Biologging tools for diving predators in R

agl_mean | Angle average |

agl_rescale | Rescale angle to [-pi; pi] |

as.bsm | General S3 utils for bsm objects |

as.data.frame.bsm | Coerce brokenstick model to data.frame |

as.ses | Creates or tests for 'ses'. |

at_ker | Test if animal is located around Kerguelen |

axisPOSIXct | Draw a correct axis for POSIXct objects |

biolum_events | Identify potential bioluminescence emission events |

BioPIC | BioPIC: bioluminescent event detection tool |

biopic.qr | BioPIC QR decomposition on a TDR sample |

bottom_delim | Find the dives' bottom start and end |

bottom_delim_bsm | Delimitate bottom phase of dive using brokenstick models |

bottom_delim_halsey | Delimitate bottom phase of dive using wiggles and steps |

bottom_delim_std | Delimitate bottom phase of dive using depth threshold |

bottom_delim_vspd | Delimitate bottom phase of dive using vertical speed... |

broadness_index | Broadness index |

brokenstick | Fitting brokenstick models |

bsmfit | Fitter function for brokenstick models |

check_nomtch | Deal with missing periods |

coef.bsm | Extract brokenstick models coefficients |

compose | Function composition |

correct_depth | Correct depth sequence from drift of values over time |

correct_duplicated_time | Fix duplicates in TDR time stamps |

correct_time | Fix jumps and duplicates in TDR time stamps |

curry | Curry |

delta | Compute difference between extremes in a set of observations |

depth_consistency_index | Depth consistency index between two dives |

depth_range_index | Depth Range Index |

df_search | Search recurssively to a data.frame |

dive_delim | Find the dives start and end |

dive_zone_index | Compute goodness of fit of brokenstick models: Dive Zone... |

drift_stat | Use brokensticks to identify potential drifts |

dynamic_acc | Dynamic (Body) acceleration DBA |

eco.mem | Subset the slots of bsm objects |

elt_delim | Extract indices corresponding to a symbol from a "delim"... |

entropy | Shannon entropy index on time at depth proportions |

exp10 | Reciprocal function of base::log10 |

exses | An tiny dataset (about 10 days) of an SES equipped with an... |

first | Return first or last element of a list of vector |

flatten_list | Flatten a list |

floorPOSIXct | floorPOSIXct |

front | Add averaged oceonagraphic fronts to an existing plot |

gcd | Greatest Common Divisor |

grapes-bw-grapes | Special operator to test if numeric values belong to a given... |

grapes-c-grapes | Operator for function composition |

grapes-else-grapes | Else special operator |

grapes-w-slash-i-grapes | x with(in/out) y |

ind | Set and get the current individual |

is_day | Use time and location to find if events occured during the... |

is_dive_truncated | Check if a dive profile is complete or truncated |

is.error | is.error |

is.injective | Check if f: X -> Y is injective |

isobath | Add isobaths to an existing plot (Kerguelen area) |

is.POSIXct | is.POSIXct |

kerbathy | Bathymetry of the Kerguelen area |

li | Linear interpolation |

list_depth | Depth of an R object |

max_dist_cost | Cost functions for automatic brokenstick models. |

max_residual | Get the maximun residual of a BSM at a given iteration |

min_n | Create a function that return a result if number of valid obs... |

nearly_equal | Vectorized predicate for near equality testing of numerics |

nNA | Count the number of NAs in a vector |

no_interpreter | Subset dive numbers with values as using indices |

nstr | nstr |

numIn | Extract numbers in character strings |

nUN | Count the number of unique values in a vector |

optBrokenstick | Fitting automatic brokenstick models |

overall_DBA | Overall Dynamic Body Acceleration (ODBA) |

pca_count | Count the number of Prey Catch Attemps (PCA) |

per | Decompose an atomic vector to its successive values and their... |

pitch | Attitude angles from static accelation |

plot.bsm | Plot brokenstick models |

plot.dzi | Plot method for "dzi" objects |

plot.tdr | plot for TDR data |

pmean | pmean |

predict.bsm | Brokenstick model predictions |

prey_catch_attempts | Identify Prey Catch attempts |

print.bsm | Print method for bsm objects |

print.dzi | Print method for dzi objects |

prof | Compute temperature profile from TDR recordings |

read.wcih | Import data from Wildlife Computers ".tab" text files |

replaceMissing | Replace values in an atomic vector. |

rescale | Scale a series between two values |

residuals.bsm | Extract brokenstick model residuals |

resize | Resize an individual |

rollapply | Apply a function along a vector or a list |

SI_light | Convert Wildlife Computers light values from/to linear W/cm^2... |

sofronts | Southern ocean climatologic fronts |

static_acc | Static acceleration |

straightness | Compute straightness index |

summary.bsm | Print summary of a brokenstick model |

sunPos | sunPos |

sun_position | Compute sun azimuth and elevation given a location and a... |

swimming_effort | Compute swimming effort |

symmetry_index | Dive/bottom symmetry index |

tdrexpand | Expand a summary variable to the length of TDR data |

tdrply | Apply function to subsets of a TDR dataset |

time_at_depth | Compute the Time Allocation at Depth (TAD) index of a dive |

time_reso | Sampling rate of a TDR dataset |

transp | Color helpers |

ty_delim | Extract indices from "delim" table using a regexp-like syntax |

ty_interpreter | Get detailed parse information from "ty" regular expressions |

update.bsm | Update and Re-fit a brokenstick model |

upd_warn | Update warning column in delim table |

vectorial_DBA | Vectorial Dynamic Body Acceleration (VeDBA) |

which.bw | Match values against a data.frame with start and end values |

which.dive | Find to which specific dive/surface a instant belongs to |

which.row | from time stamp to row number |

which.stick | To which brokenstick segment a point belongs to ? |

wiggles | Count/Extract wiggles in 2D dataset. |

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