cassava_CC: IITA Cassava Germplasm Data - Core Collection

In EvaluateCore: Quality Evaluation of Core Collections

IITA Cassava Germplasm Data - Core Collection

Description

An example germplasm characterisation data of a core collection generated from 1591 accessions of IITA Cassava collection \insertCitebenjamin_cassava_2019EvaluateCore using 10 quantitative and 48 qualitative trait data with CoreHunter3 (corehunter). The core set was generated using distance based measures giving equal weightage to Average entry-to-nearest-entry distance (EN) and Average accession-to-nearest-entry distance (AN). Includes data on 26 descriptors for 168 (10 % of cassava_EC) accessions. It is used to demonstrate the various functions of EvaluateCore package.

Usage

cassava_CC

Format

A data frame with 58 columns:

CUAL

Colour of unexpanded apical leaves

LNGS

Length of stipules

PTLC

Petiole colour

DSTA

Distribution of anthocyanin

LFRT

Leaf retention

LBTEF

Level of branching at the end of flowering

CBTR

Colour of boiled tuberous root

NMLB

Number of levels of branching

ANGB

Angle of branching

CUAL9M

Colours of unexpanded apical leaves at 9 months

LVC9M

Leaf vein colour at 9 months

TNPR9M

Total number of plants remaining per accession at 9 months

PL9M

Petiole length at 9 months

STRP

Storage root peduncle

STRC

Storage root constrictions

PSTR

Position of root

NMSR

Number of storage root per plant

TTRN

Total root number per plant

TFWSR

Total fresh weight of storage root per plant

TTRW

Total root weight per plant

TFWSS

Total fresh weight of storage shoot per plant

TTSW

Total shoot weight per plant

TTPW

Total plant weight

AVPW

Average plant weight

ARSR

Amount of rotted storage root per plant

SRDM

Storage root dry matter

Details

Further details on how the example dataset was built from the original data is available online.

References

\insertAllCited

Examples

data(cassava_CC)
summary(cassava_CC)

quant <- c("NMSR", "TTRN", "TFWSR", "TTRW", "TFWSS", "TTSW", "TTPW", "AVPW",
           "ARSR", "SRDM")
qual <- c("CUAL", "LNGS", "PTLC", "DSTA", "LFRT", "LBTEF", "CBTR", "NMLB",
          "ANGB", "CUAL9M", "LVC9M", "TNPR9M", "PL9M", "STRP", "STRC",
          "PSTR")

lapply(seq_along(cassava_CC[, qual]),
       function(i) barplot(table(cassava_CC[, qual][, i]),
                           xlab = names(cassava_CC[, qual])[i]))

lapply(seq_along(cassava_CC[, quant]),
       function(i) hist(table(cassava_CC[, quant][, i]),
                        xlab = names(cassava_CC[, quant])[i],
                        main = ""))

EvaluateCore documentation built on July 3, 2022, 5:06 p.m.