R/check_names_pt.R
In reyzaguirre/st4gi: Statistical tools for genetic improvement
Defines functions
check.names.pt
Documented in
check.names.pt
#' Check fieldbook traits names for potato
#'
#' Check that fieldbook traits names correspond with the names defined in
#' \url{https://cropontology.org/term/CO_330:ROOT},
#' and that all traits are stored as numeric.
#' @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_330:ROOT}.
#'
#' ----------------------------- Plot identifiers -----------------------------
#' \itemize{
#' \item \code{plot} : Plot number (\code{plot_number} is also valid).
#' \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} and \code{instn} are also valid).
#' \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} : Treatments.
#' }
#' ----------------------------------- Plants ---------------------------------
#' \itemize{
#' \item \code{ntp} : Number of tubers planted per plot (CO_330:0000265).
#' \item \code{npe} : Number of plants emerged per plot (CO_330:0000268).
#' \item \code{npe_15dap} : Number of plants emerged per plot, 15 days after planting (COMP:0000002).
#' \item \code{npe_30dap} : Number of plants emerged per plot, 30 days after planting (COMP:0000003).
#' \item \code{nph} : Number of plants harvested per plot (CO_330:0000287).
#' \item \code{ppe} : Proportion of plants emerged in percentage (CO_330:0000283).
#' \item \code{pph} : Proportion of plants harvested in percentage (CO_330:0000290).
#' }
#' ----------------------------- Number of tubers -----------------------------
#' \itemize{
#' \item \code{tntp} : Total number of tubers per plot (CO_330:0000304).
#' \item \code{tntpl} : Total number of tubers per plant (CO_330:0000305).
#' \item \code{nmtp} : Number of marketable tubers per plot (CO_330:0000293).
#' \item \code{nmtpl} : Number of marketable tubers per plant (CO_330:0000297).
#' \item \code{nnomtp} : Number of non-marketable tubers per plot (CO_330:0000300).
#' \item \code{nmtci} : Number of marketable tubers category I per plot.
#' \item \code{nmtcii} : Number of marketable tubers category II per plot.
#' }
#' ----------------------------- Weight of tubers -----------------------------
#' \itemize{
#' \item \code{ttwp} : Total tuber weight per plot in kg (CO_330:0000317).
#' \item \code{ttwpl} : Total tuber weight per plant in kg (CO_330:0000321).
#' \item \code{mtwp} : Marketable tuber weight per plot in kg (CO_330:0000308).
#' \item \code{mtwpl} : Marketable tuber weight per plant in kg (CO_330:0000311).
#' \item \code{nomtwp} : Non-marketable tuber weight per plot in kg (CO_330:0000314).
#' \item \code{mtwci} : Marketable tuber weight category I per plot in kg.
#' \item \code{mtwcii} : Marketable tuber weight category II per plot in kg.
#' \item \code{ttya} : Total tuber yield adjusted by number of plants harvested per plot in tons per ha (CO_330:0000323).
#' \item \code{ttyna} : Total tuber yield not adjusted in tons per ha (CO_330:0000324).
#' \item \code{mtya} : Marketable tuber yield adjusted by number of plants harvested per plot in tons per ha (CO_330:0000327).
#' \item \code{mtyna} : Marketable tuber yield not adjusted in tons per ha (CO_330:0000330).
#' \item \code{atw} : Average tuber weight in g (CO_330:0000333).
#' \item \code{atmw} : Average marketable tuber weight in g (CO_330:0000336).
#' }
#' ------------------------ Plant and tuber appearance ------------------------
#' \itemize{
#' \item \code{flowering} : Flowering degree estimating 0-7 (CO_330:0000224).
#' \item \code{flowering_45dap} : Flowering degree estimating 0-7, 45 days after planting (COMP:0000010).
#' \item \code{flowering_60dap} : Flowering degree estimating 0-7, 60 days after planting (COMP:0000011).
#' \item \code{plant_unif} : Plant uniformity estimating 1-9 (CO_330:0000272).
#' \item \code{plant_unif_45dap} : Plant uniformity estimating 1-9, 45 days after planting (COMP:0000008).
#' \item \code{plant_unif_60dap} : Plant uniformity estimating 1-9, 60 days after planting (COMP:0000009).
#' \item \code{plant_vigor} : Plant vigor estimating 1-9 (CO_330:0000276).
#' \item \code{plant_vigor_30dap} : Plant vigor estimating 1-9, 30 days after planting (COMP:0000004).
#' \item \code{plant_vigor_45dap} : Plant vigor estimating 1-9, 45 days after planting (COMP:0000005).
#' \item \code{plant_vigor_60dap} : Plant vigor estimating 1-9, 60 days after planting (COMP:0000006).
#' \item \code{se} : Senescence estimating 1-9 (CO_330:0000280).
#' \item \code{tuber_apper} : Tuber appearance estimating 1-9 (CO_330:0000348).
#' \item \code{tub_unif} : Tuber uniformity estimating 1-9 (CO_330:0000352).
#' \item \code{tub_size} : Tuber size estimating 1-9 (CO_330:0000356).
#' \item \code{tbskn1} : Predominant tuber skin color (CO_330:0000249).
#' \item \code{tbfsh1} : Predominant tuber flesh color (CO_330:0000253).
#' \item \code{tbshp1} : Tuber shape (CO_330:0000256).
#' \item \code{tbshp3} : Tuber depth eyes (CO_330:0000258).
#' \item \code{dorpd} : Tuber dormancy period (CO_330:0000397).
#' }
#' ------------------------------- Organoleptic -------------------------------
#' \itemize{
#' \item \code{chip_color} : Chips color 1-5 (CO_330:0000384).
#' \item \code{ffr} : French fries color 1-5 (CO_330:0000388).
#' \item \code{aocp} : Chips oil absorption rate (CO_330:0000395).
#' \item \code{flavour} : Tuber flavor after cooking (CO_330:0000379).
#' \item \code{textac} : Tuber texture after cooking (CO_330:0000380).
#' \item \code{cookqu} : Tuber cooking quality (CO_330:0000381).
#' \item \code{cootime} : Tuber cooking time (CO_330:0000389).
#' }
#' ---------------------------------- Biomass ---------------------------------
#' \itemize{
#' \item \code{tafw} : Total aerial fresh weight per plot in g.
#' \item \code{tbfwp} : Total biomass fresh weight per plot in g. (CO_330:0000829)
#' \item \code{tbfwpl} : Total biomass fresh weight per plant in g (CO_330:0000799).
#' \item \code{hi_fw} : Harvest index fresh weight in percentage (CO_330:0000738).
#' \item \code{tadw} : Total aerial dry weight per plot in g.
#' \item \code{tbdwp} : Total biomass dry weight per plot in g. (CO_330:0000828)
#' \item \code{tbdwpl} : Total biomass dry weight per plant in g (CO_330:0000798).
#' \item \code{hi_dw} : Harvest index dry weight in percentage (CO_330:0000735).
#' }
#' -------------------------------- Dry weight --------------------------------
#' \itemize{
#' \item \code{fwts} : Fresh weight of tuber for dry matter determination.
#' \item \code{dwts} : Dry weight of tuber for dry matter determination.
#' \item \code{fwts1} : Fresh weight of tuber sample 1.
#' \item \code{fwts2} : Fresh weight of tuber sample 2.
#' \item \code{dwts1} : Dry weight of tuber sample 1.
#' \item \code{dwts2} : Dry weight of tuber sample 2.
#' \item \code{dm1} : Tuber dry matter content sample 1.
#' \item \code{dm2} : Tuber dry matter content sample 2.
#' \item \code{dm} : Tuber dry matter content in percentage (CO_330:0000390).
#' }
#' --------------------------- Nutrients evaluations --------------------------
#' \itemize{
#' \item \code{fedw} : Tuber iron concentration on dry weight basis in mg per 100 g (CO_330:0000402).
#' \item \code{fefw} : Tuber iron concentration on fresh weight basis in mg per 100 g (CO_330:0000407).
#' \item \code{fedw_xrf} : Tuber iron concentration on dry weight basis in mg per kg by XRF (CO_330:0000404).
#' \item \code{zndw} : Tuber zinc concentration on dry weight basis in mg per 100 g (CO_330:0000408).
#' \item \code{znfw} : Tuber zinc concentration on fresh weight basis in mg per 100 g (CO_330:0000412).
#' \item \code{zndw_xrf} : Tuber zinc concentration on dry weight basis in mg per kg by XRF (CO_330:0000409).
#' \item \code{antho_dw} : Tuber anthocyanin concentration on dry weight basis in mg per 100 g (CO_330:0000414).
#' \item \code{antho_fw} : Tuber anthocyanin concentration on fresh weight basis in mg per 100 g (CO_330:0000417).
#' \item \code{aah_dw} : Tuber hydrophilic antioxidant activity on dry weight basis in ugTroloxequiv/g (CO_330:0000418).
#' \item \code{aah_fw} : Tuber hydrophilic antioxidant activity on fresh weight basis in ugTroloxequiv/g (CO_330:0000421).
#' \item \code{aal_dw} : Tuber lipophilic antioxidant activity on dry weight basis in ugTroloxequiv/g (CO_330:0000422).
#' \item \code{aal_fw} : Tuber lipophilic antioxidant activity on fresh weight basis in ugTroloxequiv/g (CO_330:0000425).
#' \item \code{asc_dw} : Tuber ascorbic acid concentration on dry weight basis in mg per 100 g (CO_330:0000426).
#' \item \code{asc_fw} : Tuber ascorbic acid concentration on fresh weight basis in mg per 100 g (CO_330:0000429).
#' \item \code{pro} : Tuber protein content in percentage (CO_330:0000432).
#' \item \code{star} : Tuber starch content in percentage (CO_330:0000435).
#' \item \code{fruc} : Tuber fructose content in percentage (CO_330:0000438).
#' \item \code{gluc} : Tuber glucose content in percentage (CO_330:0000441).
#' \item \code{sucr} : Tuber sucrose content in percentage (CO_330:0000444).
#' \item \code{malt} : Tuber maltose content in percentage (CO_330:0000447).
#' \item \code{fiber} : Tuber fiber content in percentage (CO_330:0000450).
#' \item \code{tgly_fw} : Tuber glycoalkaloid concentration on fresh weight basis in mg per 100 g (CO_330:0000661).
#' }
#' ---------------------------------- Deseases --------------------------------
#' \itemize{
#' \item \code{lb} : Late Blight severity estimating percentage (CO_330:0000359).
#' \item \code{lbi} : Late Blight severity estimating percentage evaluation i (i = 1, 2,... 8).
#' \item \code{rlb} : Late Blight resistance estimating 1-6 (CO_330:0000372).
#' \item \code{rlb_30dap} : Late Blight resistance estimating 1-6, 30 days after planting (COMP:0000012).
#' \item \code{rlb_45dap} : Late Blight resistance estimating 1-6, 45 days after planting (COMP:0000013).
#' \item \code{rlb_60dap} : Late Blight resistance estimating 1-6, 60 days after planting (COMP:0000014).
#' \item \code{rlb_75dap} : Late Blight resistance estimating 1-6, 75 days after planting (COMP:0000015).
#' \item \code{audpc} : Late blight AUDPC computed (CO_330:0000363).
#' \item \code{raudpc} : Late blight relative AUDPC computed (CO_330:0000367).
#' \item \code{saudpc} : Late blight susceptibility computed (CO_330:0000371).
#' \item \code{pvx} : Potato virus X resistance (CO_330:0000373).
#' \item \code{pvy} : Potato virus Y resistance (CO_330:0000374).
#' \item \code{prlv} : Potatoleaf roll virus resistance (CO_330:0000375).
#' \item \code{bw} : Bacterial wilt resistance (CO_330:0000376).
#' \item \code{rkn} : Root knot nematode resistance (CO_330:0000377).
#' \item \code{rlmf} : Resistance to leaf miner fly 1-5 (CO_330:0000378).
#' \item \code{rlmf_45dap} : Resistance to leaf miner fly 1-5 (COMP_0000016).
#' \item \code{rlmf_60dap} : Resistance to leaf miner fly 1-5 (COMP_0000017).
#' \item \code{rlmf_75dap} : Resistance to leaf miner fly 1-5 (COMP_0000018).
#' }
#' ------------------------------- Other traits -------------------------------
#' \itemize{
#' \item \code{rd} : Root density estimating 1-3 (CO_330:0000834).
#' \item \code{rl} : Root length in cm (CO_330:0000764).
#' \item \code{sg} : Tuber specific gravity (CO_330:0000394).
#' \item \code{dsi} : Drought susceptibility index computed (CO_330:0000776).
#' \item \code{dti} : Drought tolerance index computed (CO_330:0000779).
#' \item \code{leaflet_tw} : Leaflet turgid weight in mg (CO_330:0000818).
#' \item \code{leaflet_twi} : Leaflet turgid weight evaluation i (i = 1,..., 5).
#' \item \code{pw_ev} : Degree of canopy wilting estimating 1-9 (CO_330:0000773).
#' \item \code{pw_evi} : Degree of canopy wilting estimating 1-9 evaluation i (i = 1,..., 5).
#' \item \code{snpp} : Stem number per plant (CO_330:0000851).
#' \item \code{snppi} : Stem number per plant evaluation i (i = 1,..., 5).
#' \item \code{nipp} : Number of inflorescences per plant estimating 0-7 (CO_330:0000226).
#' \item \code{nfwp} : Number of flowers per main inflorescence estimating 0-5 (CO_330:0000227).
#' \item \code{Num_Stolon} : Number of stolons estimating 1-9 (CO_330:0000340).
#' \item \code{Leng_Stolon} : Length of stolons estimating 1-9 (CO_330:0000344).
#' \item \code{plahe_ev} : Plant height in cm (CO_330:0000758).
#' \item \code{plahe_evi} : Plant height evaluation i (i = 1,..., 5).
#' \item \code{sd_ev} : Stem diameter in mm (CO_330:0000847).
#' \item \code{sd_evi} : Stem diameter evaluation i (i = 1,..., 5)
#' \item \code{chlspad_ev} : Chlorophyll content index using SPAD-meter in SPAD units (CO_330:0000805).
#' \item \code{chlspad_evi} : Chlorophyll content index evaluation i (i = 1,..., 5).
#' \item \code{cr_ev} : Canopy reflectance using Green-Seeker-meter in NDVI units (CO_330:0000860).
#' \item \code{cr_evi} : Canopy reflectance evaluation i (i = 1,..., 5).
#' \item \code{lfa_ev} : Leaflet area using Compu Eye, Leaf Symptom Area software in cm^2 (CO_330:0000766).
#' \item \code{lfa_evi} : Leaflet area using Compu Eye, Leaf Symptom Area software in cm^2 evaluation i (i = 1,..., 5).
#' \item \code{rwc_ev} : Relative water content in percentage (CO_330:0000741).
#' \item \code{rwc_evi} : Relative water content evaluation i (i = 1,..., 5).
#' \item \code{sla_ev} : Leaflet area using EasyLeafArea software in cm^2 per g (CO_330:0000812).
#' \item \code{sla_evi} : Leaflet area using EasyLeafArea software in cm^2 per g evaluation i (i = 1,..., 5).
#' }
#' @return It returns:
#' \itemize{
#' \item The fieldbook data frame with all column names in lowercase and
#' with some possible modifications in the names. Traits that are stored
#' with a non-numeric class are transformed to numeric.
#' \item A list of warnings for all the column names that have been changed.
#' \item A list of warnings for all the column names not recognized.
#' \item A list of warnings for all the column traits that have been changed to numeric.
#' }
#' @author Raul Eyzaguirre, Johan Ninanya.
#' @examples
#' check.names.pt(potatoyield)
#' @export
check.names.pt <- function(dfr, add = NULL) {
# Valid names for factors
plot.id <- c("plot", "row", "col")
factors <- c("loc", "year", "season", "env", "geno", 'type', "rep", "block",
"treat", 'is_a_control')
# Repeated measures traits (i = 1...5)
rm.traits <- c("leaflet_tw", "pw_ev", "snpp", "plahe_ev", "sd_ev", "chlspad_ev",
"cr_ev", "lfa_ev", "rwc_ev", "sla_ev")
rm.traitsi <- c(rm.traits, sapply(rm.traits, function(x) paste0(x, 1:5)))
# Late blight evaluations
lb.ev <- paste0("lb", 1:8)
# Valid names for traits
traits <- c(ptont$Label, "nmtci", "nmtcii", "mtwci", "mtwcii", "tbskn1", "tbfsh1",
"tbshp1", "tbshp3", "dorpd", "ffr", "aocp", "flavour", "textac",
"cookqu", "cootime", "tafw", "tadw", "fwts", "dwts", "fwts1", "fwts2",
"dwts1", "dwts2", "dm1", "dm2", "avdm", "tgly_fw", "pvx", "pvy",
"prlv", "bw", "rkn", lb.ev, rm.traits, rm.traitsi, tolower(add))
# Valid names for factors and traits
colnames.valid <- c(plot.id, factors, traits)
# Factors and traits in field book (original names)
colnames.fb <- colnames(dfr)
# Convert all fieldbook names to lower case (except CO numbers)
cond <- substring(colnames(dfr), 1, 7) != 'CO_330:' & substring(colnames(dfr), 1, 5) != 'COMP:'
colnames(dfr)[cond] <- tolower(colnames(dfr))[cond]
if (sum(colnames.fb != colnames(dfr)) > 0)
warning("Some labels converted to lower case", call. = FALSE)
# Solve synonyms for factors
# All options for genotypes
old.geno <- c("accession_name", "cipno", "cip.number", 'genotype', "instn")
new.geno <- rep('geno', length(old.geno))
change.names.f <- NULL
old.names.f <- c('plot_number', 'location', "replication", 'rep_number', "block_number", "row_number", "col_number", old.geno)
new.names.f <- c('plot', 'loc', "rep", 'rep', "block", "row", "col", new.geno)
for (i in 1:length(old.names.f)) {
if (exists(old.names.f[i], dfr) & !exists(new.names.f[i], dfr)) {
change.names.f <- c(change.names.f, old.names.f[i])
colnames(dfr)[colnames(dfr) == old.names.f[i]] <- new.names.f[i]
}
}
if (!is.null(change.names.f)) {
change.names.list <- old.names.f %in% change.names.f
warning("Factors' names ", list(old.names.f[change.names.list]), " changed to ", list(new.names.f[change.names.list]), call. = FALSE)
}
# Solve synonyms for traits
change.names.t <- NULL
old.names.t <- c("mwt", "mwmt", "stfw", "stdw", "pdm", 'avdm', "protein", 'chipping')
new.names.t <- c("atw", "atmw", "sfw", "sdw", "dm", 'dm', "pro", 'chip_color')
for (i in 1:length(old.names.t)) {
if (exists(old.names.t[i], dfr) & !exists(new.names.t[i], dfr)) {
change.names.t <- c(change.names.t, old.names.t[i])
colnames(dfr)[colnames(dfr) == old.names.t[i]] <- new.names.t[i]
}
}
if (!is.null(change.names.t)) {
change.names.list <- old.names.t %in% change.names.t
warning("Traits' names ", list(old.names.t[change.names.list]), " changed to ", list(new.names.t[change.names.list]), call. = FALSE)
}
# Names not valid
names.not.valid <- !(colnames(dfr) %in% colnames.valid)
if (max(names.not.valid) == 1)
warning("Some columns with invalid names: ", list(colnames(dfr)[names.not.valid]), call. = FALSE)
# Check traits are numeric
nonumeric.list <- NULL
column.class <- unlist(lapply(dfr, class))
for(i in colnames(dfr)) {
if(i %in% traits & column.class[i] != "numeric") {
dfr[, i] <- suppressWarnings(as.numeric(as.character(dfr[, i])))
nonumeric.list <- c(nonumeric.list, i)
}
}
if (!is.null(nonumeric.list))
warning("Some traits converted to numeric: ", list(nonumeric.list), call. = FALSE)
# Return
dfr
}
reyzaguirre/st4gi documentation built on Sept. 17, 2024, 8:44 p.m.
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Defines functions check.names.pt
Documented in check.names.pt
#' Check fieldbook traits names for potato
#'
#' Check that fieldbook traits names correspond with the names defined in
#' \url{https://cropontology.org/term/CO_330:ROOT},
#' and that all traits are stored as numeric.
#' @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_330:ROOT}.
#'
#' ----------------------------- Plot identifiers -----------------------------
#' \itemize{
#' \item \code{plot} : Plot number (\code{plot_number} is also valid).
#' \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} and \code{instn} are also valid).
#' \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} : Treatments.
#' }
#' ----------------------------------- Plants ---------------------------------
#' \itemize{
#' \item \code{ntp} : Number of tubers planted per plot (CO_330:0000265).
#' \item \code{npe} : Number of plants emerged per plot (CO_330:0000268).
#' \item \code{npe_15dap} : Number of plants emerged per plot, 15 days after planting (COMP:0000002).
#' \item \code{npe_30dap} : Number of plants emerged per plot, 30 days after planting (COMP:0000003).
#' \item \code{nph} : Number of plants harvested per plot (CO_330:0000287).
#' \item \code{ppe} : Proportion of plants emerged in percentage (CO_330:0000283).
#' \item \code{pph} : Proportion of plants harvested in percentage (CO_330:0000290).
#' }
#' ----------------------------- Number of tubers -----------------------------
#' \itemize{
#' \item \code{tntp} : Total number of tubers per plot (CO_330:0000304).
#' \item \code{tntpl} : Total number of tubers per plant (CO_330:0000305).
#' \item \code{nmtp} : Number of marketable tubers per plot (CO_330:0000293).
#' \item \code{nmtpl} : Number of marketable tubers per plant (CO_330:0000297).
#' \item \code{nnomtp} : Number of non-marketable tubers per plot (CO_330:0000300).
#' \item \code{nmtci} : Number of marketable tubers category I per plot.
#' \item \code{nmtcii} : Number of marketable tubers category II per plot.
#' }
#' ----------------------------- Weight of tubers -----------------------------
#' \itemize{
#' \item \code{ttwp} : Total tuber weight per plot in kg (CO_330:0000317).
#' \item \code{ttwpl} : Total tuber weight per plant in kg (CO_330:0000321).
#' \item \code{mtwp} : Marketable tuber weight per plot in kg (CO_330:0000308).
#' \item \code{mtwpl} : Marketable tuber weight per plant in kg (CO_330:0000311).
#' \item \code{nomtwp} : Non-marketable tuber weight per plot in kg (CO_330:0000314).
#' \item \code{mtwci} : Marketable tuber weight category I per plot in kg.
#' \item \code{mtwcii} : Marketable tuber weight category II per plot in kg.
#' \item \code{ttya} : Total tuber yield adjusted by number of plants harvested per plot in tons per ha (CO_330:0000323).
#' \item \code{ttyna} : Total tuber yield not adjusted in tons per ha (CO_330:0000324).
#' \item \code{mtya} : Marketable tuber yield adjusted by number of plants harvested per plot in tons per ha (CO_330:0000327).
#' \item \code{mtyna} : Marketable tuber yield not adjusted in tons per ha (CO_330:0000330).
#' \item \code{atw} : Average tuber weight in g (CO_330:0000333).
#' \item \code{atmw} : Average marketable tuber weight in g (CO_330:0000336).
#' }
#' ------------------------ Plant and tuber appearance ------------------------
#' \itemize{
#' \item \code{flowering} : Flowering degree estimating 0-7 (CO_330:0000224).
#' \item \code{flowering_45dap} : Flowering degree estimating 0-7, 45 days after planting (COMP:0000010).
#' \item \code{flowering_60dap} : Flowering degree estimating 0-7, 60 days after planting (COMP:0000011).
#' \item \code{plant_unif} : Plant uniformity estimating 1-9 (CO_330:0000272).
#' \item \code{plant_unif_45dap} : Plant uniformity estimating 1-9, 45 days after planting (COMP:0000008).
#' \item \code{plant_unif_60dap} : Plant uniformity estimating 1-9, 60 days after planting (COMP:0000009).
#' \item \code{plant_vigor} : Plant vigor estimating 1-9 (CO_330:0000276).
#' \item \code{plant_vigor_30dap} : Plant vigor estimating 1-9, 30 days after planting (COMP:0000004).
#' \item \code{plant_vigor_45dap} : Plant vigor estimating 1-9, 45 days after planting (COMP:0000005).
#' \item \code{plant_vigor_60dap} : Plant vigor estimating 1-9, 60 days after planting (COMP:0000006).
#' \item \code{se} : Senescence estimating 1-9 (CO_330:0000280).
#' \item \code{tuber_apper} : Tuber appearance estimating 1-9 (CO_330:0000348).
#' \item \code{tub_unif} : Tuber uniformity estimating 1-9 (CO_330:0000352).
#' \item \code{tub_size} : Tuber size estimating 1-9 (CO_330:0000356).
#' \item \code{tbskn1} : Predominant tuber skin color (CO_330:0000249).
#' \item \code{tbfsh1} : Predominant tuber flesh color (CO_330:0000253).
#' \item \code{tbshp1} : Tuber shape (CO_330:0000256).
#' \item \code{tbshp3} : Tuber depth eyes (CO_330:0000258).
#' \item \code{dorpd} : Tuber dormancy period (CO_330:0000397).
#' }
#' ------------------------------- Organoleptic -------------------------------
#' \itemize{
#' \item \code{chip_color} : Chips color 1-5 (CO_330:0000384).
#' \item \code{ffr} : French fries color 1-5 (CO_330:0000388).
#' \item \code{aocp} : Chips oil absorption rate (CO_330:0000395).
#' \item \code{flavour} : Tuber flavor after cooking (CO_330:0000379).
#' \item \code{textac} : Tuber texture after cooking (CO_330:0000380).
#' \item \code{cookqu} : Tuber cooking quality (CO_330:0000381).
#' \item \code{cootime} : Tuber cooking time (CO_330:0000389).
#' }
#' ---------------------------------- Biomass ---------------------------------
#' \itemize{
#' \item \code{tafw} : Total aerial fresh weight per plot in g.
#' \item \code{tbfwp} : Total biomass fresh weight per plot in g. (CO_330:0000829)
#' \item \code{tbfwpl} : Total biomass fresh weight per plant in g (CO_330:0000799).
#' \item \code{hi_fw} : Harvest index fresh weight in percentage (CO_330:0000738).
#' \item \code{tadw} : Total aerial dry weight per plot in g.
#' \item \code{tbdwp} : Total biomass dry weight per plot in g. (CO_330:0000828)
#' \item \code{tbdwpl} : Total biomass dry weight per plant in g (CO_330:0000798).
#' \item \code{hi_dw} : Harvest index dry weight in percentage (CO_330:0000735).
#' }
#' -------------------------------- Dry weight --------------------------------
#' \itemize{
#' \item \code{fwts} : Fresh weight of tuber for dry matter determination.
#' \item \code{dwts} : Dry weight of tuber for dry matter determination.
#' \item \code{fwts1} : Fresh weight of tuber sample 1.
#' \item \code{fwts2} : Fresh weight of tuber sample 2.
#' \item \code{dwts1} : Dry weight of tuber sample 1.
#' \item \code{dwts2} : Dry weight of tuber sample 2.
#' \item \code{dm1} : Tuber dry matter content sample 1.
#' \item \code{dm2} : Tuber dry matter content sample 2.
#' \item \code{dm} : Tuber dry matter content in percentage (CO_330:0000390).
#' }
#' --------------------------- Nutrients evaluations --------------------------
#' \itemize{
#' \item \code{fedw} : Tuber iron concentration on dry weight basis in mg per 100 g (CO_330:0000402).
#' \item \code{fefw} : Tuber iron concentration on fresh weight basis in mg per 100 g (CO_330:0000407).
#' \item \code{fedw_xrf} : Tuber iron concentration on dry weight basis in mg per kg by XRF (CO_330:0000404).
#' \item \code{zndw} : Tuber zinc concentration on dry weight basis in mg per 100 g (CO_330:0000408).
#' \item \code{znfw} : Tuber zinc concentration on fresh weight basis in mg per 100 g (CO_330:0000412).
#' \item \code{zndw_xrf} : Tuber zinc concentration on dry weight basis in mg per kg by XRF (CO_330:0000409).
#' \item \code{antho_dw} : Tuber anthocyanin concentration on dry weight basis in mg per 100 g (CO_330:0000414).
#' \item \code{antho_fw} : Tuber anthocyanin concentration on fresh weight basis in mg per 100 g (CO_330:0000417).
#' \item \code{aah_dw} : Tuber hydrophilic antioxidant activity on dry weight basis in ugTroloxequiv/g (CO_330:0000418).
#' \item \code{aah_fw} : Tuber hydrophilic antioxidant activity on fresh weight basis in ugTroloxequiv/g (CO_330:0000421).
#' \item \code{aal_dw} : Tuber lipophilic antioxidant activity on dry weight basis in ugTroloxequiv/g (CO_330:0000422).
#' \item \code{aal_fw} : Tuber lipophilic antioxidant activity on fresh weight basis in ugTroloxequiv/g (CO_330:0000425).
#' \item \code{asc_dw} : Tuber ascorbic acid concentration on dry weight basis in mg per 100 g (CO_330:0000426).
#' \item \code{asc_fw} : Tuber ascorbic acid concentration on fresh weight basis in mg per 100 g (CO_330:0000429).
#' \item \code{pro} : Tuber protein content in percentage (CO_330:0000432).
#' \item \code{star} : Tuber starch content in percentage (CO_330:0000435).
#' \item \code{fruc} : Tuber fructose content in percentage (CO_330:0000438).
#' \item \code{gluc} : Tuber glucose content in percentage (CO_330:0000441).
#' \item \code{sucr} : Tuber sucrose content in percentage (CO_330:0000444).
#' \item \code{malt} : Tuber maltose content in percentage (CO_330:0000447).
#' \item \code{fiber} : Tuber fiber content in percentage (CO_330:0000450).
#' \item \code{tgly_fw} : Tuber glycoalkaloid concentration on fresh weight basis in mg per 100 g (CO_330:0000661).
#' }
#' ---------------------------------- Deseases --------------------------------
#' \itemize{
#' \item \code{lb} : Late Blight severity estimating percentage (CO_330:0000359).
#' \item \code{lbi} : Late Blight severity estimating percentage evaluation i (i = 1, 2,... 8).
#' \item \code{rlb} : Late Blight resistance estimating 1-6 (CO_330:0000372).
#' \item \code{rlb_30dap} : Late Blight resistance estimating 1-6, 30 days after planting (COMP:0000012).
#' \item \code{rlb_45dap} : Late Blight resistance estimating 1-6, 45 days after planting (COMP:0000013).
#' \item \code{rlb_60dap} : Late Blight resistance estimating 1-6, 60 days after planting (COMP:0000014).
#' \item \code{rlb_75dap} : Late Blight resistance estimating 1-6, 75 days after planting (COMP:0000015).
#' \item \code{audpc} : Late blight AUDPC computed (CO_330:0000363).
#' \item \code{raudpc} : Late blight relative AUDPC computed (CO_330:0000367).
#' \item \code{saudpc} : Late blight susceptibility computed (CO_330:0000371).
#' \item \code{pvx} : Potato virus X resistance (CO_330:0000373).
#' \item \code{pvy} : Potato virus Y resistance (CO_330:0000374).
#' \item \code{prlv} : Potatoleaf roll virus resistance (CO_330:0000375).
#' \item \code{bw} : Bacterial wilt resistance (CO_330:0000376).
#' \item \code{rkn} : Root knot nematode resistance (CO_330:0000377).
#' \item \code{rlmf} : Resistance to leaf miner fly 1-5 (CO_330:0000378).
#' \item \code{rlmf_45dap} : Resistance to leaf miner fly 1-5 (COMP_0000016).
#' \item \code{rlmf_60dap} : Resistance to leaf miner fly 1-5 (COMP_0000017).
#' \item \code{rlmf_75dap} : Resistance to leaf miner fly 1-5 (COMP_0000018).
#' }
#' ------------------------------- Other traits -------------------------------
#' \itemize{
#' \item \code{rd} : Root density estimating 1-3 (CO_330:0000834).
#' \item \code{rl} : Root length in cm (CO_330:0000764).
#' \item \code{sg} : Tuber specific gravity (CO_330:0000394).
#' \item \code{dsi} : Drought susceptibility index computed (CO_330:0000776).
#' \item \code{dti} : Drought tolerance index computed (CO_330:0000779).
#' \item \code{leaflet_tw} : Leaflet turgid weight in mg (CO_330:0000818).
#' \item \code{leaflet_twi} : Leaflet turgid weight evaluation i (i = 1,..., 5).
#' \item \code{pw_ev} : Degree of canopy wilting estimating 1-9 (CO_330:0000773).
#' \item \code{pw_evi} : Degree of canopy wilting estimating 1-9 evaluation i (i = 1,..., 5).
#' \item \code{snpp} : Stem number per plant (CO_330:0000851).
#' \item \code{snppi} : Stem number per plant evaluation i (i = 1,..., 5).
#' \item \code{nipp} : Number of inflorescences per plant estimating 0-7 (CO_330:0000226).
#' \item \code{nfwp} : Number of flowers per main inflorescence estimating 0-5 (CO_330:0000227).
#' \item \code{Num_Stolon} : Number of stolons estimating 1-9 (CO_330:0000340).
#' \item \code{Leng_Stolon} : Length of stolons estimating 1-9 (CO_330:0000344).
#' \item \code{plahe_ev} : Plant height in cm (CO_330:0000758).
#' \item \code{plahe_evi} : Plant height evaluation i (i = 1,..., 5).
#' \item \code{sd_ev} : Stem diameter in mm (CO_330:0000847).
#' \item \code{sd_evi} : Stem diameter evaluation i (i = 1,..., 5)
#' \item \code{chlspad_ev} : Chlorophyll content index using SPAD-meter in SPAD units (CO_330:0000805).
#' \item \code{chlspad_evi} : Chlorophyll content index evaluation i (i = 1,..., 5).
#' \item \code{cr_ev} : Canopy reflectance using Green-Seeker-meter in NDVI units (CO_330:0000860).
#' \item \code{cr_evi} : Canopy reflectance evaluation i (i = 1,..., 5).
#' \item \code{lfa_ev} : Leaflet area using Compu Eye, Leaf Symptom Area software in cm^2 (CO_330:0000766).
#' \item \code{lfa_evi} : Leaflet area using Compu Eye, Leaf Symptom Area software in cm^2 evaluation i (i = 1,..., 5).
#' \item \code{rwc_ev} : Relative water content in percentage (CO_330:0000741).
#' \item \code{rwc_evi} : Relative water content evaluation i (i = 1,..., 5).
#' \item \code{sla_ev} : Leaflet area using EasyLeafArea software in cm^2 per g (CO_330:0000812).
#' \item \code{sla_evi} : Leaflet area using EasyLeafArea software in cm^2 per g evaluation i (i = 1,..., 5).
#' }
#' @return It returns:
#' \itemize{
#' \item The fieldbook data frame with all column names in lowercase and
#' with some possible modifications in the names. Traits that are stored
#' with a non-numeric class are transformed to numeric.
#' \item A list of warnings for all the column names that have been changed.
#' \item A list of warnings for all the column names not recognized.
#' \item A list of warnings for all the column traits that have been changed to numeric.
#' }
#' @author Raul Eyzaguirre, Johan Ninanya.
#' @examples
#' check.names.pt(potatoyield)
#' @export
check.names.pt <- function(dfr, add = NULL) {
# Valid names for factors
plot.id <- c("plot", "row", "col")
factors <- c("loc", "year", "season", "env", "geno", 'type', "rep", "block",
"treat", 'is_a_control')
# Repeated measures traits (i = 1...5)
rm.traits <- c("leaflet_tw", "pw_ev", "snpp", "plahe_ev", "sd_ev", "chlspad_ev",
"cr_ev", "lfa_ev", "rwc_ev", "sla_ev")
rm.traitsi <- c(rm.traits, sapply(rm.traits, function(x) paste0(x, 1:5)))
# Late blight evaluations
lb.ev <- paste0("lb", 1:8)
# Valid names for traits
traits <- c(ptont$Label, "nmtci", "nmtcii", "mtwci", "mtwcii", "tbskn1", "tbfsh1",
"tbshp1", "tbshp3", "dorpd", "ffr", "aocp", "flavour", "textac",
"cookqu", "cootime", "tafw", "tadw", "fwts", "dwts", "fwts1", "fwts2",
"dwts1", "dwts2", "dm1", "dm2", "avdm", "tgly_fw", "pvx", "pvy",
"prlv", "bw", "rkn", lb.ev, rm.traits, rm.traitsi, tolower(add))
# Valid names for factors and traits
colnames.valid <- c(plot.id, factors, traits)
# Factors and traits in field book (original names)
colnames.fb <- colnames(dfr)
# Convert all fieldbook names to lower case (except CO numbers)
cond <- substring(colnames(dfr), 1, 7) != 'CO_330:' & substring(colnames(dfr), 1, 5) != 'COMP:'
colnames(dfr)[cond] <- tolower(colnames(dfr))[cond]
if (sum(colnames.fb != colnames(dfr)) > 0)
warning("Some labels converted to lower case", call. = FALSE)
# Solve synonyms for factors
# All options for genotypes
old.geno <- c("accession_name", "cipno", "cip.number", 'genotype', "instn")
new.geno <- rep('geno', length(old.geno))
change.names.f <- NULL
old.names.f <- c('plot_number', 'location', "replication", 'rep_number', "block_number", "row_number", "col_number", old.geno)
new.names.f <- c('plot', 'loc', "rep", 'rep', "block", "row", "col", new.geno)
for (i in 1:length(old.names.f)) {
if (exists(old.names.f[i], dfr) & !exists(new.names.f[i], dfr)) {
change.names.f <- c(change.names.f, old.names.f[i])
colnames(dfr)[colnames(dfr) == old.names.f[i]] <- new.names.f[i]
}
}
if (!is.null(change.names.f)) {
change.names.list <- old.names.f %in% change.names.f
warning("Factors' names ", list(old.names.f[change.names.list]), " changed to ", list(new.names.f[change.names.list]), call. = FALSE)
}
# Solve synonyms for traits
change.names.t <- NULL
old.names.t <- c("mwt", "mwmt", "stfw", "stdw", "pdm", 'avdm', "protein", 'chipping')
new.names.t <- c("atw", "atmw", "sfw", "sdw", "dm", 'dm', "pro", 'chip_color')
for (i in 1:length(old.names.t)) {
if (exists(old.names.t[i], dfr) & !exists(new.names.t[i], dfr)) {
change.names.t <- c(change.names.t, old.names.t[i])
colnames(dfr)[colnames(dfr) == old.names.t[i]] <- new.names.t[i]
}
}
if (!is.null(change.names.t)) {
change.names.list <- old.names.t %in% change.names.t
warning("Traits' names ", list(old.names.t[change.names.list]), " changed to ", list(new.names.t[change.names.list]), call. = FALSE)
}
# Names not valid
names.not.valid <- !(colnames(dfr) %in% colnames.valid)
if (max(names.not.valid) == 1)
warning("Some columns with invalid names: ", list(colnames(dfr)[names.not.valid]), call. = FALSE)
# Check traits are numeric
nonumeric.list <- NULL
column.class <- unlist(lapply(dfr, class))
for(i in colnames(dfr)) {
if(i %in% traits & column.class[i] != "numeric") {
dfr[, i] <- suppressWarnings(as.numeric(as.character(dfr[, i])))
nonumeric.list <- c(nonumeric.list, i)
}
}
if (!is.null(nonumeric.list))
warning("Some traits converted to numeric: ", list(nonumeric.list), call. = FALSE)
# Return
dfr
}
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