Package 'sunscanimport'

Title: Imports data from sunscan device
Description: Provides functions to import, convert and visualize LAI measurements from Sunscan device. An interactive shiny app is included.
Authors: Gunther Krauss <[email protected]>
Maintainer: Gunther Krauss <[email protected]>
License: GPL-3
Version: 0.3.4
Built: 2024-12-30 07:23:22 UTC
Source: https://github.com/gk-crop/sunscanimport

Help Index

Adds PlotID column to LAI data

Description

Information about PlotID is given via additional tab delimited files.

Usage

addPlotID(data, path)

Arguments

data

data.frame with LAI data
path

of the original data

Value

data.frame with PlotID column

Adds PlotID column to LAI data

Description

Information about PlotID is given via additional tab delimited files.

Usage

addPlotIDFromData(data, ids, mids)

Arguments

data

data.frame with LAI data
ids

dataframe with plotids
mids

dataframe with measurementids

Value

data.frame with PlotID column

Converts all SunScan data files in a directory (and it's subdirectories)

Description

Converts all SunScan data files in a directory (and it's subdirectories)

Usage

convertSunScanDirectory(
  directory,
  prefix = "",
  extension = ".txt",
  reportscript = ""
)

Arguments

directory

to search for data files
prefix

of files to take into accoung
extension

of files to take into account
reportscript

R script that is used to generate a report for each converted file

Converts a SunScan data file

Description

Converts a SunScan data file

Usage

convertSunscanFile(file, inputfolder, outputfolder)

Arguments

file

name of file
inputfolder

input folder
outputfolder

output folder

Value

vector with filenames of converted data

Counts measurements

Description

Counts measurements

Usage

countMeasurements(data)

Arguments

data

imported sunscan data

Value

dataframe with number of measurements

Creates a boxplot for LAI data

Description

Creates a boxplot for LAI data

Usage

createBoxplot(data, deleted = FALSE)

Arguments

data

data.frame with LAI data
deleted

include measurements marked as deleted

Value

ggplot graph with boxplot

Creates (sub)folders for converted data and reports

Description

Creates (sub)folders for converted data and reports

Usage

createFolders(file, inputfolder, outputfolder)

Arguments

file

filename
inputfolder

input folder
outputfolder

output folder

Plots the PlotNr arranged in a grid

Description

Plots the PlotNr arranged in a grid

Usage

createGridPlot(griddata)

Arguments

griddata

grid data

Plots LAI on a grid

Description

Plots LAI on a grid

Usage

createGridPlotLAI(data, griddata, deleted = FALSE)

Arguments

data

imported sunscan data
griddata

grid data
deleted

include measurements marked as deleted

Summarise information about measurement series

Description

Summarise information about measurement series

Usage

createSeriesInfo(data)

Arguments

data

imported sunscan data

Value

dataframe

Summarises data for each PlotID

Description

Summarises data for each PlotID

Usage

createSummary(data, deleted = FALSE)

Arguments

data

data.frame with LAI data
deleted

include measurements marked as deleted

Value

data.frame with summary information

Plots measurements over time

Description

Plots measurements over time

Usage

createTimePlot(data, stripes = 11)

Arguments

data

imported sunscan data
stripes

number of color stripes

Plots measurements over time

Description

Plots measurements over time

Usage

createTimePlotLAI(data, stripes = 11)

Arguments

data

imported sunscan data
stripes

number of color stripes

Creates initial grid data

Description

Creates initial grid data

Usage

generateInitialGridData(data, rows = 1, rowwise = FALSE)

Arguments

data

converted sunscan data
rows

number of rows of the field
rowwise

TRUE if the numbering is rowwise

Value

data frame with grids (col/row)

Generates report concerning converted data

Description

If one does not provide a report script, then the default report script is used.

Usage

generateReport(
  file,
  inputfolder,
  outputfolder,
  reportscript = system.file("reports", "default_report.R", package = "sunscanimport")
)

Arguments

file

filename
inputfolder

input folder
outputfolder

output folder
reportscript

script to generate the report

Details

A report script is an R script that may contain RMarkdown. Inside the script one can use the variable param with its elements param$file, param$inputfolder and param$outputfolder. The report will be placed in the outputfolder in the subdirectory report.

Notice that the package rmarkdown and knitr have to be installed to generate a report.

Creates Sample MeasurementID data

Description

Creates Sample MeasurementID data

Usage

generateSampleMeasurementIdData(data, interval = 0)

Arguments

data

converted sunscan data
interval

time interval after which a new PlotNR is assumed

Value

data frame with ids

Generates sample ID data

Description

Generates sample data to relate PlotNr to grids, PlotIDs or MeasurementIDs

Usage

generateSamplePlotIdData(data)

generateInitialPlotIdData(data)

generateInitialMeasurementIdData(data)

Arguments

data

LAI-Data from SunscanFile

Value

dataframe with IDs

Extracts LAI data from the file lines

Description

Extracts LAI data from the file lines

Usage

getData(lines, date)

Arguments

lines

vector of lines read from the data file
date

start date of measurements from meta data

Value

data.frame with LAI measurements

Fetches recursively all possible data files from a directory

Description

Fetches recursively all possible data files from a directory

Usage

getFileList(
  directory,
  prefix = "",
  extension = ".TXT",
  excludedir = "converted"
)

Arguments

directory

to search for data files
prefix

of files to take into account
extension

of files to take into account
excludedir

subdirectory name to exclude

Value

vector of potential data files

Gets meta data from the file header

Description

Gets meta data from the file header

Usage

getHeader(lines, path)

Arguments

lines

vector of lines read from the data file
path

path of the file

Value

named vector with meta data

Extracts PAR data from the file lines

Description

Extracts PAR data from the file lines

Usage

getParData(lines, date)

Arguments

lines

vector of lines read from the data file
date

start date of measurements from meta data

Value

data.frame with PAR measurements

Gets meta data from the file header

Description

Gets meta data from the file header

Usage

getSmallHeader(lines)

Arguments

lines

vector of lines read from the data file

Value

named vector with meta data

File name for the metadata file

Description

File name for the metadata file

File name for the LAI data file

File name for the PAR data file

File name for the summary file

File name for the boxplot image

File name for the report

Usage

headerFileName(file, outputfolder)

dataFileName(file, outputfolder)

pardataFileName(file, outputfolder)

summaryFileName(file, outputfolder)

boxplotFileName(file, outputfolder)

reportFileName(file, outputfolder)

Arguments

file

filename of data file
outputfolder

output folder

Value

filename

Checks if the line is a data line

Description

Data lines begin with a date

Usage

isDataLine(line)

Arguments

line

a line of text

Value

TRUE if data line

Checks if the data file has been moved to subfolder 'original'

Description

Checks if the data file has been moved to subfolder 'original'

Usage

isMovedFile(file, inputfolder, target = "original")

Arguments

file

filename
inputfolder

input folder
target

target folder

Value

TRUE if file has been moved to original folder

Checks if given file is a valid SunScan file

Description

Checks if file starts with 'Created by SunData' and if the files has at least 14 lines

Usage

isSunscanFile(path)

Arguments

path

path to the file

Value

TRUE if valid SunScan file

Checks if the line is a title line

Description

A title line starts a new metatdata section in the sunscan data file.

Usage

isTitleLine(line)

Arguments

line

a line of text

Value

TRUE if title line

Returns path for the data file moved to 'original' subfolder

Description

Returns path for the data file moved to 'original' subfolder

Usage

movedFileName(file, inputfolder, target = "original")

Arguments

file

filename
inputfolder

input folder
target

target folder

Value

path to data file

Moves data file to subfolder 'original'

Description

Moves data file to subfolder 'original'

Usage

moveFilesToSubfolders(file, inputfolder, target = "original")

Arguments

file

filename
inputfolder

input folder
target

target folder

Moves data file to subfolder 'original'

Description

Moves data file to subfolder 'original'

Usage

moveOriginalFile(file, inputfolder, target = "original")

Arguments

file

filename
inputfolder

input folder
target

target folder

Reads converted data

Description

Reads converted data

Usage

readConvertedHeader(file, outputfolder)

readConvertedData(file, outputfolder)

readConvertedParData(file, outputfolder)

readConvertedSummary(file, outputfolder)

readConvertedFiles(file, outputfolder)

Arguments

file

filename
outputfolder

output folder

Value

dataframe with converted data

Read dataframe with PlotID column

Description

Read dataframe with PlotID column

Usage

readIdData(file)

Arguments

file

filename

Value

data frame with the ids

Reorders columns in converted data

Description

Reorders columns in converted data

Usage

reorderDataColumns(data)

Arguments

data

imported sunscan data

Value

dataframe with reordered columns

Runs Shiny app

Description

Runs Shiny app

Usage

runSunscanApp(...)

Arguments

...

parameters passed to shiny::runApp

Saves metadata to file

Description

Saves metadata to file

Saves LAI data

Saves PAR data

Saves summary

Saves boxplot

Usage

saveHeader(data, file, outputfolder)

saveData(data, file, outputfolder)

saveParData(data, file, outputfolder)

saveSummary(data, file, outputfolder)

saveBoxplot(data, file, outputfolder)

Arguments

data

data frame
file

filename of original file
outputfolder

output folder

Splits the data when file contains multiple headers

Description

Splits the data when file contains multiple headers

Usage

splitLines(lines)

Arguments

lines

vector of lines from the data file

Value

list of line vectors

Strips the file extension

Description

Strips the file extension

Usage

stripFileExtension(file)

Arguments

file

filename

Value

file name without path and extension

Functions to import, convert and visualise data from LAI Sunscan device

Description

The package provides functions to:

  • convert a file or a directory

  • summarize or transform converted data

  • create reports for converted data

  • run a shiny app for interactive conversion

Author(s)

Gunther Krauss

Examples

## Not run: 
  runSunscanApp()
## End(Not run)

## Not run: 
  file <- "paulinenaue.TXT"
  inputfolder <-  "data/210908/original/"
  outputfolder <- "data/210908/"
  convfile <- convertSunscanFile(file,inputfolder, outputfolder)
  generateReport(convfile, inputfolder, outputfolder)
## End(Not run)

## Not run: 
  convertSunScanDirectory("data/")
## End(Not run)

## Not run: 
  data <- readr::read_delim("data/210908/converted/data_paulinenaue.txt", delim="\t")
  data_summary <- createSummary(data)
  data_wide <- transformToWideFormat(data)
## End(Not run)

Transform LAI data to wide format (1 row per PlotID)

Description

Each PlotID has only one row where each individual LAI measurements is in an own column. Number of columns is determined by the maxiumum number of measurements per PlotID. Measurements are populated from left to right and filled up by NAs.

Usage

transformToWideFormat(data, deleted = FALSE)

Arguments

data

data.frame with LAI data
deleted

include measurements marked as deleted

Value

data.frame in wide format