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

check.names.sp

R Documentation

Check fieldbook traits names for sweetpotato

Description

Check that fieldbook factors and traits names correspond with the names defined in 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.

Usage

check.names.sp(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_331:ROOT or COMP numbers defined in https://sweetpotatobase.org/.

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

plot : Plot number.
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 is also valid).
cipno : Institutional CIP number.
type : Entry type (clon, check, progeny, parent).
rep : Replications (rep_number is also valid).
block : Blocks (block_number is also valid).
treat : Treatment.
harvest : Harvest time.

—————————— Roots and vines —————————–

nops : Number of plants planted per plot (CO_331:0000678).
nope : Number of plants established per plot (CO_331:0000192).
noph : Number of plants harvested per plot (CO_331:0000679).
vir : Virus symptoms estimating 1-9 (CO_331:0000193).
vir1 : Virus symptoms estimating 1-9, first evaluation, 1 month after planting (COMP:0000023).
vir2 : Virus symptoms estimating 1-9, second evaluation, 1 month before harvest (COMP:0000024).
alt : Alternaria symptoms estimating 1-9 (CO_331:0000198).
alt1 : Alternaria symptoms estimating 1-9, first evaluation, 1 month after planting (COMP:0000026).
alt2 : Alternaria symptoms estimating 1-9, second evaluation, 1 month before harvest (COMP:0000022).
vv : Vine vigor estimating 1-9 (CO_331:0000197).
vw : Weight of vines per plot in kg (CO_331:0000227).
nopr : Number of plants with storage roots per plot (CO_331:0000211).
nocr : Number of commercial storage roots per plot (CO_331:0000214).
nonc : Number of non-commercial storage roots per plot (CO_331:0000217).
crw : Weight of commercial storage roots per plot in kg (CO_331:0000220).
ncrw : Weight of non-commercial storage roots per plot in kg (CO_331:0000223).
scol : Storage root predominant skin color estimating 1-9 (CO_331:0000175).
fcol : Storage root predominant flesh color estimating 1-9 (CO_331:0000178).
fcol2 : Storage root secondary flesh color estimating 0-9 (CO_331:0000179).
fcol.cc : Root flesh color from RHS color chart, 1-30.
rs : Storage root size estimating 1-9 (CO_331:0000184).
rf : Storage root appearance estimating 1-9 (CO_331:0000202).
rtshp : Storage root shape estimating 1-9 (CO_331:0000181).
damr : Storage root damage estimating 1-9 (CO_331:0000206).
rspr : Sprouting ability estimating 1-9 (CO_331:0000277).
alcdam : Alcidodes sp. damage estimating 1-9 (CO_331:0000806).
wed : Reaction to sweet potato weevil estimating 1-9 (CO_331:0000207).
stspwv : Reaction to striped sweet potato weevil estimating 1-9 (CO_331:0000720).
milldam : Millipede damage estimating 1-9 (CO_331:0000805).

————————— Dry matter assesment —————————

dmf : Fresh weight of storage root samples for dry matter assessment measuring g (CO_331:0000243).
dmd : Dry weight of storage root samples for dry matter assessment measuring g (CO_331:0000247).
dm : Storage root dry matter content computing percent (CO_331:0000297).
dmvf : Fresh weight of vines samples for dry matter assessment measuring g (CO_331:0000251).
dmvd : Dry weight of vines samples for dry matter assessment measuring g (CO_331:0000255).
dmv : Vine dry matter content computing percent (CO_331:0001014).

———————- Raw and cooked roots attributes ———————

fraw : Fiber content in raw storage roots estimating 1-9 (CO_331:0001038).
suraw : Content of total sugars in raw storage roots estimating 1-9 (CO_331:0000766).
straw : Content of starch in raw storage roots estimating 1-9 (CO_331:0001055).
coof : Fiber content in boiled storage roots estimating 1-9 (CO_331:0000259).
coosu : Storage root sweetness in cooked samples estimating 1-9 (CO_331:0000261).
coost : Storage root texture in boiled samples estimating 1-9 (CO_331:0000265).
coot : Boiled storage root flesh taste estimating 1-9 (CO_331:0000269).
cooap : Boiled storage root overall appearance estimating 1-9 (CO_331:0000273).

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

prot : Content of protein in dry weight basis in raw storage roots measuring percentage (CO_331:0000278).
fe : Content of iron in dry weight basis measuring mg per 100 g (CO_331:0001016).
zn : Content of zinc in dry weight basis measuring mg per 100 g (CO_331:0001017).
ca : Content of calcium in dry weight basis measuring mg per 100 g (CO_331:0001029).
mg : Content of magnesium in dry weight basis measuring mg per 100 g (CO_331:0001030).
bc : Content of beta-carotene in dry weight basis in raw storage roots measuring mg per 100 g (CO_331:0000289).
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).
tc : Content of total carotenoids in dry weight basis in raw storage roots measuring mg per 100 g (CO_331:0000290).
star : Content of starch in dry weight basis in raw storage roots measuring percentage (CO_331:0000291).
star.b : Content of starch in dry weight basis in boiled storage roots measuring percentage (CO_331:2000027).
fruc : Content of fructose in dry weight basis in raw storage roots measuring g per 100 g (CO_331:0001045).
fruc.b : Content of fructose in dry weight basis in boiled storage roots measuring g per 100 g (CO_331:0001046).
gluc : Content of glucose in dry weight basis in raw storage roots measuring g per 100 g (CO_331:0001047).
gluc.b : Content of glucose in dry weight basis in boiled storage roots measuring g per 100 g (CO_331:0001048).
sucr : Content of sucrose in dry weight basis in raw storage roots measuring g per 100 g (CO_331:0001049).
sucr.b : Content of sucrose in dry weight basis in boiled storage roots measuring g per 100 g (CO_331:0001050).
malt : Content of maltose in dry weight basis in raw storage roots measuring g per 100 g (CO_331:0001051).
malt.b : Content of maltose in dry weight basis in boiled storage roots measuring g per 100 g (CO_331:0001052).

—————————– Calculated traits —————————-

tnr : Total number of storage roots per plot (CO_331:0000233).
trw : Total storage root weight per plot in kg (CO_331:0000237).
trw.d : Total storage root weight in dry weight basis per plot in kg (CO_331:0000995).
biom : Biomass yield per plot in kg (CO_331:0000683).
biom.d : Biomass yield in dry weight basis per plot in kg (CO_331:0000997).
cytha : Commercial storage root yield in tons per ha (CO_331:0000809).
cytha.aj : Commercial storage root yield adjusted by number of harvested plants per plot in tons per ha (CO_331:0000998).
rytha : Total storage roots yield in tons per ha (CO_331:0000296).
rytha.aj : Total storage roots yield adjusted by number of harvested plants per plot in tons per ha (CO_331:0000999).
dmry : Storage root dry matter yield in tons per ha (CO_331:0001000).
dmry.aj : Storage root dry matter yield adjusted by number of harvested plants per plot in tons per ha (CO_331:0001001).
vw.d : Dry weight of vines per plot in kg (CO_331:0000996).
fytha : Total foliage yield in tons per ha (CO_331:0000684).
fytha.aj : Total foliage yield adjusted by number of harvested plants per plot in tons per ha (CO_331:0001002).
dmvy : Vine dry matter yield in tons per ha (CO_331:0001005).
dmvy.aj : Vine dry matter yield adjusted by number of harvested plants per plot in tons per ha (CO_331:0001006).
bytha : Biomass yield in tons per ha (CO_331:0001003).
bytha.aj : Biomass yield adjusted by number of harvested plants per plot in tons per ha (CO_331:0001004).
dmby : Biomass dry matter yield in tons per ha (CO_331:0001007).
dmby.aj : Biomass dry matter yield adjusted by number of harvested plants per plot in tons per ha (CO_331:0001008).
acrw : Average commercial storage root weight in kg (CO_331:0000680).
ancrw : Average non-commercial storage root weight in kg (CO_331:0002039).
atrw : Average total storage root weight in kg (CO_331:0002040).
nrpp : Number of storage roots per plant harvested (CO_331:0000230).
nrpsp : Number of storage roots per plant planted (CO_331:0000994).
ncrpp : Number of commercial storage roots per plant harvested (CO_331:0006024).
ncrpsp : Number of commercial storage roots per plant planted (CO_331:0000993).
ypp : Storage roots yield per plant harvested in kg (CO_331:0000681).
ypsp : Storage roots yield per plant planted in kg (CO_331:0000989).
vpp : Vine weight per plant harvested in kg (CO_331:0000990).
vpsp : Vine weight per sowed plant in kg (CO_331:0000991).
rtyldpct : Yield as percent of check (CO_331:0000792).
ci : Commercial index in percentage (CO_331:0000682).
hi : Harvest index in percentage (CO_331:0000302).
shi : Survival index in percentage (CO_331:0000301).
rfr : Root foliage ratio in percentage (CO_331:0001015).