# mousetrap 3.2.0 2021-06-05

## General changes to existing functions

• The mt_spatialize function has been replaced with mt_length_normalize (to achieve consistent naming analogous to mt_time_normalize). The new function offers the same functionality with the exception that the created trajectories are now by default called ln_trajectories (instead of sp_trajectories), which stands for length-normalized trajectories and should ensure consistency in naming with time-normalized trajectories.
• Because of the renaming of sp_trajectories to ln_trajectories, all functions that by default were using the sp_trajectories are now by default using ln_trajectories (e.g., mt_cluster and mt_map). Additionally, to ease the transition many mousetrap functions now internally flexibly exchange ln_trajectories and sp_trajectories in the use argument (if the specified trajectories are missing and the other trajectories are found) and throw a warning if they replace one with the other.

## Changes in specific functions

• mt_spatialize: function is deprecated and replaced with mt_length_normalize. The reason for this is to achieve consistent naming analogous to mt_time_normalize. The mt_length_normalize function offers the same functionality as mt_spatialize with the exception that the created trajectories are now by default called ln_trajectories (instead of sp_trajectories), which stands for length-normalized trajectories and should ensure consistency in naming with time-normalized trajectories.
• mt_import_mousetrap: Now can also import trajectory coordinates when they are stored in scientific notation in the raw data (e.g., 2.98e-8).
• mt_plot and mt_plot_aggregate: Replaced only_ggplot with return_type argument. The new return_type argument allows for further customization of the plots: If return_type == "plot" (the default), a new ggplot is created and the trajectories are plotted using geom_path (corresponds to the old default behavior, where only_ggplot was set to FALSE). If return_type == "mapping", only the ggplot object containing the mapping but without any geoms is returned (corresponds to the old behavior where only_ggplot was set to TRUE). If return_type == "geoms", only the geoms are returned, which allows adding the plotted trajectories to an existing ggplot (new functionality).

## Bugs fixed

• mt_exclude_initiation: Bug fixed so that the correct initial position is used when removing the initial period without movement in a trial. Previously, mt_exclude_initiation was only behaving as intended when the initial position was (0,0), which probably was the case in many settings (in particular, if the trajectories were aligned using mt_align_start with default start values). If the initial position in a trial corresponded to a different value, the initial period without movement in most cases was simply not removed. This has now been fixed (closes #14).

# mousetrap 3.1.5 2020-08-26

## Changes in specific functions

• mt_measures: Introduced initiation_threshold argument to allow specifying a minimum distance from the start point of the trajectory that needs to be exceeded for calculating the initiation time.
• mt_import_mousetrap and mt_check_resolution: Introduced digits argument. If specified, timestamps will be rounded which can potentially be useful if timestamps are recorded with submillisecond precision.
• mt_import_mousetrap: Introduced unordered argument that allows for different options to handle unordered, that is, non-monotonically increasing timestamps within a trial.
• mt_plot and mt_plot_aggregate: Introduced wrap_var and wrap_ncol arguments that add wrapping to trajectory plots (i.e., splitting a plot across multiple columns and rows based on the levels of a single variable or a combination of variables).
• mt_plot_riverbed: Introduced na.rm argument which, if set to TRUE, allows the creation of riverbed plots from trajectories with unequal length (whether this is in practice desirable or not is an open question).

## Internal changes

• mt_import_long: Replaced dplyr/tidyr standard evaluation functions by using embracing and pivoting.
• mt_reshape: Replaced dplyr/tidyr standard evaluation functions by using embracing and pivoting.
• mt_plot_riverbed and mt_heatmap_ggplot: Replaced geom_raster with geom_tile.

# mousetrap 3.1.4 2019-12-05

## Announcements

• A book chapter on the mousetrap software packages has been published. It covers many common analyses using the mousetrap R package. Please cite it as follows when using mousetrap in your research:
• Kieslich, P. J., Henninger, F., Wulff, D. U., Haslbeck, J. M. B., & Schulte-Mecklenbeck, M. (2019). Mouse-tracking: A practical guide to implementation and analysis. In M. Schulte-Mecklenbeck, A. Kühberger, & J. G. Johnson (Eds.), A Handbook of Process Tracing Methods (pp. 111-130). New York, NY: Routledge.
• Besides, if you use functions for clustering and mapping trajectories, please also include the following reference:
• Wulff, D. U., Haslbeck, J. M. B., Kieslich, P. J., Henninger, F., & Schulte-Mecklenbeck, M. (2019). Mouse-tracking: Detecting types in movement trajectories. In M. Schulte-Mecklenbeck, A. Kühberger, & J. G. Johnson (Eds.), A Handbook of Process Tracing Methods (pp. 131-145). New York, NY: Routledge.

## Changes in specific functions

• mt_measures: Introduced hover_incl_intial argument to make inclusion of a potential initial phase without movement optional when calculating hovers. By default, this initial phase is included (as in previous versions).
• mt_measures: Multiple values can now be specified in the hover_threshold argument. If this is done, hovers and hover_time will be returned in separate variables for each threshold value (the variable name will be suffixed with the threshold value).
• mt_measures: Multiple values can now be specified in the flip_threshold argument. If this is done, flips (e.g., xpos_flips) will be returned in separate variables for each threshold value (the variable name will be suffixed with the threshold value).

## Internal changes

• When checking the class of an object, inherits is now used consistently instead of the class function to avoid problems with future R releases (>=4.0.0).

# mousetrap 3.1.3 2019-10-04

## Changes in specific functions

• mt_sample_entropy: By default, sample entropy is calculated based on the differences of the position values (following Hehman et al., 2015). An optional argument use_diff now has been introduced to allow users to override this behavior and use the untransformed values instead, by setting use_diff=FALSE.
• mt_align_start_end: Now checks, if start and end points are equal for a trial (separately per dimension). If so, returns a warning message as the aligned trajectory values for the respective dimension will be NaN/Inf/-Inf.

# mousetrap 3.1.2 2019-02-02

## Changes in documentation

• citation("mousetrap") now returns the correct citation for the mousetrap package.
• Updated mousetrap book chapter citations (see announcements above for correct citation).

## Changes in specific functions

• mt_import_long: internal change (prefix row_number() function with dplyr) to accomodate changes in dplyr 0.8.0.

# mousetrap 3.1.1 2018-07-06

## Announcements

• Book chapters on the mousetrap software packages have been accepted for publication. See version 3.1.3 above for updated references (as the book chapters meanwhile have been published).
• If you have any questions when using mousetrap, you can now ask them in the mousetrap forum at https://forum.cogsci.nl/index.php?p=/categories/mousetrap

## Changes in specific functions

• mt_map: now allows for mapping trajectories onto prototypes separately for different groups of trajectories (the prototypes will be rescaled separately to match the coordinate system of each group).
• mt_heatmap_ggplot: now allows for faceting using the facet_row and facet_col arguments.
• mt_diffmap: the condition can now simply be specified by providing the corresponding variable name (and the condition values can now be any type, provided that they only contain two levels).
• mt_plot and mt_plot_aggregate: transparency and line width can now be varied via the alpha and size arguments.
• mt_plot_riverbed: introduced grid_colors argument for setting the grid colors (use grid_colors = NA to omit grid lines).
• mt_reshape: internal changes reflecting changes in dplyr::summarize_at.
• mt_align_start and mt_align_start_end: if start is computed internally, it is now ensured that it is a named vector.
• mt_plot_add_rect: it is now ensured that this function does not influence the legend (previously, this could happen if the linetype argument was used in mt_plot)

# mousetrap 3.1.0 2017-05-20

## Announcements

• A first paper on the mousetrap software packages has been published. It presents the mousetrap plugin for creating mouse-tracking experiments in OpenSesame and also includes a short demonstration of basic analyses using the mousetrap R package. Please cite it as follows when using the mousetrap plugin in your research.
• Kieslich, P. J., & Henninger, F. (2017). Mousetrap: An integrated, open-source mouse-tracking package. Behavior Research Methods, 49(5), 1652-1667. https://doi.org/10.3758/s13428-017-0900-z
• The reference for the mousetrap R package has been updated as Zenodo now supports version independent DOIs.
• Kieslich, P. J., Wulff, D. U., Henninger, F., Haslbeck, J. M. B., & Schulte-Mecklenbeck, M. (2016). Mousetrap: An R package for processing and analyzing mouse-tracking data. https://doi.org/10.5281/zenodo.596640

## Changes in specific functions

• mt_derivatives: now always reports acceleration as difference in absolute velocity (the argument acc_on_abs_vel has been removed). Besides, the argument absolute has been introduced that indicates if absolute values for distances and velocities should be reported (by default, this is not the case). All of this is only relevant if a single dimension is specified in dimensions.
• mt_sample_entropy: the default values reported have changed (cf. bug fix below). mt_sample_entropy now only uses a custom function for computing sample entropy (which is faster and produces virtually identical results as pracma::sample_entropy if the same parameters are used). Therefore, the method argument has been removed. Besides, the lag argument has been renamed to m.
• mt_distmat, mt_cluster, mt_cluster_k, and mt_map: now provide the option to remove trajectory points containing missing values (by setting the na_rm argument to TRUE). Removal is done column-wise. That is, if any trajectory has a missing value at, e.g., the 10th recorded position, the 10th position is removed for all trajectories.
• mt_distmat, mt_cluster, mt_cluster_k, and mt_map: now allow for specifying the relative importance of each trajectory dimension via the weights argument. Technically, each variable is rescaled so that the standard deviation matches the corresponding value in weights. By default, weights is a vector of 1s implying equal importance of each dimension (i.e., all dimensions are standardized to a standard deviation of 1). This changes the default behavior of the functions compared to the previous release where the original variables were used without standardization. To use the original variables, set weights = NULL.
• mt_map: uses mousetrap::mt_prototypes as default for prototypes if no prototypes are provided.
• mt_average: now internally replaces NaNs with NAs. NaNs only occur if a specific dimension contains only NAs for an interval (which in practice only happens for acc values if the trial stops at the interval boundary).
• mt_standardize: now by default standardizes mouse-tracking measures across all trials if no within variable is specified.

## Bugs fixed

• mt_sample_entropy: Bug fixed for method="pracma" (the default method): The window size argument (which used to be specified using the lag argument - now this has been renamed to m) was incorrectly passed on to the tau argument of pracma::sample_entropy. It should have beend passed on to the edim argument. After fixing this, both methods in mt_sample_entropy provided virtually identical results (which is why the method argument has been dropped, see above).

## New functions

• bezier: create Bezier-curves using the Bernstein approximation.
• mt_scale_trajectories: standardize variables in a mouse trajectory array.
• mt_heatmap_raw: create high-resolution heatmap of trajectory data.
• mt_heatmap: plot trajectory heatmap using base plots.
• mt_heatmap_ggplot: plot trajectory heatmap using ggplot.
• mt_diffmap: create a difference-heatmap of two trajectory heatmap images.
• mt_animate: create a gif trajectory animation.
• Please note that although these functions have been tested extensively, they still have beta status.

## New data

• KH2017_raw: Raw mouse-tracking dataset from Kieslich & Henninger (in press).
• KH2017: Mouse-tracking dataset from Kieslich & Henninger (in press).

# mousetrap 3.0.0 2017-02-10

## Announcements

• We are delighted that Dirk Wulff and Jonas Haslbeck have joined the mousetrap team! They are contributing a number of new functions, particularly for clustering and visualization.
• The documentation of the mousetrap package can now also be found online at http://pascalkieslich.github.io/mousetrap/

## General changes to existing functions

• Introduction of class mousetrap for mousetrap data objects (such as mt_example). This facilitates, among other things, checking of the data class.
• Change of dimension order for all trajectory arrays: The old order was 1) trials, 2) variables, 3) samples. The new order is 1) trials, 2) samples, 3) variables. All functions and example data have been modified accordingly.
• Many reshape, aggregation, export, and plotting functions now accept a trajectory array as direct input to data.
• In case an analysis function adds measures to an existing data.frame, existing columns of the same name are now replaced and a warning is displayed (instead of merging the data.frames and adding generic suffixes).
• Arguments that were already deprecated and replaced (e.g., show_progress was replaced with verbose) have been removed.

## Changes in specific functions

• mt_align_start: function is now vectorized and allows for optionally aligning to mean start position across trials; default for save_as argument is set to use.
• mt_space_normalize: function is deprecated and replaced with mt_align_start_end. It offers similar functionality but is vectorized and allows for optionally aligning to mean start/end position across trials.
• mt_resample: now provides option to perform partial constant interpolation. Thanks to @sbrockhaus for the suggestion (cf. #7, #9).
• mt_derivatives: now provides option to additionally return timestamp differences.
• mt_measures: now optionally determines the number and duration of hovers (cf. #9), improved documentation and report of time measures (cf. #6).
• mt_plot: introduced facet_row and facet_col arguments for faceting.
• mt_plot_add_rect: internal change to avoid warning message (due to changes in ggplot2).
• mt_plot_riverbed: explicitly remove zero frequencies instead of relying on the alpha parameter.

## New functions

• read_mt: read MouseTracker raw data (.mt files).
• mt_align: general purpose function for aligning and rescaling trajectories. For specific operations, you can rely on the specialized functions mt_align_start and mt_align_start_end.
• mt_spatialize: re-represent each trajectory spatially so that adjacent points become equidistant to each other.
• mt_add_trajectory: add a new trajectory to a trajectory array.
• mt_bind: join two trajectory arrays.
• mt_count: count the number of observations for each trajectory.
• mt_angles: calculate movement angles for trajectories.
• mt_distmat: compute the distance matrix for each pair of trajectories.
• mt_cluster: perform trajectory clustering with a specified number of clusters.
• mt_cluster_k: estimate the optimal number of clusters using various methods.
• mt_map: map trajectories onto a predefined set of prototype trajectories (a core set is provided in mt_prototypes).

## Bugs fixed

• mt_measures: make checks for timestamps > 0 and < 0 independent. Thanks to Regina Köhler for pointing this out.
• mt_plot_per_trajectory: fix bug that all trajectories were plotted on each page (introduced through previous change in mt_reshape). Thanks to Bence Palfi for discovering this.
• create_results (internal function): Explicitly select mt_id column (instead of assuming that it is the first column - which is, e.g., often not the case in data[["data"]]); ensure for case overwrite=FALSE that function also works when multiple columns are merged and when all columns except mt_id are dropped beforehand.

## Removed functions

• read_mousetracker: removed as it is recommended to directly import the MouseTracker raw data using the new function read_mt.
• mt_movement_angle: removed as it is replaced with new and more general function mt_angles.
• mt_calculate_derivatives, mt_calculate_deviations, mt_calculate_measures: removed as they were previously deprecated and replaced with mt_derivatives, mt_deviations, mt_measures.

# mousetrap 2.0.0 2016-10-25

## General changes to all existing functions

• Renamed show_progress argument to verbose (+ set default to FALSE).
• Introduced dimensions argument to explicitly specify the names of the columns in the trajectory array that contain the mouse positions. In most cases, the default is c("xpos","ypos") as the x- and y-positions should be used. Note that in some functions (as specified in the documentation) the order of the labels matters, the first value will be taken as the label of the x-positions, the second as the label of the y-positions.
• Introduced timestamps argument to explicitly specify the dimension in the trajectory array containing the timestamps.
• Perform merging of trial and trajectory data (e.g., in mt_subset and mt_reshape) based on the rownames. Therefore, the mt_id column in data.frames is not needed anymore - but is kept for the convenience of the user. The column is called "mt_id" in import and measures functions. mt_reshape allows the user to specify the label of the mt_id column explicitly.
• As a consequence of the previous changes: Removal of the internal variables mt_variable_labels and mt_id.
• Removed calculate from all mt_calculate functions: mt_calculate_measures, mt_calculate_derivatives, mt_calculate_deviations are now called mt_measures, mt_derivatives, mt_deviations.
• Introduction of internal utils function create_results (that simplifies including the newly created trajectories or measures in the existing mousetrap data object).
• Performance improvement of reshaping, aggregation, and visualization functions through internal changes in mt_reshape: base::merge and reshape2 functions are replaced with functions from the tidyr and dplyr packages (and custom functions). Package dependencies were adjusted accordingly. As the dplyr functions may introduce additional classes for the reshaped data (such as grouped_df and tbl_df), a new argument (convert_df) is introduced that converts the reshaped data to pure data.frames by default (thereby dropping additional classes).

## Changes in specific functions

• mt_import_mousetrap, mt_import_long, mt_import_wide: Allow specifying several variables for the trial identifier in mt_id_label. A new ID variable will be created by combining the values of each variable.
• mt_import_mousetrap: Make import more robust against variables with empty logs (warning message is returned in the end) (closes #5, thanks to @sbrockhaus).
• mt_import_long, mt_import_wide: Import any number of additional variables using add_labels (closes #4).
• mt_import_long: Timestamps are no longer used for ordering if mt_seq_label is not provided. Instead, data will be imported in the order in which they were stored in raw_data.
• mt_import_long: Improved speed by relying on functions from the tidyr and dplyr packages.
• mt_space_normalize, mt_align_start: Introduction of dimensions argument and the corresponding arguments start and end (deprecate xpos_start/xpos_end/ypos_start/ypos_end). This also fixes the internal bug that in mt_align_start xpos_start was passed on as ypos_start to mt_space_normalize (instead of ypos_start).
• mt_derivatives: Rename dimension argument to dimensions, enable function to work with an arbitrary number of dimensions.
• mt_deviations: Vectorized function point_to_line for time speed up (closes #2, thanks to @sbrockhaus).
• mt_measures: Allow for flexible dimension labels and rename all measures columns relating only to x- or y-positions depending on the values in dimensions (e.g., x_max becomes xpos_max, x_flips becomes xpos_flips). Change column label xy_dist to total_dist.
• mt_measures: Simplify AUC calculation using the actual x- and y-positions . New AUC values correlate to 1.00 with old values in mt_example, but in some cases extremely small differences are possible (maximum difference of 2.328e-10 in mt_example).
• mt_reshape, mt_aggregate, mt_aggregate_per_subject: Replace aggregation_function argument with .funs, which is passed on to the aggregation function(summarize_at). .funs also allows for specifying several aggregation functions.
• mt_plot_per_trajectory: New arguments xlim and ylim for specifying the axes limits explicitly and axes_exact for plotting exact axes.
• mt_plot_per_trajectory: New arguments rect, color, and fill for plotting rectangles (usually representing the response buttons).
• mt_plot (and related functions): New argument points allows for plotting points.

## New functions

• mt_add_variables: add new variables to trajectory array.
• mt_export_long: export mouse-tracking data in long format (wrapper for mt_reshape).
• mt_export_wide: export mouse-tracking data in wide format (wrapper for mt_reshape).

## Bugs fixed

• mt_align_start: Fixed bug that xpos_start (instead of ypos_start) was passed on as ypos_start to mt_space_normalize.
• mt_average: Fixed bug that if intervals were specified explicitly using intervals, the wrong interval size was used when averaging (the default size of 100 was used).

# mousetrap 1.2.0 2016-07-09

• New function mt_align_start adjusts trajectories so that they have the same start position (wrapper for mt_space_normalize)
• New function mt_calculate_deviations calculates the idealized trajectory and the perpendicular deviations of the actual trajectory from it for each position in the trajectory array
• For many functions, a trajectory array can now be provided directly via the data argument. In this case, the use argument will be ignored and only the resulting trajectory array will be returned
• mt_plot_riverbed now preserves factor levels for facets
• mt_calculate_derivatives now allows for custom dimension names using the prefix argument
• mt_plot_per_trajectory now receives the file name as the first argument

# mousetrap 1.1.0 2016-06-09

• mt_import_mousetrap now offers possibility to combine several variables in mouse-tracking raw data
• mt_plot_riverbed now allows for faceting
• mt_check_resolution now offers possibility to check (relative) frequencies of desired timestamp differences
• Improved preprocessing of mouse-tracking raw data for mt_import_mousetrap
• Change of default scale for fill in mt_plot_riverbed
• Custom x and y axis labels for mt_plot_riverbed can no longer be set via x_label and y_label (but can be added using the ggplot2 functions xlab() and ylab(), see Examples)
• Minor fix in package documentation (#1) (thanks to @sbrockhaus)
• Minor fix in documentation of x/y reversals (thanks to Barnabas Szaszi)

# mousetrap 1.0.0 2016-03-19

• First release