OsteoBioR

https://pandora-isomemo.github.io/OsteoBioR/
Admin
OsteoBioR is an R package designed to estimate isotopic values in the past and analyze their changes...
Tokens:23,925
Snippets:260
Trust Score:9.7
Update:5 days ago
Show doc for...
Tokens:
Raw
### getExampleDataMatrix()

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/index.html

Get Example Matrix of Data.

```APIDOC
## getExampleDataMatrix()

### Description
Get Example Matrix of Data.
```

--------------------------------

### Example: create renewal rates dataset and call estimateIntervals

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/estimateIntervals.html

Example usage wrapped in \dontrun, showing how to create a dataframe with renewal rates for two bones and two teeth over six time intervals, then call estimateIntervals. The example is not run by default.

```r
if (FALSE) { # \dontrun{
#dataset with renewal rates
data <- data.frame(
 intStart = 0:5,
 intEnd = 1:6,
 bone1 = c(100, 50, 20, 10, 5, 2),
 bone2 = c(100, 10, 5, 1, 1, 1),
 tooth1 = c(0, 100, 0, 0, 0, 0),
 tooth2 = c(0, 0, 100, 0, 0, 0)
)
```

--------------------------------

### startApplication()

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/index.html

Start Application.

```APIDOC
## startApplication()

### Description
Start Application.
```

--------------------------------

### getExampleDataMatrix(sd = FALSE)

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/getExampleDataMatrix.html

Returns an example data matrix. If sd is TRUE, returns uncertainty renewal rates example data.

```APIDOC
## getExampleDataMatrix(sd = FALSE)

### Description
Returns an example data matrix. If `sd` is TRUE, returns uncertainty renewal rates example data.

### Usage
```r
getExampleDataMatrix(sd = FALSE)
```

### Arguments
- **sd** (boolean) - Optional - If TRUE, get uncertainty renewal rates example data.

```

--------------------------------

### computeResult example with test data

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/computeResult.html

Example usage of computeResult with a test dataframe. The output shows the resulting mean and standard deviation for the bone.

```R
testDat <- data.frame(
  t = 1:3,
  bone = c(100, 50, 0),
  mean = c(1, 3, 50),
  sd = c(1, 3, 50)
)
  computeResult(
  data = testDat,
  timeVars = "t",
  boneVars = "bone",
  meanVar = "mean",
  sdVar = "sd"
)
#>          mean      sd
#> bone 1.999994 1.80277
```

--------------------------------

### getEntry()

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/index.html

Get Entry.

```APIDOC
## getEntry()

### Description
Get Entry.
```

--------------------------------

### Interactive Program Startup Notice

Source: https://pandora-isomemo.github.io/OsteoBioR/LICENSE.html

Use this notice when your program starts in interactive mode. It includes placeholders for the program name, year, and author name. The commands 'show w' and 'show c' should display the appropriate parts of the GNU General Public License.

```plaintext
<program>  Copyright (C) <year>  <name of author>
This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'.
This is free software, and you are welcome to redistribute it
under certain conditions; type 'show c' for details.

```

--------------------------------

### getExampleIsotopeVals()

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/getExampleIsotopeVals.html

Returns an example matrix of isotopic values. This function is called with no arguments and provides a sample dataset for demonstration purposes.

```APIDOC
## getExampleIsotopeVals()

### Description
Returns an example matrix of isotopic values.

### Usage
```r
getExampleIsotopeVals()
```

### Arguments
None.

### Value
A matrix of isotopic values (example data).
```

--------------------------------

### startApplication(port = 4242)

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/startApplication.html

Starts the OsteoBioR web application on the specified port. The port argument defaults to 4242.

```APIDOC
## startApplication(port = 4242)

### Description
Starts the OsteoBioR web application on the specified port.

### Usage
```r
startApplication(port = 4242)
```

### Arguments
- **port** - Port of web application. Default is 4242.

```

--------------------------------

### getSeed()

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/index.html

Get Seed.

```APIDOC
## getSeed()

### Description
Get Seed.
```

--------------------------------

### getLabel()

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/index.html

Get Label.

```APIDOC
## getLabel()

### Description
Get Label.
```

--------------------------------

### getTimeMin()

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/index.html

Get Time Minimum.

```APIDOC
## getTimeMin()

### Description
Get Time Minimum.
```

--------------------------------

### getBreaks()

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/index.html

Get Breaks.

```APIDOC
## getBreaks()

### Description
Get Breaks.
```

--------------------------------

### getSiteStayTimes(object, siteMeans, siteSigma, intervalLengths = NULL, print = TRUE)

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/getSiteStayTimes.html

Calculates points in time where large changes happen in isotopic values. It uses posterior distributions to estimate the probability of changes to be (absolutely or relatively) large. Returns a data.frame containing the interval starts (intStart) and ends (intEnd) of changes.

```APIDOC
## getSiteStayTimes(object, siteMeans, siteSigma, intervalLengths = NULL, print = TRUE)

### Description
Calculates points in time where large changes happen in the isotopic values. It uses the posterior distributions to estimate the probability of changes to be (absolutely or relatively) large.

### Usage
```r
getSiteStayTimes(
  object,
  siteMeans,
  siteSigma,
  intervalLengths = NULL,
  print = TRUE
)
```

### Arguments
- **object** - model of class `TemporalIso`
- **siteMeans** - numeric vector. Isotopic mean values of sites/locations.
- **siteSigma** - numeric vector. Isotopic standard deviation values of sites/locations.
- **intervalLengths** - numeric vector. Vector of time interval lengths. Optional (if not given equal length intervals are assumed)
- **print** - boolean. If output should be printed. Defaults to TRUE.

### Value
A data.frame containing the interval starts (intStart) and ends (intEnd) of changes.
```

--------------------------------

### getTimeMax()

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/index.html

Get Time Maximum.

```APIDOC
## getTimeMax()

### Description
Get Time Maximum.
```

--------------------------------

### getPlotData()

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/index.html

Get Plot Data.

```APIDOC
## getPlotData()

### Description
Get Plot Data.
```

--------------------------------

### joinTimeForDerivation()

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/index.html

Get Breaks for Derivation.

```APIDOC
## joinTimeForDerivation()

### Description
Get Breaks for Derivation.
```

--------------------------------

### getXAxisData()

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/index.html

Get X-Axis Data.

```APIDOC
## getXAxisData()

### Description
Get X-Axis Data.
```

--------------------------------

### Define isotope values and standard deviations

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/estimateIntervals.html

Sets up the mean and standard deviation vectors for isotopic values used in the estimateIntervals example.

```R
y_mean <- c(-10, -7, -12, -9)
y_sigma <- c(2, 1.5, 2.5, 2.5)
```

--------------------------------

### Run Shiny app

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/estimateIntervals.html

Launches the OsteoBioR Shiny application.

```R
shiny::runApp(paste0(system.file(package = "OsteoBioR"),"/app"))
```

--------------------------------

### config()

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/index.html

Config.

```APIDOC
## config()

### Description
Config.
```

--------------------------------

### logging()

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/index.html

Logging.

```APIDOC
## logging()

### Description
Logging.
```

--------------------------------

### shinyModule

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/index.html

Server and UI Functions for Shiny Module.

```APIDOC
## shinyModule

### Description
Server and UI Functions for Shiny Module.
```

--------------------------------

### defaultInputsForUI()

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/index.html

Default Inputs for UI.

```APIDOC
## defaultInputsForUI()

### Description
Default Inputs for UI.
```

--------------------------------

### logWarn()

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/index.html

LogWarn.

```APIDOC
## logWarn()

### Description
LogWarn.
```

--------------------------------

### Get shift time with getShiftTime

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/estimateIntervals.html

Returns the estimated shift time for the fitted model using a threshold of 0.5.

```R
getShiftTime(fit, threshold = 0.5)
```

--------------------------------

### Estimate site stay times with getSiteStayTimes

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/estimateIntervals.html

Computes estimated staying times for sites with given means and standard deviations.

```R
estimatedStayTimes <- getSiteStayTimes(object = fit,
                                      siteMeans = c(-8, -10),
                                      siteSigma = c(1, 1.5))
```

--------------------------------

### getShiftTime(object, type = TRUE, slope = FALSE, threshold = NULL, probability = 0.5)

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/getShiftTime.html

Calculates time points where large changes occur in isotopic values based on posterior distributions. Returns a data frame with interval starts and ends of changes.

```APIDOC
## getShiftTime(object, type = TRUE, slope = FALSE, threshold = NULL, probability = 0.5)

### Description
Calculates points in time where large changes happen in the isotopic values. It uses the posterior distributions to estimate the probability of changes to be (absolutely or relatively) large.

### Usage
```r
getShiftTime(
  object,
  type = TRUE,
  slope = FALSE,
  threshold = NULL,
  probability = 0.5
)
```

### Arguments
- **object** (model of class `TemporalIso`) - Required - Model of class `TemporalIso`.
- **type** (boolean) - Optional - If the calculation shall be based on absolute or relative differences. Defaults to TRUE.
- **slope** (boolean) - Optional - If the calculation shall be based on differences or slopes. Defaults to FALSE (differences).
- **threshold** (numeric) - Optional - The threshold for a shift to be considered "large". Defaults to 1.5 for absolute isotopic values and 15 percent for relative changes.
- **probability** (numeric) - Optional - The probability for the differences to be larger than the threshold. Defaults to 50 percent.

### Value
A data.frame containing the interval starts (intStart) and ends (intEnd) of changes.
```

--------------------------------

### modelSpecificationsServer(id, dataMatrix, uploadedModelSpecInputs = reactiveVal())

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/modelSpecificationsServer.html

Server function for the modelSpecifications module. It initializes the module's server logic using the provided ID, reactive data matrix, and optional reactive model specification inputs.

```APIDOC
## modelSpecificationsServer(id, dataMatrix, uploadedModelSpecInputs = reactiveVal())

### Description
Server function of the modelSpecifications module. This function is called to set up the server-side logic for the module.

### Usage
```r
modelSpecificationsServer(
  id,
  dataMatrix,
  uploadedModelSpecInputs = reactiveVal()
)
```

### Arguments
- **id** (character) - Required - An ID string that corresponds with the ID used to call the module's UI function.
- **dataMatrix** (reactive) - Required - A reactive shinyMatrix matrixInput, see `estimateIntervals`: specifying the renewal rates of different probes for each time interval. The renewalRates should be between 0 and 100 (percentages). The dataframe should include a column specifying a time-index (e.g. 1, 2, 3, ...) as well as columns for the different bones. The renewal rates should contain the times of origin, containing 100.
- **uploadedModelSpecInputs** (reactive) - Optional - Model specifications for the current fit.
```

--------------------------------

### Estimate intervals with estimateIntervals

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/estimateIntervals.html

Fits the model using renewal rates data, time variable 'intStart', and bone variables. Prints the fit, plots time intervals, and estimates values at specific time points.

```R
fit <- estimateIntervals(renewalRates = data,
                        timeVars = "intStart",
                        boneVars = c("bone1", "bone2", "tooth1", "tooth2"),
                        isoMean = y_mean,
                      isoSigma = y_sigma)
print(fit)
# implemented Methods
plotTime(fit)
#get estimates for specific time points
estimateTimePoint(fit, time = seq(0,5, by = 0.5))
```

--------------------------------

### timePlotFormattingServer(id, savedModels)

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/timePlotFormattingServer.html

Backend for plot formatting module. This function is called to initialize the server-side logic for the plot formatting module.

```APIDOC
## timePlotFormattingServer(id, savedModels)

### Description
Backend for plot formatting module.

### Usage
```r
timePlotFormattingServer(id, savedModels)
```

### Arguments
- **id** - namespace id
- **savedModels** - list of models of class `TemporalIso`

```

--------------------------------

### export(<TemporalIso>)

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/index.html

Export of TemporalIso samples as csv.

```APIDOC
## export(<TemporalIso>)

### Description
Export of TemporalIso samples as csv.
```

--------------------------------

### modelSpecificationsServer()

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/index.html

Server function of modelSpecifications module.

```APIDOC
## modelSpecificationsServer()

### Description
Server function of modelSpecifications module.
```

--------------------------------

### getSiteStayTimes()

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/index.html

Calculate estimated stay times for locations given isotopic values.

```APIDOC
## getSiteStayTimes()

### Description
Calculate estimated stay times for locations given isotopic values.
```

--------------------------------

### export(fit, file, interval = NULL, ...)

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/export.html

Writes the interval samples of a TemporalIso object to a CSV file. The method takes a TemporalIso object, a file path, and optional interval filtering and additional arguments passed to write.csv.

```APIDOC
## export(fit, file, interval = NULL, ...)

### Description
Writes the interval samples of a TemporalIso object to a .csv file.

### Usage
```r
# S4 method for class 'TemporalIso'
export(fit, file, interval = NULL, ...)
```

### Arguments
- **fit** (TemporalIso) - Required - An instance of class TemporalIso, generated from `estimateIntervals`.
- **file** (character) - Required - A character string specifying the path to a .csv file.
- **interval** (numeric) - Optional - Numeric values which are part of the specified time intervals. Defaults to all intervals being exported.
- **...** - Optional - Optional arguments to write.csv.

### See Also
write.csv
```

--------------------------------

### computeResult function usage

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/computeResult.html

Shows the function signature with all arguments and defaults. The cor argument defaults to 0.5.

```R
computeResult(data, timeVars, boneVars = NULL, meanVar, sdVar, cor = 0.5)
```

--------------------------------

### logging(msg, ...)

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/logging.html

Logs a message. The msg argument is the message to log, and additional arguments can be used to populate the format string.

```APIDOC
## logging(msg, ...)

### Description
Logs a message with optional formatting arguments.

### Usage
```r
logging(msg, ...)
```

### Arguments
- **msg** - The message to log.
- **...** - Optional arguments to populate the format string.

```

--------------------------------

### logDebug()

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/index.html

LogDebug.

```APIDOC
## logDebug()

### Description
LogDebug.
```

--------------------------------

### computeResult(data, timeVars, boneVars = NULL, meanVar, sdVar, cor = 0.5)

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/computeResult.html

Computes the resulting mean and standard deviation for each bone/tooth as well as the covariances, based on renewal rates and isotopic value distributions over time.

```APIDOC
## computeResult(data, timeVars, boneVars = NULL, meanVar, sdVar, cor = 0.5)

### Description
Given renewal rates for different isotopic probes over time and normal distributions of isotopic values over time, resulting normal distributions of the isotopic probes are calculated.

### Usage
```r
computeResult(data, timeVars, boneVars = NULL, meanVar, sdVar, cor = 0.5)
```

### Arguments
- **data** (data.frame) - Required - A dataframe specifying the renewal rates of different probes for each time interval. The renewal rates should be between 0 and 100 (percentages). The dataframe should include a column specifying a time-index (e.g. 1, 2, 3, ...) as well as columns for the different bones. Furthermore, the dataframe should contain the mean and sd values for each time interval.
- **timeVars** (character string) - Required - A character string specifying the name of the column indicating the time.
- **boneVars** (vector of character strings) - Optional - A vector of character strings indicating the relevant variables containing the renewal rates of bones and teeth.
- **meanVar** (character string) - Required - A character string specifying the name of the column indicating the mean values of the isotopic probes over time.
- **sdVar** (character string) - Required - A character string specifying the name of the column indicating the standard deviation of the isotopic probes over time.
- **cor** (numeric) - Optional - The temporal correlation between neighbouring time points. Defaults to 0.5.

### Value
A data.frame containing the resulting mean and standard deviation for each bone/tooth as well as the covariances.

### Examples
```r
testDat <- data.frame(
  t = 1:3,
  bone = c(100, 50, 0),
  mean = c(1, 3, 50),
  sd = c(1, 3, 50)
)
computeResult(
  data = testDat,
  timeVars = "t",
  boneVars = "bone",
  meanVar = "mean",
  sdVar = "sd"
)
#>          mean      sd
#> bone 1.999994 1.80277
```

### See also
estimateIntervals
```

--------------------------------

### timePlotFormattingServer()

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/index.html

Server function of time plot formatting.

```APIDOC
## timePlotFormattingServer()

### Description
Server function of time plot formatting.
```

--------------------------------

### combineDataAndModelOutputs()

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/index.html

Combine Data and Model Outputs.

```APIDOC
## combineDataAndModelOutputs()

### Description
Combine Data and Model Outputs.
```

--------------------------------

### OsteoBioR-package

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/index.html

The 'OsteoBioR' package.

```APIDOC
## OsteoBioR-package

### Description
The 'OsteoBioR' package.
```

--------------------------------

### modelSpecificationsUI()

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/index.html

UI function of modelSpecifications module.

```APIDOC
## modelSpecificationsUI()

### Description
UI function of modelSpecifications module.
```

--------------------------------

### extendXAxis()

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/index.html

Extend X Axis.

```APIDOC
## extendXAxis()

### Description
Extend X Axis.
```

--------------------------------

### cleanAndSplitData()

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/index.html

Clean and Split Data.

```APIDOC
## cleanAndSplitData()

### Description
Clean and Split Data.
```

--------------------------------

### Compute resulting isotopic values with computeResult

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/estimateIntervals.html

Creates a test data frame and computes resulting isotopic values using the computeResult function.

```R
testDat <- data.frame(
 t = 1:3,
 bone1 = c(100, 50, 10, 10, 10, 10),
 bone2 = c(0, 20, 20, 20, 20, 20),
 teeth1 = c(0, 0, 0, 10, 50, 60),
 mean = c(1, 3, 3,0, -1, - 5),
 sd = c(1, 3, 1, 1.5, 2, 3)
)

computeResult(
 data = testDat,
 timeVars = "t",
 boneVars = c("bone1","bone2","teeth1"),
 meanVar = "mean",
 sdVar = "sd"
)
```

--------------------------------

### modelSpecificationsUI(id, title)

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/modelSpecificationsUI.html

This function creates the UI for the modelSpecifications module. It is called with a namespace id and a title to display in the tab.

```APIDOC
## modelSpecificationsUI(id, title)

### Description
Creates the UI for the modelSpecifications module.

### Usage
```r
modelSpecificationsUI(id, title)
```

### Arguments
- **id** - namespace
- **title** - title in tab

### Details
This function is part of the modelSpecifications module and is used to generate the user interface for that module.
```

--------------------------------

### getShiftTime()

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/index.html

Calculate time points of shifted isotopic values.

```APIDOC
## getShiftTime()

### Description
Calculate time points of shifted isotopic values.
```

--------------------------------

### timePlotFormattingUI()

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/index.html

UI function of time plot formatting.

```APIDOC
## timePlotFormattingUI()

### Description
UI function of time plot formatting.
```

--------------------------------

### logDebug(msg, ...)

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/logDebug.html

Logs a debug message with optional format arguments.

```APIDOC
## logDebug(msg, ...)

### Description
Logs a debug message. The message can include format specifiers that are populated by the optional arguments.

### Usage
```r
logDebug(msg, ...)
```

### Arguments
- **msg** (character) - Required - The message to log.
- **...** - Optional - Optional arguments to populate the format string.

```

--------------------------------

### getTimeMin(mtrx, timeVars, default = 0)

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/getTimeMin.html

Returns the minimal time from a data matrix. The function accepts a data matrix, column names of time variables, and an optional default value.

```APIDOC
## getTimeMin(mtrx, timeVars, default = 0)

### Description
Returns the minimal time from a data matrix.

### Usage
```r
getTimeMin(mtrx, timeVars, default = 0)
```

### Arguments
- **mtrx** (matrix) - Required - data matrix
- **timeVars** (character) - Required - column names of time variables
- **default** (numeric) - Optional - default result

### Value
(numeric) minimal time

```

--------------------------------

### logWarn(msg, ...)

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/logWarn.html

Logs a warning message. The message can contain format specifiers that are populated by the optional arguments.

```APIDOC
## logWarn(msg, ...)

### Description
Logs a warning message. The message can contain format specifiers that are populated by the optional arguments.

### Usage
```r
logWarn(msg, ...)
```

### Arguments
- **msg** - The message to log.
- **...** - Optional arguments to populate the format string.

```

--------------------------------

### setVarsForUncMatrix()

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/index.html

Set Vars For Unc Matrix.

```APIDOC
## setVarsForUncMatrix()

### Description
Set Vars For Unc Matrix.
```

--------------------------------

### estimateIntervals function signature

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/estimateIntervals.html

The usage signature for estimateIntervals, showing all parameters and their defaults. Note that the defaults for mu_df, mu_sd, adapt_delta, and max_treedepth in the signature differ from those described in the Arguments section.

```r
estimateIntervals(
  renewalRates,
  timeVars,
  boneVars = NULL,
  indVar = "",
  isoMean,
  isoSigma,
  renewalRatesSD = NULL,
  mu_df = 3,
  mu_mean = 0,
  mu_sd = 20,
  rho_mean = 1,
  rho_sd = 0.25,
  alpha_mean = 2,
  alpha_sd = 0.5,
  mc = TRUE,
  adapt_delta = 0.98,
  max_treedepth = 15,
  chains = 4,
  iter = 2000,
  burnin = 500,
  ...
)
```

--------------------------------

### add_na_row()

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/index.html

Add NA Row.

```APIDOC
## add_na_row()

### Description
Add NA Row.
```

--------------------------------

### timePlotFormattingUI(id)

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/timePlotFormattingUI.html

UI function of time plot formatting. This function returns an actionButton for time plot formatting.

```APIDOC
## timePlotFormattingUI(id)

### Description
UI function of time plot formatting.

### Usage
```r
timePlotFormattingUI(id)
```

### Arguments
- **id** - module id

### Value
actionButton
```

--------------------------------

### getSeed(fixSeed, seedValue)

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/getSeed.html

Returns a seed value for model fitting. If fixSeed is TRUE, returns the provided seedValue; otherwise, returns a random seed.

```APIDOC
## getSeed(fixSeed, seedValue)

### Description
Returns a seed value for model fitting. If `fixSeed` is TRUE, returns the provided `seedValue`; otherwise, returns a random seed.

### Usage
```r
getSeed(fixSeed, seedValue)
```

### Arguments
- **fixSeed** (logical) - Required - If TRUE use fixed seed, if FALSE use random seed when fitting the model.
- **seedValue** (numeric) - Required - Value for seed if `fixSeed == TRUE`.

### Return Value
A numeric seed value.
```

--------------------------------

### plot(<TemporalIso>,<missing>)

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/index.html

Plots for TemporalIso objects.

```APIDOC
## plot(<TemporalIso>,<missing>)

### Description
Plots for TemporalIso objects.
```

--------------------------------

### getEntry(modelList, entry)

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/getEntry.html

Retrieves all list elements named 'entry' from a list of model objects. The function takes a list of saved model objects and a character string specifying the name of the list element to extract.

```APIDOC
## getEntry(modelList, entry)

### Description
Get all list elements "entry" of a list of models.

### Usage
```r
getEntry(modelList, entry)
```

### Arguments
- **modelList** (list) - Required - List of saved model objects.
- **entry** (character) - Required - Name of the list element, e.g. "fit".

```

--------------------------------

### getUserDefinedEst(object, minim = 0, maxim = 1, type = "1")

Source: https://pandora-isomemo.github.io/OsteoBioR/reference/getUserDefinedEst.html

Calculates estimates for user defined intervals from a TemporalIso model object. Returns a data.frame containing mean and sd within the interval.

```APIDOC
## getUserDefinedEst(object, minim = 0, maxim = 1, type = "1")

### Description
Calculate estimates for user defined intervals.

### Usage
```r
getUserDefinedEst(object, minim = 0, maxim = 1, type = "1")
```

### Arguments
- **object** (model of class `TemporalIso`) - Required - Model of class `TemporalIso`.
- **minim** (numeric) - Optional - Numeric lower interval point. Default is 0.
- **maxim** (numeric) - Optional - Numeric upper interval point. Default is 1.
- **type** (character) - Optional - "1" for absolute values, "2" for total turnover. Default is "1".

### Value
A data.frame containing mean and sd within the interval.
```
Tokens:
Raw