In KeachMurakami/kagari:

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-"
)

kagari (縢り)

This package organizes individual data from various measuring instruments into tidy dataset. kagari is a Japanese word meaning sew (c.f 和綴じ). The author hope to sew a user-friendly book---i.e. tidy dataset---from individual pages---i.e. messy raw data.

You can install:

• the latest development version from github with

# install.packages("devtools") # if not installed
devtools::install_github("KeachMurakami/kagari")

Prerequisite

library(tidyverse)
library(kagari)

Data load

read_*** deals with raw data obtained by ***---a name of the software or the device:

• read_li6400(): reads .txt/.csv/.tsv format data obtained by LI6400/LI6400XT (LI-COR) with Xterm.

• read_junior_pam(): reads .csv format data obtained by JUNIOR-PAM (Heinz Walz) with WinControl.

• read_field_lambda(): reads .csv format data obtained by field-lambda with color viewer.

• read_color_reader(): reads .csv format data obtained by CR-10 Plus (Konica Minolta).

The first argument is always a file path. The output is wide format data containing the measured variables and measured times.

Data manipulation

mutate_*** calculates parameters from raw data obtained by ***---a name of the software or the device---and adds new columns to the input tibble.

• mutate_oxy(): calculates and adds maximum gross photosynthetic O~2~ evolution rate, functional PSII content, and cytochrome content from data obtained by liquid phase oxygen electrode system (Hansatech) with single-turnover.

tibble(o2_calibration = c(1.3, 1.31),
       pn_under_saturing_irradiance = c(.3, .51),
       pn_under_dark = c(-.11, -.05),
       pn_under_fr_and_flash = c(.1, .09),
       pn_under_fr = c(-.002, 0)) %>%
  mutate_oxy(.tbl = ., calb = o2_calibration,
             positive_pmax = pn_under_saturing_irradiance, negative_pmax = pn_under_dark,
             positive_psii = pn_under_fr_and_flash, negative_psii = pn_under_fr,
             leaf_area = 2.22*10^-4, hz = 10) %>%
  knitr::kable(format = "markdown")

The first argument is always a tibble.

Session information

devtools::session_info()

KeachMurakami/kagari documentation built on May 29, 2019, 2:26 p.m.