mm_model_by_ply: Split and label data into >=24-hr days for fitting daily...

In USGS-R/streamMetabolizer: Models for Estimating Aquatic Photosynthesis and Respiration

Split and label data into >=24-hr days for fitting daily metabolism

Description

Splits up to two data.frames, data and data_daily, into date-specific chunks. These are passed to model_fun. If day_tests is not empty, those validity checks are run and the results are also passed to model_fun (in validity). The results of model_fun (which must be a data.frame) are modified to include the data as a first column, then row-bound together into a single data.frame containing results from all days.

Usage

mm_model_by_ply(
  model_fun,
  data,
  data_daily = NULL,
  day_start,
  day_end,
  day_tests = c("full_day", "even_timesteps", "complete_data", "pos_discharge",
    "pos_depth"),
  required_timestep = NA,
  timestep_days = TRUE,
  ...
)

Arguments

model_fun	the function to apply to each data ply. This function should accept the arguments c(data, data_daily, ..., day_start, day_end, ply_date) where data_daily is NULL when the data_daily argument to mm_model_by_ply is missing or NULL
data	required. A data.frame to split into chunks by date, where a 'date' begins on the hour day_start and ends at the hour day_end. The solar.time column must be present.
data_daily	optional. A data.frame containing inputs with a daily timestep, each row of which will be passed to the corresponding date chunk from data. The date column must be present.
day_start	start time (inclusive) of a day's data in number of hours from the midnight that begins the date. For example, day_start=-1.5 indicates that data describing 2006-06-26 begin at 2006-06-25 22:30, or at the first observation time that occurs after that time if day_start doesn't fall exactly on an observation time. For metabolism models working with single days of input data, it is conventional/useful to begin the day the evening before, e.g., -1.5, and to end just before the next sunrise, e.g., 30. For multiple consecutive days, it may make the most sense to start just before sunrise (e.g., 4) and to end 24 hours later. For nighttime regression, the date assigned to a chunk of data should be the date whose evening contains the data. The default is therefore 12 to 36 for metab_night, of which the times of darkness will be used.
day_end	end time (exclusive) of a day's data in number of hours from the midnight that begins the date. For example, day_end=30 indicates that data describing 2006-06-26 end at the last observation time that occurs before 2006-06-27 06:00. See day_start for recommended start and end times.
day_tests	list of tests to conduct to determine whether each date worth of data is valid for modeling. The results of these tests will be combined with the result of the test implied if required_timestep is numeric and then will be passed to model_fun as the ply_validity argument to that function.
required_timestep	NA or numeric (length 1). If numeric, the timestep length in days that a date must have to pass the validity check (to within a tolerance of 0.2% of the value of required_timestep). The result of this test will be combined with the results of the tests listed in day_tests and reported to model_fun as the ply_validity argument to that function.
timestep_days	TRUE if you would like the mean timestep length to be calculated for each data ply and passed to model_fun as the timestep_days argument to that function. Alternatively, this may be numeric as a specifically expected timestep length in days; for example, a 1-hour timestep is 1/24 is 0.0416667.
...	other args to be passed through mm_model_by_ply to model_fun

Value

a data.frame of model results

Examples

dat <- data_metab('10')
mm_model_by_ply(mm_model_by_ply_prototype, data=dat, day_start=2, day_end=28)$date
mm_model_by_ply(function(...) { data.frame(text='hi')},
  data=dat, day_start=2, day_end=28)

USGS-R/streamMetabolizer documentation built on Aug. 15, 2023, 7:50 a.m.