proximetricsR (version 0.6.5)

add_application_metadata: A function for adding application metadata to a list of spectral_model objects

Description

This function has two use cases:

i. If object (a list of spectral_model objects) is passed to the function, it returns the same object with the specified application metadata added to it.

ii. Otherwise, the function can be used to create a list of application metadata that can be used as input for the argument metadata of the proximate_write_nax function.

Usage

add_application_metadata(object, key = UUIDgenerate(),
                         name = c(name = "Untitled", alias = NULL),
                         view = c("Up", "Down"), 
                         measurement_mode = c("DrIwr", "TrIwr"),
                         measurement_time = 15,
                         absorbmask_low = c(min = 0, max = 0),
                         absorbmask_high = c(min = 0, max = 0),
                         rotate_sample = TRUE,
                         selectable = TRUE, created, changed,
                         composition = NULL,
                         description = "created with proximetricsR",
                         sop = "",
                         presentation_id = "Default")

Value

Either the list of spectral_model objects with the added application metadata (if object is provided), or the application metadata as a named list.

Arguments

object

an optional object, consisting of a list of objects of class spectral_model. See details.

key

a string for the key of the application. Defaults to a newly generated key using UUIDgenerate.

name

a vector length at most 2, consisting of characters for the name and alias of the application. Defaults to "Untitled".

view

a string for the type of view in the application. Has to be either "Up" (default) or "Down".

measurement_mode

a string, indicating how the samples were measured. Has to be either Diffuse Reflection ("DrIwr", default) or Transflection ("TrIwr").

measurement_time

a numeric for the time each sample in the application should be measured, in seconds. Defaults to 15 seconds.

absorbmask_low

a vector of numerics of length 2 for the minimum and maximum of the lower absorbance mask. Defaults to a vector of zeros.

absorbmask_high

a vector of numerics of length 2 for the minimum and maximum of the higher absorbance mask. Defaults to a vector of zeros.

rotate_sample

a logical. Should the sample be rotated? Defaults to TRUE.

selectable

a logical, whether the application should be selectable. Defaults to TRUE.

created

a string of date and time of the creation of the application. Default is the current date and time of the system. See details for the format in which it has to be provided.

changed

a string of date and time when the application was changed. Defaults to the current date and time of the system. See details for the format in which it has to be provided.

composition

an optional string for the composition of the application. Defaults to NULL.

description

an optional string for the description of the application. Defaults to "created with proximetricsR".

sop

a string for the standard operating procedure (sop) for this particular application. Defaults to an empty character.

presentation_id

a string for the sample presentation ID of the application. Default is "Default".

Author

Claudio Orellano, Leonardo Ramirez-Lopez

Details

This function has two functionalities:

• If object (a list of spectral_model objects) is passed to the function, it returns the same object with the specified application metadata added to it.

• Otherwise, the function can be used to create a list of application metadata that can be used as input for the argument metadata of the proximate_write_nax function.

The application metadata is required for the import of an application into a ProxiMate device.

The two-fold functionality of this function allows to add application metadata during the construction of the models, or after the model-building processes have been finished. In the former case, a list of models of class spectral_model must be passed in object. Then, the returned object of this function contains the same list of models, including the specified metadata. Models can also be added or removed from that list, without changing the application metadata. In the latter case, the returned value of this function may be passed to the parameter metadata of function proximate_write_nax.

A lot of the parameters can be left unchanged and may be adjusted at a later stage of the application development (e.g. in a ProxiMate device). However, several parameters are of great importance for a successful migration of the application:

The parameter view describes if the spectrum is measured by either up-view "Up" or down-view "Down".

The measurement_mode describes how the samples are measured, with the following possibilities: Diffuse Reflection "DrIwr" or Transflection "TrIwr".

The parameters created and changed must contain the date (YYYY-MM-DD) and time (HH:MM:SS), seperated by a single "T" (without any spaces). For example, the following code returns the correct format (both created and changed default to this value):

gsub(" ", "T", format(Sys.time()))

See Also

calibrate, proximate_write_nax

Examples

# \donttest{
data(NIRcannabis)

# Downview Absorbance of CBDA in percentage
downview_metadata <- add_application_metadata(
  name = "CBDA Downview",
  view = "Down",
  measurement_mode = "DrIwr"
)

# Create a simple model with default model metadata
simple_model <- calibrate(CBDA ~ spc,
  data = NIRcannabis, preprocess = preprocess_recipe(),
  method = fit_plsr(5), control = calibration_control(),
  metadata = add_model_metadata(), verbose = FALSE
)

# Two ways to add application metadata to a list of spectral_model objects:
model_list <- list(simple_model)

# Using the add_application_metadata 'object' argument
model_list <- add_application_metadata(
  object = model_list,
  name = "CBDA Downview",
  view = "Down",
  measurement_mode = "TrIwr"
)

# Adding it manually
model_list$metadata <- downview_metadata

# Alternatively, if you are creating an application, you can also pass
# application metadata to 'proximate_write_nax':
proximate_write_nax(
  object = model_list,
  path = tempdir(),
  metadata = downview_metadata,
  tsv_name = "some_tsv",
  empty_tsv_name = "another_tsv",
  report = TRUE,
  verbose = FALSE
)
# }