mousetrap 3.0.0

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

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

Changes

• 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

Changes

• 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 Barnabás Szászi)

mousetrap 1.0.0

This is the first release of the mousetrap package.
We hope that the package enables users to easily import, preprocess, analyze, aggregate and visualize mouse-tracking data in R.
We are looking forward to your feedback!