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Make dataframe with variance measures

Source: R/Process-data.R
make_variance_data.Rd

make_variance_data creates a dataframe containing variance measures at two time points. They are the baseline period and a user-specified interval after a hormone or protocol has been applied. The variance measures are the inverse coefficient of variation squared and the variance-to-mean ratio (VMR). A "before vs. after" comparison of these two variance measures is useful to determine which mechanism is involved in modifying synaptic plasticity. For more information, please see Huijstee & Kessels (2020).

Usage

make_variance_data(
  data,
  df_category,
  include_all_treatments = "yes",
  list_of_treatments = NULL,
  baseline_interval = "t0to5",
  post_hormone_interval = "t20to25",
  treatment_colour_theme,
  save_output_as_RDS = "no"
)

Arguments

data

A dataframe containing the summary data generated from make_summary_EPSC_data(). If current_type is "eEPSC", this must be the $summary_data element of the list produced by make_summary_EPSC_data().

df_category

A numeric value describing the experimental category. In the sample dataset for this package, 2 represents experiments where insulin was applied continuously after a 5-minute baseline period. Here, plot_treatment represents antagonists that were present on the brain slice, or the animals were fasted, etc.

include_all_treatments

A character ("yes" or "no") specifying if the plot will include data from all treatments. If "no", you must specify a list of treatments in list_of_treatments.

list_of_treatments

A list of character values describing the treatments that will be in the plot. Defaults to NULL, since include_all_treatments is "yes" by default.

baseline_interval

A character value indicating the name of the interval used as the baseline. Defaults to "t0to5", but can be changed. Make sure that this matches the baseline interval that you set in make_normalized_EPSC_data().

post_hormone_interval

A character value indicating the name of the interval used as "after" timepoint for comparison. Defaults to "t20to25", but can be changed. Make sure that this matches an interval present in data

treatment_colour_theme

A dataframe containing treatment names and their associated colours as hex values. See sample_treatment_names_and_colours for an example of what this dataframe should look like.

save_output_as_RDS

A character ("yes" or "no") describing if the resulting object should be saved as an RDS file in the raw data folder.

Value

A dataframe containing all of the columns within the summary data (see sample_summary_eEPSC_df for a detailed description of these columns) plus three additional columns:

  • state A character value describing if a data point belongs to the baseline interval ("Baseline") or an interval after a hormone or protocol has been applied ("Post-modification"). These intervals are selected from baseline_interval and post_hormone_interval.

  • mean_cv_inverse_square The mean inverse coefficient of variation squared within a specific state and sex.

  • mean_VMR The mean variance-to-mean ratio within a specific state and sex.

See also

plot_variance_comparison_data() to plot this data.

Examples


make_variance_data(
  data = sample_summary_eEPSC_df$summary_data,
  df_category = 2,
  include_all_treatments = "yes",
  list_of_treatments = NULL,
  baseline_interval = "t0to5",
  post_hormone_interval = "t20to25",
  treatment_colour_theme = sample_treatment_names_and_colours,
  save_output_as_RDS = "no"
)
#> # A tibble: 38 × 25
#> # Groups:   treatment, state, sex [16]
#>    category letter sex    treatment interval mean_P1_transformed mean_P1_raw
#>    <fct>    <fct>  <fct>  <fct>     <fct>                  <dbl>       <dbl>
#>  1 2        AO     Male   Control   t0to5                 100          36.8 
#>  2 2        AO     Male   Control   t20to25                21.3         7.82
#>  3 2        AZ     Female Control   t0to5                 100          44.3 
#>  4 2        AZ     Female Control   t20to25                50.7        22.4 
#>  5 2        BN     Male   Control   t0to5                 100          72.1 
#>  6 2        BN     Male   Control   t20to25                19.1        13.8 
#>  7 2        L      Male   Control   t0to5                 100          77.0 
#>  8 2        L      Male   Control   t20to25                 5.75        4.43
#>  9 2        BO     Male   HNMPA     t0to5                 100          87.7 
#> 10 2        BO     Male   HNMPA     t20to25                24.3        21.4 
#> # ℹ 28 more rows
#> # ℹ 18 more variables: n <dbl>, sd <dbl>, cv <dbl>, se <dbl>,
#> #   cv_inverse_square <dbl>, variance <dbl>, VMR <dbl>, age <dbl>,
#> #   animal <dbl>, X <dbl>, Y <dbl>, time <dbl>, synapses <fct>,
#> #   days_alone <fct>, animal_or_slicing_problems <fct>, state <chr>,
#> #   mean_cv_inverse_square <dbl>, mean_VMR <dbl>