Summarize Ovulation Confirmation and Imputation — summary

This function provides a summary of how ovulation was identified across the dataset – either through direct confirmation using an ovulation biomarker or via imputation based on menstrual cycle timing.

Usage

summary_ovulation(data)

Arguments

data: A dataframe containing the output of pacts_scaling() – specifically id, cyclenum, ovtoday, ovtoday_impute, and mcyclength_complete. (See examples below)

Value

A list with two data frames:

ovstatus_total: A dataset-level summary showing:
1. The number of cycles with confirmed ovulation (ovtoday == 1).
2. The number of cycles with imputed ovulation (ovtoday_impute == 1).
ovstatus_id: A participant-level summary showing, for each unique ID:
1. The number of cycles whose length falls outside 21-35 days. Descriptive only: a confirmed-ovulation cycle outside that range is still scaled, gated by its phase lengths instead (see lower_cyclength_bound in ?pacts_scaling). Still-open trailing cycles, whose length is not yet knowable, are not counted.
2. The number of cycles with confirmed ovulation.
3. The number of cycles with imputed ovulation.

Details

Specifically, it counts the number of cycles in which ovulation was:

Confirmed using an ovulation biomarker (i.e., a 1 in the ovtoday column), such as urinary LH surge tests or basal body temperature (BBT).
Imputed using the backward-count method, which estimates ovulation as 15 days before the subsequent menses onset (ovtoday_impute == 1), based on the typical length of the luteal phase.

The output includes both:

Overall summary counts across the entire dataset.
Per-individual summaries to support participant-level quality checks and reporting.

Report this summary in publications: it states how often ovulation timing was measured versus estimated. Ovulation-biomarker confirmation is preferred where available. Note that a positive LH-surge test or a basal body temperature (BBT) nadir does not pinpoint the day of ovulation, which would require ultrasound; it indicates that ovulation occurred within 24 to 36 hours (Nagpal et al., 2025, Section 2.1.2), and the width of that window depends on the detection method.

When ovulation biomarkers are unavailable, the -15 day backward count is recommended over a cycle-midpoint assumption, because the luteal phase varies less in length than the follicular phase. Against 33 hormone-confirmed cycles it was off by a mean absolute 0.97 days (SD 0.88; Nagpal et al., 2025, Section 3.2).

For further guidance on ovulation identification and the rationale for the -15 day imputation method, see:

Nagpal et al. (2025). Studying the Menstrual Cycle as a Continuous Variable: Implementing Phase-Aligned Cycle Time Scaling (PACTS) with the menstrualcycleR package. Psychoneuroendocrinology, 107584. https://doi.org/10.1016/j.psyneuen.2025.107584
Schmalenberger et al. (2021). How to study the menstrual cycle: Practical tools and recommendations. Psychoneuroendocrinology, 123, 104895. https://doi.org/10.1016/j.psyneuen.2020.104895

Examples

cycle_df = cycledata

data_with_scaling <- pacts_scaling(
  cycle_df, 
  id = id, 
  date = daterated, 
  menses = menses, 
  ovtoday = ovtoday, 
  lower_cyclength_bound = 21, 
  upper_cyclength_bound = 35
)

ov_summary = summary_ovulation(data_with_scaling)
print(ov_summary)
#> $ovstatus_total
#>          Total Confirmed Ovulation
#> N cycles                        14
#>          Total Estimated Ovulation via 15day Backward Count
#> N cycles                                                 11
#> 
#> $ovstatus_id
#> # A tibble: 25 × 4
#>       id Total cycles with cycle…¹ Total cycles with co…² Total cycles with im…³
#>    <int>                     <dbl>                  <dbl>                  <dbl>
#>  1     1                         0                      0                      1
#>  2     2                         0                      1                      0
#>  3     3                         0                      1                      0
#>  4     4                         0                      0                      1
#>  5     5                         0                      1                      0
#>  6     6                         0                      0                      1
#>  7     7                         0                      1                      0
#>  8     8                         0                      1                      0
#>  9     9                         0                      0                      1
#> 10    10                         0                      1                      0
#> # ℹ 15 more rows
#> # ℹ abbreviated names: ¹`Total cycles with cycle length < 21 or > 35`,
#> #   ²`Total cycles with confirmed ovulation`,
#> #   ³`Total cycles with imputed ovulation via 15day Backward Count`
#> 
ov_summary$ovstatus_total
#>          Total Confirmed Ovulation
#> N cycles                        14
#>          Total Estimated Ovulation via 15day Backward Count
#> N cycles                                                 11
ov_summary$ovstatus_id
#> # A tibble: 25 × 4
#>       id Total cycles with cycle…¹ Total cycles with co…² Total cycles with im…³
#>    <int>                     <dbl>                  <dbl>                  <dbl>
#>  1     1                         0                      0                      1
#>  2     2                         0                      1                      0
#>  3     3                         0                      1                      0
#>  4     4                         0                      0                      1
#>  5     5                         0                      1                      0
#>  6     6                         0                      0                      1
#>  7     7                         0                      1                      0
#>  8     8                         0                      1                      0
#>  9     9                         0                      0                      1
#> 10    10                         0                      1                      0
#> # ℹ 15 more rows
#> # ℹ abbreviated names: ¹`Total cycles with cycle length < 21 or > 35`,
#> #   ²`Total cycles with confirmed ovulation`,
#> #   ³`Total cycles with imputed ovulation via 15day Backward Count`