Closed Rafnuss closed 1 year ago
pam
pam
(pressure-acceleration-magnetism)tag
(https://www.movebank.org/cms/movebank-content/movebank-attribute-dictionary#tag_terms), but use data logger in the textgl
used in papergdl
from gdl_id
. seems to be mainly used by SOI.gls
global location sensordl
for dataloggerlog
, logger
sensor
sta
Need to think of the elevation/alitutde/local period.
sta
stap
sp
stpe
GeoLight
Utilisation: solar
, refracted
, find_twilights
, light2mat
gl_*
geopressure_*
gp_*
geopressure_map()
geopressure_mismatch_mask()
geopressure_mse_mask()
geopressure_error()
geopressure_mismatch()
geopressure_prob_map()
geopressure_ll()
geopressure_likelihood()
geopressure_ts_*()
geopressure_timeseries()
geopressure_timeseries_path()
prob
prob
likelihood
L
lh
, ~~lm
for likelihood mapplm
llhd
or ll
graph
graph
trajectory
hmm
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
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")
See https://github.com/Rafnuss/GeoPressureR/wiki/Migration-v2-%E2%80%90--v3 π Indicates import new exiting feature to check out! β οΈ Might be confusing at first coming from the v2. β Removed
GeoPressureR object
pam
tag
sta
stap
grl
graph
map
tag
.marginal
is the only map not stored intag
path
graph_simulation()
,graph_most_likely()
ortag2path()
. Data.framepressurepath
param
tag
andgraph
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
pam_read
tag_create
pam_read_check
pam_read_delim_dto
tag_create_dto
tag_label
tag_label_*
functions for a more efficient workflowpam_classify
tag_label_auto
trainset_read
tag_label_read
trainset_read
is not the same as the previous (see Utility section)trainset_write
tag_label_write
trainset_read
is not the same as the previouspam_sta
tag_label_stap
tag_set_map
tag_update
tag
with a new label file. Allows to recompute pressure maps only for stap that have change.tag_assert
print.tag
plot.tag
plot_tag_pressure
plot_tag_light
plot_tag_twilight
plot_tag_acceleration
geopressure_map2path
tag2path
tag2map
map
from atag
GeoPressure
geopressure_map
geopressure_mismatch
andgeopressure_likelihood
together to make the workflow more efficient. Also doesn't storemse
andmask
by default to save space.geopressure_map
geopressure_map_mismatch
geopressure_prob_map
geopressure_map_likelihood
geopressure_map_preprocess
geopressure_ts
geopressure_timseries
GeoLight
find_twilights
twilight_create
twilight_label_write
twilight_label_read
geolight_map
tag
, similar togeopressure_map
.solar
geolight_solar
zenith
geolight_zenith
refracted
geolight_refracted
ligh2mat
Graph
graph_create
graph_trim
graph_create_prune
graph_download_wind
tag_download_wind
tag
object and notgraph
graph_add_wind
graph_set_movement
graph_transition
flight_bird
create_bird
print.bird
flight_power
speed2power
flight_prob
speed2prob
graph_marginal
graph_simulation
graph_most_likely
igraph
package.graph_assert
print.graph
Map
map_create
map
are now S3 objectsprint.map
plot.map
rast.map
map
to aterra::rast
map_expend
map
are defined by only extend and scale, this function allows to compute lat, lon and dimPath
path2df
ind2path
graph_path2edge
path2edge
plot.path
Pressurepath
geopressure_ts_path
pressurepath_create
pressurepath
)pressurepath_update
pressurepath
with a new label file. similar totag_update
.plot.pressurepath
pressurepath2altitude
Param
param_create
print.param
Flight
β Avoid
flight
which can be computed "on the fly" fromstap
usingstap2flight()
Utility
trainset_read
tag_label
andtwilight_label
. Not exportedtrainset_write
tag_label
andtwilight_label
. Not exportedstap2flight
stap2duration
graph_path2lonlat
geopressureviz
Variables
Tag
pam
tag
id
min_duration
pathname
directory
file
basename
would be better but less user friendly see thispressure_file
light_file
acceleration_file
path
sensor_path
crop_start
crop_end
skip
col
date_format
Set map
extent
scale
known
include_stap_id
include_min_duration
GeoPressure
pressure
max_sample
margin
timeout
workers
presssure_maps
geostap
s
sd
thr
thr_mask
fun_w
log_linear_pooling_weight
keep_mse_mask
lon
lat
start_time
end_time
verbose
quiet
path
include_flight
Geolight
light
threshold
twl_thr
shift_k
twl_offset
TwGeos
but adds twl in fronttwl
twilight
adjust_calib
twl_calib_adjust
w_llp
twl_llp
zenith
sun
tm
date
Graph
grl
graph
static_prob
tag_set_map
field
thr_prob_percentile
thr_likelihood
thr_gs
thr_as
area
extent
cds_key
cds_user
type
nj
Field of
graph
s
t
as
gs
andws
)gs
ws
ps
obs
p
transition
movement
which can compute trans on the flight withgraph_trans
and save memorymovement
graph_trans
graph_trans
sz
equipment
retrieval
flight_duration
stap2flight
lat
extent_scale2grid
lon
extent_scale2grid
extent
resolution
temporal_extent
stap
scale
mask_water
Utility
species_name
mass
wing_span
wing_aspect
wing_area
body_frontal_area
bird
speed
method
shape
scale
location
fun_power
power2prob
low_speed_fix