README.md
In KeachMurakami/kagari:
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)
#>
#> Some coefficient for ‘Oxygen electrode measurements’ were attached
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 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.
Session information
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)
KeachMurakami/kagari documentation built on May 29, 2019, 2:26 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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)
#>
#> Some coefficient for ‘Oxygen electrode measurements’ were attached
Data load
read_*** deals with raw data obtained by ***---a name of the software or the device:
-
read_li6400(): reads.txt/.csv/.tsvformat data obtained by LI6400/LI6400XT (LI-COR) with Xterm. -
read_junior_pam(): reads.csvformat data obtained by JUNIOR-PAM (Heinz Walz) with WinControl. -
read_field_lambda(): reads.csvformat data obtained by field-lambda with color viewer. -
read_color_reader(): reads.csvformat 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 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")
The first argument is always a tibble.
Session information
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)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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