Generate Report for Daily Cosinor and Generate Summary Plot

A multi-wrapper function which generate data trend using geom_smooth and model plot using CosinorM or CosinorM.KDE. All daily results could be found in the exported report. A summary file in .csv format is also generated to update the original `Bdf` with cosinor model coefficients for each day.

Usage

write.cosinor(
  Dir,
  ID,
  DailyAct,
  Bdf,
  VAct = NULL,
  VTm = NULL,
  method = "OLS",
  tau = 24,
  ph = FALSE,
  overwrite = FALSE
)

Arguments

Dir

The directory where the recordings to be exported <e.g. "C:/Users/___YOUR USERNAME___/UPSTREAM FOLDER/.../FOLDER NAME/">

ID

The subject's ID which would be used to create a folder.

DailyAct

A data.frame list generated by `Act2Daily()`

Bdf

A BriefSum object. Note, if jet lag occurred during the recording, please, update the metadata using TAdjust before passing to this function.

VAct

Optional character. Name of the activity column in each data.frame object (`df`) in `DailyAct`. If NULL, defaults to the second column of `df`.

VTm

Optional character. Name of the activity column in each data.frame object (`df`) in `DailyAct`. If NULL, defaults to the first column of `df`.

method

Character string specifying estimation method

"OLS": Ordinary least square cosinor model via CosinorM. (default)
"FGLS": Feasible generalized least squares cosinor model via CosinorM.
"KDE": Gaussian kernel density estimate (KDE) on circular time (hours of day) via CosinorM.KDE.

tau

Numeric scalar or vector for the assumed circadian period, passed to CosinorM. Default is 24 for single-phase; multiple phases can be supplied via [c()].

ph

Optional logical scaler; if only a single period is assigned to tau, TRUE will force the function to append the post-hoc circadian estimates instead of the model estimates. (default: FALSE)

overwrite

Logical; if TRUE, existing files with the same name will be overwritten. Default = FALSE.

Value

Creates a multi-page `.pdf` visual document and a text-based `.csv` summary.

PDF A multi-page PDF written to `pdfDir` (one file per `ID`). Each page corresponds to a recording day and contains two panels: the top panel shows the raw activity (points) and a smoothed trend; the bottom panel shows the model fit for the same day
`Summary.csv` An updated `Bdf` documentation with one row per recording day. Model-based circadian parameters are appened at the end of the file for each day.

Examples

if (FALSE) { # \dontrun{

# Import data
data (FlyEast)


# Create quick summary of the recording with adjustment for daylight saving.
BdfList <-
    BriefSum (
        df = FlyEast,
        SR = 1 / 60,
        Start = "2017-10-24 13:45:00"
    )


# Let's extract the quick summary of the recording
Bdf <- BdfList$Bdf
df <- BdfList$df

### Note that since the original data was affected by travel-induced time
### shift, the recordings would not be properly segmented from 2017-11-02.

## To avoid time shift due to travelling, we will keep only the first 8 days.
Bdf <- Bdf [1:8, ]


## Segment Data by Day
dfList <-
    Act2Daily (
        df = df,
        Bdf = Bdf,
        VAct = "Activity",
        VTm = "Time",
        Incomplete = TRUE,
        Travel = TRUE
    )


## Generate graphic summary of daily recordings in pdf with an addition
## `Summary` file just like write.act
write.cosinor (
    Dir = getwd (), ## Export to the current working directory
    ID = "JD",
    DailyAct = dfList$Daily_df,
    Bdf = Bdf,
    VAct = "Activity",
    VTm = "Time"
)

## To see what was exported copy the path generated by the code below and
## paste it as an url in a web browser or the file explorer.
getwd ()
} # }

Generate Report for Daily Cosinor and Generate Summary Plot

Usage

Arguments

Value

See also

Examples