.b} : Content of maltose in dry weight basis in boiled storage roots measuring g per 100 g (CO_331:0001052).
#' }
#' ----------------------------- Calculated traits ----------------------------
#' \itemize{
#' \item \code{tnr} : Total number of storage roots per plot (CO_331:0000233).
#' \item \code{trw} : Total storage root weight per plot in kg (CO_331:0000237).
#' \item \code{trw.d} : Total storage root weight in dry weight basis per plot in kg (CO_331:0000995).
#' \item \code{biom} : Biomass yield per plot in kg (CO_331:0000683).
#' \item \code{biom.d} : Biomass yield in dry weight basis per plot in kg (CO_331:0000997).
#' \item \code{cytha} : Commercial storage root yield in tons per ha (CO_331:0000809).
#' \item \code{cytha.aj} : Commercial storage root yield adjusted by number of harvested plants per plot in tons per ha (CO_331:0000998).
#' \item \code{rytha} : Total storage roots yield in tons per ha (CO_331:0000296).
#' \item \code{rytha.aj} : Total storage roots yield adjusted by number of harvested plants per plot in tons per ha (CO_331:0000999).
#' \item \code{dmry} : Storage root dry matter yield in tons per ha (CO_331:0001000).
#' \item \code{dmry.aj} : Storage root dry matter yield adjusted by number of harvested plants per plot in tons per ha (CO_331:0001001).
#' \item \code{vw.d} : Dry weight of vines per plot in kg (CO_331:0000996).
#' \item \code{fytha} : Total foliage yield in tons per ha (CO_331:0000684).
#' \item \code{fytha.aj} : Total foliage yield adjusted by number of harvested plants per plot in tons per ha (CO_331:0001002).
#' \item \code{dmvy} : Vine dry matter yield in tons per ha (CO_331:0001005).
#' \item \code{dmvy.aj} : Vine dry matter yield adjusted by number of harvested plants per plot in tons per ha (CO_331:0001006).
#' \item \code{bytha} : Biomass yield in tons per ha (CO_331:0001003).
#' \item \code{bytha.aj} : Biomass yield adjusted by number of harvested plants per plot in tons per ha (CO_331:0001004).
#' \item \code{dmby} : Biomass dry matter yield in tons per ha (CO_331:0001007).
#' \item \code{dmby.aj} : Biomass dry matter yield adjusted by number of harvested plants per plot in tons per ha (CO_331:0001008).
#' \item \code{acrw} : Average commercial storage root weight in kg (CO_331:0000680).
#' \item \code{ancrw} : Average non-commercial storage root weight in kg (CO_331:0002039).
#' \item \code{atrw} : Average total storage root weight in kg (CO_331:0002040).
#' \item \code{nrpp} : Number of storage roots per plant harvested (CO_331:0000230).
#' \item \code{nrpsp} : Number of storage roots per plant planted (CO_331:0000994).
#' \item \code{ncrpp} : Number of commercial storage roots per plant harvested (CO_331:0006024).
#' \item \code{ncrpsp} : Number of commercial storage roots per plant planted (CO_331:0000993).
#' \item \code{ypp} : Storage roots yield per plant harvested in kg (CO_331:0000681).
#' \item \code{ypsp} : Storage roots yield per plant planted in kg (CO_331:0000989).
#' \item \code{vpp} : Vine weight per plant harvested in kg (CO_331:0000990).
#' \item \code{vpsp} : Vine weight per sowed plant in kg (CO_331:0000991).
#' \item \code{rtyldpct} : Yield as percent of check (CO_331:0000792).
#' \item \code{ci} : Commercial index in percentage (CO_331:0000682).
#' \item \code{hi} : Harvest index in percentage (CO_331:0000302).
#' \item \code{shi} : Survival index in percentage (CO_331:0000301).
#' \item \code{rfr} : Root foliage ratio in percentage (CO_331:0001015).
#' }
#' @return It returns a data frame with all traits names in lower case, and a list of the
#' traits with names not included in the list shown above.
#' @author Raul Eyzaguirre.
#' @examples
#' check.names.sp(pjpz09)
#' @export
check.names.sp <- function(dfr, add = NULL) {
# Valid names for factors
plot.id <- c('observationunit_name', "plot", "row", 'row_number', "col", 'col_number')
factors <- c("loc", "year", "season", "env",
"geno", 'accession_name', "cipno", 'type',
"rep", 'rep_number', "block", 'block_number',
"treat", "harvest")
# Valid names for traits
traits <- c("nops", "nope", "noph", "vir", "vir1", "vir2", "alt", "alt1", "alt2",
"vv", "vw", "nopr", "nocr", "nonc", "crw", "ncrw", "scol", "fcol",
"fcol2", "fcol.cc", "rs", "rf", "rtshp", "damr", "rspr", "alcdam",
"wed", "stspwv", "milldam", "dmf", "dmd", "dm", "dmvf", "dmvd",
"dmv", "fraw", "suraw", "straw", "coof", "coosu", "coost", "coot",
"cooap", "prot", "fe", "zn", "ca", "mg", "bc", "bc.cc", "tc", "star",
"star.b", "fruc", "fruc.b", "gluc", "gluc.b", "sucr", "sucr.b",
"malt", "malt.b", "tnr", "trw", "trw.d", "biom",
"biom.d", "cytha", "cytha.aj", "rytha", "rytha.aj", "dmry",
"dmry.aj", "vw.d", "fytha", "fytha.aj", "dmvy", "dmvy.aj", "bytha",
"bytha.aj", "dmby", "dmby.aj", "acrw", "ancrw", "atrw", "nrpp",
"nrpsp", "ncrpp", "ncrpsp", "ypp", "ypsp", "vpp", "vpsp", "rtyldpct",
"ci", "hi", "shi", "rfr")
# Valid names for factors and traits
colnames.valid <- c(plot.id, factors, traits, tolower(add))
# Factors and traits in field book
colnames.fb <- colnames(dfr)
# check.list.1: mark names not valid
check.list.1 <- !(tolower(colnames.fb) %in% colnames.valid)
# check.list.2: mark valid names but upper case to be converted to lower case
colnames.fb.valid <- colnames.fb[!check.list.1]
check.list.2 <- !(colnames.fb.valid %in% colnames.valid)
# Convert all fieldbook names to lower case
colnames(dfr) <- tolower(colnames(dfr))
# Warnings
if (max(check.list.1) == 1)
warning("Some columns with invalid names: ", list(colnames.fb[check.list.1]), call. = FALSE)
if (max(check.list.2) == 1)
warning("Some labels converted to lower case: ", list(colnames.fb.valid[check.list.2]), call. = FALSE)
# Return
dfr
}
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