check.names.pt: Check fieldbook traits names for potato
In reyzaguirre/st4gi: Statistical tools for genetic improvement

check.names.pt

R Documentation

Check fieldbook traits names for potato

Description

Check that fieldbook traits names correspond with the names defined in https://cropontology.org/term/CO_330:ROOT, and that all traits are stored as numeric.

Usage

check.names.pt(dfr, add = NULL)

Arguments

`dfr`	The name of the data frame.
`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 https://cropontology.org/term/CO_330:ROOT.

—————————– Plot identifiers —————————–

plot : Plot number (plot_number is also valid).
row : Row number position of the plot (row_number is also valid).
col : Column number position of the plot (col_number is also valid).

————————— Classification factors————————–

loc : Locations.
year : Years.
season : Seasons.
env : Environments.
geno : Genotypes (accession_name and instn are also valid).
type : Entry type (clon, check, progeny, parent).
rep : Replications (rep_number is also valid).
block : Blocks (block_number is also valid).
treat : Treatments.

———————————– Plants ———————————

ntp : Number of tubers planted per plot (CO_330:0000265).
npe : Number of plants emerged per plot (CO_330:0000268).
npe_15dap : Number of plants emerged per plot, 15 days after planting (COMP:0000002).
npe_30dap : Number of plants emerged per plot, 30 days after planting (COMP:0000003).
nph : Number of plants harvested per plot (CO_330:0000287).
ppe : Proportion of plants emerged in percentage (CO_330:0000283).
pph : Proportion of plants harvested in percentage (CO_330:0000290).

—————————– Number of tubers —————————–

tntp : Total number of tubers per plot (CO_330:0000304).
tntpl : Total number of tubers per plant (CO_330:0000305).
nmtp : Number of marketable tubers per plot (CO_330:0000293).
nmtpl : Number of marketable tubers per plant (CO_330:0000297).
nnomtp : Number of non-marketable tubers per plot (CO_330:0000300).
nmtci : Number of marketable tubers category I per plot.
nmtcii : Number of marketable tubers category II per plot.

—————————– Weight of tubers —————————–

ttwp : Total tuber weight per plot in kg (CO_330:0000317).
ttwpl : Total tuber weight per plant in kg (CO_330:0000321).
mtwp : Marketable tuber weight per plot in kg (CO_330:0000308).
mtwpl : Marketable tuber weight per plant in kg (CO_330:0000311).
nomtwp : Non-marketable tuber weight per plot in kg (CO_330:0000314).
mtwci : Marketable tuber weight category I per plot in kg.
mtwcii : Marketable tuber weight category II per plot in kg.
ttya : Total tuber yield adjusted by number of plants harvested per plot in tons per ha (CO_330:0000323).
ttyna : Total tuber yield not adjusted in tons per ha (CO_330:0000324).
mtya : Marketable tuber yield adjusted by number of plants harvested per plot in tons per ha (CO_330:0000327).
mtyna : Marketable tuber yield not adjusted in tons per ha (CO_330:0000330).
atw : Average tuber weight in g (CO_330:0000333).
atmw : Average marketable tuber weight in g (CO_330:0000336).

———————— Plant and tuber appearance ————————

flowering : Flowering degree estimating 0-7 (CO_330:0000224).
flowering_45dap : Flowering degree estimating 0-7, 45 days after planting (COMP:0000010).
flowering_60dap : Flowering degree estimating 0-7, 60 days after planting (COMP:0000011).
plant_unif : Plant uniformity estimating 1-9 (CO_330:0000272).
plant_unif_45dap : Plant uniformity estimating 1-9, 45 days after planting (COMP:0000008).
plant_unif_60dap : Plant uniformity estimating 1-9, 60 days after planting (COMP:0000009).
plant_vigor : Plant vigor estimating 1-9 (CO_330:0000276).
plant_vigor_30dap : Plant vigor estimating 1-9, 30 days after planting (COMP:0000004).
plant_vigor_45dap : Plant vigor estimating 1-9, 45 days after planting (COMP:0000005).
plant_vigor_60dap : Plant vigor estimating 1-9, 60 days after planting (COMP:0000006).
se : Senescence estimating 1-9 (CO_330:0000280).
tuber_apper : Tuber appearance estimating 1-9 (CO_330:0000348).
tub_unif : Tuber uniformity estimating 1-9 (CO_330:0000352).
tub_size : Tuber size estimating 1-9 (CO_330:0000356).
tbskn1 : Predominant tuber skin color (CO_330:0000249).
tbfsh1 : Predominant tuber flesh color (CO_330:0000253).
tbshp1 : Tuber shape (CO_330:0000256).
tbshp3 : Tuber depth eyes (CO_330:0000258).
dorpd : Tuber dormancy period (CO_330:0000397).

——————————- Organoleptic ——————————-

chip_color : Chips color 1-5 (CO_330:0000384).
ffr : French fries color 1-5 (CO_330:0000388).
aocp : Chips oil absorption rate (CO_330:0000395).
flavour : Tuber flavor after cooking (CO_330:0000379).
textac : Tuber texture after cooking (CO_330:0000380).
cookqu : Tuber cooking quality (CO_330:0000381).
cootime : Tuber cooking time (CO_330:0000389).

———————————- Biomass ———————————

tafw : Total aerial fresh weight per plot in g.
tbfwp : Total biomass fresh weight per plot in g. (CO_330:0000829)
tbfwpl : Total biomass fresh weight per plant in g (CO_330:0000799).
hi_fw : Harvest index fresh weight in percentage (CO_330:0000738).
tadw : Total aerial dry weight per plot in g.
tbdwp : Total biomass dry weight per plot in g. (CO_330:0000828)
tbdwpl : Total biomass dry weight per plant in g (CO_330:0000798).
hi_dw : Harvest index dry weight in percentage (CO_330:0000735).

——————————– Dry weight ——————————–

fwts : Fresh weight of tuber for dry matter determination.
dwts : Dry weight of tuber for dry matter determination.
fwts1 : Fresh weight of tuber sample 1.
fwts2 : Fresh weight of tuber sample 2.
dwts1 : Dry weight of tuber sample 1.
dwts2 : Dry weight of tuber sample 2.
dm1 : Tuber dry matter content sample 1.
dm2 : Tuber dry matter content sample 2.
dm : Tuber dry matter content in percentage (CO_330:0000390).

————————— Nutrients evaluations ————————–

fedw : Tuber iron concentration on dry weight basis in mg per 100 g (CO_330:0000402).
fefw : Tuber iron concentration on fresh weight basis in mg per 100 g (CO_330:0000407).
fedw_xrf : Tuber iron concentration on dry weight basis in mg per kg by XRF (CO_330:0000404).
zndw : Tuber zinc concentration on dry weight basis in mg per 100 g (CO_330:0000408).
znfw : Tuber zinc concentration on fresh weight basis in mg per 100 g (CO_330:0000412).
zndw_xrf : Tuber zinc concentration on dry weight basis in mg per kg by XRF (CO_330:0000409).
antho_dw : Tuber anthocyanin concentration on dry weight basis in mg per 100 g (CO_330:0000414).
antho_fw : Tuber anthocyanin concentration on fresh weight basis in mg per 100 g (CO_330:0000417).
aah_dw : Tuber hydrophilic antioxidant activity on dry weight basis in ugTroloxequiv/g (CO_330:0000418).
aah_fw : Tuber hydrophilic antioxidant activity on fresh weight basis in ugTroloxequiv/g (CO_330:0000421).
aal_dw : Tuber lipophilic antioxidant activity on dry weight basis in ugTroloxequiv/g (CO_330:0000422).
aal_fw : Tuber lipophilic antioxidant activity on fresh weight basis in ugTroloxequiv/g (CO_330:0000425).
asc_dw : Tuber ascorbic acid concentration on dry weight basis in mg per 100 g (CO_330:0000426).
asc_fw : Tuber ascorbic acid concentration on fresh weight basis in mg per 100 g (CO_330:0000429).
pro : Tuber protein content in percentage (CO_330:0000432).
star : Tuber starch content in percentage (CO_330:0000435).
fruc : Tuber fructose content in percentage (CO_330:0000438).
gluc : Tuber glucose content in percentage (CO_330:0000441).
sucr : Tuber sucrose content in percentage (CO_330:0000444).
malt : Tuber maltose content in percentage (CO_330:0000447).
fiber : Tuber fiber content in percentage (CO_330:0000450).
tgly_fw : Tuber glycoalkaloid concentration on fresh weight basis in mg per 100 g (CO_330:0000661).

———————————- Deseases ——————————–

lb : Late Blight severity estimating percentage (CO_330:0000359).
lbi : Late Blight severity estimating percentage evaluation i (i = 1, 2,... 8).
rlb : Late Blight resistance estimating 1-6 (CO_330:0000372).
rlb_30dap : Late Blight resistance estimating 1-6, 30 days after planting (COMP:0000012).
rlb_45dap : Late Blight resistance estimating 1-6, 45 days after planting (COMP:0000013).
rlb_60dap : Late Blight resistance estimating 1-6, 60 days after planting (COMP:0000014).
rlb_75dap : Late Blight resistance estimating 1-6, 75 days after planting (COMP:0000015).
audpc : Late blight AUDPC computed (CO_330:0000363).
raudpc : Late blight relative AUDPC computed (CO_330:0000367).
saudpc : Late blight susceptibility computed (CO_330:0000371).
pvx : Potato virus X resistance (CO_330:0000373).
pvy : Potato virus Y resistance (CO_330:0000374).
prlv : Potatoleaf roll virus resistance (CO_330:0000375).
bw : Bacterial wilt resistance (CO_330:0000376).
rkn : Root knot nematode resistance (CO_330:0000377).
rlmf : Resistance to leaf miner fly 1-5 (CO_330:0000378).
rlmf_45dap : Resistance to leaf miner fly 1-5 (COMP_0000016).
rlmf_60dap : Resistance to leaf miner fly 1-5 (COMP_0000017).
rlmf_75dap : Resistance to leaf miner fly 1-5 (COMP_0000018).

——————————- Other traits ——————————-

rd : Root density estimating 1-3 (CO_330:0000834).
rl : Root length in cm (CO_330:0000764).
sg : Tuber specific gravity (CO_330:0000394).
dsi : Drought susceptibility index computed (CO_330:0000776).
dti : Drought tolerance index computed (CO_330:0000779).
leaflet_tw : Leaflet turgid weight in mg (CO_330:0000818).
leaflet_twi : Leaflet turgid weight evaluation i (i = 1,..., 5).
pw_ev : Degree of canopy wilting estimating 1-9 (CO_330:0000773).
pw_evi : Degree of canopy wilting estimating 1-9 evaluation i (i = 1,..., 5).
snpp : Stem number per plant (CO_330:0000851).
snppi : Stem number per plant evaluation i (i = 1,..., 5).
nipp : Number of inflorescences per plant estimating 0-7 (CO_330:0000226).
nfwp : Number of flowers per main inflorescence estimating 0-5 (CO_330:0000227).
Num_Stolon : Number of stolons estimating 1-9 (CO_330:0000340).
Leng_Stolon : Length of stolons estimating 1-9 (CO_330:0000344).
plahe_ev : Plant height in cm (CO_330:0000758).
plahe_evi : Plant height evaluation i (i = 1,..., 5).
sd_ev : Stem diameter in mm (CO_330:0000847).
sd_evi : Stem diameter evaluation i (i = 1,..., 5)
chlspad_ev : Chlorophyll content index using SPAD-meter in SPAD units (CO_330:0000805).
chlspad_evi : Chlorophyll content index evaluation i (i = 1,..., 5).
cr_ev : Canopy reflectance using Green-Seeker-meter in NDVI units (CO_330:0000860).
cr_evi : Canopy reflectance evaluation i (i = 1,..., 5).
lfa_ev : Leaflet area using Compu Eye, Leaf Symptom Area software in cm^2 (CO_330:0000766).
lfa_evi : Leaflet area using Compu Eye, Leaf Symptom Area software in cm^2 evaluation i (i = 1,..., 5).
rwc_ev : Relative water content in percentage (CO_330:0000741).
rwc_evi : Relative water content evaluation i (i = 1,..., 5).
sla_ev : Leaflet area using EasyLeafArea software in cm^2 per g (CO_330:0000812).
sla_evi : Leaflet area using EasyLeafArea software in cm^2 per g evaluation i (i = 1,..., 5).

Value

It returns:

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.
A list of warnings for all the column names that have been changed.
A list of warnings for all the column names not recognized.
A list of warnings for all the column traits that have been changed to numeric.