def setup_pages(self, model, last_analysis):
self.choose_effect_size_page = ChooseEffectSizePage(
add_generic_effect=True,
data_type=last_analysis['data_type'],
metric=last_analysis['metric'],
var_groups = model.get_variable_groups())
self.setPage(Page_ChooseEffectSize, self.choose_effect_size_page)
self.data_location_page = DataLocationPage(model=model)
self.setPage(Page_DataLocation, self.data_location_page)
self.refine_studies_page = RefineStudiesPage(model=model)
self.setPage(Page_RefineStudies, self.refine_studies_page)
self.meta_reg_details_page = MetaRegDetailsPage(
fixed_effects=last_analysis['fixed_effects'],
random_effects_method=last_analysis['random_effects_method'],
analysis_type=last_analysis['analysis_type'], # PARAMETRIC or BOOTSTRAP
conf_level=last_analysis['conf_level'],
phylogen=last_analysis['phylogen'],
disable_analysis_type_groupbox=True,
disable_output_type_groupbox=True)
self.setPage(Page_MetaRegDetails, self.meta_reg_details_page)
self.ma_details_page = MADetailsPage()
self.setPage(Page_MADetails, self.ma_details_page)
self.perm_pg = PermuationPage()
self.setPage(Page_Permutation, self.perm_pg)
self.select_covariates_page = SelectCovariatesPage(
model=model,
previously_included_covs=last_analysis['included_covariates'],
disable_require_categorical=True)
self.setPage(Page_SelectCovariates, self.select_covariates_page)
self.reference_value_page = ReferenceValuePage(
model=model,
prev_cov_to_ref_level=last_analysis['cov_2_ref_values'])
self.setPage(Page_ReferenceValues, self.reference_value_page)
self.summary_page = SummaryPage()
self.setPage(Page_Summary, self.summary_page)
class PermutationWizard(QtGui.QWizard):
# if meta_reg mode is True, the wizard will do a permutation
# test for a meta-regression, otherwise it does a standard
# meta-analysis
def __init__(self, model, meta_reg_mode=False, parent=None):
super(PermutationWizard, self).__init__(parent)
self.model = model
last_analysis = model.get_last_analysis_selections()
self.meta_reg_mode = meta_reg_mode
# Set window title
if meta_reg_mode:
self.analysis_label = "Permuted Meta-Regression"
else:
self.analysis_label = "Permuted Meta-Analysis"
self.setWindowTitle(self.analysis_label)
self.setup_pages(model=model, last_analysis=last_analysis)
self.setWizardStyle(QWizard.ClassicStyle)
# Automatically resize wizard on each page flip
self.currentIdChanged.connect(self.adjustSize)
def setup_pages(self, model, last_analysis):
self.choose_effect_size_page = ChooseEffectSizePage(
add_generic_effect=True,
data_type=last_analysis['data_type'],
metric=last_analysis['metric'],
var_groups = model.get_variable_groups())
self.setPage(Page_ChooseEffectSize, self.choose_effect_size_page)
self.data_location_page = DataLocationPage(model=model)
self.setPage(Page_DataLocation, self.data_location_page)
self.refine_studies_page = RefineStudiesPage(model=model)
self.setPage(Page_RefineStudies, self.refine_studies_page)
self.meta_reg_details_page = MetaRegDetailsPage(
fixed_effects=last_analysis['fixed_effects'],
random_effects_method=last_analysis['random_effects_method'],
analysis_type=last_analysis['analysis_type'], # PARAMETRIC or BOOTSTRAP
conf_level=last_analysis['conf_level'],
phylogen=last_analysis['phylogen'],
disable_analysis_type_groupbox=True,
disable_output_type_groupbox=True)
self.setPage(Page_MetaRegDetails, self.meta_reg_details_page)
self.ma_details_page = MADetailsPage()
self.setPage(Page_MADetails, self.ma_details_page)
self.perm_pg = PermuationPage()
self.setPage(Page_Permutation, self.perm_pg)
self.select_covariates_page = SelectCovariatesPage(
model=model,
previously_included_covs=last_analysis['included_covariates'],
disable_require_categorical=True)
self.setPage(Page_SelectCovariates, self.select_covariates_page)
self.reference_value_page = ReferenceValuePage(
model=model,
prev_cov_to_ref_level=last_analysis['cov_2_ref_values'])
self.setPage(Page_ReferenceValues, self.reference_value_page)
self.summary_page = SummaryPage()
self.setPage(Page_Summary, self.summary_page)
def nextId(self):
current_id = self.currentId()
return self.nextId_helper(current_id)
def nextId_helper(self, page_id):
if self.meta_reg_mode:
if page_id == Page_ChooseEffectSize:
return Page_DataLocation
elif page_id == Page_DataLocation:
return Page_RefineStudies
elif page_id == Page_RefineStudies:
return Page_SelectCovariates
elif page_id == Page_SelectCovariates:
return Page_MetaRegDetails
elif page_id == Page_MetaRegDetails:
if self._categorical_covariates_selected():
return Page_ReferenceValues
else:
return Page_Permutation
elif page_id == Page_ReferenceValues:
return Page_Permutation
elif page_id == Page_Permutation:
return Page_Summary
elif page_id == Page_Summary:
return -1
else: # non-meta regression mode (no moderators)
if page_id == Page_ChooseEffectSize:
return Page_DataLocation
elif page_id == Page_DataLocation:
return Page_RefineStudies
elif page_id == Page_RefineStudies:
return Page_MADetails
elif page_id == Page_MADetails:
return Page_Permutation
elif page_id == Page_ReferenceValues:
return Page_Permutation
elif page_id == Page_Permutation:
return Page_Summary
elif page_id == Page_Summary:
return -1
def _categorical_covariates_selected(self):
'''are categorical variables selected?'''
included_covariates = self.get_included_covariates()
categorical_covariates = [cov for cov in included_covariates if cov.get_type()==CATEGORICAL]
return len(categorical_covariates) > 0
################# getters #########################
def get_parameters(self):
data_type_and_metric = self.choose_effect_size_page.get_data_type_and_metric()
data_location = self.data_location_page.get_data_locations()
studies = self.refine_studies_page.get_included_studies_in_proper_order()
parameters = {
'data_type_and_metric': data_type_and_metric,
'data_location': data_location,
'studies': studies,
}
parameters.update(self.perm_pg.get_choices())
# meta-regression specific
if self.meta_reg_mode:
covariates = self.select_covariates_page.get_included_covariates()
interactions = self.select_covariates_page.get_interactions()
_fixed_effects = self.meta_reg_details_page.get_using_fixed_effects()
level = self.meta_reg_details_page.get_confidence_level()
_random_effects_method = self.meta_reg_details_page.get_random_effects_method()
method = _random_effects_method if not _fixed_effects else FIXED_EFFECTS_METHOD_STR
phylogen = self.meta_reg_details_page.get_phylogen()
btt = self.meta_reg_details_page.get_btt()
reference_values = self.reference_value_page.get_covariate_reference_levels()
parameters.update({
'covariates': covariates,
'interactions': interactions,
'level': level,
'method': method,
'phylogen': phylogen,
'btt': btt,
'reference_values': reference_values,
})
else:
# ma specific (no moderators)
method = self.ma_details_page.get_method()
intercept = self.ma_details_page.get_intercept()
weighted = self.ma_details_page.get_weighted_least_squares()
knha = self.ma_details_page.get_knha()
level = self.ma_details_page.get_confidence_level()
digits = self.ma_details_page.get_digits()
parameters.update({
'method':method,
'intercept':intercept,
'weighted':weighted,
'knha':knha,
'level':level,
'digits':digits,
})
return parameters
# Summary page
def save_selections(self):
return self.summary_page.save_selections()
# Effect Size Page
def get_data_type_and_metric(self):
''' returns tuple (data_type, metric) '''
return self.choose_effect_size_page.get_data_type_and_metric()
# Data location page
def get_data_location(self):
return self.data_location_page.get_data_locations()
# Refine studies page
def get_included_studies_in_proper_order(self):
all_studies = self.model.get_studies_in_current_order()
included_studies = self.refine_studies_page.get_included_studies()
included_studies_in_order = [study for study in all_studies if study in included_studies]
return included_studies_in_order
# Select covariates Page
def get_included_covariates(self):
return self.select_covariates_page.get_included_covariates()
def get_included_interactions(self):
return self.select_covariates_page.get_interactions()
######################### end of getters #################################
# Summary Page
def get_summary(self):
''' Make a summary string to show the user at the end of the wizard summarizing most of the user selections '''
summary = wizard_summary(
wizard=self,
next_id_helper=self.nextId_helper,
summary_page_id=Page_Summary,
analysis_label=self.analysis_label
)
return summary