ikeogu.2017: Example vis-NIRS and reference dataset

In GoreLab/waves: Vis-NIR Spectral Analysis Wrapper

Example vis-NIRS and reference dataset

Description

The 'ikeogu.2017' data set contains raw vis-NIRS scans, total carotenoid content, and cassava root dry matter content (using the oven method) from the 2017 PLOS One paper by Ikeogu et al. This dataset contains a subset of the original scans and reference values from the supplementary files of the paper. 'ikeogu.2017' is a 'data.frame' that contains the following columns:

• study.name = Name of the study as described in Ikeogu et al. (2017).

• sample.id = Unique identifier for each individual root sample

• DMC.oven = Cassava root dry matter content, the percentage of dry weight relative to fresh weight of a sample after oven drying.

• TCC = Total carotenoid content (\mu g/g, unknown whether on a fresh or dry weight basis) as measured by high performance liquid chromatography

• X350:X2500 = spectral reflectance measured with the QualitySpec Trek: S-10016 vis-NIR spectrometer. Each cell represents the mean of 150 scans on a single root at a single wavelength.

Usage

ikeogu.2017

Format

An object of class tbl_df (inherits from tbl, data.frame) with 175 rows and 2155 columns.

Author(s)

Original authors: Ikeogu, U.N., F. Davrieux, D. Dufour, H. Ceballos, C.N. Egesi, and J. Jannink. Reformatted by Jenna Hershberger.

References

Ikeogu, U.N., F. Davrieux, D. Dufour, H. Ceballos, C.N. Egesi, et al. 2017. Rapid analyses of dry matter content and carotenoids in fresh cassava roots using a portable visible and near infrared spectrometer (Vis/NIRS). PLOS One 12(12): 1–17. doi: 10.1371/journal.pone.0188918.

Examples

library(magrittr)
library(ggplot2)
data(ikeogu.2017)
ikeogu.2017[1:10, 1:10]
ikeogu.2017 %>%
  dplyr::select(-starts_with("X")) %>%
  dplyr::group_by(study.name) %>%
  tidyr::gather(trait, value, c(DMC.oven:TCC), na.rm = TRUE) %>%
  ggplot2::ggplot(aes(x = study.name, y = value, fill = study.name)) +
  facet_wrap(~trait, scales = "free_y", nrow = 2) +
  geom_boxplot()

GoreLab/waves documentation built on April 15, 2024, 3:28 p.m.