pré 4.0-3 submission fixes

CHANGES

@@ -1,6 +1,8 @@
 4.0-3
-- fixed bug in ezMixed when family=gaussian (default)
-- changed author email address
+- Fixed bug in ezMixed when family=gaussian (default)
+- Fixed bug in ezMixed use of gam_args and mer_args
+- Added ability to use bam instead of gam via argument to ezMixed
+- Changed author email address
 
 4.0-2
 - updated .Rbuildignore to ignore .gitignore

R/ezMixed.R

@@ -12,6 +12,7 @@ function(
 	, gam_smooth = c('s','te')
 	, gam_bs = 'ts'
 	, gam_k = Inf
+	, use_bam = FALSE
 	, alarm = FALSE
 	, term_labels = NULL
 	, highest = Inf
@@ -187,35 +188,37 @@ function(
 				)
 				, '+'
 			)
-			if(is.null(covariates[covariates %in% numeric_covariates])){
-				formula_base = paste(
-					formula_base
-					, '+'
-					, paste(
-						gam_smooth[1]
-						,'('
-						, covariates[covariates %in% numeric_covariates]
-						, ',bs="'
-						, gam_bs
-						, '")'
-						, collapse = '+'
+			if(!is.null(covariates)){
+				if(!is.null(covariates[covariates %in% numeric_covariates])){
+					formula_base = paste(
+						formula_base
+						, '+'
+						, paste(
+							gam_smooth[1]
+							,'('
+							, covariates[covariates %in% numeric_covariates]
+							, ',bs="'
+							, gam_bs
+							, '")'
+							, collapse = '+'
+							, sep = ''
+						)
+						, '+'
 						, sep = ''
 					)
-					, '+'
-					, sep = ''
-				)
-			}
-			if(is.null(covariates[!(covariates %in% numeric_covariates)])){
-				formula_base = paste(
-					formula_base
-					, '+'
-					, paste(
-						covariates[!(covariates %in% numeric_covariates)]
-						, collapse = '+'
-					)
-					, '+'
-					, sep = ''
-				)			
+				}
+				if(!is.null(covariates[!(covariates %in% numeric_covariates)])){
+					formula_base = paste(
+						formula_base
+						, '+'
+						, paste(
+							covariates[!(covariates %in% numeric_covariates)]
+							, collapse = '+'
+						)
+						, '+'
+						, sep = ''
+					)			
+				}
 			}
 		}else{
 			formula_base = paste(
@@ -362,11 +365,21 @@ function(
 					fit <- withCallingHandlers(
 						{ 
 							eval(parse(text=paste(
-								"bam( formula ="
+								ifelse(
+									use_bam
+									, 'bam'
+									, 'gam'
+								)
+								, "( formula ="
 								, formula
-								, ", data = this_data , method = 'ML' "
-								, gam_args
+								, ", data = this_data , method = 'ML' , family = family"
+								, ifelse(
+									!is.null(gam_args)
+									, paste(',',gam_args)
+									, ''
+								)
 								, ")"
+								, sep = ''
 							)))
 						}
 						, warning = function(x) {w<<-c(w,x$message)}
@@ -378,20 +391,28 @@ function(
 				try(
 					fit <- withCallingHandlers(
 						{ 
-							if(identical(family,gaussian)|(family=='gaussian')){
+							if(!identical(family,gaussian)|identical(family,'gaussian')){
 								eval(parse(text=paste(
 									"lmer( formula = "
 									, formula
 									, ", data = this_data , REML = FALSE"
-									, mer_args
+									, ifelse(
+										!is.null(mer_args)
+										, paste(',',mer_args)
+										, ''
+									)
 									, ")"
 								)))
 							}else{
 								eval(parse(text=paste(
 									"glmer( formula ="
 									, formula
 									, ", data = this_data, family = family"
-									, mer_args
+									, ifelse(
+										!is.null(mer_args)
+										, paste(',',mer_args)
+										, ''
+									)
 									, ")"
 								)))
 							}

man/ezMixed.Rd

@@ -18,6 +18,7 @@ ezMixed(
     , gam_smooth = c('s','te')
     , gam_bs = 'ts'
     , gam_k = Inf
+	, use_bam = FALSE
     , alarm = FALSE
     , term_labels = NULL
     , highest = Inf
@@ -67,6 +68,9 @@ Character specifying the name of the smooth term to use when using gam.
 \item{gam_k}{
 Numeric value specifying the maximum value for \code{k} to supply to calls to gam. Higher values yield longer computation times but may better capture non-linear phenomena. If set to \code{Inf} (default), \code{ezMixed} will automatically use the maximum possible value for k given the number of unique combinations of values in the numeric predictors being evaluated. If a finite positive value is supplied, k will be set to that value or less (if the supplied k exceeds the maximum possible k for a given effect).
 }
+\item{use_bam}{
+Logical. If TRUE, \code{\link[mgcv]{bam}} is used rather than \code{\link[mgcv]{gam}}.
+}
 \item{alarm}{
 Logical. If TRUE, call the \code{\link[utils]{alarm}} function when \code{\link{ezMixed}} completes.
 }