[Stacomir-commits] r292 - in pkg/stacomir: . R

[noreply at r-forge.r-project.org]

Author: briand
Date: 2017-02-12 20:18:28 +0100 (Sun, 12 Feb 2017)
New Revision: 292

Modified:
   pkg/stacomir/DESCRIPTION
   pkg/stacomir/R/BilanFonctionnementDC.r
   pkg/stacomir/R/BilanFonctionnementDF.r
   pkg/stacomir/R/Bilan_poids_moyen.r
   pkg/stacomir/R/stacomi.r
Log:
changes to pass R check

Modified: pkg/stacomir/DESCRIPTION
===================================================================
--- pkg/stacomir/DESCRIPTION	2017-02-12 19:05:34 UTC (rev 291)
+++ pkg/stacomir/DESCRIPTION	2017-02-12 19:18:28 UTC (rev 292)
@@ -110,7 +110,7 @@
     testthat,
     viridis
 Author: Cedric Briand [aut, cre],
-    Marion Legrand [aut]
+    Marion Legrand [aut],
     Timothee Besse [aut]
 Maintainer: Cedric Briand <cedric.briand00 at gmail.com>
 RoxygenNote: 5.0.1

Modified: pkg/stacomir/R/BilanFonctionnementDC.r
===================================================================
--- pkg/stacomir/R/BilanFonctionnementDC.r	2017-02-12 19:05:34 UTC (rev 291)
+++ pkg/stacomir/R/BilanFonctionnementDC.r	2017-02-12 19:18:28 UTC (rev 292)
@@ -556,7 +556,7 @@
 			write.table(t_periodefonctdispositif_per,file=path1,row.names=FALSE,col.names=TRUE,sep=";")
 			funout(gettext("Writing of %s \n",path1,domain="R-stacomiR"))
 			path1html<-file.path(path.expand(get("datawd",envir=envir_stacomi)),paste("t_periodefonctdispositif_per_DC_",bilanFonctionnementDC at dc@dc_selectionne,"_",annee,".html",sep=""),fsep ="\\")
-			funout(gettextf("Writing of %s this might take a while, please be patient …\n",path1html))
+			funout(gettextf("Writing of %s this might take a while, please be patient ...\n",path1html))
 			funhtml(t_periodefonctdispositif_per,
 					caption=gettextf("t_periodefonctdispositif_per_DC_%s_%s",bilanFonctionnementDC at dc@dc_selectionne,annee),
 					top=TRUE,

Modified: pkg/stacomir/R/BilanFonctionnementDF.r
===================================================================
--- pkg/stacomir/R/BilanFonctionnementDF.r	2017-02-12 19:05:34 UTC (rev 291)
+++ pkg/stacomir/R/BilanFonctionnementDF.r	2017-02-12 19:18:28 UTC (rev 292)
@@ -537,7 +537,7 @@
 			write.table(t_periodefonctdispositif_per,file=path1,row.names=FALSE,col.names=TRUE,sep=";")
 			if(!silent) funout(gettextf("Writing of %s \n",path1))
 			path1html=file.path(path.expand(get("datawd",envir=envir_stacomi)),paste("t_periodefonctdispositif_per_DF_",bilanFonctionnementDF at df@df_selectionne,"_",annee,".html",sep=""),fsep ="\\")
-			if(!silent) funout(gettextf("Writing of %s this might take a while, please be patient …\n",path1html))
+			if(!silent) funout(gettextf("Writing of %s this might take a while, please be patient ...\n",path1html))
 			funhtml(t_periodefonctdispositif_per,
 					caption=paste("t_periodefonctdispositif_per_DF_",bilanFonctionnementDF at df@df_selectionne,"_",annee,sep=""),
 					top=TRUE,

Modified: pkg/stacomir/R/Bilan_poids_moyen.r
===================================================================
--- pkg/stacomir/R/Bilan_poids_moyen.r	2017-02-12 19:05:34 UTC (rev 291)
+++ pkg/stacomir/R/Bilan_poids_moyen.r	2017-02-12 19:18:28 UTC (rev 292)
@@ -299,9 +299,9 @@
 #' 			This model was considered as the best to model size variations by Diaz & Briand in prep. but using a large set of values
 #' 			over years.}
 #' 		\item{model.type="seasonal2". The seasonal trend in the previous model is now modelled with a sine
-#' 			curve similar to the sine curve used in seasonal.  The formula for this is ‘sin(ωvt) + cos(ωvt)’, 
-#'			where vt is the time index variable ω is a constant that describes how the index variable relates to the full period
-#' 			(here, 2π/365=0.0172). the model is written as following w~cos(0.0172*doy)+sin(0.0172*doy)+s(time).}
+#' 			curve similar to the sine curve used in seasonal.  The formula for this is \eqn{sin(\omega vt) + cos(\omega vt)}{{sin(omega vt) + cos(omega vt)}, 
+#'			where vt is the time index variable \eqn{\omega}{omega} is a constant that describes how the index variable relates to the full period
+#' 			(here, \eqn{2\pi/365=0.0172}{2pi/365=0.0172}). The model is written as following w~cos(0.0172*doy)+sin(0.0172*doy)+s(time).}
 #' 		\item{model.type="manual", The dataset don (the raw data), coe (the coefficients already present in the
 #' 			database, and newcoe the dataset to make the predictions from, are written to the environment envir_stacomi. 
 #' 			please see example for further description on how to fit your own model, build the table of coefficients,
@@ -419,8 +419,8 @@
 				com="model seasonal1 = gam(w~s(yday,bs='cc')+s(time), knots = list(yday = c(1, 365)))"
 			} else 	if (model.type=="seasonal2"){
 				#########################################################
-				# seasonal effects with a continuous sine-cosine wave,.  The formula for this is ‘sin(ωvt) + cos(ωvt)’, where vt is the time index variable 
-				#	ω is a constant that describes how the index variable relates to the full period (here, 2π/365=0.0172).
+				# seasonal effects with a continuous sine-cosine wave,.  The formula for this is ‘sin(omegavt) + cos(omegavt)’, where vt is the time index variable 
+				#	omega is a constant that describes how the index variable relates to the full period (here, 2pi/365=0.0172).
 				############################################################
 				g2 = mgcv::gam(w~cos(0.0172*doy)+sin(0.0172*doy)+s(time),data=don)
 				print(gettext("One model per year, doy starts in november",domain="R-stacomiR"))
@@ -446,7 +446,7 @@
 				if (!silent) funout(gettext("gam model g2 assigned to envir_stacomi",domain="R-stacomiR"))
 					
 				###################################################################
-				# comparison with Guérault and Désaunay (summary table in latex)
+				# comparison with Guerault and Desaunay (summary table in latex)
 				######################################################################
 				gamma=as.numeric(sqrt(g2$coefficients["cos(0.0172 * doy)"]^2+g2$coefficients["sin(0.0172 * doy)"]^2)) #0.386
 				#compared with 0.111

Modified: pkg/stacomir/R/stacomi.r
===================================================================
--- pkg/stacomir/R/stacomi.r	2017-02-12 19:05:34 UTC (rev 291)
+++ pkg/stacomir/R/stacomi.r	2017-02-12 19:18:28 UTC (rev 292)
@@ -26,7 +26,7 @@
 #' @param ... additional parameters
 hDFDC=function(h,...){
 	# TODO developper cette fonction
-	funout(gettext("Summary between the operating fishway and the counting device … to do\n",domain="R-stacomiR"),wash=TRUE)
+	funout(gettext("Summary between the operating fishway and the counting device ... to do\n",domain="R-stacomiR"),wash=TRUE)
 }
 #' handler function used by the main interface
 #' @param h handler