From fee09fe50de87ece95295a925f4c06d9e40493c1 Mon Sep 17 00:00:00 2001 From: "Pascal J. Kieslich" Date: Thu, 5 Dec 2019 18:02:53 +0100 Subject: [PATCH] Update online documentation --- DESCRIPTION | 2 +- docs/404.html | 2 +- docs/LICENSE-text.html | 2 +- docs/authors.html | 2 +- docs/index.html | 4 +- docs/news/index.html | 51 ++++++++++++++----- docs/reference/KH2017.html | 2 +- docs/reference/KH2017_raw.html | 2 +- docs/reference/bezier.html | 2 +- docs/reference/bimodality_coefficient.html | 2 +- docs/reference/index.html | 2 +- docs/reference/mousetrap.html | 2 +- docs/reference/mt_add_trajectory.html | 13 +++-- docs/reference/mt_add_variables.html | 2 +- docs/reference/mt_aggregate.html | 15 ++++-- docs/reference/mt_aggregate_per_subject.html | 15 ++++-- docs/reference/mt_align.html | 17 +++++-- docs/reference/mt_align_start.html | 12 +++-- docs/reference/mt_align_start_end.html | 14 +++-- docs/reference/mt_angles.html | 14 +++-- docs/reference/mt_animate.html | 37 ++++++++++---- docs/reference/mt_average.html | 18 +++++-- docs/reference/mt_bind.html | 2 +- docs/reference/mt_check_bimodality.html | 13 +++-- docs/reference/mt_check_resolution.html | 10 ++-- docs/reference/mt_cluster.html | 23 ++++++--- docs/reference/mt_cluster_k.html | 26 +++++++--- docs/reference/mt_count.html | 5 +- docs/reference/mt_derivatives.html | 17 +++++-- docs/reference/mt_deviations.html | 15 ++++-- docs/reference/mt_diffmap.html | 25 ++++++--- docs/reference/mt_distmat.html | 15 ++++-- docs/reference/mt_example.html | 2 +- docs/reference/mt_example_raw.html | 2 +- docs/reference/mt_exclude_initiation.html | 14 +++-- docs/reference/mt_export_long.html | 24 ++++++--- docs/reference/mt_heatmap.html | 15 ++++-- docs/reference/mt_heatmap_ggplot.html | 13 +++-- docs/reference/mt_heatmap_raw.html | 31 ++++++++--- docs/reference/mt_import_long.html | 18 +++++-- docs/reference/mt_import_mousetrap.html | 17 +++++-- docs/reference/mt_import_wide.html | 19 +++++-- docs/reference/mt_map.html | 18 +++++-- docs/reference/mt_measures.html | 33 +++++++++--- docs/reference/mt_plot.html | 46 +++++++++++++---- docs/reference/mt_plot_add_rect.html | 2 +- docs/reference/mt_plot_per_trajectory.html | 22 ++++++-- docs/reference/mt_plot_riverbed-1.png | Bin 55416 -> 55421 bytes docs/reference/mt_plot_riverbed.html | 18 +++++-- docs/reference/mt_prototypes.html | 2 +- docs/reference/mt_qeffect.html | 14 +++-- docs/reference/mt_remap_symmetric.html | 13 +++-- docs/reference/mt_resample.html | 17 +++++-- docs/reference/mt_reshape.html | 25 ++++++--- docs/reference/mt_sample_entropy.html | 15 ++++-- docs/reference/mt_scale_trajectories.html | 16 ++++-- docs/reference/mt_space_normalize.html | 14 +++-- docs/reference/mt_spatialize.html | 11 ++-- docs/reference/mt_standardize.html | 13 +++-- docs/reference/mt_subset.html | 2 +- docs/reference/mt_time_normalize.html | 14 +++-- docs/reference/print.mt_heatmap_raw.html | 2 +- docs/reference/read_mt.html | 5 +- docs/reference/reexports.html | 2 +- docs/reference/scale_within.html | 12 +++-- man/mousetrap.Rd | 1 - man/mt_add_trajectory.Rd | 11 +++- man/mt_aggregate.Rd | 13 +++-- man/mt_aggregate_per_subject.Rd | 13 +++-- man/mt_align.Rd | 15 ++++-- man/mt_align_start.Rd | 10 +++- man/mt_align_start_end.Rd | 12 +++-- man/mt_angles.Rd | 12 +++-- man/mt_animate.Rd | 35 ++++++++++--- man/mt_average.Rd | 16 ++++-- man/mt_check_bimodality.Rd | 11 +++- man/mt_check_resolution.Rd | 8 ++- man/mt_cluster.Rd | 21 ++++++-- man/mt_cluster_k.Rd | 24 ++++++--- man/mt_count.Rd | 3 +- man/mt_derivatives.Rd | 15 ++++-- man/mt_deviations.Rd | 13 +++-- man/mt_diffmap.Rd | 23 +++++++-- man/mt_distmat.Rd | 13 +++-- man/mt_exclude_initiation.Rd | 12 +++-- man/mt_export_long.Rd | 20 ++++++-- man/mt_heatmap.Rd | 13 +++-- man/mt_heatmap_ggplot.Rd | 11 +++- man/mt_heatmap_raw.Rd | 29 ++++++++--- man/mt_import_long.Rd | 16 ++++-- man/mt_import_mousetrap.Rd | 15 ++++-- man/mt_import_wide.Rd | 17 +++++-- man/mt_map.Rd | 16 ++++-- man/mt_measures.Rd | 15 ++++-- man/mt_plot.Rd | 44 ++++++++++++---- man/mt_plot_per_trajectory.Rd | 20 ++++++-- man/mt_plot_riverbed.Rd | 14 +++-- man/mt_qeffect.Rd | 12 ++++- man/mt_remap_symmetric.Rd | 11 ++-- man/mt_resample.Rd | 15 ++++-- man/mt_reshape.Rd | 23 ++++++--- man/mt_sample_entropy.Rd | 13 +++-- man/mt_scale_trajectories.Rd | 14 +++-- man/mt_space_normalize.Rd | 12 +++-- man/mt_spatialize.Rd | 9 +++- man/mt_standardize.Rd | 11 +++- man/mt_time_normalize.Rd | 12 +++-- man/read_mt.Rd | 3 +- man/scale_within.Rd | 10 +++- 109 files changed, 1120 insertions(+), 390 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 3fd2d5b..aba3bf8 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -52,4 +52,4 @@ Suggests: LinkingTo: Rcpp Encoding: UTF-8 LazyData: TRUE -RoxygenNote: 6.1.1 +RoxygenNote: 7.0.2 diff --git a/docs/404.html b/docs/404.html index 62ea22c..c363e7d 100644 --- a/docs/404.html +++ b/docs/404.html @@ -67,7 +67,7 @@ mousetrap - 3.1.3 + 3.1.4 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 67aba17..e7c1742 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -67,7 +67,7 @@ mousetrap - 3.1.3 + 3.1.4 diff --git a/docs/authors.html b/docs/authors.html index 2b509e0..6199fec 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -67,7 +67,7 @@ mousetrap - 3.1.3 + 3.1.4 diff --git a/docs/index.html b/docs/index.html index dfbc1f3..4daa008 100644 --- a/docs/index.html +++ b/docs/index.html @@ -34,7 +34,7 @@ mousetrap - 3.1.3 + 3.1.4 @@ -78,7 +78,7 @@

General Information

The mousetrap package is developed by Pascal Kieslich, Dirk Wulff, Felix Henninger, and Jonas Haslbeck. It is published under the GNU General Public License (version 3).

-

An overview of the functions in this package can be found online. It can also be accessed from within R using package?mousetrap once the package has been installed. Please see news for a summary of changes in the package. Questions about using mousetrap can be asked in the forum.

+

An overview of the functions in this package can be found online. It can also be accessed from within R using package?mousetrap once the package has been installed. Please see news for a summary of changes in the package. Questions about using mousetrap can be asked in the forum.

The mousetrap package offers functions for importing mouse-tracking data in different formats and from various sources. One option to collect mouse-tracking data is by using the open-source graphical experiment builder OpenSesame in combination with the mousetrap-os plugin.

diff --git a/docs/news/index.html b/docs/news/index.html index 3f0522a..bb578c4 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -67,7 +67,7 @@ mousetrap - 3.1.3 + 3.1.4
@@ -107,9 +107,9 @@

Changelog

Source: NEWS.md -
+

-mousetrap 3.1.3 2019-10-04 +mousetrap 3.1.4 Unreleased

@@ -126,6 +126,30 @@

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.
    • @@ -145,9 +169,9 @@

  • Updated mousetrap book chapter citations (see announcements above for correct citation).

-
+

-Changes in specific functions

+Changes in specific functions
  • mt_import_long: internal change (prefix row_number() function with dplyr) to accomodate changes in dplyr 0.8.0.
    • @@ -167,9 +191,9 @@

-
+

-Changes in specific functions

+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).
    • @@ -206,9 +230,9 @@

-
+

-Changes in specific functions

+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.
    • @@ -290,9 +314,9 @@

  • Arguments that were already deprecated and replaced (e.g., show_progress was replaced with verbose) have been removed.

-
+

-Changes in specific functions

+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.
    • @@ -383,9 +407,9 @@

  • 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

+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.
    • @@ -490,6 +514,7 @@

    Contents

      +
    • 3.1.4
    • 3.1.3
    • 3.1.2
    • 3.1.1
      • diff --git a/docs/reference/KH2017.html b/docs/reference/KH2017.html index ff05fa5..2c45529 100644 --- a/docs/reference/KH2017.html +++ b/docs/reference/KH2017.html @@ -71,7 +71,7 @@ mousetrap - 3.1.3 + 3.1.4
    diff --git a/docs/reference/KH2017_raw.html b/docs/reference/KH2017_raw.html index 32a649f..ea89a09 100644 --- a/docs/reference/KH2017_raw.html +++ b/docs/reference/KH2017_raw.html @@ -72,7 +72,7 @@ mousetrap - 3.1.3 + 3.1.4

diff --git a/docs/reference/bezier.html b/docs/reference/bezier.html index b90ac61..946f732 100644 --- a/docs/reference/bezier.html +++ b/docs/reference/bezier.html @@ -71,7 +71,7 @@ mousetrap - 3.1.3 + 3.1.4
diff --git a/docs/reference/bimodality_coefficient.html b/docs/reference/bimodality_coefficient.html index b0bde35..6daf391 100644 --- a/docs/reference/bimodality_coefficient.html +++ b/docs/reference/bimodality_coefficient.html @@ -70,7 +70,7 @@ mousetrap - 3.1.3 + 3.1.4
diff --git a/docs/reference/index.html b/docs/reference/index.html index 8d47925..02ea161 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -67,7 +67,7 @@ mousetrap - 3.1.3 + 3.1.4
diff --git a/docs/reference/mousetrap.html b/docs/reference/mousetrap.html index cff8852..923a891 100644 --- a/docs/reference/mousetrap.html +++ b/docs/reference/mousetrap.html @@ -71,7 +71,7 @@ mousetrap - 3.1.3 + 3.1.4
diff --git a/docs/reference/mt_add_trajectory.html b/docs/reference/mt_add_trajectory.html index 2a7f035..4ba20ab 100644 --- a/docs/reference/mt_add_trajectory.html +++ b/docs/reference/mt_add_trajectory.html @@ -69,7 +69,7 @@ mousetrap - 3.1.3 + 3.1.4
@@ -114,8 +114,15 @@

Add new trajectory to trajectory array.

Add a single new trajectory to trajectory array.

- 
mt_add_trajectory(data, use = "trajectories", save_as = use,
-  xpos = NULL, ypos = NULL, xypos = NULL, id = "new")
+ 
mt_add_trajectory(
+  data,
+  use = "trajectories",
+  save_as = use,
+  xpos = NULL,
+  ypos = NULL,
+  xypos = NULL,
+  id = "new"
+)

Arguments

diff --git a/docs/reference/mt_add_variables.html b/docs/reference/mt_add_variables.html index 999c26a..6542613 100644 --- a/docs/reference/mt_add_variables.html +++ b/docs/reference/mt_add_variables.html @@ -73,7 +73,7 @@ mousetrap - 3.1.3 + 3.1.4 diff --git a/docs/reference/mt_aggregate.html b/docs/reference/mt_aggregate.html index ad76d43..672307a 100644 --- a/docs/reference/mt_aggregate.html +++ b/docs/reference/mt_aggregate.html @@ -73,7 +73,7 @@ mousetrap - 3.1.3 + 3.1.4 @@ -122,9 +122,16 @@

Aggregate mouse-tracking data per condition.

a wrapper function for mt_reshape.

- 
mt_aggregate(data, use = "measures", use_variables = NULL,
-  use2 = "data", use2_variables = NULL, subject_id = NULL,
-  trajectories_long = TRUE, ...)
+ 
mt_aggregate(
+  data,
+  use = "measures",
+  use_variables = NULL,
+  use2 = "data",
+  use2_variables = NULL,
+  subject_id = NULL,
+  trajectories_long = TRUE,
+  ...
+)

Arguments

diff --git a/docs/reference/mt_aggregate_per_subject.html b/docs/reference/mt_aggregate_per_subject.html index 4234e9f..664058d 100644 --- a/docs/reference/mt_aggregate_per_subject.html +++ b/docs/reference/mt_aggregate_per_subject.html @@ -74,7 +74,7 @@ mousetrap - 3.1.3 + 3.1.4 @@ -124,9 +124,16 @@

Aggregate mouse-tracking data per condition separately for each subject.

mt_reshape.

- 
mt_aggregate_per_subject(data, use = "measures", use_variables = NULL,
-  use2 = "data", use2_variables = NULL, subject_id,
-  trajectories_long = TRUE, ...)
+ 
mt_aggregate_per_subject(
+  data,
+  use = "measures",
+  use_variables = NULL,
+  use2 = "data",
+  use2_variables = NULL,
+  subject_id,
+  trajectories_long = TRUE,
+  ...
+)

Arguments

diff --git a/docs/reference/mt_align.html b/docs/reference/mt_align.html index e97e255..16d6ef5 100644 --- a/docs/reference/mt_align.html +++ b/docs/reference/mt_align.html @@ -70,7 +70,7 @@ mousetrap - 3.1.3 + 3.1.4 @@ -116,10 +116,17 @@

Align trajectories.

or coordinate system.

- 
mt_align(data, use = "trajectories", save_as = use,
-  dimensions = c("xpos", "ypos"), coordinates = "isotropic",
-  align_start = FALSE, align_end = FALSE, align_side = "no",
-  verbose = FALSE)
+ 
mt_align(
+  data,
+  use = "trajectories",
+  save_as = use,
+  dimensions = c("xpos", "ypos"),
+  coordinates = "isotropic",
+  align_start = FALSE,
+  align_end = FALSE,
+  align_side = "no",
+  verbose = FALSE
+)

Arguments

diff --git a/docs/reference/mt_align_start.html b/docs/reference/mt_align_start.html index aeabda7..eab15fd 100644 --- a/docs/reference/mt_align_start.html +++ b/docs/reference/mt_align_start.html @@ -69,7 +69,7 @@ mousetrap - 3.1.3 + 3.1.4 @@ -114,8 +114,14 @@

Align start position of trajectories.

Adjust trajectories so that all trajectories have the same start position.

- 
mt_align_start(data, use = "trajectories", save_as = use,
-  dimensions = c("xpos", "ypos"), start = c(0, 0), verbose = FALSE)
+ 
mt_align_start(
+  data,
+  use = "trajectories",
+  save_as = use,
+  dimensions = c("xpos", "ypos"),
+  start = c(0, 0),
+  verbose = FALSE
+)

Arguments

diff --git a/docs/reference/mt_align_start_end.html b/docs/reference/mt_align_start_end.html index 0371e3b..1264093 100644 --- a/docs/reference/mt_align_start_end.html +++ b/docs/reference/mt_align_start_end.html @@ -71,7 +71,7 @@ mousetrap - 3.1.3 + 3.1.4 @@ -118,9 +118,15 @@

Align start and end position of trajectories.

(e.g. Dale et al., 2007).

- 
mt_align_start_end(data, use = "trajectories", save_as = use,
-  dimensions = c("xpos", "ypos"), start = c(0, 0), end = c(-1, 1),
-  verbose = FALSE)
+ 
mt_align_start_end(
+  data,
+  use = "trajectories",
+  save_as = use,
+  dimensions = c("xpos", "ypos"),
+  start = c(0, 0),
+  end = c(-1, 1),
+  verbose = FALSE
+)

Arguments

diff --git a/docs/reference/mt_angles.html b/docs/reference/mt_angles.html index 0511636..7c2a0ce 100644 --- a/docs/reference/mt_angles.html +++ b/docs/reference/mt_angles.html @@ -72,7 +72,7 @@ mousetrap - 3.1.3 + 3.1.4 @@ -120,9 +120,15 @@

Calculate movement angles.

between two subsequent points and the vertical axis.

- 
mt_angles(data, use = "trajectories", dimensions = c("xpos", "ypos"),
-  save_as = use, na_replace = FALSE, unit = "radian",
-  verbose = FALSE)
+ 
mt_angles(
+  data,
+  use = "trajectories",
+  dimensions = c("xpos", "ypos"),
+  save_as = use,
+  na_replace = FALSE,
+  unit = "radian",
+  verbose = FALSE
+)

Arguments

diff --git a/docs/reference/mt_animate.html b/docs/reference/mt_animate.html index c9141f5..6d4da21 100644 --- a/docs/reference/mt_animate.html +++ b/docs/reference/mt_animate.html @@ -70,7 +70,7 @@ mousetrap - 3.1.3 + 3.1.4 @@ -116,14 +116,33 @@

Create gif trajectory animation.

that this function has beta status.

- 
mt_animate(data, use = "trajectories", dimensions = c("xpos", "ypos"),
-  timestamps = "timestamps", filename = "trajectory_animation.gif",
-  xres = 1000, seconds = 3, framerate = 24, speed = 0.5,
-  density = 3, jitter = TRUE, remove = FALSE, bg = "black",
-  col = "white", lwd = 1, loop = FALSE, bounds = NULL,
-  norm = FALSE, upscale = 1, decay = 10, max_intensity = 5,
-  discard_images = TRUE, im_path = NULL, parallel = TRUE,
-  verbose = FALSE)
+ 
mt_animate(
+  data,
+  use = "trajectories",
+  dimensions = c("xpos", "ypos"),
+  timestamps = "timestamps",
+  filename = "trajectory_animation.gif",
+  xres = 1000,
+  seconds = 3,
+  framerate = 24,
+  speed = 0.5,
+  density = 3,
+  jitter = TRUE,
+  remove = FALSE,
+  bg = "black",
+  col = "white",
+  lwd = 1,
+  loop = FALSE,
+  bounds = NULL,
+  norm = FALSE,
+  upscale = 1,
+  decay = 10,
+  max_intensity = 5,
+  discard_images = TRUE,
+  im_path = NULL,
+  parallel = TRUE,
+  verbose = FALSE
+)

Arguments

diff --git a/docs/reference/mt_average.html b/docs/reference/mt_average.html index 387b6d5..8a02e27 100644 --- a/docs/reference/mt_average.html +++ b/docs/reference/mt_average.html @@ -73,7 +73,7 @@ mousetrap - 3.1.3 + 3.1.4 @@ -122,10 +122,18 @@

Average trajectories across intervals.

(see Details for information regarding the exact averaging procedure).

- 
mt_average(data, use = "trajectories", save_as = "av_trajectories",
-  dimensions = "all", av_dimension = "timestamps", intervals = NULL,
-  interval_size = 100, max_interval = NULL, verbose = FALSE,
-  dimension = NULL)
+ 
mt_average(
+  data,
+  use = "trajectories",
+  save_as = "av_trajectories",
+  dimensions = "all",
+  av_dimension = "timestamps",
+  intervals = NULL,
+  interval_size = 100,
+  max_interval = NULL,
+  verbose = FALSE,
+  dimension = NULL
+)

Arguments

diff --git a/docs/reference/mt_bind.html b/docs/reference/mt_bind.html index f0e66b9..6727dbe 100644 --- a/docs/reference/mt_bind.html +++ b/docs/reference/mt_bind.html @@ -71,7 +71,7 @@ mousetrap - 3.1.3 + 3.1.4 diff --git a/docs/reference/mt_check_bimodality.html b/docs/reference/mt_check_bimodality.html index 6b39526..f209991 100644 --- a/docs/reference/mt_check_bimodality.html +++ b/docs/reference/mt_check_bimodality.html @@ -72,7 +72,7 @@ mousetrap - 3.1.3 + 3.1.4 @@ -120,8 +120,15 @@

Assess bimodality of mouse-tracking measure distributions.

corresponding variables can be specified under grouping_variables.

- 
mt_check_bimodality(data, use = "measures", use_variables = NULL,
-  methods = c("BC", "HDS"), B = 2000, grouping_variables = NULL, ...)
+ 
mt_check_bimodality(
+  data,
+  use = "measures",
+  use_variables = NULL,
+  methods = c("BC", "HDS"),
+  B = 2000,
+  grouping_variables = NULL,
+  ...
+)

Arguments

diff --git a/docs/reference/mt_check_resolution.html b/docs/reference/mt_check_resolution.html index efdaf94..07879ff 100644 --- a/docs/reference/mt_check_resolution.html +++ b/docs/reference/mt_check_resolution.html @@ -71,7 +71,7 @@ mousetrap - 3.1.3 + 3.1.4 @@ -118,8 +118,12 @@

Check logging resolution by looking at timestamp differences.

the logging resolution.

- 
mt_check_resolution(data, use = "trajectories",
-  timestamps = "timestamps", desired = NULL)
+ 
mt_check_resolution(
+  data,
+  use = "trajectories",
+  timestamps = "timestamps",
+  desired = NULL
+)

Arguments

diff --git a/docs/reference/mt_cluster.html b/docs/reference/mt_cluster.html index 3ac0e83..b513eb5 100644 --- a/docs/reference/mt_cluster.html +++ b/docs/reference/mt_cluster.html @@ -71,7 +71,7 @@ mousetrap - 3.1.3 + 3.1.4 @@ -118,11 +118,22 @@

Cluster trajectories.

the resulting dissimilarity matrix using a predefined number of clusters.

- 
mt_cluster(data, use = "sp_trajectories", save_as = "clustering",
-  dimensions = c("xpos", "ypos"), n_cluster = 5, method = "hclust",
-  weights = rep(1, length(dimensions)), pointwise = TRUE,
-  minkowski_p = 2, hclust_method = "ward.D", kmeans_nstart = 10,
-  na_rm = FALSE, cluster_output = FALSE, verbose = FALSE)
+ 
mt_cluster(
+  data,
+  use = "sp_trajectories",
+  save_as = "clustering",
+  dimensions = c("xpos", "ypos"),
+  n_cluster = 5,
+  method = "hclust",
+  weights = rep(1, length(dimensions)),
+  pointwise = TRUE,
+  minkowski_p = 2,
+  hclust_method = "ward.D",
+  kmeans_nstart = 10,
+  na_rm = FALSE,
+  cluster_output = FALSE,
+  verbose = FALSE
+)

Arguments

diff --git a/docs/reference/mt_cluster_k.html b/docs/reference/mt_cluster_k.html index 66a2567..0bdce94 100644 --- a/docs/reference/mt_cluster_k.html +++ b/docs/reference/mt_cluster_k.html @@ -69,7 +69,7 @@ mousetrap - 3.1.3 + 3.1.4 @@ -114,12 +114,24 @@

Estimate optimal number of clusters.

Estimates the optimal number of clusters (k) using various methods.

- 
mt_cluster_k(data, use = "sp_trajectories", dimensions = c("xpos",
-  "ypos"), kseq = 2:15, compute = c("stability", "gap", "jump",
-  "slope"), method = "hclust", weights = rep(1, length(dimensions)),
-  pointwise = TRUE, minkowski_p = 2, hclust_method = "ward.D",
-  kmeans_nstart = 10, n_bootstrap = 10, model_based = FALSE,
-  n_gap = 10, na_rm = FALSE, verbose = FALSE)
+ 
mt_cluster_k(
+  data,
+  use = "sp_trajectories",
+  dimensions = c("xpos", "ypos"),
+  kseq = 2:15,
+  compute = c("stability", "gap", "jump", "slope"),
+  method = "hclust",
+  weights = rep(1, length(dimensions)),
+  pointwise = TRUE,
+  minkowski_p = 2,
+  hclust_method = "ward.D",
+  kmeans_nstart = 10,
+  n_bootstrap = 10,
+  model_based = FALSE,
+  n_gap = 10,
+  na_rm = FALSE,
+  verbose = FALSE
+)

Arguments

diff --git a/docs/reference/mt_count.html b/docs/reference/mt_count.html index 2157ab9..02f3769 100644 --- a/docs/reference/mt_count.html +++ b/docs/reference/mt_count.html @@ -71,7 +71,7 @@ mousetrap - 3.1.3 + 3.1.4 @@ -118,8 +118,7 @@

Count number of observations.

functions in this package.

- 
mt_count(data, use = "trajectories", save_as = "measures",
-  dimensions = "xpos")
+ 
mt_count(data, use = "trajectories", save_as = "measures", dimensions = "xpos")

Arguments

diff --git a/docs/reference/mt_derivatives.html b/docs/reference/mt_derivatives.html index 2f715b3..1e4e301 100644 --- a/docs/reference/mt_derivatives.html +++ b/docs/reference/mt_derivatives.html @@ -73,7 +73,7 @@ mousetrap - 3.1.3 + 3.1.4 @@ -122,10 +122,17 @@

Calculate distance, velocity, and acceleration.

per time.

- 
mt_derivatives(data, use = "trajectories", save_as = use,
-  dimensions = c("xpos", "ypos"), timestamps = "timestamps",
-  prefix = "", absolute = FALSE, return_delta_time = FALSE,
-  verbose = FALSE)
+ 
mt_derivatives(
+  data,
+  use = "trajectories",
+  save_as = use,
+  dimensions = c("xpos", "ypos"),
+  timestamps = "timestamps",
+  prefix = "",
+  absolute = FALSE,
+  return_delta_time = FALSE,
+  verbose = FALSE
+)

Arguments

diff --git a/docs/reference/mt_deviations.html b/docs/reference/mt_deviations.html index 1ca9acb..35556ea 100644 --- a/docs/reference/mt_deviations.html +++ b/docs/reference/mt_deviations.html @@ -70,7 +70,7 @@ mousetrap - 3.1.3 + 3.1.4 @@ -116,9 +116,16 @@

Calculate deviations from idealized trajectory.

actual trajectory from it for each logged position.

- 
mt_deviations(data, use = "trajectories", save_as = use,
-  dimensions = c("xpos", "ypos"), start_ideal = NULL,
-  end_ideal = NULL, prefix = "", verbose = FALSE)
+ 
mt_deviations(
+  data,
+  use = "trajectories",
+  save_as = use,
+  dimensions = c("xpos", "ypos"),
+  start_ideal = NULL,
+  end_ideal = NULL,
+  prefix = "",
+  verbose = FALSE
+)

Arguments

diff --git a/docs/reference/mt_diffmap.html b/docs/reference/mt_diffmap.html index 9eb78fd..c8940e3 100644 --- a/docs/reference/mt_diffmap.html +++ b/docs/reference/mt_diffmap.html @@ -70,7 +70,7 @@ mousetrap - 3.1.3 + 3.1.4 @@ -116,11 +116,24 @@

Creates a difference-heatmap of two trajectory heatmap images.

gaussian smoothing. Note that this function has beta status.

- 
mt_diffmap(x, y = NULL, condition = NULL, use = "trajectories",
-  dimensions = c("xpos", "ypos"), use2 = "data", filename = NULL,
-  bounds = NULL, xres = 500, upscale = 4, smooth_radius = 10,
-  colors = c("#00863F", "#000000", "#FF1900"), n_shades = 1000,
-  plot = TRUE, ..., verbose = TRUE)
+ 
mt_diffmap(
+  x,
+  y = NULL,
+  condition = NULL,
+  use = "trajectories",
+  dimensions = c("xpos", "ypos"),
+  use2 = "data",
+  filename = NULL,
+  bounds = NULL,
+  xres = 500,
+  upscale = 4,
+  smooth_radius = 10,
+  colors = c("#00863F", "#000000", "#FF1900"),
+  n_shades = 1000,
+  plot = TRUE,
+  ...,
+  verbose = TRUE
+)

Arguments

diff --git a/docs/reference/mt_distmat.html b/docs/reference/mt_distmat.html index a9903b3..4c012fb 100644 --- a/docs/reference/mt_distmat.html +++ b/docs/reference/mt_distmat.html @@ -70,7 +70,7 @@ mousetrap - 3.1.3 + 3.1.4 @@ -116,9 +116,16 @@

Compute distance matrix.

trajectories.

- 
mt_distmat(data, use = "sp_trajectories", save_as = "distmat",
-  dimensions = c("xpos", "ypos"), weights = rep(1, length(dimensions)),
-  pointwise = TRUE, minkowski_p = 2, na_rm = FALSE)
+ 
mt_distmat(
+  data,
+  use = "sp_trajectories",
+  save_as = "distmat",
+  dimensions = c("xpos", "ypos"),
+  weights = rep(1, length(dimensions)),
+  pointwise = TRUE,
+  minkowski_p = 2,
+  na_rm = FALSE
+)

Arguments

diff --git a/docs/reference/mt_example.html b/docs/reference/mt_example.html index 86d957d..52fc76a 100644 --- a/docs/reference/mt_example.html +++ b/docs/reference/mt_example.html @@ -70,7 +70,7 @@ mousetrap - 3.1.3 + 3.1.4 diff --git a/docs/reference/mt_example_raw.html b/docs/reference/mt_example_raw.html index ad78f80..1f8e712 100644 --- a/docs/reference/mt_example_raw.html +++ b/docs/reference/mt_example_raw.html @@ -73,7 +73,7 @@ mousetrap - 3.1.3 + 3.1.4 diff --git a/docs/reference/mt_exclude_initiation.html b/docs/reference/mt_exclude_initiation.html index a2337bb..d1dcdeb 100644 --- a/docs/reference/mt_exclude_initiation.html +++ b/docs/reference/mt_exclude_initiation.html @@ -71,7 +71,7 @@ mousetrap - 3.1.3 + 3.1.4 @@ -118,9 +118,15 @@

Exclude initial phase without mouse movement.

data will be removed.

- 
mt_exclude_initiation(data, use = "trajectories", save_as = use,
-  dimensions = c("xpos", "ypos"), timestamps = "timestamps",
-  reset_timestamps = TRUE, verbose = FALSE)
+ 
mt_exclude_initiation(
+  data,
+  use = "trajectories",
+  save_as = use,
+  dimensions = c("xpos", "ypos"),
+  timestamps = "timestamps",
+  reset_timestamps = TRUE,
+  verbose = FALSE
+)

Arguments

diff --git a/docs/reference/mt_export_long.html b/docs/reference/mt_export_long.html index 43d1b08..80f53ec 100644 --- a/docs/reference/mt_export_long.html +++ b/docs/reference/mt_export_long.html @@ -73,7 +73,7 @@ mousetrap - 3.1.3 + 3.1.4 @@ -122,11 +122,23 @@

Export mouse-tracking data.

mt_export_wide are wrapper functions for mt_reshape.

- 
mt_export_long(data, use = "trajectories", use_variables = NULL,
-  use2 = "data", use2_variables = NULL, ...)
-
-mt_export_wide(data, use = "trajectories", use_variables = NULL,
-  use2 = "data", use2_variables = NULL, ...)
+ 
mt_export_long(
+  data,
+  use = "trajectories",
+  use_variables = NULL,
+  use2 = "data",
+  use2_variables = NULL,
+  ...
+)
+
+mt_export_wide(
+  data,
+  use = "trajectories",
+  use_variables = NULL,
+  use2 = "data",
+  use2_variables = NULL,
+  ...
+)

Arguments

diff --git a/docs/reference/mt_heatmap.html b/docs/reference/mt_heatmap.html index 8f19e16..64ac712 100644 --- a/docs/reference/mt_heatmap.html +++ b/docs/reference/mt_heatmap.html @@ -70,7 +70,7 @@ mousetrap - 3.1.3 + 3.1.4 @@ -116,9 +116,16 @@

Plot trajectory heatmap.

function has beta status.

- 
mt_heatmap(x, use = "trajectories", dimensions = c("xpos", "ypos"),
-  filename = NULL, ..., upscale = 1, plot_dims = FALSE,
-  verbose = TRUE)
+ 
mt_heatmap(
+  x,
+  use = "trajectories",
+  dimensions = c("xpos", "ypos"),
+  filename = NULL,
+  ...,
+  upscale = 1,
+  plot_dims = FALSE,
+  verbose = TRUE
+)

Arguments

diff --git a/docs/reference/mt_heatmap_ggplot.html b/docs/reference/mt_heatmap_ggplot.html index dd911de..075f9e2 100644 --- a/docs/reference/mt_heatmap_ggplot.html +++ b/docs/reference/mt_heatmap_ggplot.html @@ -70,7 +70,7 @@ mousetrap - 3.1.3 + 3.1.4 @@ -116,8 +116,15 @@

Plot trajectory heatmap using ggplot.

this function has beta status.

- 
mt_heatmap_ggplot(data, use = "trajectories", dimensions = c("xpos",
-  "ypos"), use2 = "data", facet_row = NULL, facet_col = NULL, ...)
+ 
mt_heatmap_ggplot(
+  data,
+  use = "trajectories",
+  dimensions = c("xpos", "ypos"),
+  use2 = "data",
+  facet_row = NULL,
+  facet_col = NULL,
+  ...
+)

Arguments

diff --git a/docs/reference/mt_heatmap_raw.html b/docs/reference/mt_heatmap_raw.html index d7d3153..9e8eded 100644 --- a/docs/reference/mt_heatmap_raw.html +++ b/docs/reference/mt_heatmap_raw.html @@ -71,7 +71,7 @@ mousetrap - 3.1.3 + 3.1.4 @@ -118,13 +118,28 @@

Creates high-resolution heatmap of trajectory data.

status.

- 
mt_heatmap_raw(data, use = "trajectories", dimensions = c("xpos",
-  "ypos"), variable = NULL, bounds = NULL, xres = 1000,
-  upsample = 1, norm = FALSE, colors = c("black", "blue", "white"),
-  n_shades = c(1000, 1000), smooth_radius = 1.5, low_pass = 200,
-  auto_enhance = TRUE, mean_image = 0.15, mean_color = 0.25,
-  aggregate_lwd = 0, aggregate_col = "black", n_trajectories = NULL,
-  seed = NULL, verbose = TRUE)
+ 
mt_heatmap_raw(
+  data,
+  use = "trajectories",
+  dimensions = c("xpos", "ypos"),
+  variable = NULL,
+  bounds = NULL,
+  xres = 1000,
+  upsample = 1,
+  norm = FALSE,
+  colors = c("black", "blue", "white"),
+  n_shades = c(1000, 1000),
+  smooth_radius = 1.5,
+  low_pass = 200,
+  auto_enhance = TRUE,
+  mean_image = 0.15,
+  mean_color = 0.25,
+  aggregate_lwd = 0,
+  aggregate_col = "black",
+  n_trajectories = NULL,
+  seed = NULL,
+  verbose = TRUE
+)

Arguments

diff --git a/docs/reference/mt_import_long.html b/docs/reference/mt_import_long.html index 2de6d3b..6b5c4fa 100644 --- a/docs/reference/mt_import_long.html +++ b/docs/reference/mt_import_long.html @@ -79,7 +79,7 @@ mousetrap - 3.1.3 + 3.1.4 @@ -134,10 +134,18 @@

Import mouse-tracking data saved in long format.

functions within this package (see mousetrap for an overview).

- 
mt_import_long(raw_data, xpos_label = "xpos", ypos_label = "ypos",
-  zpos_label = NULL, timestamps_label = "timestamps",
-  add_labels = NULL, mt_id_label = "mt_id", mt_seq_label = "mt_seq",
-  reset_timestamps = TRUE, verbose = TRUE)
+ 
mt_import_long(
+  raw_data,
+  xpos_label = "xpos",
+  ypos_label = "ypos",
+  zpos_label = NULL,
+  timestamps_label = "timestamps",
+  add_labels = NULL,
+  mt_id_label = "mt_id",
+  mt_seq_label = "mt_seq",
+  reset_timestamps = TRUE,
+  verbose = TRUE
+)

Arguments

diff --git a/docs/reference/mt_import_mousetrap.html b/docs/reference/mt_import_mousetrap.html index 503d866..2c354b0 100644 --- a/docs/reference/mt_import_mousetrap.html +++ b/docs/reference/mt_import_mousetrap.html @@ -79,7 +79,7 @@ mousetrap - 3.1.3 + 3.1.4 @@ -134,10 +134,17 @@

Import mouse-tracking data recorded using the mousetrap plug-ins in OpenSesa functions within this package (see mousetrap for an overview).

- 
mt_import_mousetrap(raw_data, xpos_label = "xpos", ypos_label = "ypos",
-  timestamps_label = "timestamps", mt_id_label = NULL, split = ",",
-  duplicates = "remove_first", reset_timestamps = TRUE,
-  verbose = FALSE)
+ 
mt_import_mousetrap(
+  raw_data,
+  xpos_label = "xpos",
+  ypos_label = "ypos",
+  timestamps_label = "timestamps",
+  mt_id_label = NULL,
+  split = ",",
+  duplicates = "remove_first",
+  reset_timestamps = TRUE,
+  verbose = FALSE
+)

Arguments

diff --git a/docs/reference/mt_import_wide.html b/docs/reference/mt_import_wide.html index 41df79c..d2ad052 100644 --- a/docs/reference/mt_import_wide.html +++ b/docs/reference/mt_import_wide.html @@ -80,7 +80,7 @@ mousetrap - 3.1.3 + 3.1.4 @@ -136,10 +136,19 @@

Import mouse-tracking data saved in wide format.

within this package (see mousetrap for an overview).

- 
mt_import_wide(raw_data, xpos_label = "X", ypos_label = "Y",
-  zpos_label = NULL, timestamps_label = "T", add_labels = NULL,
-  mt_id_label = NULL, pos_sep = "_", pos_ids = NULL,
-  reset_timestamps = TRUE, verbose = TRUE)
+ 
mt_import_wide(
+  raw_data,
+  xpos_label = "X",
+  ypos_label = "Y",
+  zpos_label = NULL,
+  timestamps_label = "T",
+  add_labels = NULL,
+  mt_id_label = NULL,
+  pos_sep = "_",
+  pos_ids = NULL,
+  reset_timestamps = TRUE,
+  verbose = TRUE
+)

Arguments

diff --git a/docs/reference/mt_map.html b/docs/reference/mt_map.html index bbb14d3..dedab27 100644 --- a/docs/reference/mt_map.html +++ b/docs/reference/mt_map.html @@ -72,7 +72,7 @@ mousetrap - 3.1.3 + 3.1.4 @@ -120,11 +120,19 @@

Map trajectories to prototypes.

prototype that produced the smallest distance.

- 
mt_map(data, use = "sp_trajectories", save_as = "prototyping",
+    
mt_map(
+  data,
+  use = "sp_trajectories",
+  save_as = "prototyping",
   dimensions = c("xpos", "ypos"),
-  prototypes = mousetrap::mt_prototypes, weights = rep(1,
-  length(dimensions)), pointwise = TRUE, na_rm = FALSE,
-  minkowski_p = 2, use2 = "data", grouping_variables = NULL)

+  prototypes = mousetrap::mt_prototypes,
+  weights = rep(1, length(dimensions)),
+  pointwise = TRUE,
+  na_rm = FALSE,
+  minkowski_p = 2,
+  use2 = "data",
+  grouping_variables = NULL
+)

Arguments

diff --git a/docs/reference/mt_measures.html b/docs/reference/mt_measures.html index 9d8f00c..eb63016 100644 --- a/docs/reference/mt_measures.html +++ b/docs/reference/mt_measures.html @@ -75,7 +75,7 @@ mousetrap - 3.1.3 + 3.1.4 @@ -126,9 +126,17 @@

Calculate mouse-tracking measures.

Values sections.

- 
mt_measures(data, use = "trajectories", save_as = "measures",
-  dimensions = c("xpos", "ypos"), timestamps = "timestamps",
-  flip_threshold = 0, hover_threshold = NULL, verbose = FALSE)
+ 
mt_measures(
+  data,
+  use = "trajectories",
+  save_as = "measures",
+  dimensions = c("xpos", "ypos"),
+  timestamps = "timestamps",
+  flip_threshold = 0,
+  hover_threshold = NULL,
+  hover_incl_initial = TRUE,
+  verbose = FALSE
+)

Arguments

@@ -163,16 +171,27 @@

Arg

- +flip. If several thresholds are specified, flips will be returned in +separate variables for each threshold value (the variable name will be +suffixed with the threshold value).

+specified in hover_threshold). If several thresholds are specified, +hovers and hover_time will be returned in separate variables for each +threshold value (the variable name will be suffixed with the threshold +value).

+ + + + diff --git a/docs/reference/mt_plot.html b/docs/reference/mt_plot.html index faeb7ac..40e157a 100644 --- a/docs/reference/mt_plot.html +++ b/docs/reference/mt_plot.html @@ -74,7 +74,7 @@ mousetrap - 3.1.3 + 3.1.4 @@ -124,15 +124,41 @@

Plot trajectory data.

for plotting velocity and acceleration profiles.

- 
mt_plot(data, use = "trajectories", use2 = "data", x = "xpos",
-  y = "ypos", color = NULL, linetype = NULL, alpha = NA,
-  size = 0.5, facet_row = NULL, facet_col = NULL, points = FALSE,
-  only_ggplot = FALSE, mt_id = "mt_id", ...)
-
-mt_plot_aggregate(data, use = "trajectories", use2 = "data",
-  x = "xpos", y = "ypos", color = NULL, linetype = NULL,
-  alpha = NA, size = 0.5, facet_row = NULL, facet_col = NULL,
-  points = FALSE, only_ggplot = FALSE, subject_id = NULL, ...)
+ 
mt_plot(
+  data,
+  use = "trajectories",
+  use2 = "data",
+  x = "xpos",
+  y = "ypos",
+  color = NULL,
+  linetype = NULL,
+  alpha = NA,
+  size = 0.5,
+  facet_row = NULL,
+  facet_col = NULL,
+  points = FALSE,
+  only_ggplot = FALSE,
+  mt_id = "mt_id",
+  ...
+)
+
+mt_plot_aggregate(
+  data,
+  use = "trajectories",
+  use2 = "data",
+  x = "xpos",
+  y = "ypos",
+  color = NULL,
+  linetype = NULL,
+  alpha = NA,
+  size = 0.5,
+  facet_row = NULL,
+  facet_col = NULL,
+  points = FALSE,
+  only_ggplot = FALSE,
+  subject_id = NULL,
+  ...
+)

Arguments

flip_threshold

a numeric value specifying the distance that needs to +

a numeric value specifying the distance that needs to be exceeded in one direction so that a change in direction counts as a -flip.
hover_threshold

an optional numeric value. If specified, hovers (and hover_time) will be calculated as the number (and total time) of periods without movement in a trial (whose duration exceeds the value -specified in hover_threshold).

hover_incl_initial

logical indicating if the calculation of hovers +should include a potential initial phase in the trial without mouse +movements (this initial phase is included by default).
verbose
diff --git a/docs/reference/mt_plot_add_rect.html b/docs/reference/mt_plot_add_rect.html index 5bc644b..cdd96ad 100644 --- a/docs/reference/mt_plot_add_rect.html +++ b/docs/reference/mt_plot_add_rect.html @@ -72,7 +72,7 @@ mousetrap - 3.1.3 + 3.1.4 diff --git a/docs/reference/mt_plot_per_trajectory.html b/docs/reference/mt_plot_per_trajectory.html index c88b93a..961e634 100644 --- a/docs/reference/mt_plot_per_trajectory.html +++ b/docs/reference/mt_plot_per_trajectory.html @@ -74,7 +74,7 @@ mousetrap - 3.1.3 + 3.1.4 @@ -124,10 +124,22 @@

Create PDF with separate plots per trajectory.

acceleration profiles.

- 
mt_plot_per_trajectory(file, data, use = "trajectories", x = "xpos",
-  y = "ypos", xlim = NULL, ylim = NULL, axes_exact = FALSE,
-  points = FALSE, rect = NULL, color = "black", fill = NA,
-  verbose = FALSE, ...)
+ 
mt_plot_per_trajectory(
+  file,
+  data,
+  use = "trajectories",
+  x = "xpos",
+  y = "ypos",
+  xlim = NULL,
+  ylim = NULL,
+  axes_exact = FALSE,
+  points = FALSE,
+  rect = NULL,
+  color = "black",
+  fill = NA,
+  verbose = FALSE,
+  ...
+)

Arguments

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Plot density of mouse positions across time steps.

trajectory variable (e.g., the x-positions or velocity) per time step.

- 
mt_plot_riverbed(data, use = "tn_trajectories", y = "xpos",
-  y_range = NULL, y_bins = 250, facet_row = NULL, facet_col = NULL,
-  facet_data = "data", grid_colors = c("gray30", "gray10"))
+ 
mt_plot_riverbed(
+  data,
+  use = "tn_trajectories",
+  y = "xpos",
+  y_range = NULL,
+  y_bins = 250,
+  facet_row = NULL,
+  facet_col = NULL,
+  facet_data = "data",
+  grid_colors = c("gray30", "gray10")
+)

Arguments

@@ -218,7 +226,7 @@

Examp # default scale for fill with a custom scale mt_plot_riverbed(mt_example, facet_col="Condition") + ggplot2::scale_fill_gradientn(colours=grDevices::heat.colors(9), - name="Frequency", trans="log", labels=scales::percent) + name="Frequency", trans="log", labels=scales::percent) } diff --git a/docs/reference/mt_qeffect.html b/docs/reference/mt_qeffect.html index c1df028..0c12913 100644 --- a/docs/reference/mt_qeffect.html +++ b/docs/reference/mt_qeffect.html @@ -69,7 +69,7 @@ mousetrap - 3.1.3 + 3.1.4 @@ -114,8 +114,16 @@

Create quantile-effect plot

Function in beta and currently only for internal purposes.

- 
mt_qeffect(data, compare, use = "measures", measure = "MAD",
-  direction = "upward", n_steps = 100, return_data = FALSE, ...)
+ 
mt_qeffect(
+  data,
+  compare,
+  use = "measures",
+  measure = "MAD",
+  direction = "upward",
+  n_steps = 100,
+  return_data = FALSE,
+  ...
+)

Arguments

diff --git a/docs/reference/mt_remap_symmetric.html b/docs/reference/mt_remap_symmetric.html index 15b3518..e57545a 100644 --- a/docs/reference/mt_remap_symmetric.html +++ b/docs/reference/mt_remap_symmetric.html @@ -71,7 +71,7 @@ mousetrap - 3.1.3 + 3.1.4 @@ -118,9 +118,14 @@

Remap mouse trajectories.

system and a symmetric design of the response buttons (see Details).

- 
mt_remap_symmetric(data, use = "trajectories", save_as = use,
-  dimensions = c("xpos", "ypos"), remap_xpos = "left",
-  remap_ypos = "up")
+ 
mt_remap_symmetric(
+  data,
+  use = "trajectories",
+  save_as = use,
+  dimensions = c("xpos", "ypos"),
+  remap_xpos = "left",
+  remap_ypos = "up"
+)

Arguments

diff --git a/docs/reference/mt_resample.html b/docs/reference/mt_resample.html index 4236446..9d3fdba 100644 --- a/docs/reference/mt_resample.html +++ b/docs/reference/mt_resample.html @@ -71,7 +71,7 @@ mousetrap - 3.1.3 + 3.1.4 @@ -118,10 +118,17 @@

Resample trajectories using a constant time interval.

interpolation is performed using the two adjacent timestamps.

- 
mt_resample(data, use = "trajectories", save_as = "rs_trajectories",
-  dimensions = c("xpos", "ypos"), timestamps = "timestamps",
-  step_size = 10, exact_last_timestamp = TRUE,
-  constant_interpolation = NULL, verbose = FALSE)
+ 
mt_resample(
+  data,
+  use = "trajectories",
+  save_as = "rs_trajectories",
+  dimensions = c("xpos", "ypos"),
+  timestamps = "timestamps",
+  step_size = 10,
+  exact_last_timestamp = TRUE,
+  constant_interpolation = NULL,
+  verbose = FALSE
+)

Arguments

diff --git a/docs/reference/mt_reshape.html b/docs/reference/mt_reshape.html index 990a265..f461469 100644 --- a/docs/reference/mt_reshape.html +++ b/docs/reference/mt_reshape.html @@ -73,7 +73,7 @@ mousetrap - 3.1.3 + 3.1.4 @@ -122,12 +122,23 @@

General-purpose reshape and aggregation function for mousetrap data.

are available.

- 
mt_reshape(data, use = "trajectories", use_variables = NULL,
-  use2 = "data", use2_variables = NULL, subset = NULL,
-  subject_id = NULL, aggregate = FALSE,
-  aggregate_subjects_only = FALSE, .funs = "mean",
-  trajectories_long = TRUE, convert_df = TRUE, mt_id = "mt_id",
-  mt_seq = "mt_seq", aggregation_function = NULL)
+ 
mt_reshape(
+  data,
+  use = "trajectories",
+  use_variables = NULL,
+  use2 = "data",
+  use2_variables = NULL,
+  subset = NULL,
+  subject_id = NULL,
+  aggregate = FALSE,
+  aggregate_subjects_only = FALSE,
+  .funs = "mean",
+  trajectories_long = TRUE,
+  convert_df = TRUE,
+  mt_id = "mt_id",
+  mt_seq = "mt_seq",
+  aggregation_function = NULL
+)

Arguments

diff --git a/docs/reference/mt_sample_entropy.html b/docs/reference/mt_sample_entropy.html index 83b996f..3a0ad68 100644 --- a/docs/reference/mt_sample_entropy.html +++ b/docs/reference/mt_sample_entropy.html @@ -70,7 +70,7 @@ mousetrap - 3.1.3 + 3.1.4 @@ -116,9 +116,16 @@

Calculate sample entropy.

of movements along one specific dimension.

- 
mt_sample_entropy(data, use = "tn_trajectories", save_as = "measures",
-  dimension = "xpos", m = 3, r = NULL, use_diff = TRUE,
-  verbose = FALSE)
+ 
mt_sample_entropy(
+  data,
+  use = "tn_trajectories",
+  save_as = "measures",
+  dimension = "xpos",
+  m = 3,
+  r = NULL,
+  use_diff = TRUE,
+  verbose = FALSE
+)

Arguments

diff --git a/docs/reference/mt_scale_trajectories.html b/docs/reference/mt_scale_trajectories.html index 5657508..91e26bb 100644 --- a/docs/reference/mt_scale_trajectories.html +++ b/docs/reference/mt_scale_trajectories.html @@ -70,7 +70,7 @@ mousetrap - 3.1.3 + 3.1.4 @@ -116,9 +116,17 @@

Standardize variables in mouse trajectory array.

trajectory variables within or across trajectories.

- 
mt_scale_trajectories(data, use = "trajectories", save_as = use,
-  var_names, center = TRUE, scale = TRUE, within_trajectory = FALSE,
-  prefix = "z_", transform = NULL)
+ 
mt_scale_trajectories(
+  data,
+  use = "trajectories",
+  save_as = use,
+  var_names,
+  center = TRUE,
+  scale = TRUE,
+  within_trajectory = FALSE,
+  prefix = "z_",
+  transform = NULL
+)

Arguments

diff --git a/docs/reference/mt_space_normalize.html b/docs/reference/mt_space_normalize.html index 7a03b06..8ff658e 100644 --- a/docs/reference/mt_space_normalize.html +++ b/docs/reference/mt_space_normalize.html @@ -73,7 +73,7 @@ mousetrap - 3.1.3 + 3.1.4 @@ -122,9 +122,15 @@

Space normalize trajectories.

instead, which provides the same (and additional) functionality.

- 
mt_space_normalize(data, use = "trajectories",
-  save_as = "sn_trajectories", dimensions = c("xpos", "ypos"),
-  start = c(0, 0), end = NULL, verbose = FALSE)
+ 
mt_space_normalize(
+  data,
+  use = "trajectories",
+  save_as = "sn_trajectories",
+  dimensions = c("xpos", "ypos"),
+  start = c(0, 0),
+  end = NULL,
+  verbose = FALSE
+)

Arguments

diff --git a/docs/reference/mt_spatialize.html b/docs/reference/mt_spatialize.html index aba353b..6680ff8 100644 --- a/docs/reference/mt_spatialize.html +++ b/docs/reference/mt_spatialize.html @@ -70,7 +70,7 @@ mousetrap - 3.1.3 + 3.1.4 @@ -116,8 +116,13 @@

Spatialize trajectories.

that adjacent points on the trajectory become equidistant to each other.

- 
mt_spatialize(data, use = "trajectories", dimensions = c("xpos",
-  "ypos"), save_as = "sp_trajectories", n_points = 20)
+ 
mt_spatialize(
+  data,
+  use = "trajectories",
+  dimensions = c("xpos", "ypos"),
+  save_as = "sp_trajectories",
+  n_points = 20
+)

Arguments

diff --git a/docs/reference/mt_standardize.html b/docs/reference/mt_standardize.html index 17878ff..fb51d22 100644 --- a/docs/reference/mt_standardize.html +++ b/docs/reference/mt_standardize.html @@ -72,7 +72,7 @@ mousetrap - 3.1.3 + 3.1.4 @@ -120,8 +120,15 @@

Standardize mouse-tracking measures per level of other variables.

stored in a mousetrap data object.

- 
mt_standardize(data, use = "measures", use_variables = NULL,
-  within = NULL, prefix = "z_", center = TRUE, scale = TRUE)
+ 
mt_standardize(
+  data,
+  use = "measures",
+  use_variables = NULL,
+  within = NULL,
+  prefix = "z_",
+  center = TRUE,
+  scale = TRUE
+)

Arguments

diff --git a/docs/reference/mt_subset.html b/docs/reference/mt_subset.html index 4638e93..05ba464 100644 --- a/docs/reference/mt_subset.html +++ b/docs/reference/mt_subset.html @@ -71,7 +71,7 @@ mousetrap - 3.1.3 + 3.1.4 diff --git a/docs/reference/mt_time_normalize.html b/docs/reference/mt_time_normalize.html index 3e4186e..ffb06d8 100644 --- a/docs/reference/mt_time_normalize.html +++ b/docs/reference/mt_time_normalize.html @@ -73,7 +73,7 @@ mousetrap - 3.1.3 + 3.1.4 @@ -122,9 +122,15 @@

Time normalize trajectories.

(following Spivey et al., 2005).

- 
mt_time_normalize(data, use = "trajectories",
-  save_as = "tn_trajectories", dimensions = c("xpos", "ypos"),
-  timestamps = "timestamps", nsteps = 101, verbose = FALSE)
+ 
mt_time_normalize(
+  data,
+  use = "trajectories",
+  save_as = "tn_trajectories",
+  dimensions = c("xpos", "ypos"),
+  timestamps = "timestamps",
+  nsteps = 101,
+  verbose = FALSE
+)

Arguments

diff --git a/docs/reference/print.mt_heatmap_raw.html b/docs/reference/print.mt_heatmap_raw.html index 2cb5145..9a3f2dc 100644 --- a/docs/reference/print.mt_heatmap_raw.html +++ b/docs/reference/print.mt_heatmap_raw.html @@ -69,7 +69,7 @@ mousetrap - 3.1.3 + 3.1.4 diff --git a/docs/reference/read_mt.html b/docs/reference/read_mt.html index 399a299..418dec0 100644 --- a/docs/reference/read_mt.html +++ b/docs/reference/read_mt.html @@ -78,7 +78,7 @@ mousetrap - 3.1.3 + 3.1.4 @@ -132,8 +132,7 @@

Read MouseTracker raw data.

Version 2.84 - but please be sure to double-check.

- 
read_mt(file, columns = "all", add_trialid = FALSE,
-  add_filename = FALSE)
+ 
read_mt(file, columns = "all", add_trialid = FALSE, add_filename = FALSE)

Arguments

diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html index 9c6875d..0e7cce4 100644 --- a/docs/reference/reexports.html +++ b/docs/reference/reexports.html @@ -74,7 +74,7 @@ mousetrap - 3.1.3 + 3.1.4 diff --git a/docs/reference/scale_within.html b/docs/reference/scale_within.html index aff5100..60e718c 100644 --- a/docs/reference/scale_within.html +++ b/docs/reference/scale_within.html @@ -73,7 +73,7 @@ mousetrap - 3.1.3 + 3.1.4 @@ -122,8 +122,14 @@

Scale and center variables within the levels of another variable.

measures design.

- 
scale_within(data, variables = NULL, within = NULL, prefix = "",
-  center = TRUE, scale = TRUE)
+ 
scale_within(
+  data,
+  variables = NULL,
+  within = NULL,
+  prefix = "",
+  center = TRUE,
+  scale = TRUE
+)

Arguments

diff --git a/man/mousetrap.Rd b/man/mousetrap.Rd index a783e3f..8791a93 100644 --- a/man/mousetrap.Rd +++ b/man/mousetrap.Rd @@ -3,7 +3,6 @@ \docType{package} \name{mousetrap} \alias{mousetrap} -\alias{mousetrap-package} \title{Process and analyze mouse-tracking data} \description{ The mousetrap package provides functions for importing, preprocessing, diff --git a/man/mt_add_trajectory.Rd b/man/mt_add_trajectory.Rd index 1e1513f..8db16f7 100644 --- a/man/mt_add_trajectory.Rd +++ b/man/mt_add_trajectory.Rd @@ -4,8 +4,15 @@ \alias{mt_add_trajectory} \title{Add new trajectory to trajectory array.} \usage{ -mt_add_trajectory(data, use = "trajectories", save_as = use, - xpos = NULL, ypos = NULL, xypos = NULL, id = "new") +mt_add_trajectory( + data, + use = "trajectories", + save_as = use, + xpos = NULL, + ypos = NULL, + xypos = NULL, + id = "new" +) } \arguments{ \item{data}{a mousetrap data object created using one of the mt_import diff --git a/man/mt_aggregate.Rd b/man/mt_aggregate.Rd index b5d88c9..1a4936a 100644 --- a/man/mt_aggregate.Rd +++ b/man/mt_aggregate.Rd @@ -4,9 +4,16 @@ \alias{mt_aggregate} \title{Aggregate mouse-tracking data per condition.} \usage{ -mt_aggregate(data, use = "measures", use_variables = NULL, - use2 = "data", use2_variables = NULL, subject_id = NULL, - trajectories_long = TRUE, ...) +mt_aggregate( + data, + use = "measures", + use_variables = NULL, + use2 = "data", + use2_variables = NULL, + subject_id = NULL, + trajectories_long = TRUE, + ... +) } \arguments{ \item{data}{a mousetrap data object created using one of the mt_import diff --git a/man/mt_aggregate_per_subject.Rd b/man/mt_aggregate_per_subject.Rd index 8ee1029..db91679 100644 --- a/man/mt_aggregate_per_subject.Rd +++ b/man/mt_aggregate_per_subject.Rd @@ -4,9 +4,16 @@ \alias{mt_aggregate_per_subject} \title{Aggregate mouse-tracking data per condition separately for each subject.} \usage{ -mt_aggregate_per_subject(data, use = "measures", use_variables = NULL, - use2 = "data", use2_variables = NULL, subject_id, - trajectories_long = TRUE, ...) +mt_aggregate_per_subject( + data, + use = "measures", + use_variables = NULL, + use2 = "data", + use2_variables = NULL, + subject_id, + trajectories_long = TRUE, + ... +) } \arguments{ \item{data}{a mousetrap data object created using one of the mt_import diff --git a/man/mt_align.Rd b/man/mt_align.Rd index 70133a7..5d4a2ff 100644 --- a/man/mt_align.Rd +++ b/man/mt_align.Rd @@ -4,10 +4,17 @@ \alias{mt_align} \title{Align trajectories.} \usage{ -mt_align(data, use = "trajectories", save_as = use, - dimensions = c("xpos", "ypos"), coordinates = "isotropic", - align_start = FALSE, align_end = FALSE, align_side = "no", - verbose = FALSE) +mt_align( + data, + use = "trajectories", + save_as = use, + dimensions = c("xpos", "ypos"), + coordinates = "isotropic", + align_start = FALSE, + align_end = FALSE, + align_side = "no", + verbose = FALSE +) } \arguments{ \item{data}{a mousetrap data object created using one of the mt_import diff --git a/man/mt_align_start.Rd b/man/mt_align_start.Rd index 1186130..5e56dfc 100644 --- a/man/mt_align_start.Rd +++ b/man/mt_align_start.Rd @@ -4,8 +4,14 @@ \alias{mt_align_start} \title{Align start position of trajectories.} \usage{ -mt_align_start(data, use = "trajectories", save_as = use, - dimensions = c("xpos", "ypos"), start = c(0, 0), verbose = FALSE) +mt_align_start( + data, + use = "trajectories", + save_as = use, + dimensions = c("xpos", "ypos"), + start = c(0, 0), + verbose = FALSE +) } \arguments{ \item{data}{a mousetrap data object created using one of the mt_import diff --git a/man/mt_align_start_end.Rd b/man/mt_align_start_end.Rd index 8ca6ced..6e639e2 100644 --- a/man/mt_align_start_end.Rd +++ b/man/mt_align_start_end.Rd @@ -4,9 +4,15 @@ \alias{mt_align_start_end} \title{Align start and end position of trajectories.} \usage{ -mt_align_start_end(data, use = "trajectories", save_as = use, - dimensions = c("xpos", "ypos"), start = c(0, 0), end = c(-1, 1), - verbose = FALSE) +mt_align_start_end( + data, + use = "trajectories", + save_as = use, + dimensions = c("xpos", "ypos"), + start = c(0, 0), + end = c(-1, 1), + verbose = FALSE +) } \arguments{ \item{data}{a mousetrap data object created using one of the mt_import diff --git a/man/mt_angles.Rd b/man/mt_angles.Rd index f46e420..bf79372 100644 --- a/man/mt_angles.Rd +++ b/man/mt_angles.Rd @@ -4,9 +4,15 @@ \alias{mt_angles} \title{Calculate movement angles.} \usage{ -mt_angles(data, use = "trajectories", dimensions = c("xpos", "ypos"), - save_as = use, na_replace = FALSE, unit = "radian", - verbose = FALSE) +mt_angles( + data, + use = "trajectories", + dimensions = c("xpos", "ypos"), + save_as = use, + na_replace = FALSE, + unit = "radian", + verbose = FALSE +) } \arguments{ \item{data}{a mousetrap data object created using one of the mt_import diff --git a/man/mt_animate.Rd b/man/mt_animate.Rd index bda0857..b2ff5b8 100644 --- a/man/mt_animate.Rd +++ b/man/mt_animate.Rd @@ -4,14 +4,33 @@ \alias{mt_animate} \title{Create gif trajectory animation.} \usage{ -mt_animate(data, use = "trajectories", dimensions = c("xpos", "ypos"), - timestamps = "timestamps", filename = "trajectory_animation.gif", - xres = 1000, seconds = 3, framerate = 24, speed = 0.5, - density = 3, jitter = TRUE, remove = FALSE, bg = "black", - col = "white", lwd = 1, loop = FALSE, bounds = NULL, - norm = FALSE, upscale = 1, decay = 10, max_intensity = 5, - discard_images = TRUE, im_path = NULL, parallel = TRUE, - verbose = FALSE) +mt_animate( + data, + use = "trajectories", + dimensions = c("xpos", "ypos"), + timestamps = "timestamps", + filename = "trajectory_animation.gif", + xres = 1000, + seconds = 3, + framerate = 24, + speed = 0.5, + density = 3, + jitter = TRUE, + remove = FALSE, + bg = "black", + col = "white", + lwd = 1, + loop = FALSE, + bounds = NULL, + norm = FALSE, + upscale = 1, + decay = 10, + max_intensity = 5, + discard_images = TRUE, + im_path = NULL, + parallel = TRUE, + verbose = FALSE +) } \arguments{ \item{data}{a mousetrap data object created using one of the mt_import diff --git a/man/mt_average.Rd b/man/mt_average.Rd index bb609ca..760997c 100644 --- a/man/mt_average.Rd +++ b/man/mt_average.Rd @@ -4,10 +4,18 @@ \alias{mt_average} \title{Average trajectories across intervals.} \usage{ -mt_average(data, use = "trajectories", save_as = "av_trajectories", - dimensions = "all", av_dimension = "timestamps", intervals = NULL, - interval_size = 100, max_interval = NULL, verbose = FALSE, - dimension = NULL) +mt_average( + data, + use = "trajectories", + save_as = "av_trajectories", + dimensions = "all", + av_dimension = "timestamps", + intervals = NULL, + interval_size = 100, + max_interval = NULL, + verbose = FALSE, + dimension = NULL +) } \arguments{ \item{data}{a mousetrap data object created using one of the mt_import diff --git a/man/mt_check_bimodality.Rd b/man/mt_check_bimodality.Rd index d56b98c..d85be22 100644 --- a/man/mt_check_bimodality.Rd +++ b/man/mt_check_bimodality.Rd @@ -4,8 +4,15 @@ \alias{mt_check_bimodality} \title{Assess bimodality of mouse-tracking measure distributions.} \usage{ -mt_check_bimodality(data, use = "measures", use_variables = NULL, - methods = c("BC", "HDS"), B = 2000, grouping_variables = NULL, ...) +mt_check_bimodality( + data, + use = "measures", + use_variables = NULL, + methods = c("BC", "HDS"), + B = 2000, + grouping_variables = NULL, + ... +) } \arguments{ \item{data}{a mousetrap data object created using one of the mt_import diff --git a/man/mt_check_resolution.Rd b/man/mt_check_resolution.Rd index 42f2f81..f7129d3 100644 --- a/man/mt_check_resolution.Rd +++ b/man/mt_check_resolution.Rd @@ -4,8 +4,12 @@ \alias{mt_check_resolution} \title{Check logging resolution by looking at timestamp differences.} \usage{ -mt_check_resolution(data, use = "trajectories", - timestamps = "timestamps", desired = NULL) +mt_check_resolution( + data, + use = "trajectories", + timestamps = "timestamps", + desired = NULL +) } \arguments{ \item{data}{a mousetrap data object created using one of the mt_import diff --git a/man/mt_cluster.Rd b/man/mt_cluster.Rd index 61159dc..84ac16c 100644 --- a/man/mt_cluster.Rd +++ b/man/mt_cluster.Rd @@ -4,11 +4,22 @@ \alias{mt_cluster} \title{Cluster trajectories.} \usage{ -mt_cluster(data, use = "sp_trajectories", save_as = "clustering", - dimensions = c("xpos", "ypos"), n_cluster = 5, method = "hclust", - weights = rep(1, length(dimensions)), pointwise = TRUE, - minkowski_p = 2, hclust_method = "ward.D", kmeans_nstart = 10, - na_rm = FALSE, cluster_output = FALSE, verbose = FALSE) +mt_cluster( + data, + use = "sp_trajectories", + save_as = "clustering", + dimensions = c("xpos", "ypos"), + n_cluster = 5, + method = "hclust", + weights = rep(1, length(dimensions)), + pointwise = TRUE, + minkowski_p = 2, + hclust_method = "ward.D", + kmeans_nstart = 10, + na_rm = FALSE, + cluster_output = FALSE, + verbose = FALSE +) } \arguments{ \item{data}{a mousetrap data object created using one of the mt_import diff --git a/man/mt_cluster_k.Rd b/man/mt_cluster_k.Rd index 4e57000..03b4933 100644 --- a/man/mt_cluster_k.Rd +++ b/man/mt_cluster_k.Rd @@ -4,12 +4,24 @@ \alias{mt_cluster_k} \title{Estimate optimal number of clusters.} \usage{ -mt_cluster_k(data, use = "sp_trajectories", dimensions = c("xpos", - "ypos"), kseq = 2:15, compute = c("stability", "gap", "jump", - "slope"), method = "hclust", weights = rep(1, length(dimensions)), - pointwise = TRUE, minkowski_p = 2, hclust_method = "ward.D", - kmeans_nstart = 10, n_bootstrap = 10, model_based = FALSE, - n_gap = 10, na_rm = FALSE, verbose = FALSE) +mt_cluster_k( + data, + use = "sp_trajectories", + dimensions = c("xpos", "ypos"), + kseq = 2:15, + compute = c("stability", "gap", "jump", "slope"), + method = "hclust", + weights = rep(1, length(dimensions)), + pointwise = TRUE, + minkowski_p = 2, + hclust_method = "ward.D", + kmeans_nstart = 10, + n_bootstrap = 10, + model_based = FALSE, + n_gap = 10, + na_rm = FALSE, + verbose = FALSE +) } \arguments{ \item{data}{a mousetrap data object created using one of the mt_import diff --git a/man/mt_count.Rd b/man/mt_count.Rd index 668e2bd..829d3c9 100644 --- a/man/mt_count.Rd +++ b/man/mt_count.Rd @@ -4,8 +4,7 @@ \alias{mt_count} \title{Count number of observations.} \usage{ -mt_count(data, use = "trajectories", save_as = "measures", - dimensions = "xpos") +mt_count(data, use = "trajectories", save_as = "measures", dimensions = "xpos") } \arguments{ \item{data}{a mousetrap data object created using one of the mt_import diff --git a/man/mt_derivatives.Rd b/man/mt_derivatives.Rd index 2ed96e0..5dcb8bb 100644 --- a/man/mt_derivatives.Rd +++ b/man/mt_derivatives.Rd @@ -4,10 +4,17 @@ \alias{mt_derivatives} \title{Calculate distance, velocity, and acceleration.} \usage{ -mt_derivatives(data, use = "trajectories", save_as = use, - dimensions = c("xpos", "ypos"), timestamps = "timestamps", - prefix = "", absolute = FALSE, return_delta_time = FALSE, - verbose = FALSE) +mt_derivatives( + data, + use = "trajectories", + save_as = use, + dimensions = c("xpos", "ypos"), + timestamps = "timestamps", + prefix = "", + absolute = FALSE, + return_delta_time = FALSE, + verbose = FALSE +) } \arguments{ \item{data}{a mousetrap data object created using one of the mt_import diff --git a/man/mt_deviations.Rd b/man/mt_deviations.Rd index b79c70f..abf0ea0 100644 --- a/man/mt_deviations.Rd +++ b/man/mt_deviations.Rd @@ -4,9 +4,16 @@ \alias{mt_deviations} \title{Calculate deviations from idealized trajectory.} \usage{ -mt_deviations(data, use = "trajectories", save_as = use, - dimensions = c("xpos", "ypos"), start_ideal = NULL, - end_ideal = NULL, prefix = "", verbose = FALSE) +mt_deviations( + data, + use = "trajectories", + save_as = use, + dimensions = c("xpos", "ypos"), + start_ideal = NULL, + end_ideal = NULL, + prefix = "", + verbose = FALSE +) } \arguments{ \item{data}{a mousetrap data object created using one of the mt_import diff --git a/man/mt_diffmap.Rd b/man/mt_diffmap.Rd index 2adb690..8ad436d 100644 --- a/man/mt_diffmap.Rd +++ b/man/mt_diffmap.Rd @@ -4,11 +4,24 @@ \alias{mt_diffmap} \title{Creates a difference-heatmap of two trajectory heatmap images.} \usage{ -mt_diffmap(x, y = NULL, condition = NULL, use = "trajectories", - dimensions = c("xpos", "ypos"), use2 = "data", filename = NULL, - bounds = NULL, xres = 500, upscale = 4, smooth_radius = 10, - colors = c("#00863F", "#000000", "#FF1900"), n_shades = 1000, - plot = TRUE, ..., verbose = TRUE) +mt_diffmap( + x, + y = NULL, + condition = NULL, + use = "trajectories", + dimensions = c("xpos", "ypos"), + use2 = "data", + filename = NULL, + bounds = NULL, + xres = 500, + upscale = 4, + smooth_radius = 10, + colors = c("#00863F", "#000000", "#FF1900"), + n_shades = 1000, + plot = TRUE, + ..., + verbose = TRUE +) } \arguments{ \item{x}{an object of class \code{mousetrap}), a trajectory object of class diff --git a/man/mt_distmat.Rd b/man/mt_distmat.Rd index 659ca35..0966750 100644 --- a/man/mt_distmat.Rd +++ b/man/mt_distmat.Rd @@ -4,9 +4,16 @@ \alias{mt_distmat} \title{Compute distance matrix.} \usage{ -mt_distmat(data, use = "sp_trajectories", save_as = "distmat", - dimensions = c("xpos", "ypos"), weights = rep(1, length(dimensions)), - pointwise = TRUE, minkowski_p = 2, na_rm = FALSE) +mt_distmat( + data, + use = "sp_trajectories", + save_as = "distmat", + dimensions = c("xpos", "ypos"), + weights = rep(1, length(dimensions)), + pointwise = TRUE, + minkowski_p = 2, + na_rm = FALSE +) } \arguments{ \item{data}{a mousetrap data object created using one of the mt_import diff --git a/man/mt_exclude_initiation.Rd b/man/mt_exclude_initiation.Rd index c6114ab..c6558ca 100644 --- a/man/mt_exclude_initiation.Rd +++ b/man/mt_exclude_initiation.Rd @@ -4,9 +4,15 @@ \alias{mt_exclude_initiation} \title{Exclude initial phase without mouse movement.} \usage{ -mt_exclude_initiation(data, use = "trajectories", save_as = use, - dimensions = c("xpos", "ypos"), timestamps = "timestamps", - reset_timestamps = TRUE, verbose = FALSE) +mt_exclude_initiation( + data, + use = "trajectories", + save_as = use, + dimensions = c("xpos", "ypos"), + timestamps = "timestamps", + reset_timestamps = TRUE, + verbose = FALSE +) } \arguments{ \item{data}{a mousetrap data object created using one of the mt_import diff --git a/man/mt_export_long.Rd b/man/mt_export_long.Rd index 612d332..15af034 100644 --- a/man/mt_export_long.Rd +++ b/man/mt_export_long.Rd @@ -5,11 +5,23 @@ \alias{mt_export_wide} \title{Export mouse-tracking data.} \usage{ -mt_export_long(data, use = "trajectories", use_variables = NULL, - use2 = "data", use2_variables = NULL, ...) +mt_export_long( + data, + use = "trajectories", + use_variables = NULL, + use2 = "data", + use2_variables = NULL, + ... +) -mt_export_wide(data, use = "trajectories", use_variables = NULL, - use2 = "data", use2_variables = NULL, ...) +mt_export_wide( + data, + use = "trajectories", + use_variables = NULL, + use2 = "data", + use2_variables = NULL, + ... +) } \arguments{ \item{data}{a mousetrap data object created using one of the mt_import diff --git a/man/mt_heatmap.Rd b/man/mt_heatmap.Rd index cbd535d..014cf10 100644 --- a/man/mt_heatmap.Rd +++ b/man/mt_heatmap.Rd @@ -4,9 +4,16 @@ \alias{mt_heatmap} \title{Plot trajectory heatmap.} \usage{ -mt_heatmap(x, use = "trajectories", dimensions = c("xpos", "ypos"), - filename = NULL, ..., upscale = 1, plot_dims = FALSE, - verbose = TRUE) +mt_heatmap( + x, + use = "trajectories", + dimensions = c("xpos", "ypos"), + filename = NULL, + ..., + upscale = 1, + plot_dims = FALSE, + verbose = TRUE +) } \arguments{ \item{x}{usually an object of class \code{mousetrap}. Alternatively, a diff --git a/man/mt_heatmap_ggplot.Rd b/man/mt_heatmap_ggplot.Rd index dd949e3..74509a3 100644 --- a/man/mt_heatmap_ggplot.Rd +++ b/man/mt_heatmap_ggplot.Rd @@ -4,8 +4,15 @@ \alias{mt_heatmap_ggplot} \title{Plot trajectory heatmap using ggplot.} \usage{ -mt_heatmap_ggplot(data, use = "trajectories", dimensions = c("xpos", - "ypos"), use2 = "data", facet_row = NULL, facet_col = NULL, ...) +mt_heatmap_ggplot( + data, + use = "trajectories", + dimensions = c("xpos", "ypos"), + use2 = "data", + facet_row = NULL, + facet_col = NULL, + ... +) } \arguments{ \item{data}{a mousetrap data object created using one of the mt_import diff --git a/man/mt_heatmap_raw.Rd b/man/mt_heatmap_raw.Rd index 7233b4e..7f63cb0 100644 --- a/man/mt_heatmap_raw.Rd +++ b/man/mt_heatmap_raw.Rd @@ -4,13 +4,28 @@ \alias{mt_heatmap_raw} \title{Creates high-resolution heatmap of trajectory data.} \usage{ -mt_heatmap_raw(data, use = "trajectories", dimensions = c("xpos", - "ypos"), variable = NULL, bounds = NULL, xres = 1000, - upsample = 1, norm = FALSE, colors = c("black", "blue", "white"), - n_shades = c(1000, 1000), smooth_radius = 1.5, low_pass = 200, - auto_enhance = TRUE, mean_image = 0.15, mean_color = 0.25, - aggregate_lwd = 0, aggregate_col = "black", n_trajectories = NULL, - seed = NULL, verbose = TRUE) +mt_heatmap_raw( + data, + use = "trajectories", + dimensions = c("xpos", "ypos"), + variable = NULL, + bounds = NULL, + xres = 1000, + upsample = 1, + norm = FALSE, + colors = c("black", "blue", "white"), + n_shades = c(1000, 1000), + smooth_radius = 1.5, + low_pass = 200, + auto_enhance = TRUE, + mean_image = 0.15, + mean_color = 0.25, + aggregate_lwd = 0, + aggregate_col = "black", + n_trajectories = NULL, + seed = NULL, + verbose = TRUE +) } \arguments{ \item{data}{a mousetrap data object created using one of the mt_import diff --git a/man/mt_import_long.Rd b/man/mt_import_long.Rd index 5e7f433..8f39c0c 100644 --- a/man/mt_import_long.Rd +++ b/man/mt_import_long.Rd @@ -4,10 +4,18 @@ \alias{mt_import_long} \title{Import mouse-tracking data saved in long format.} \usage{ -mt_import_long(raw_data, xpos_label = "xpos", ypos_label = "ypos", - zpos_label = NULL, timestamps_label = "timestamps", - add_labels = NULL, mt_id_label = "mt_id", mt_seq_label = "mt_seq", - reset_timestamps = TRUE, verbose = TRUE) +mt_import_long( + raw_data, + xpos_label = "xpos", + ypos_label = "ypos", + zpos_label = NULL, + timestamps_label = "timestamps", + add_labels = NULL, + mt_id_label = "mt_id", + mt_seq_label = "mt_seq", + reset_timestamps = TRUE, + verbose = TRUE +) } \arguments{ \item{raw_data}{a data.frame in long format, containing the raw data.} diff --git a/man/mt_import_mousetrap.Rd b/man/mt_import_mousetrap.Rd index b2438cc..0b46379 100644 --- a/man/mt_import_mousetrap.Rd +++ b/man/mt_import_mousetrap.Rd @@ -4,10 +4,17 @@ \alias{mt_import_mousetrap} \title{Import mouse-tracking data recorded using the mousetrap plug-ins in OpenSesame.} \usage{ -mt_import_mousetrap(raw_data, xpos_label = "xpos", ypos_label = "ypos", - timestamps_label = "timestamps", mt_id_label = NULL, split = ",", - duplicates = "remove_first", reset_timestamps = TRUE, - verbose = FALSE) +mt_import_mousetrap( + raw_data, + xpos_label = "xpos", + ypos_label = "ypos", + timestamps_label = "timestamps", + mt_id_label = NULL, + split = ",", + duplicates = "remove_first", + reset_timestamps = TRUE, + verbose = FALSE +) } \arguments{ \item{raw_data}{a data.frame containing the raw data.} diff --git a/man/mt_import_wide.Rd b/man/mt_import_wide.Rd index 905b8b6..9869af2 100644 --- a/man/mt_import_wide.Rd +++ b/man/mt_import_wide.Rd @@ -4,10 +4,19 @@ \alias{mt_import_wide} \title{Import mouse-tracking data saved in wide format.} \usage{ -mt_import_wide(raw_data, xpos_label = "X", ypos_label = "Y", - zpos_label = NULL, timestamps_label = "T", add_labels = NULL, - mt_id_label = NULL, pos_sep = "_", pos_ids = NULL, - reset_timestamps = TRUE, verbose = TRUE) +mt_import_wide( + raw_data, + xpos_label = "X", + ypos_label = "Y", + zpos_label = NULL, + timestamps_label = "T", + add_labels = NULL, + mt_id_label = NULL, + pos_sep = "_", + pos_ids = NULL, + reset_timestamps = TRUE, + verbose = TRUE +) } \arguments{ \item{raw_data}{a data.frame containing the raw data.} diff --git a/man/mt_map.Rd b/man/mt_map.Rd index e3990c5..e4a2a3d 100644 --- a/man/mt_map.Rd +++ b/man/mt_map.Rd @@ -4,11 +4,19 @@ \alias{mt_map} \title{Map trajectories to prototypes.} \usage{ -mt_map(data, use = "sp_trajectories", save_as = "prototyping", +mt_map( + data, + use = "sp_trajectories", + save_as = "prototyping", dimensions = c("xpos", "ypos"), - prototypes = mousetrap::mt_prototypes, weights = rep(1, - length(dimensions)), pointwise = TRUE, na_rm = FALSE, - minkowski_p = 2, use2 = "data", grouping_variables = NULL) + prototypes = mousetrap::mt_prototypes, + weights = rep(1, length(dimensions)), + pointwise = TRUE, + na_rm = FALSE, + minkowski_p = 2, + use2 = "data", + grouping_variables = NULL +) } \arguments{ \item{data}{a mousetrap data object created using one of the mt_import diff --git a/man/mt_measures.Rd b/man/mt_measures.Rd index f0e6628..48143de 100644 --- a/man/mt_measures.Rd +++ b/man/mt_measures.Rd @@ -4,10 +4,17 @@ \alias{mt_measures} \title{Calculate mouse-tracking measures.} \usage{ -mt_measures(data, use = "trajectories", save_as = "measures", - dimensions = c("xpos", "ypos"), timestamps = "timestamps", - flip_threshold = 0, hover_threshold = NULL, - hover_incl_initial = TRUE, verbose = FALSE) +mt_measures( + data, + use = "trajectories", + save_as = "measures", + dimensions = c("xpos", "ypos"), + timestamps = "timestamps", + flip_threshold = 0, + hover_threshold = NULL, + hover_incl_initial = TRUE, + verbose = FALSE +) } \arguments{ \item{data}{a mousetrap data object created using one of the mt_import diff --git a/man/mt_plot.Rd b/man/mt_plot.Rd index 6022072..1d03f0a 100644 --- a/man/mt_plot.Rd +++ b/man/mt_plot.Rd @@ -5,15 +5,41 @@ \alias{mt_plot_aggregate} \title{Plot trajectory data.} \usage{ -mt_plot(data, use = "trajectories", use2 = "data", x = "xpos", - y = "ypos", color = NULL, linetype = NULL, alpha = NA, - size = 0.5, facet_row = NULL, facet_col = NULL, points = FALSE, - only_ggplot = FALSE, mt_id = "mt_id", ...) - -mt_plot_aggregate(data, use = "trajectories", use2 = "data", - x = "xpos", y = "ypos", color = NULL, linetype = NULL, - alpha = NA, size = 0.5, facet_row = NULL, facet_col = NULL, - points = FALSE, only_ggplot = FALSE, subject_id = NULL, ...) +mt_plot( + data, + use = "trajectories", + use2 = "data", + x = "xpos", + y = "ypos", + color = NULL, + linetype = NULL, + alpha = NA, + size = 0.5, + facet_row = NULL, + facet_col = NULL, + points = FALSE, + only_ggplot = FALSE, + mt_id = "mt_id", + ... +) + +mt_plot_aggregate( + data, + use = "trajectories", + use2 = "data", + x = "xpos", + y = "ypos", + color = NULL, + linetype = NULL, + alpha = NA, + size = 0.5, + facet_row = NULL, + facet_col = NULL, + points = FALSE, + only_ggplot = FALSE, + subject_id = NULL, + ... +) } \arguments{ \item{data}{a mousetrap data object created using one of the mt_import diff --git a/man/mt_plot_per_trajectory.Rd b/man/mt_plot_per_trajectory.Rd index 146220c..6a218eb 100644 --- a/man/mt_plot_per_trajectory.Rd +++ b/man/mt_plot_per_trajectory.Rd @@ -4,10 +4,22 @@ \alias{mt_plot_per_trajectory} \title{Create PDF with separate plots per trajectory.} \usage{ -mt_plot_per_trajectory(file, data, use = "trajectories", x = "xpos", - y = "ypos", xlim = NULL, ylim = NULL, axes_exact = FALSE, - points = FALSE, rect = NULL, color = "black", fill = NA, - verbose = FALSE, ...) +mt_plot_per_trajectory( + file, + data, + use = "trajectories", + x = "xpos", + y = "ypos", + xlim = NULL, + ylim = NULL, + axes_exact = FALSE, + points = FALSE, + rect = NULL, + color = "black", + fill = NA, + verbose = FALSE, + ... +) } \arguments{ \item{file}{a character string specifying the name of the PDF file. Passed on diff --git a/man/mt_plot_riverbed.Rd b/man/mt_plot_riverbed.Rd index a1cbebe..a620187 100644 --- a/man/mt_plot_riverbed.Rd +++ b/man/mt_plot_riverbed.Rd @@ -4,9 +4,17 @@ \alias{mt_plot_riverbed} \title{Plot density of mouse positions across time steps.} \usage{ -mt_plot_riverbed(data, use = "tn_trajectories", y = "xpos", - y_range = NULL, y_bins = 250, facet_row = NULL, facet_col = NULL, - facet_data = "data", grid_colors = c("gray30", "gray10")) +mt_plot_riverbed( + data, + use = "tn_trajectories", + y = "xpos", + y_range = NULL, + y_bins = 250, + facet_row = NULL, + facet_col = NULL, + facet_data = "data", + grid_colors = c("gray30", "gray10") +) } \arguments{ \item{data}{mousetrap data object containing the data to be plotted.} diff --git a/man/mt_qeffect.Rd b/man/mt_qeffect.Rd index 19a92f2..afe3af7 100644 --- a/man/mt_qeffect.Rd +++ b/man/mt_qeffect.Rd @@ -4,8 +4,16 @@ \alias{mt_qeffect} \title{Create quantile-effect plot} \usage{ -mt_qeffect(data, compare, use = "measures", measure = "MAD", - direction = "upward", n_steps = 100, return_data = FALSE, ...) +mt_qeffect( + data, + compare, + use = "measures", + measure = "MAD", + direction = "upward", + n_steps = 100, + return_data = FALSE, + ... +) } \arguments{ \item{data}{a mousetrap data object created using one of the mt_import diff --git a/man/mt_remap_symmetric.Rd b/man/mt_remap_symmetric.Rd index 4792888..2065724 100644 --- a/man/mt_remap_symmetric.Rd +++ b/man/mt_remap_symmetric.Rd @@ -4,9 +4,14 @@ \alias{mt_remap_symmetric} \title{Remap mouse trajectories.} \usage{ -mt_remap_symmetric(data, use = "trajectories", save_as = use, - dimensions = c("xpos", "ypos"), remap_xpos = "left", - remap_ypos = "up") +mt_remap_symmetric( + data, + use = "trajectories", + save_as = use, + dimensions = c("xpos", "ypos"), + remap_xpos = "left", + remap_ypos = "up" +) } \arguments{ \item{data}{a mousetrap data object created using one of the mt_import diff --git a/man/mt_resample.Rd b/man/mt_resample.Rd index f18bde1..0b06a16 100644 --- a/man/mt_resample.Rd +++ b/man/mt_resample.Rd @@ -4,10 +4,17 @@ \alias{mt_resample} \title{Resample trajectories using a constant time interval.} \usage{ -mt_resample(data, use = "trajectories", save_as = "rs_trajectories", - dimensions = c("xpos", "ypos"), timestamps = "timestamps", - step_size = 10, exact_last_timestamp = TRUE, - constant_interpolation = NULL, verbose = FALSE) +mt_resample( + data, + use = "trajectories", + save_as = "rs_trajectories", + dimensions = c("xpos", "ypos"), + timestamps = "timestamps", + step_size = 10, + exact_last_timestamp = TRUE, + constant_interpolation = NULL, + verbose = FALSE +) } \arguments{ \item{data}{a mousetrap data object created using one of the mt_import diff --git a/man/mt_reshape.Rd b/man/mt_reshape.Rd index 2643c74..c5a83e1 100644 --- a/man/mt_reshape.Rd +++ b/man/mt_reshape.Rd @@ -4,12 +4,23 @@ \alias{mt_reshape} \title{General-purpose reshape and aggregation function for mousetrap data.} \usage{ -mt_reshape(data, use = "trajectories", use_variables = NULL, - use2 = "data", use2_variables = NULL, subset = NULL, - subject_id = NULL, aggregate = FALSE, - aggregate_subjects_only = FALSE, .funs = "mean", - trajectories_long = TRUE, convert_df = TRUE, mt_id = "mt_id", - mt_seq = "mt_seq", aggregation_function = NULL) +mt_reshape( + data, + use = "trajectories", + use_variables = NULL, + use2 = "data", + use2_variables = NULL, + subset = NULL, + subject_id = NULL, + aggregate = FALSE, + aggregate_subjects_only = FALSE, + .funs = "mean", + trajectories_long = TRUE, + convert_df = TRUE, + mt_id = "mt_id", + mt_seq = "mt_seq", + aggregation_function = NULL +) } \arguments{ \item{data}{a mousetrap data object created using one of the mt_import diff --git a/man/mt_sample_entropy.Rd b/man/mt_sample_entropy.Rd index bda0337..e5ced33 100644 --- a/man/mt_sample_entropy.Rd +++ b/man/mt_sample_entropy.Rd @@ -4,9 +4,16 @@ \alias{mt_sample_entropy} \title{Calculate sample entropy.} \usage{ -mt_sample_entropy(data, use = "tn_trajectories", save_as = "measures", - dimension = "xpos", m = 3, r = NULL, use_diff = TRUE, - verbose = FALSE) +mt_sample_entropy( + data, + use = "tn_trajectories", + save_as = "measures", + dimension = "xpos", + m = 3, + r = NULL, + use_diff = TRUE, + verbose = FALSE +) } \arguments{ \item{data}{a mousetrap data object created using one of the mt_import diff --git a/man/mt_scale_trajectories.Rd b/man/mt_scale_trajectories.Rd index 39e4dd9..037c8dc 100644 --- a/man/mt_scale_trajectories.Rd +++ b/man/mt_scale_trajectories.Rd @@ -4,9 +4,17 @@ \alias{mt_scale_trajectories} \title{Standardize variables in mouse trajectory array.} \usage{ -mt_scale_trajectories(data, use = "trajectories", save_as = use, - var_names, center = TRUE, scale = TRUE, within_trajectory = FALSE, - prefix = "z_", transform = NULL) +mt_scale_trajectories( + data, + use = "trajectories", + save_as = use, + var_names, + center = TRUE, + scale = TRUE, + within_trajectory = FALSE, + prefix = "z_", + transform = NULL +) } \arguments{ \item{data}{a mousetrap data object created using one of the mt_import diff --git a/man/mt_space_normalize.Rd b/man/mt_space_normalize.Rd index bef9389..dc1f14d 100644 --- a/man/mt_space_normalize.Rd +++ b/man/mt_space_normalize.Rd @@ -4,9 +4,15 @@ \alias{mt_space_normalize} \title{Space normalize trajectories.} \usage{ -mt_space_normalize(data, use = "trajectories", - save_as = "sn_trajectories", dimensions = c("xpos", "ypos"), - start = c(0, 0), end = NULL, verbose = FALSE) +mt_space_normalize( + data, + use = "trajectories", + save_as = "sn_trajectories", + dimensions = c("xpos", "ypos"), + start = c(0, 0), + end = NULL, + verbose = FALSE +) } \arguments{ \item{data}{a mousetrap data object created using one of the mt_import diff --git a/man/mt_spatialize.Rd b/man/mt_spatialize.Rd index 2de4a29..aa193d5 100644 --- a/man/mt_spatialize.Rd +++ b/man/mt_spatialize.Rd @@ -4,8 +4,13 @@ \alias{mt_spatialize} \title{Spatialize trajectories.} \usage{ -mt_spatialize(data, use = "trajectories", dimensions = c("xpos", - "ypos"), save_as = "sp_trajectories", n_points = 20) +mt_spatialize( + data, + use = "trajectories", + dimensions = c("xpos", "ypos"), + save_as = "sp_trajectories", + n_points = 20 +) } \arguments{ \item{data}{a mousetrap data object created using one of the mt_import diff --git a/man/mt_standardize.Rd b/man/mt_standardize.Rd index d82fb7d..e44d929 100644 --- a/man/mt_standardize.Rd +++ b/man/mt_standardize.Rd @@ -4,8 +4,15 @@ \alias{mt_standardize} \title{Standardize mouse-tracking measures per level of other variables.} \usage{ -mt_standardize(data, use = "measures", use_variables = NULL, - within = NULL, prefix = "z_", center = TRUE, scale = TRUE) +mt_standardize( + data, + use = "measures", + use_variables = NULL, + within = NULL, + prefix = "z_", + center = TRUE, + scale = TRUE +) } \arguments{ \item{data}{a mousetrap data object created using one of the mt_import diff --git a/man/mt_time_normalize.Rd b/man/mt_time_normalize.Rd index 4068910..0a10185 100644 --- a/man/mt_time_normalize.Rd +++ b/man/mt_time_normalize.Rd @@ -4,9 +4,15 @@ \alias{mt_time_normalize} \title{Time normalize trajectories.} \usage{ -mt_time_normalize(data, use = "trajectories", - save_as = "tn_trajectories", dimensions = c("xpos", "ypos"), - timestamps = "timestamps", nsteps = 101, verbose = FALSE) +mt_time_normalize( + data, + use = "trajectories", + save_as = "tn_trajectories", + dimensions = c("xpos", "ypos"), + timestamps = "timestamps", + nsteps = 101, + verbose = FALSE +) } \arguments{ \item{data}{a mousetrap data object created using one of the mt_import diff --git a/man/read_mt.Rd b/man/read_mt.Rd index c87dc93..85380e9 100644 --- a/man/read_mt.Rd +++ b/man/read_mt.Rd @@ -4,8 +4,7 @@ \alias{read_mt} \title{Read MouseTracker raw data.} \usage{ -read_mt(file, columns = "all", add_trialid = FALSE, - add_filename = FALSE) +read_mt(file, columns = "all", add_trialid = FALSE, add_filename = FALSE) } \arguments{ \item{file}{a character string specifying the filename of the .mt file.} diff --git a/man/scale_within.Rd b/man/scale_within.Rd index 929c91a..204aa82 100644 --- a/man/scale_within.Rd +++ b/man/scale_within.Rd @@ -4,8 +4,14 @@ \alias{scale_within} \title{Scale and center variables within the levels of another variable.} \usage{ -scale_within(data, variables = NULL, within = NULL, prefix = "", - center = TRUE, scale = TRUE) +scale_within( + data, + variables = NULL, + within = NULL, + prefix = "", + center = TRUE, + scale = TRUE +) } \arguments{ \item{data}{a \link{data.frame}.}