Description Usage Arguments Details Value Examples

`autoGoldy`

Define the most stable set of observations in time-series infrared
gas exchange data. Currently optimized for LICOR 6400 .rtf data output.

1 2 3 |

`filename` |
The path and name of a file to parse and optimize |

`trait1` |
Character string that matches the name of a column in the input dataset. This data will be used for optimization computation |

`trait2` |
A (optional) second trait to assist with optimization |

`window` |
The size of the window in the sliding window optimization protocol |

`verbose` |
Logical, should updates be printed |

`weights` |
A numeric vector of length 4. These values indicate the weighting of the slope [1] and coeficient of variation (cv) [2] of trait1 and trait2 [3,4] |

`...` |
additional arguments, not currently in use. |

This function runs the following pipeline:

1. Import and parse rtf LICOR datasets

2. Standardize (0-1) and plot the raw data

3. Run sliding window analysis to calculate the slope and CV of standardized data

4. Find the most stable window

5. Plot diagnostics

6. Output the optimal data

a single row dataframe that gives the most stable data from the time series data input originally. A single page figure with some information is also printed.

1 | ```
## Not Run out<-autoGoldy(filename="./data/RO_052714_rr11_h57s", window=4, weights=c(1,1,.5,.5))
``` |

jtlovell/goldy documentation built on May 20, 2019, 3:14 a.m.

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