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:
# install.packages("devtools") # if not installed
devtools::install_github("KeachMurakami/kagari")
library(tidyverse)
library(kagari)
#>
#> Some coefficient for ‘Oxygen electrode measurements’ were attached
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.
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 O2 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")
o2_calibration
pn_under_saturing_irradiance
pn_under_dark
pn_under_fr_and_flash
pn_under_fr
pmax
psii
cytf
1.30
0.30
-0.11
0.10
-0.002
19.99018
0.8395877
0.4794487
1.31
0.51
-0.05
0.09
0.000
33.53936
0.7216268
0.8940091
The first argument is always a tibble.
devtools::session_info()
#> Session info -------------------------------------------------------------
#> setting value
#> version R version 3.5.0 (2018-04-23)
#> system x86_64, darwin15.6.0
#> ui X11
#> language (EN)
#> collate en_US.UTF-8
#> tz Australia/Brisbane
#> date 2018-07-18
#> Packages -----------------------------------------------------------------
#> package * version date source
#> assertthat 0.2.0 2017-04-11 CRAN (R 3.5.0)
#> backports 1.1.2 2017-12-13 CRAN (R 3.5.0)
#> base * 3.5.0 2018-04-24 local
#> bindr 0.1.1 2018-03-13 CRAN (R 3.5.0)
#> bindrcpp * 0.2.2 2018-03-29 CRAN (R 3.5.0)
#> broom * 0.4.4.9000 2018-06-21 Github (tidyverse/broom@2721de4)
#> cellranger 1.1.0 2016-07-27 CRAN (R 3.5.0)
#> cli 1.0.0 2017-11-05 CRAN (R 3.5.0)
#> colorspace 1.3-2 2016-12-14 CRAN (R 3.5.0)
#> compiler 3.5.0 2018-04-24 local
#> crayon 1.3.4 2017-09-16 CRAN (R 3.5.0)
#> datasets * 3.5.0 2018-04-24 local
#> devtools * 1.13.5 2018-02-18 CRAN (R 3.5.0)
#> digest 0.6.15 2018-01-28 CRAN (R 3.5.0)
#> dplyr * 0.7.5 2018-05-19 CRAN (R 3.5.0)
#> evaluate 0.10.1 2017-06-24 CRAN (R 3.5.0)
#> forcats * 0.3.0 2018-02-19 CRAN (R 3.5.0)
#> ggplot2 * 3.0.0.9000 2018-07-16 Github (hadley/ggplot2@79e8b45)
#> glue 1.2.0 2017-10-29 CRAN (R 3.5.0)
#> graphics * 3.5.0 2018-04-24 local
#> grDevices * 3.5.0 2018-04-24 local
#> grid 3.5.0 2018-04-24 local
#> gtable 0.2.0 2016-02-26 CRAN (R 3.5.0)
#> haven 1.1.1 2018-01-18 CRAN (R 3.5.0)
#> highr 0.6 2016-05-09 CRAN (R 3.5.0)
#> hms 0.4.2 2018-03-10 CRAN (R 3.5.0)
#> htmltools 0.3.6 2017-04-28 CRAN (R 3.5.0)
#> httr 1.3.1 2017-08-20 CRAN (R 3.5.0)
#> jsonlite 1.5 2017-06-01 CRAN (R 3.5.0)
#> kagari * 0.1.0 2018-07-18 Github (KeachMurakami/kagari@6f2bc3c)
#> knitr * 1.20 2018-02-20 CRAN (R 3.5.0)
#> lattice 0.20-35 2017-03-25 CRAN (R 3.5.0)
#> lazyeval 0.2.1 2017-10-29 CRAN (R 3.5.0)
#> lubridate * 1.7.4 2018-04-11 CRAN (R 3.5.0)
#> magrittr * 1.5 2014-11-22 CRAN (R 3.5.0)
#> MASS * 7.3-49 2018-02-23 CRAN (R 3.5.0)
#> memoise 1.1.0 2017-04-21 CRAN (R 3.5.0)
#> methods * 3.5.0 2018-04-24 local
#> modelr 0.1.2 2018-05-11 cran (@0.1.2)
#> munsell 0.4.3 2016-02-13 CRAN (R 3.5.0)
#> nlme 3.1-137 2018-04-07 CRAN (R 3.5.0)
#> pillar 1.2.3 2018-05-25 cran (@1.2.3)
#> pkgconfig 2.0.1 2017-03-21 CRAN (R 3.5.0)
#> plyr 1.8.4 2016-06-08 CRAN (R 3.5.0)
#> purrr * 0.2.5 2018-05-29 CRAN (R 3.5.0)
#> R6 2.2.2 2017-06-17 CRAN (R 3.5.0)
#> Rcpp 0.12.17 2018-05-18 cran (@0.12.17)
#> readr * 1.1.1 2017-05-16 CRAN (R 3.5.0)
#> readxl 1.1.0 2018-04-20 CRAN (R 3.5.0)
#> reshape2 1.4.3 2017-12-11 CRAN (R 3.5.0)
#> rlang 0.2.1 2018-05-30 cran (@0.2.1)
#> rmarkdown 1.10 2018-06-11 cran (@1.10)
#> rprojroot 1.3-2 2018-01-03 CRAN (R 3.5.0)
#> rstudioapi 0.7 2017-09-07 CRAN (R 3.5.0)
#> rvest 0.3.2 2016-06-17 CRAN (R 3.5.0)
#> scales 0.5.0 2017-08-24 CRAN (R 3.5.0)
#> stats * 3.5.0 2018-04-24 local
#> stringi 1.2.3 2018-06-12 cran (@1.2.3)
#> stringr * 1.3.1 2018-05-10 cran (@1.3.1)
#> tibble * 1.4.2 2018-01-22 CRAN (R 3.5.0)
#> tidyr * 0.8.1 2018-05-18 cran (@0.8.1)
#> tidyselect 0.2.4 2018-02-26 CRAN (R 3.5.0)
#> tidyverse * 1.2.1 2017-11-14 CRAN (R 3.5.0)
#> tools 3.5.0 2018-04-24 local
#> utils * 3.5.0 2018-04-24 local
#> withr 2.1.2 2018-03-15 CRAN (R 3.5.0)
#> xml2 1.2.0 2018-01-24 CRAN (R 3.5.0)
#> yaml 2.1.19 2018-05-01 cran (@2.1.19)
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