TAT-frequency data
In RchivalTag: Analyzing and Interactive Visualization of Archival Tagging Data

merge_histos

R Documentation

merge and/or rebin TAD/TAT-frequency data

Description

The joint analysis of archival tagging data from different tagging programs is often hampered by differences in the tags' setups, e.g. by the user-specified temporal resolution of time series data or the definition of summary data products. The latter particuarly concerns different selected bin breaks of Time-at-Depth (TAD) and Time-at-Temperature (TAT) frequency data from archival tags by Wildlife Computers.

The purpose of this function is to allow:

1) a grouping of TAD and TAT data from multiple tags based on similiar bin breaks (For this, run the function with default statements, i.e. force_merge is FALSE),

2) merging (rebinning) of TAD and TAT data from multiple tags based on the bin breaks that all tags have in common (To do so, run the function with force_merge set TRUE).

3) merging (rebinning) of TAD and TAT data from multiple tags based on new user-specified tad_breaks and/or tat_breaks. In this case, the force_merge-statements TRUE and FALSE will omit or seperately group tags that do not share all user-specified bin breaks, respectively.

To combine of TAD/TAT data of several hist_lists, see combine_histos.

To visualize Time-at-Temperature (TaT) and Time-at-Depth (TaD) data, please see hist_tat and hist_tad, respectively.

Usage

merge_histos(hist_list, tad_breaks=NULL, tat_breaks=NULL, force_merge=FALSE)
rebin_histos(hist_list, tad_breaks=NULL, tat_breaks=NULL, force_merge=FALSE)

Arguments

`hist_list`	A list-of-lists containing the TAD and TAT frequency data and the corresponding `bin_breaks` from one or several tags.
`tad_breaks`	a numeric vector defining the `bin_breaks` for the merging (rebinning) of the TAD frequency data. In case that the additional argument `force_merge` is set `TRUE`, only tags whose original TAD bin breaks included all of the user-specified `tad_breaks` will be merged in a single group ('merged') based on the new bin breaks, while other tags will be omitted in the output. By contrast, if `force_merge` is set `FALSE`, tags that do not contain all specified `tad_breaks` will be merged in seperate groups (group2, group3, etc.), based on similar `bin_breaks`.
`tat_breaks`	a numeric vector defining the `bin_breaks` for the merging (rebinning) of the TAT frequency data. In case that the additional argument `force_merge` is set `TRUE`, only tags whose original TAT bin breaks included all of the user-specified `tat_breaks` will be merged in a single group ('merged') based on the new bin breaks, while other tags will be omitted in the output. By contrast, if `force_merge` is set `FALSE`, tags that do not contain all specified `tat_breaks` will be merged in seperate groups (group2, group3, etc.), based on similar `bin_breaks`.
`force_merge`	If `FALSE` (default), groups of tags with similar TAD and TAT-`bin_breaks` will be combined (no merging on new bin breaks) and identifier labels renamed as group1, group2, etc. If set `TRUE`, TAD and TAT frequency data will be merged on user-specified `tad/tat_breaks` or, if those arguments are missing, on the `bin_breaks` that all tags have in common. In both latter cases, identifier labels will be renamed "merged".

Value

A list-of-lists of grouped or merged TAD and TAT frequency data.

$ TAD:List
..$ group1 : List of 2
.. ..$ bin_breaks: num
.. ..$ df : data.frame
$ TAT:List
..$ group1 : List of 2
.. ..$ bin_breaks: num
.. ..$ df : data.frame
..$ group2 : List of 2
...

Author(s)

Robert K. Bauer

Examples

## example 1) read, merge and plot TAD frequency data from several files:
## part I - read histogram data from two files:
hist_dat_1 <- read_histos(system.file("example_files/104659-Histos.csv",package="RchivalTag"))
hist_dat_2 <- read_histos(system.file("example_files/104659b-Histos.csv",package="RchivalTag"))
## note the second list is based on the same data (tag), but on different bin_breaks

## part II - combine TAD/TAT frecuency data from seperate files in one list:
hist_dat_combined <- combine_histos(hist_dat_1, hist_dat_2)
par(mfrow=c(2,1))
hist_tad(hist_dat_combined)
hist_tat(hist_dat_combined)

## part III - force merge TAD/TAT frecuency data from seperate files 
# in one list, by applying common bin_breaks:
hist_dat_merged <- merge_histos(hist_dat_combined,force_merge = TRUE)
hist_tad(hist_dat_merged)
hist_tat(hist_dat_merged)

## part IV - plot merged data:
hist_tad(hist_dat_merged) # of all tags
unique(hist_dat_merged$TAD$merged$df$DeployID) ## list unique tags in merged list
hist_tad(hist_dat_merged, select_id = "15P1019b", select_from = 'DeployID') # of one tag

## part V - unmerge data:
unmerge_histos(hist_dat_merged)

RchivalTag documentation built on Nov. 10, 2023, 5:06 p.m.