
# Rcmdr menus for meta-analysis
# When the plug-in is loaded, these menus are merged with the standard Rcmdr menus 

# last modified: 03.11.2013 by AC Del Re

##===================== MAIN MA MENU ========================##

#type    menu/item  operation/parent  label                              command/menu                activation            	install?

#menu    MAdMenu	  topMenu     		  ""                                  ""                           ""				    ""
#item    topMenu    cascade         	"MA"                                MAdMenu                      ""			        ""

# main MA menu
menu    MAdMenu	    topMenu     		 ""                                   ""                           ""				    ""
menu    aboutMenu   MAdMenu     		 ""                                  	"" 			                 ""				   ""
menu    startMenu  MAdMenu     		 ""                                  	"" 			                 ""				   ""
menu    CalcESMenu	MAdMenu     		 ""                                  	"" 			                 ""				   ""
menu    depMenu  	  MAdMenu     		 ""                                   "" 			                 ""				   ""
menu    ModMenu		 	MAdMenu     		 ""                            		  	""                          ""						""
menu 	  GraphMenu		MAdMenu     	   ""                                   ""                          ""						""
menu   	diagMenu		MAdMenu     	   ""                                   ""                         ""						""
#menu 		OtherMenu		MAdMenu     	   ""                                   ""                         ""						""
 
item    topMenu     cascade         "MA"                                 MAdMenu                      ""			        ""
#item    MAdMenu 		cascade         "About the package"                  aboutMenu                   	 ""				    ""
#item    MAdMenu   	cascade         "Getting started"                    startMenu                   	 ""				    ""
item    MAdMenu   	cascade         "Calculate effect sizes"             CalcESMenu                   	 ""				    ""
item    MAdMenu     cascade         "Handling dependencies"              depMenu                        ""					""
item    MAdMenu     cascade         "Moderator analysis"                 ModMenu                 	""						""
item    MAdMenu     cascade         "Graphics"           				   			 GraphMenu                   ""						""
item    MAdMenu     cascade         "Diagnostics"        			   	       diagMenu                   ""						""
#item    MAdMenu     cascade         "Inter-rater agreement"      				 OtherMenu                   ""						""

#== ABOUT ==#

#type    menu/item    operation/parent   	label                         					command/menu                activation    				install?

item    MAdMenu		  command         		"About the package"        	  						aboutcmd			          ""                     		""

#== STARTED ==#

#type    menu/item    operation/parent     label                         					command/menu                activation    				install?

item    MAdMenu		  command         		"Getting started"        	  						startcmd			          ""                     		""


#== Calculate ES ==#  

# Calculate ES menu

# Correlation
menu    corMenu			  CalcESMenu          		""																		""							 						""						 ""
item    CalcESMenu	  cascade             "Correlational"        		  	      	 corMenu 										""							""
item    corMenu	   		command         		"r from chi-squared"        		   	   r_from_chicmd     		      ""             "packageAvailable('MAd')"
item    corMenu	      command       	    "r from d (n of both grps same)"       r_from_dcmd				 	 			""              "packageAvailable('MAd')"
item    corMenu	      command             "r from d (n of both grps not same)"   r_from_d1cmd               ""              "packageAvailable('MAd')"
item    corMenu	      command             "r from t-statistic"                   r_from_tcmd                ""             "packageAvailable('MAd')"
item    corMenu	      command             "r to d"						                   r_to_dcmd              		  ""             "packageAvailable('MAd')"

# Mean Differences
menu     mnMenu		  CalcESMenu          ""																				""							 						""						 					""
item     CalcESMenu	cascade             "Mean Differences"        		  	   	 mnMenu 		        				 ""                      ""
item     mnMenu	    command       	    "Vector of mean differences (d & g)"   MeanDiffgcmd				 	 				""                      "packageAvailable('MAd')"
#item    mnMenu	    command             "Automated mean differences (d)"       MeanDiffdcmd                  ""                      "packageAvailable('MAd')"
#item    mnMenu	    command             "Automated mean differences (g)"       MeanDiffgcmd                   ""                      "packageAvailable('MAd')"
item     mnMenu	    command         	  "ancova to d (adj SD)" 				     	   ancova_to_d1cmd     		     		""                      "packageAvailable('MAd')"
item     mnMenu	    command       	    "ancova to d (pooled SD)"				       ancova_to_d2cmd				 	 				""                      "packageAvailable('MAd')"
item     mnMenu	    command             "d to unbiased g"       							 d_to_gcmd                  ""                      "packageAvailable('MAd')"
item     mnMenu	    command             "f-value (ANCOVA) to d"                f.ancova_to_dcmd                   ""                      "packageAvailable('MAd')"
item     mnMenu	    command         	  "f to d"				          		  			 f_to_dcmd     		     		""                      "packageAvailable('MAd')"
item     mnMenu	    command       	    "raw means and SDs to d"               mean_to_dcmd				 	 				""                      "packageAvailable('MAd')"
item     mnMenu	    command             "means with pooled SD to d"            mean_to_d2cmd                  ""                      "packageAvailable('MAd')"
item     mnMenu	    command             "one-tailed p-value (ANCOVA) to d"     p.ancova_to_d1cmd                   ""                      "packageAvailable('MAd')"
item     mnMenu	    command       	    "two-tailed p-value (ANCOVA) to d"     p.ancova_to_d2cmd				 	 				""                      "packageAvailable('MAd')"
item     mnMenu	    command             "one-tailed p-value to d"     				 p_to_d1cmd                   ""                      "packageAvailable('MAd')"
item     mnMenu	    command       	    "two-tailed p-value to d"     				 p_to_d2cmd				 	 				""                      "packageAvailable('MAd')"
item     mnMenu	    command             "t-test to d"    									     t_to_dcmd                  ""                      "packageAvailable('MAd')"
item     mnMenu	    command             "t-test (ANCOVA) to d"                 tt.ancova_to_dcmd                   ""                      "packageAvailable('MAd')"
item     mnMenu	    command       	    "r from d (n of both grps same)"       r_from_dcmd				 	 			""              "packageAvailable('MAd')"
item     mnMenu	    command             "r from d (n of both grps not same)"   r_from_d1cmd               ""              "packageAvailable('MAd')"
item     mnMenu	    command             "r to d"						                   r_to_dcmd              		  ""             "packageAvailable('MAd')"
item     mnMenu		  command         	  "log odds ratio to d"        		   		 lor_to_dcmd     		      ""                      "packageAvailable('MAd')"
item     mnMenu	 	  command       	    "proportions to d"                     prop_to_dcmd				 	 				""                      "packageAvailable('MAd')"

# Odds Ratio
menu    orMenu			CalcESMenu            ""																				""													""										 ""
item    CalcESMenu 	  cascade             "Odds Ratios"			              		 	   orMenu 	               		 ""         							 ""
item    orMenu		    command         	  "log odds ratio to d"        		   			 lor_to_dcmd     		      ""                      "packageAvailable('MAd')"
item    orMenu	 	    command       	    "proportions to d"                       prop_to_dcmd				 	 				""                      "packageAvailable('MAd')"
item    orMenu		    command             "proportions to odds ratio"              prop_to_orcmd                 ""                      "packageAvailable('MAd')"


#== Within-Study Aggregation ==#

#type    menu/item  operation/parent  label                              					command/menu                activation    		  	install?

# ROBUST SE
menu    robMenu  		depMenu            ""																				""													""										 ""
item    depMenu     command         "Robust standard errors"         				    robustSEcmd         		     ""                      "packageAvailable('MAd')"

# WITHIN STUDY AGG
menu    AggMenu    	depMenu            ""																				""													""										 ""
item    depMenu     cascade         "Aggregate dependencies"			              AggMenu 	               		 ""         							 ""
item    AggMenu     command         "Correlational effect sizes"       					MetaCcmd         		     ""                      "packageAvailable('RcmdrPlugin.MA')"
item    AggMenu     command         "Mean Difference effect sizes"        		  MetaGcmd 		        	 	 ""                      "packageAvailable('MAd')"


#== Omnibus Analysis ==#

#type    menu/item    operation/parent 		label                         					command/menu                activation    				install?

item    MAdMenu		  command         		"Omnibus analysis"        	  						OmnibusEScmd			          ""                     		"packageAvailable('MAd') "


#== Moderator Analysis ==#

#type    menu/item   	operation/parent  label                             		  	command/menu                activation  			  	install?

#menu   ModMenu		 	  MAdMenu     			""                            		  			""                          ""						""
item    ModMenu	     	command         "Categoical moderation"       							CatModcmd         			""                      "packageAvailable('MAd') "
item    ModMenu     	command         "Direct comparison: cat mod"		 	  				CatCompcmd                 ""                      "packageAvailable('MAd') "
#item   ModMenu     	command         "Single predictor meta-regression"    	  	MAreg1cmd                   ""                      "packageAvailable('MAd') "
item    ModMenu     	command         "Meta-regression"  	  	                    MAreg2cmd                   ""                      "packageAvailable('MAd')"
#item   ModMenu     	command         "Meta-regression model fit"  	  						MRfitcmd                   ""                      "packageAvailable('MAd')"
#item   MAdMenu      	cascade         "Moderator analysis"                 		  	ModMenu                 	""						""


#== Graphics ==#

#type    menu/item      operation/parent  label                              		command/menu                activation   				 install?

#menu 	GraphMenu		  MAdMenu     	""                                     		""                          ""						""
item    GraphMenu	    command         "Categorical moderator graph"          		CatModGraphcmd       		""                      "packageAvailable('MAd') "
item    GraphMenu	    command         "Forest plot"				           						ForestPlotcmd 				""                      "packageAvailable('MAd') "
item    GraphMenu	    command         "Meta-regression graph"                		MAregGraphcmd               ""                      "packageAvailable('MAd') "
item    GraphMenu     command         "Multiple predictor moderator graph"  	  MultiModGraphcmd            ""                      "packageAvailable('MAd') "
item    GraphMenu      command        "Funnel plot"       				   						FunnelPlotcmd               ""                      "packageAvailable('MAd') "
item    GraphMenu      command        "Radial plot"                             radialcmd               	        ""                "packageAvailable('metafor')"
item    GraphMenu      command        "Influential studies plots"					      influencecmd			 		        ""                "packageAvailable('metafor')"

#item    MAdMenu       cascade         "Graphics"           				   					  GraphMenu                   ""						""

##== DIAGNOSTIC ==##

##menu   diagMenu			MAdMenu     	  ""                                    		 			""                         ""						""
item    diagMenu      command         "Funnel plot"       				   						FunnelPlotcmd               ""                      "packageAvailable('metafor') "
item    diagMenu	    command         "Influential studies plots"					       			influencecmd			 		        ""                "packageAvailable('metafor')"
item    diagMenu      command         "Externally standardized residuals"				rstudentcmd			   		        ""                "packageAvailable('metafor')"
item    diagMenu      command         "Internally standardized residuals"  			rstandardcmd			 		        ""                "packageAvailable('metafor')"
item    diagMenu      command         "Trim and fill"    		                    trimcmd		      	 		        ""                "packageAvailable('metafor')"
item    diagMenu      command         "Regression test (funnel plot asymmetry)" regcmd		      	 		        ""                "packageAvailable('metafor')"
item    diagMenu      command         "Rank corr test (funnel plot asymmetry)"  rankcmd  	      	 		        ""                "packageAvailable('metafor')"
item    diagMenu      command         "Normal Q-Q plot"                         qqnormcmd          	 		        ""                "packageAvailable('metafor')"
item    diagMenu      command         "Radial plot"                             radialcmd             		        ""                "packageAvailable('metafor')"


## == Inter-rater agreement == ##

##menu   diagMenu  		MAdMenu     	  ""                                    		 			""                         ""						""
#item    OtherMenu      command         "ICC (for continuous moderators)"       				   						FunnelPlotcmd               ""                      "packageAvailable('MAd')"
#item    OtherMenu	    command         "Kappa (for categrical moderators)"					       			influencecmd			 		        ""                "packageAvailable('MAd')"



## DEPRICATED ##
##== Other ==##

#menu 	OtherMenu			MAdMenu     	  ""                                    		 			""                         ""						""
#item    OtherMenu	    command         "Complete dataset"					       			  ComplDatacmd			 		 ""                ""
#item    OtherMenu	    command         "Add weights to dataset"					        Wifuncmd			 		 ""                ""
#item    OtherMenu     command         "Convert to Categorical Variable"         factscmd						        ""          ""
#item    OtherMenu	    command         "Correction for attenuation"           		CorAttencmd         			""                  "packageAvailable('MAd')"
#item    OtherMenu     command         "Agreement: Kappa (cat data)"   	        Kappacmd                    ""                      "packageAvailable('MAd')"
#item    OtherMenu     command         "Publication Bias"						   	        PubBiascmd                    ""                      "packageAvailable('MAd')"
#item    MAdMenu       cascade         "Other functions"      				   	   		  OtherMenu                   ""						""

 
