Rafnuss commented 1 year ago

See https://github.com/Rafnuss/GeoPressureR/wiki/Migration-v2-%E2%80%90--v3 🎉 Indicates import new exiting feature to check out! ⚠️ Might be confusing at first coming from the v2. ❌ Removed

GeoPressureR object

Old	New	Comment
`pam`	`tag`	⚠️ Generic term see this
`sta`	`stap`	Better suited for STAtionary Period.
`grl`	`graph`	More explicit name.
	`map`	⚠️ New likelihood map are stored inside `tag`. `marginal` is the only map not stored in `tag`
	`path`	New created by `graph_simulation()`, `graph_most_likely()` or `tag2path()`. Data.frame
	`pressurepath`	New Data.frame
	`param`	⚠️ New named list stored inside `tag` and `graph` keeping track of all parameters used in all functions. Do not edit manually, but useful to export at the end as json file.

Functions

Tag

Old	New	Comment
`pam_read`	`tag_create`
`pam_read_check`	❌
`pam_read_delim_dto`	`tag_create_dto`	Not exported
	`tag_label`	🎉 New This new single function group all the `tag_label_*` functions for a more efficient workflow
`pam_classify`	`tag_label_auto`
`trainset_read`	`tag_label_read`	⚠️ Note the new `trainset_read` is not the same as the previous (see Utility section)
`trainset_write`	`tag_label_write`	⚠️ Note the new `trainset_read` is not the same as the previous
`pam_sta`	`tag_label_stap`
	`tag_set_map`	🎉 New Define parameters for the map and stap
	`tag_update`	🎉 New Update a `tag` with a new label file. Allows to recompute pressure maps only for stap that have change.
	`tag_assert`	New Check status of a tag object. Not exported
	`print.tag`	New
	`plot.tag`	New
	`plot_tag_pressure`	New
	`plot_tag_light`	New
	`plot_tag_twilight`	New
	`plot_tag_acceleration`	New
`geopressure_map2path`	`tag2path`
	`tag2map`	New return a GeoPressureR `map` from a `tag`

GeoPressure

Old	New	Comment
	`geopressure_map`	🎉 Run both `geopressure_mismatch` and `geopressure_likelihood` together to make the workflow more efficient. Also doesn't store `mse` and `mask` by default to save space.
`geopressure_map`	`geopressure_map_mismatch`	make more explicit and consider mismatch to incorporate both mse and mask
`geopressure_prob_map`	`geopressure_map_likelihood`	replace probability by likelihood
	`geopressure_map_preprocess`	New Convert the pressure timeseries into an optimal pressure for geopressureapi
`geopressure_ts`	`geopressure_timseries`	⚠️ Make name more explicit despite long.

GeoLight

Old	New	Comment
`find_twilights`	`twilight_create`
	`twilight_label_write`	New
	`twilight_label_read`	New
	`geolight_map`	🎉 New function that create the light likelihood map in `tag`, similar to `geopressure_map`.
`solar`	`geolight_solar`
`zenith`	`geolight_zenith`
`refracted`	`geolight_refracted`
	`ligh2mat`	New Convert a timeserie of light into a matrix of day of year, time of day

Graph

Old	New	Comment
`graph_create`
`graph_trim`	`graph_create_prune`	Not exported
`graph_download_wind`	`tag_download_wind`	⚠️ Use `tag` object and not `graph`
`graph_add_wind`
	`graph_set_movement`	🎉 New Defining all parameters for the movement model without actually computin anything.
	`graph_transition`	New Allow to compute the transition matrix on the fly, thus saving memory
`flight_bird`	`create_bird`
	`print.bird`	New Check a bird object
`flight_power`	`speed2power`	Not exported
`flight_prob`	`speed2prob`	More descriptive of what the function does
`graph_marginal`
`graph_simulation`
	`graph_most_likely`	🎉 New more efficient implementation than using the `igraph` package.
	`graph_assert`	New Check status of a graph object
	`print.graph`	New

Map

Old	New	Comment
	`map_create`	🎉 New GeoPreussreR `map` are now S3 objects
	`print.map`	New
	`plot.map`	New
	`rast.map`	New convert a `map` to a `terra::rast`
	`map_expend`	New `map` are defined by only extend and scale, this function allows to compute lat, lon and dim

Path

Old	New	Comment
`path2df`	`ind2path`
`graph_path2edge`	`path2edge`
	`plot.path`	New

Pressurepath

Old	New	Comment
`geopressure_ts_path`	`pressurepath_create`	⚠️ Focus on the main outcome (`pressurepath`)
	`pressurepath_update`	🎉 New Update a `pressurepath` with a new label file. similar to `tag_update`.
	`plot.pressurepath`	New
	`pressurepath2altitude`	New

Param

Old	New	Comment
	`param_create`	New
	`print.param`	New

Flight

❌ Avoid flight which can be computed "on the fly" from stap using stap2flight()

Utility

Old	New	Comment
	`trainset_read`	New more generic function taking any df as input as to work with `tag_label` and `twilight_label`. Not exported
	`trainset_write`	New more generic function taking any df as input as to work with `tag_label` and `twilight_label`. Not exported
	`stap2flight`	New
	`stap2duration`	New
`graph_path2lonlat`	❌
`geopressureviz`

Variables

Tag

Old	New	Comment
`pam`	`tag`
`id`
`min_duration`
`pathname`	`directory`	see this
`file`		`basename` would be better but less user friendly see this
`pressure_file`
`light_file`
`acceleration_file`
`path`	`sensor_path`	dirname+basename
`crop_start`
`crop_end`
`skip`
`col`
`date_format`

Set map

Old	New	Comment
`extent`
`scale`
	`known`	New data.frame defining the knwon position (e.g., equipement and retrieval). Use to avoid computing the likelihood map for nothing and calibration of light
	`include_stap_id`	New
	`include_min_duration`	New

GeoPressure

Old	New	Comment
`pressure`
`max_sample`
`margin`
`timeout`
`workers`
`presssure_maps`	❌	⚠️ Remove and integreated within `geostap`
`s`	`sd`	Match classic R base function name for standard deviation.
`thr`	`thr_mask`	Make more explicit
`fun_w`	`log_linear_pooling_weight`	Aligned with geolight aggregation
	`keep_mse_mask`
`lon`
`lat`
`start_time`
`end_time`
`verbose`	`quiet`
`path`
`include_flight`

Geolight

Old	New	Comment
`light`
`threshold`	`twl_thr`
`shift_k`	`twl_offset`	Align with `TwGeos` but adds twl in front
`twl`	`twilight`	⚠️ more explicit
`adjust_calib`	`twl_calib_adjust`
`w_llp`	`twl_llp`	⚠️ Not to confuse with llp in geopressure
`zenith`
`sun`
`tm`	`date`	Align with the format

Graph

Old	New	Comment
`grl`	`graph`
`static_prob`	❌	⚠️ Remove and integreated within `tag_set_map`
	`field`	Define which field in geostap should be use as likelihood
`thr_prob_percentile`	`thr_likelihood`
`thr_gs`
`thr_as`
`area`	`extent`
`cds_key`
`cds_user`
	`type`
`nj`

Field of graph

Old	New	Comment
`s`
`t`
`as`	❌	avoid storing unnecessary (computable from `gs` and `ws`)
`gs`
`ws`
`ps`	`obs`	Stored as 3D matrix rather than edge level for memory efficiency.
`p`	`transition`	⚠️ Now optional. When possible, use `movement` which can compute trans on the flight with `graph_trans` and save memory
	`movement`	Parameter to be used in `graph_trans`
		Parameter to be used in `graph_trans`
`sz`
`equipment`
`retrieval`
`flight_duration`	❌	Computable with `stap2flight`
`lat`	❌	Computable with `extent_scale2grid`
`lon`	❌	Computable with `extent_scale2grid`
`extent`
`resolution`	❌
`temporal_extent`	❌
	`stap`
	`scale`
	`mask_water`

Utility

Old	New	Comment
`species_name`
`mass`
`wing_span`
`wing_aspect`
`wing_area`
`body_frontal_area`
`bird`		not super specific
`speed`		slightly different than as,gs, ws
`method`
`shape`
`scale`			⚠️ Not to confuse with scale in geostap
`location`
`fun_power`	`power2prob`
`low_speed_fix`

Rafnuss commented 1 year ago

Brainstorm

`pam`

~~pam (pressure-acceleration-magnetism)~~
:white_check_mark: tag (https://www.movebank.org/cms/movebank-content/movebank-attribute-dictionary#tag_terms), but use data logger in the text
~~gl used in paper~~
~~gdl from gdl_id. seems to be mainly used by SOI.~~
~~gls global location sensor~~
~~dl for datalogger~~
~~log, logger~~
~~sensor~~

`sta`

Need to think of the elevation/alitutde/local period.

~~keep sta~~
:white_check_mark: stap
~~sp~~
~~stpe~~

`GeoLight`

Utilisation: solar, refracted, find_twilights, light2mat

:white_checkmark: `geolight*`
~~gl_*~~

`geopressure_*`

:white_checkmark: `geopressure*`
~~gp_*~~

`geopressure_map()`

~~geopressure_mismatch_mask()~~
~~geopressure_mse_mask()~~
~~geopressure_error()~~
:white_check_mark: geopressure_mismatch()

`geopressure_prob_map()`

~~geopressure_ll()~~
:white_check_mark: geopressure_likelihood()

`geopressure_ts_*()`

:white_check_mark:geopressure_timeseries()
:white_check_mark:geopressure_timeseries_path()

`prob`

keep ~~prob~~
:white_check_mark: likelihood
~~L lh, ~~
~~lm for likelihood map~~
~~plm~~
~~llhdor ll~~

`graph`

:white_check_mark: keep graph
trajectory
hmm
Static probability static_prob, grl$ps -> observation likelihood obs_likelihood grl$O
grl$ps -> grl$likelihood (target likelihood and not source).
thr_prob_percentile -> thr_likelihood
thr_gs -> thr_gs

Rafnuss commented 1 year ago

Script to get all arguements

tmp <- do.call(rbind, lapply(ls("package:GeoPressureR"), function(fn_name){
  fn <- tryCatch(get(fn_name, mode = "function", envir = asNamespace('GeoPressureR')), error = function(e) NULL)
  tmp <- data.frame(
    arg = names(formals(fn))
  )
  tmp$fun <- fn_name
  return(tmp)
}))
write.csv(tmp, file = "~/Downloads/arg.csv")

Rafnuss / GeoPressureR

Renaming function and variables #55

GeoPressureR object

Functions

Tag

GeoPressure

GeoLight

Graph

Map

Path

Pressurepath

Param

Flight

Utility

Variables

Tag

Set map

GeoPressure

Geolight

Graph

Utility

Brainstorm

`pam`

`sta`

`GeoLight`

`geopressure_*`

`geopressure_map()`

`geopressure_prob_map()`

`geopressure_ts_*()`

`prob`

`graph`