EVRISCRIPT Module and Evri faq: Difference between pages

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===Purpose===
__TOC___
==Importing / Exporting==


EVRISCRIPT_Module objects wrap Eigenvector code and objects into "steps" used in an [[Evriscript]] Object. Each step defines the operation, inputs, outputs, and options.
[[faq_concatenate_multiple_files|How do I concatenate multiple files into a single DataSet?]]


[[EVRISCRIPT_Module]]) to perform.
[[faq_create_multivariate_image_from_separate_images|How do I create a multivariate image from separate images?]]


===Description===
[[faq_export_PCA_scores_and_loadings_to_text_file|How do I export PCA scores and loadings to a text file (to read into MS Excel, for example)?]]
====Creating a modules====
Create an empty instance of a module:
module = evriscript_module;
After creating instance of evriscript_module, the following operations can be done to customize the module for its particular operation.
====Using Keywords====
Specify the keyword to instance the module through evriscript objects:
module.keyword = 'knn';
====Description====
Provide a description of the module:
module.description = 'KNN K-nearest neighbor classifier';
====Module Modes====
For any particular module you can add modes to define operations in the step. For example, a module for calculating a PLS model would include "calibrate", "apply", and "test" modes. An example to create a "calibrate" mode for KNN:
module.command.calibrate = 'var.model = knn(var.x,var.k,options);';
* Creating a new mode starts by defining the "command" property for the mode. This consists of specifying the command property, followed by the mode name ("calibrate" in the example above) and the command to execute for this mode. The mode name is also used to specify mode-specific settings in the "required", "optional" and "outputs" properties of the EVRISCRIPT_MODULE object.


* Note that inputs and outputs from the function are prefixed with "var." to indicate these are properties on the evriscript object (see "required" and "optional" properties below). The "options" input never has a var. prefix as it refers to the EVRISCRIPT_STEP options specifically.
[[faq_import_three-way_data|How do I import three-way data into Solo or PLS_Toolbox?]]


* Any number of modes can be defined for a given module. If only one is defined, this will be the default mode when the given module is added to a script. Otherwise, the default mode will be empty and the user will be forced to choose a mode before the script step containing this module is run.
[[faq_import_horiba_NGC_64bit |Why can't I import a Horiba NGC file on my 64-bit computer?]]


====Required Inputs====
[[faq_SPCREADR_cant_read_multiple_files |Why can't SPCREADR read multiple files I've selected?]]
This cell array indicates what inputs MUST be defined prior to executing the module in this mode.
module.required.calibrate = {'x'};


====Optional Inputs====
[[faq_some_EXCEL_files_fail_to_import |Why do some Excel files fail to import?]]
Define the list of optional inputs for the mode:
module.optional.calibrate = {'k'};
This cell array indicates what inputs can be left undefined prior to executing the module in this mode. An optional input, if not defined by the caller, is passed with the value defined in the "default" field (see below). Options are always considered "optional" and need not be listed. The options listed in the "options" field will be passed for these values.
====Default Values====
Defining default values for optional inputs:
module.default.k = 3;
Provide values which are used if the given optional input is not provided by the user. If no inputs are optional, this field will be empty. Note that the default is the same for all modes (this field is not indexed by the mode name.)
====Outputs====
Define the list of outputs expected from the mode:
module.outputs.calibrate  = {'model'};
This cell array indicates the outputs expected. Outputs will be mapped to properties of the evriscript object and, unless listed as a required or optional input for this mode, will be marked as "read only".
====Options====
Define the options:
module.options = knn('options');
Provides a sub-structure which will contain the default options for this function. Only one set of default options can be provided and that will be used for all modes. If different modes of calling this module require different options, then separate modules must be created.
====Renaming====
To rename a mode:
module = rename(module,'onecall','mycall')
Renames the mode 'onecall' to be 'mycall'.


====Locking====
==General==
To lock a module:
module.lock = 1
Forces the module into "read-only" mode indicating that no additional changes can be made to the object.


===Examples===
[[faq_PARALIND_in_PLS_Toolbox |Can I do PARALIND in PLS_Toolbox?]]
module = evriscript_module %empty module
 
  module = evriscript_module('pls') %return module for this keyword predefined for PLS model
[[faq_install_on_more_than_one_PC | Can I install PLS_Toolbox (or Solo) on more than one PC, such as on my desktop and laptop computer?]]
===See Also===
 
[[EVRISCRIPT]]
[[faq_multiple_class_sets_together_in_SIMCA_PLSDA_LDA | Can I use multiple class sets (categorical variables) together in a SIMCA, PLSDA, or LDA model?]]
 
[[faq_more_info_on_R_Squared_statistic | Can you give me more information on the R-Squared statistic?]]
 
[[faq_how_RMSEC_and_RMSECV_related to R2Y_and_Q2Y_seen_other_software | How are RMSEC and RMSECV related to R2Y and Q2Y I see in other software?]]
 
[[faq_convergence_of_PARAFAC| Convergence of PARAFAC. How much variation between models is expected a particular PARAFAC is fit multiple times with the same settings?]]
 
[[faq_does_software_stop_working_if_maintenance_expires | Does the software stop working if my maintenance expires?]]
 
[[faq_report_a_problem_with_PLS_Toolbox | How and where do I report a problem with PLS_Toolbox?]]
 
[[faq_how_are_T_contributions_calculated | How are T-contributions calculated?]]
 
[[faq_how_are_ROC_curves_calculated_for_PLSDA | How are the ROC curves calculated for PLSDA?]]
 
[[faq_how_are_error_bars_calculated_regression_model | How are the error bars calculated for a regression model and can they be related to a confidence limit (confidence in the prediction)?]]
 
[[faq_improve_performance_with_PLS_Toolbx_and_Matlab_on_Mac | How can I improve performance with PLS_Toolbox and Matlab on the Mac platform?]]
 
[[faq_assign_classes_for_samples_in_a_DataSet | How do I assign classes for samples in a DataSet?]]
 
[[faq_build_a_classification_model_from_class_set_other_than_the_first | How do I build a classification model from a class set other than the first?]]
 
[[faq_choose_between_different_cross_validation_leave_out_options | How do I choose between the different cross-validation leave-out options?]]
 
[[faq_reference_Eigenvector| How do I cite/reference Eigenvector?]]
 
[[faq_interpret_ROC_curves_and_Sensitivity_Specificity_plots_from_PLSDA | How do I interpret the ROC curves and Sensitivity / Specificity plots from PLSDA?]]
 
[[faq_make_DataSet_backwards_compatible | How do I make a DataSet backwards compatible?]]
 
[[faq_obtain_or_use_recompilation_license_for_PLS_Toolbox | How do I obtain or use a recompilation license for PLS_Toolbox?]]
 
[[faq_use_custom_cross_validation_option | How do I use the "custom" cross-validation option?]]
 
[[faq_out_of_memory_error_when_analyzing_data | I keep getting "out of memory" errors when analyzing my data. What can I do?]]
 
[[faq_java_lang_OutOfMemoryError| What can I do if I get a java.lang.OutOfMemoryError error?]]
 
[[faq_why_get_negative_scores_when_all_modes_are_set_to_nonnegativity | Nonnegativity (PARAFAC, PARAFAC2, Tucker): Why do I get negative scores when all modes are set to nonnegativity?]]
 
[[faq_what_are_relative_contributions | What are "Relative Contributions"?]]
 
[[faq_what_are_reduced_T^2_and_Q_Statistics | What are the "Reduced" T<sup>2</sup> and Q Statistics?]]
 
[[faq_units_for_RMSEC_and_RMSECV_for_PLSDA | What are the units used for RMSEC and RMSECV when cross-validating PLSDA models?  Why do the cross-validation curves look strange for PLSDA?]]
 
[[faq_what_do_the_four_Fit_/_Unique_Fit_stats_mean_in_MCR_PARAFAC | What do the four Fit/Unique Fit statistics mean in MCR and PARAFAC models?]]
 
[[faq_internal_tests_used_to_select_suggested_number_of_PCs | What internal tests are used to select "suggested" number of PCs?]]
 
[[faq_what_is_PLS1_v_PLS2_and_how_to_create_separate_PLS1_models_from_multi_column_y_block | What is PLS1 vs PLS2 and how do I create separate PLS1 models when I have a multi-column y-block?]]
 
[[faq_difference_between_a_loading_and_a_weighting | What is the difference between a loading and a weighting?]]
 
[[faq_why_some_axis_labels_and_titles_upside_down_in_MIA_Toolbox | Why are some axis labels and titles on my axes upside-down when I'm viewing images in MIA_Toolbox?]]
 
[[faq_why_can't_I_recompile_PLS_Toolbox_functions | Why can't I recompile the PLS_Toolbox functions?]]
 
[[faq_why_get_missing_data_warning| Why do I get the warning/notice "Missing Data Found - Replacing with "best guess" from existing model. Results may be affected by this action."]]
 
[[faq_why_PLS_Toolbox_have_a_boxplot_function_that_conflicts_with_Stats_Toolbox | Why does PLS_Toolbox have a "boxplot" function that conflicts with the Mathworks Statistics Toolbox function of the same name?]]
 
[[faq_why_R2014b_give_error_cannot_convert_double_value_to_a_handle | Why does R2014b give me "Error using matlab.ui.Figure... Cannot convert double value to a handle" (or similar)?]]
 
==Command Line==
[[faq_specify_all_options_of_a_function_or_only_those_different_from_defaults | Do I have to specify all the options to a function or only the ones that are different from the defaults?]]
 
[[faq_how_are_Q_residuals_and_Hotellings_T2_calculated_in_PLS_models | How are the Q-residuals and Hotelling's T<sup>2</sup> values calculated for PLS models?]]
 
[[faq_how_to_automate_PCA_analysis_for_multiple_images | How do I automate PCA analysis for multiple images?]]
 
[[faq_how_do_I_calculate_my_own_T2_and_Q_limits | How do I calculate my own T<sup>2</sup> and Q limits?]]
 
[[faq_how_do_manually_calculate_the_limits_for_scores | How do I manually calculate the limits for scores?]]
 
[[faq_how_do_I_calculate_scores_from_a_PLS_or_PLSDA_model | How do I calculate scores from a PLS or PLSDA model?]]
 
[[faq_how_do_I_change_the_default_options_for_a_function | How do I change the default options for a function?]]
 
[[faq_how_do_I_interpret_the_misclassification_results_reported_by_crossval | How do I interpret the Misclassification results reported by crossval?]]
 
[[faq_how_do_I_make_PlotGUI_send_plot_to_a_new_figure_and_not_overwrite_current_figure | How do I make PlotGUI send its plot to a new figure and not overwrite the current figure?]]
 
[[faq_how_do_I_retrieve_and_display_predictions_from_a_model_structure_in_command_window | How do I retrieve and display predictions from a model structure in the command window?]]
 
==Manual==
==GUI==
==Installation==
 
 
 
 
 
 
 
[[Category:FAQ]]

Revision as of 13:26, 5 December 2018

_

Importing / Exporting

How do I concatenate multiple files into a single DataSet?

How do I create a multivariate image from separate images?

How do I export PCA scores and loadings to a text file (to read into MS Excel, for example)?

How do I import three-way data into Solo or PLS_Toolbox?

Why can't I import a Horiba NGC file on my 64-bit computer?

Why can't SPCREADR read multiple files I've selected?

Why do some Excel files fail to import?

General

Can I do PARALIND in PLS_Toolbox?

Can I install PLS_Toolbox (or Solo) on more than one PC, such as on my desktop and laptop computer?

Can I use multiple class sets (categorical variables) together in a SIMCA, PLSDA, or LDA model?

Can you give me more information on the R-Squared statistic?

How are RMSEC and RMSECV related to R2Y and Q2Y I see in other software?

Convergence of PARAFAC. How much variation between models is expected a particular PARAFAC is fit multiple times with the same settings?

Does the software stop working if my maintenance expires?

How and where do I report a problem with PLS_Toolbox?

How are T-contributions calculated?

How are the ROC curves calculated for PLSDA?

How are the error bars calculated for a regression model and can they be related to a confidence limit (confidence in the prediction)?

How can I improve performance with PLS_Toolbox and Matlab on the Mac platform?

How do I assign classes for samples in a DataSet?

How do I build a classification model from a class set other than the first?

How do I choose between the different cross-validation leave-out options?

How do I cite/reference Eigenvector?

How do I interpret the ROC curves and Sensitivity / Specificity plots from PLSDA?

How do I make a DataSet backwards compatible?

How do I obtain or use a recompilation license for PLS_Toolbox?

How do I use the "custom" cross-validation option?

I keep getting "out of memory" errors when analyzing my data. What can I do?

What can I do if I get a java.lang.OutOfMemoryError error?

Nonnegativity (PARAFAC, PARAFAC2, Tucker): Why do I get negative scores when all modes are set to nonnegativity?

What are "Relative Contributions"?

What are the "Reduced" T2 and Q Statistics?

What are the units used for RMSEC and RMSECV when cross-validating PLSDA models? Why do the cross-validation curves look strange for PLSDA?

What do the four Fit/Unique Fit statistics mean in MCR and PARAFAC models?

What internal tests are used to select "suggested" number of PCs?

What is PLS1 vs PLS2 and how do I create separate PLS1 models when I have a multi-column y-block?

What is the difference between a loading and a weighting?

Why are some axis labels and titles on my axes upside-down when I'm viewing images in MIA_Toolbox?

Why can't I recompile the PLS_Toolbox functions?

Why do I get the warning/notice "Missing Data Found - Replacing with "best guess" from existing model. Results may be affected by this action."

Why does PLS_Toolbox have a "boxplot" function that conflicts with the Mathworks Statistics Toolbox function of the same name?

Why does R2014b give me "Error using matlab.ui.Figure... Cannot convert double value to a handle" (or similar)?

Command Line

Do I have to specify all the options to a function or only the ones that are different from the defaults?

How are the Q-residuals and Hotelling's T2 values calculated for PLS models?

How do I automate PCA analysis for multiple images?

How do I calculate my own T2 and Q limits?

How do I manually calculate the limits for scores?

How do I calculate scores from a PLS or PLSDA model?

How do I change the default options for a function?

How do I interpret the Misclassification results reported by crossval?

How do I make PlotGUI send its plot to a new figure and not overwrite the current figure?

How do I retrieve and display predictions from a model structure in the command window?

Manual

GUI

Installation