Find out the main highlights of each update.
Fixes: * Fix printLastSection() crash for very large
datasets. * Fix printCircular() crash if there are six or
more groups but only one is present at the array. * Fix actel missing
some efficiency peers as per issue #72. * Fix
comments not being appended to status.df in the residency()
analysis. * Fix minor bug where comments could not be saved after
interacting with the graphical interface. * Prevent crash in
migration() if an array has 0 efficiency and there are no
arrays coming before it. * Prevent crash if the dot file/string line
breaks are coded as \r\n. * Prevent crash while printing
circular plots for the reports on Macs where the svg engines are not
working. * Prevent crash in residency() if one group has no
valid detections at all. * Fix bug in plotRatios() brought
up in issue #77 which
would occur when the user specified a section for which not all groups
were detected. * Prevent crashes in residency() when the
data has an unusually high percentage of exact-time detections
(e.g. midnight). * Prevent crash if only some tags have multiple sensors
and Sensor.unit is only included for those tags. * Prevent crash if the
study area/population is so large that it clashes with ggplot’s size
limit failsafes. * Fix message overflow reported in issue #78.
Changes: * Changed the inner mechanics of the graphical widgets from
RGtk2 to tcltk, as RGtk2 is now gone from CRAN. Should not affect user
experience. * Renamed createWorkspace() to
blankWorkspace() following cases of confusion regarding
function purpose. Closes #80 * Removed
dependency from package RGDAL; updated distance calculations code
accordingly. * Moved package vignettes to
https://hugomflavio.github.io/actel-website/index.html. * Removed
deprecated argument plot.detections.by. *
minimum.detections has been replaced by
min.total.detections and min.per.event. *
section.minimum has been replaced by
section.warning and section.error.
Enhancements: * Improve handling of manually set
section.warning and section.error arguments
when the set values don’t respect the
section.warning >= section.error rule. * Implement
area-based scales for circular plots. To obtain reports with the legacy
linear circular scale, users can still run
options(actel.circular.scale = "linear") before running
analyses. plotTimes() received a new argument
circular.scale. * Improve handling of manually set
jump.warning and jump.error arguments when the
set values don’t respect the jump.warning <= jump.error
rule. * Change the behaviour of recoverLog() so it attempts
to save the log to actel_job_log.txt if a file
argument is not provided. * Added new force argument to
blankWorkspace() and exampleWorkspace(). * New
Code.space column in the biometrics allows the user to
specify the code space of the target tags. * New arguments in
plotArray(): by.group and
y.style. See function documentation for more details. *
Include preload() log in reports where preloaded data is
used. * plotRatios() can now subset multiple groups and
sections simultaneously. The user can also decide to either colour the
plot by group or by section using the new col.by argument
(issue #77)).
Fixes: * Prevent crash in residency if the overall data period starts in winter time but the data for a given fish starts in summer time. * Prevent crash in residency caused by missing “save.tables.locally” argument. * Fix bug related to wrong type of detections object in preload(). * Fix bad formatting of the summary section in reports produced in Linux OS’s.
Changes: * The argument plot.detections.by in functions
explore(), migration() and residency() has been renamed to
detections.y.axis. * The argument type in the
function plotDetections() has been renamed to y.axis.
Enhancements: * Verify that deployments do not end before they start.
* Improve verification of station and array names, to avoid troublesome
characters slipping through and potentially crashing the analyses. * The
function plotDetections() has been expanded with the following
arguments: section.alias, x.label.format,
only.valid and like.migration.
Fixes: * Prevent warning during printing of the progression flowchart, related to overlapping array names (that could also lead to an actual error). * Fix undesired behaviour in unknown receiver mechanisms and improve unknown handling. * Prevent crash in array efficiency estimation if release sites have spaces. * Prevent wrong output in array efficiency estimations if array names are contained within each other. * Prevent missing arrays when finding array paths due to overlapping array names. * Prevent crash in distancesMatrix if spatial contains a “longitude” or “latitude” column. * Fix silent bug that could cause array efficiency estimates to be misplaced in the output. * Prevent crash during circular plot saving caused by illegal characters in the file name.
Enhancements: * New functionality: expand events and edit the
validity of individual detections. * Added Section information to the
detections and the movement tables. * Automatically convert “-” to NA in
the Data column of Thelma log files. * Automatically rename Y axis in
plotDetections to “Array” if type = “arrays”. * Added possibility to
save orphan detection files for later inspection. * Include detections
source file in a new “Source.file” column. * New argument
‘save.tables.locally’ allows the user to save temporary tables in the
current working directory. Particularly useful for Mac users that cannot
activate the graphical user interface. * Improve job log recovery method
so it is not as intrusive. Including new function recoverLog(). * Only
display GUI windows once they are ready. * Check for impassable jumps
between release and first event too. * Array live times are now
calculated and included in the ‘arrays’ object. * The ‘deployments’
object has been extended and now includes array and standard station
name. * actel can now dynamically check for array live times when
checking jump distances, to avoid triggering warnings and errors simply
because some arrays were not active. * New plotLive()
function allows the user to plot the periods during which each array was
active. The option ‘show.stations’ can be used to plot each individual
station live time as well. * Group warnings if more than four of the
same type of warnings shows up for any given tag. * The argument
plot.detections.by now defaults to ‘auto’, so actel can try
to optimize space use in the detection plots. * Included citation
information for the recently accepted paper describing actel.
Fixes: * Prevent crash if data used as input for
preload() contains factors. * Prevent crash during
individual plot printing if number of stations is higher than 29. *
Prevent bad structuring of the legend in individual plots if
plot.detections.by = 'arrays'. * Prevent crash of CJS
functions when running tags with multiple sensors. * Prevent CJS crash
due to overlapping array names. * Prevent crash if spatial has release
sites, but biometrics doesn’t (in CJS calculations of migration). *
Fixed a bug where the sensor data would get scrambled when reading
standard format detection files. * Fixed visual bug where the progress
bar for sensor plots would not reach 100%.
Changes: * plotMoves() has been renamed to
plotDetections() * In the residency analysis, the
following output objects have changed name: *
daily.ratios is now time.ratios *
daily.positions is now time.positions * In the
residency analysis report, the section ‘Section progression’ has been
renamed to ‘Global residency’.
Enhancements: * Never show unknown events during movement table
display. * Show how many invalid events were omitted in the message that
opens movement events. * Expand unknown receiver options to allow
discarding unknown detections and repeating the same action for all
occurrences. * Improve error messages when something fails during
detections loading. * Improve detection file recognition mechanics. *
New function plotSensors() can be used to plot the sensor
data for each tag. * Sensor plots are now painted by array or section
(matching the detection plots). * New function plotMoves()
can be used to plot the movement evolution of multiple tags
simultaneously. * New function plotArray() can be used to
plot the simultaneous number of fish present at a subset of arrays or,
if cumulative = TRUE, the cumulative number of individual
fish to have reached that subset of arrays per unit of time. * New
argument in the residency() analysis: timestep
allows the user to decide whether residency calculations should be done
on a daily basis (default) or an hourly basis (at cost of computing
time). * New fail-safe prevents unhandled function failure if arrays
were accidentally assigned to more than one section. * Introduced
fail-safes so report compiling does not fail when R is not being able to
produce SVG graphics. * Improved cleanliness by moving temporary report
files to a dedicated actel folder. * New function
plotResidency() can be used to plot the individual
residency for each fish. * The column order in global.ratios now follows
the section order. * New output in the residency analysis: group.ratios
(similar to global.ratios, but per group). * New function
plotRatios() can be used to plot the global and group
residency. * Improve handling of very long legends in the global
residency plots. * Display times as hh:mm:ss in the movement tables to
avoid ambiguity in interpretation. * Colour the SEM ranges in the
circular plots (matching the respective groups). The level of darkening
can be controlled with the new mean.range.darken.factor
argument in plotTimes().
Fixes: * Prevent crash if all detections for a given stray tag were removed during detection quality checks. * Prevent migration crash if all movement events are rendered invalid before section movements are created. * Prevent crash related with circular plotting when running an analysis on more than eight fish groups. * Prevent bug in older R versions where actel did not display all table rows, for long tables displayed in the console. * Fixed ‘last to last’ speed calculations. A bug was found where this speed method was accidentally matching first stations for distance calculation, rather than last stations. * Fix bug where valid.movements would retain the invalid speed values if the fish no longer moved between arrays. * Fix bug where the wrong tags would be stored in stray_tags.csv. * Fig bug where stray tags from previous runs would leak into stray_tags.csv.
Changes * stripCodeSpaces() has been replaced with
extractSignals(). * Sections are now set up using a
‘Section’ column in the spatial.csv file. The ‘sections’
argument has been deprecated. See the updated vignettes for details. *
Arrays can now be named freely (short names are still
recommended). * Perform quality checks on the ‘replicates’ argument
earlier in the analyses. * User decisions no longer have default
options. * Users must now list only the tag signals in
the ‘override’ argument.
Enhancements: * The shapefiles of the study areas can now be water or
land polygons. Use the new argument “type” in loadShape()
to switch from land shapefiles (the default) to water shapefiles. *
Paint groups consistently in circular plots. * Improved handling of long
array lists in individual detection plots. * Display event number on
inactiveness checks. * New argument discard.first allows
the user to discard detections that happen before a given amount of time
has passed after release. * New function
extractCodeSpaces() has been implemented. * New
preload() function allows advanced users to run actel
without requiring input files. See more in the new dedicated vignette. *
New argument section.order allows the user to specify the
order by which the sections should be listed. * plotTimes()
has been expanded with new arguments and better compatibility for
multiple groups. * New argument plot.detections.by allows
the user to plot the detections by array, rather than by station.
Applied both to the analyses and to plotMoves(). * User
decisions can now be followed by a in-line comment (started with “#”).
Additionally, actel automatically adds default comments to decisions so
these are easier to read through in the job log. * Message that opens
movement events now includes the respective tag and the type of
movements displayed (section or array movements). * Include user
comments in the txt job logs. * In case of error, the user can now save
a copy of the log up to the point where the function crashed. * Verify
number of columns on all detection files. * Run quality checks on
standard detection files. * New getSpeeds() function allows
the user to quickly extract all speed information from the analyses.
Fixes: * Sort deployment rows by start time. Avoids false triggering of redeployment-before-retrieval errors. * Prevent failure to identify receivers if the model-serial combination has two or more “-” characters. * Prevent residence crash if no fish entered a given section. * Prevent crash if study area only has one array. * Fix replicates argument formulation in the log’s function call carbon copy. * Prevent crash if array names contain regex characters. * Fix bug causing crash when attempting to save a movements table to a temporary file.
Changes: * maximum efficiency estimates in residency now only take
into account known missed events and recorded events in the denominator
(previously, potentially missed events were being included as well). *
GUI interaction mechanisms were changed as a consequence of updating
from package gWidgets to gWidgets2. * The argument ‘path’ has been
removed from explore, migration and
residency. The user must now move to the target directory
using setwd() before running the analyses. * Analysis files
are saved in a temporary folder and are only made permanent by user
request. * The ‘report’ argument now defaults to FALSE. By setting
‘report’ to TRUE, the user acknowledges that a file will be written in
the current working directory. * Auxiliary files to the report are now
saved in a temporary directory. The user can still access the report
figures by right-clicking them in the html report and saving them. *
actel no longer saves compiled detections to the user’s working
directory by default. A new argument ‘save.detections’ (defaults to
FALSE) was added to allow users to mimic the old behaviour. * actel no
longer saves the stray tags summary to the user’s working directory by
default. If there are stray tags in the data, the users will be asked if
they would like to save a copy of the summary. * transitionLayer no
longer saves the output automatically into the working directory. *
distancesMatrix now receives the transition layer as an R object rather
than a file name. * distancesMatrix now requires user confirmation
before writing a ‘distances.csv’ file into the working directory. *
createMatrix and completeMatrix now work with R objects rather than
files. The user must manually save the function output to a
‘distances.csv’ file to include it in the next analysis. * The possible
values of speed.method have been changed to ‘last to first’ and ‘last to
last’, for a more logical interpretation of the results. The explore
vignette has been updated accordingly. * Separated part of
transitionLayer into a preceding function
loadShape. * exampleWorkspace and
createWorkspace now require a target directory.
Enhancements: * Perform early quality checks on the content of
‘sections’ before advancing with migration and residency analysis. *
Allow user to hide release sites from the study area diagrams. * Improve
spatial.csv vs spatial.txt mismatch error messaging by showing missing
arrays. * Improve colour and caption handling on individual residency
plots for study areas with many sections. * Improve handling of spatial
file in distancesMatrix (including new fail-safes). * Added support for
tags that emit multiple signals (i.e. multi-sensor tags). * Plot sensor
data in the reports. * Allow intra-array efficiency to be calculated
even if no inter-array efficiency could be calculated. * Allow the GUI
to pop up if the number of lines to display goes over
getOptions(“max.print”). * Hide biometrics’ section from the report if
no biometric data was found. * New advEfficiency function
allows user to calculate more robust efficiency estimates. * Improved
release.overview and group.overview objects so they can be used as an
input to advEfficiency(). * New plotTimes function allows
the user to create circular plots of specific subsets of the time data,
with the ability to include night shades too. * getTimes
and timesToCircular are now exported, allowing the user to
quickly format the input for plotTimes. * A new page has
been included in the vignettes aiming to explore what can be done with
the results of actel’s analyses. * Included usage examples on exported
functions. * Verify the names of the release site arrays as soon as the
spatial.csv is loaded. * Added support for timestamps using a “T”
separator between date and time in the biometrics and deployments files.
* new ‘discard.orphans’ argument allows the user to automatically
discard all detections that do not fall within receiver deployment
periods. * Users can now create and use a generic detections file.
Details for the format of this file are provided in the “Detections”
section of vignette 1.0. * migration() has been upgraded to be capable
of handling backwards movements. The status.df has also been improved,
and a new graphic was included to the report (last array). * new
plotMoves function allows the user to create personalised
detection plots for specific tags. * EPSGcode argument has been removed
from all distances matrix related functions. actel now looks for the
coordinate system within the shape file supplied. * distances matrix
functions can now work with degree-based coordinate systems too.
Fixes: * Force R to assume detection files are separated by commas (prevents occasional Thelma log crash). * Fix bug where fish whose data started in summer time and extended into winter time would cause one day to be lost in the daily positions during residency analysis. * Prevent arrays from having maximum estimated fish passing through greater than previous arrays (unless new fish are released). * Fix internal bug where efficiency matrices did not have “1” at Release for all fish (did not impact results). * Fix bug where arrays with no detections for a group*release combination would cause skewed estimates. * Fix estimation of passed fish when using intra-array estimates. * Fix split CJS’s not receiving information about intra-array estimates. * Avoid crash if a fish makes a U turn without being detected in all sections. * Avoid crash if group names have ‘.’ characters in them. * Avoid crash if some group names are entirely contained within other groups. * Fix bug where ‘disregard.parallels’ was ironically disregarded and parallels always blocked peer assignment. * Prevent crash if the spatial.csv file cannot be updated due to being open elsewhere. * Fix bug where the presence of multiple instantaneous shifts in section would mess up the residency lists. * Fix bug preventing distancesMatrix from recognising the transition layer object. * Fix bug where the temporary detections object would be overwritten during inactiveness checks with a distance matrix present. * Fix bug causing speed calculations to crash in the presence of unknown detections. * Fix bug where the Invalid.detections and Invalid.events columns in the status.df of residency would always return 0. * Prevent invalid detections from being considered during intra-array efficiency estimations. * Fix bug where fish with only one movement event would not count towards efficiency calculations. * Fix very specific bug where 8 shaped study areas would not have the bottleneck array accounted as a “known” failure in case a fish moved from one side of the constriction to the other without being detected.
Changes: * array.overview is now called
group.overview. * Fish that never entered a section now
have NA total and average times for that section during residency
analysis. This allows to distinguish between fish that never entered a
section (NA time) and fish that only had one detection at a section (0
time).
Enhancements: * The object detections now contains a
“Valid” column, similarly to the movements objects. *
Invalid detections are now painted in grey in the individual detection
plots. * Check for duplicated detections and give the user a chance to
clear them out before continuing. * Prevent unhandled crashes if the
‘replicates’ argument is badly structured. * Show number of released
fish per release location in the release sites table. * Detailed
progression per group and release site is now exported through a
release.overview object. * Prevent migration from
continuing if some arrays are not associated to a section. * Warn user
if override is requested for a fish that is not detected. * Improve
mechanics behind suggestions to linearise movements. * Movement tables
can now be visualised in a new window with the argument GUI. * Improve
handling of partially empty groups and release sites in the biometrics
file. * Improve flexibility in handling shape files with dimensions
incompatible with the requested pixel size. * Improve the distances
matrix so it can cope with unspecified release sites. * transitionLayer
can now take into account the station positions and expand the study
area as needed. * transitionLayer now has a “buffer” argument, which can
be used to expand the study area beyond the limits of the shape file. *
distancesMatrix will now warn the user if some stations are completely
cut off from the rest (i.e. there is no water path). * Reports are now
opened using utils::browseURL, allowing the report to be open even when
the computer is not connected to the internet. * Sensor values are now
transported through the analysis and returned in the valid detections
(for Vemco loggers only for now). * Ensure the legend in the residency
graphics follows the order specified in the sections argument. * Improve
Thelma .csv file handling for files exported with new column structure.
* Allow for multiple expected first arrays (e.g. if fish are released in
a lake whose exits are covered with receivers).
Fixes: * Fix mechanisms that deal with unknown receivers * Edge arrays are now recognized if sections are provided * The columns “Backwards.movements” and “Backwards.movements” now display correct values * Prevent crash if inactive.warning is set but inactive.error is left null (applicable for speed checks as well) * Prevent crash when calculating multi-way efficiency estimations for fish that jumped at release * Prevent crash during residency analysis if a fish had more than one detection but all at the exact same time * Prevent crash when loading empty detection files * Display correct event numbers and names when speed warnings are triggered
Changes: * ‘maximum.time’ has been renamed to ‘max.interval’ *
‘tz.study.area’ has been renamed to ‘tz’ * ‘start.timestamp’ has been
renamed to ‘start.time’ * ‘end.timestamp’ has been renamed to
‘stop.time’ * After a transition period, actel function has
been removed * ‘cautious.assignment’ has been removed from the migration
analysis * Analysis run with ‘override’ are no longer saved with a
“_corrected” appendix
Enhancements: * ‘tz’ is now checked against the output of
OlsonNames to ensure a valid time zone is entered. *
messages and warnings are now printed using message and
warning * Stop if any of the input files has duplicated
column names * Warn user if success.arrays is not defined in
migration * ‘minimum.detections’ is now available in all
functions. * ‘override’ is now available in all functions, and allows
the user to directly invalidate specific events. * ‘Detections’ column
in the object status.df (migration analysis) has been split
into ‘Valid.detections’ and ‘Invalid.detections’. * Package-level
documentation has been implemented (can be found using ?actel). *
explore, migration and residency
documentation has been expanded. * Force all individual residency plots
to include all used locations in the caption, to ensure locations always
show up with the same colour. * Stations are now grouped by array in the
individual plots, following the array order provided either by the
spatial.csv file or the spatial.txt file. * Improved links between the
report plots and the R objects by naming the objects containing the data
used in the plots.
Fixes: * Make checkInactiveness start counting time in the right event. * Remove spaces in bio’s release sites before matching with stations’ standard names.
Enhancements: * explore(), migration() and residency() now output auxiliary information for the upcoming RSP functions.