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Primary Model Selection

Node extensions for KNIME Workbench version 1.0.0.202102171221 by BfR

View and select estimated primary models and the associated microbial data.

Options

Graph
Visualizes values (e.g. microbial concentrations) over time.

Mouse zoom: To view a part of the graph in detail left click and simultaneously drag the mouse right and down. Another way is to use the zoom options in the context menu.

Context Menu (Right click in the graph):
Properties: Change font (type, size, color) and labels as well as the appearance of the graph. These changes are lost as soon as the options dialog is closed. To save a graph with changed properties (e.g. for a publication) use the "Save as..." option in the context menu.
Copy: Copies the graph to the clipboard enabling you to paste it in a graphical editor.
Save as...: Saves the graph as PNG (a bitmap image) or as SVG (a vector image). Compared to the PNG image in the outport (which has a resolution of 640x480 pixels) this PNG is saved with the same size as on the screen.
Print: Print the graph directly from Knime PMM-Lab.
Zoom: Zoom in and out or auto range the view for one or both axes.
Display Options
Draw Lines: Connect data points with lines which helps to distinguish between different sets of data.
Display Highlighted Row: If checked, only the highlighted row in the table on the right is displayed. A comfortable way to select sets of data is to highlight a row and then navigate with the arrow keys (up/down) through the table. Using the keyboard, the space bar can be used to select/unselect a set of data.
Show Legend: Display the model name together with symbol and color.
Add Info in Legend: Adds the formula to the legend. This option is only available when the legend is displayed.
Export as SVG: If checked, the graph outport contains a SVG file and not a PNG file after execution of the node.
Show Confidence Interval: Computes and displays confidence intervals. This is computed live and for all displayed models at once. For faster display only select few primary models or choose "Display Highlighted Row" and view models one after another. For details about the calculation of the confidence interval please see Tijskens, Hertog, Nicolai (eds) (2001): "Food Process Modelling". Woodhead Publishing Limited and CRC Press LLC.
Range
Set the minimum and maximum values for the x and y axes.
Variables on Display
X and Y: Time is on the x-axis and value (e.g. bacterial concentrations) on the y-axis.
X Unit: Change the time unit to seconds (s), minutes (min), hours (h), days (d), weeks (wk), months (mo) or years (a).
Y Unit: For some diagnostic tests it is necessary to know the amount of bacteria in 25g. For this case and others the value unit can be changed.
X and Y Transform: Transforms the data on the X and Y axis (square root, ln, log10, basis e, basis 10). This is useful if a display of data other than the PMM-Lab default (log10) is wished for (e.g. as actual cell counts -> 10^).
Filter
Filter the rows in the table to be displayed for model formula name, microbial data ID and model estimation status. Possible status of the model estimation:
'Model Name' If several model formulas were used for fitting data, this option reduces the rows in the table to those containing the selected formula.
'DataID' The DataID is an arbitrary negative number or shows the name of a ComBase dataset. In both cases the ID represents one dataset to which parameters of a primary model were fitted. This filter can be used to compare how well parameters of different model formulas could be fitted to the same dataset.
'Status' Filters for different model estimation results.
Ok = fitting successful;
No Covariance Matrix = Confidence intervals cannot be calculated. Editing the expert settings in the Model Fitting node or choosing a different formula may help;
Coeff out of limit = The fitting was successful, but only because the minimum/maximum values of the parameters given in the model formula were ignored;
Failed = Fitting was not successful. Editing the expert settings in the Model Fitting node or choosing a different formula may help.
Select
Either select all sets of data, unselect chosen data sets or invert the current selection.
Columns
Click on 'Customize' to select the columns to be displayed, e.g. model name, quality criteria (R2, AIC) and assay conditions (temperature, pH, aW).
'Set optimal width' changes the width of the columns such that the whole text is visible in each cell.
Table
The table shows the available sets of data, whether they are currently being displayed (selected), the color and shape of the symbol and other information (see "Columns"). Clicking on a column header sorts the rows. To change the order of the columns drag the column headline. This is temporarily and not saved when the node dialog is closed.

Input Ports

Icon
Primary models and microbial data (via Model Fitting, Model Reader, ComBase Reader or XLS Model Reader)

Output Ports

Icon
Selected primary models and corresponding data
Icon
Graph with selected data; the image is a PNG file (default) or a SVG file (see section 'Display Options')

Best Friends (Incoming)

Best Friends (Outgoing)

Installation

To use this node in KNIME, install PMM Nodes from the following update site:

KNIME 4.3

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Developers

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