Code style update

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: diveMove
 Type: Package
 Title: Dive Analysis and Calibration
-Version: 1.6.4
+Version: 1.6.5
 Depends: R (>= 4.4.0), methods, stats4
 Suggests: knitr, lattice, pander, rmarkdown, tinytest
 Imports: geosphere, KernSmooth, plotly, quantreg, uniReg

R/AllMethod.R

@@ -437,9 +437,9 @@ setMethod("plotDiveModel",
                     depths[a.crit:length(x)], col="lightblue")
               legend("top", ncol=2, title=paste("Dive:", diveNo),
                      legend=c("original", "smoothed",
-                       "descent", "ascent"), lty=c(1, 2, 1, 1),
+                              "descent", "ascent"), lty=c(1, 2, 1, 1),
                      col=c("black", "green",
-                       "blue", "lightblue"), cex=0.7)
+                           "blue", "lightblue"), cex=0.7)
               plot(times.deriv, depths.deriv, xlab="Time index",
                    ylab="First derivative", type="l", cex=0.3)
               points(times.deriv[descent], depths.deriv[descent],
@@ -450,7 +450,7 @@ setMethod("plotDiveModel",
                      v=c(times[d.crit], times[a.crit]), lty=2)
               text(2, c(d.crit.rate, a.crit.rate),
                    labels=c(expression(paste("descent ", hat(q))),
-                     expression(paste("ascent ", hat(q)))),
+                            expression(paste("ascent ", hat(q)))),
                    pos=c(3, 1), cex=0.7)
               text(c(times[d.crit], times[a.crit]), 0,
                    labels=c("descent", "ascent"), pos=1, cex=0.7)
@@ -527,7 +527,7 @@ setMethod("boutsNLSll", signature(obj="numeric"),
 setMethod("boutinit", signature(obj="data.frame"),
           function(obj, x.break, plot=TRUE, ...) {
               nproc <- length(x.break)
-              if (nproc > 2) stop ("x.break must be of length 1 or 2")
+              if (nproc > 2) stop("x.break must be of length 1 or 2")
               procf <- cut(obj$x, breaks=c(min(obj$x), x.break,
                                            max(obj$x)),
                            include.lowest=TRUE, right=TRUE)
@@ -838,7 +838,7 @@ setMethod("plotBouts", signature(fit="mle", obj="Bouts"),
         for (bec.i in seq_len(length(becx))) {
             text(becx[bec.i], becy[bec.i], pos=4, offset=1,
                  paste(paste("bec_", bec.i - 1, "=", sep=""),
-                   round(becx[bec.i], 2), sep=""),
+                       round(becx[bec.i], 2), sep=""),
                  bty="n", cex=0.8)
         }
     }
@@ -1435,11 +1435,11 @@ setReplaceMethod("ccData", signature(x="TDR", value="data.frame"),
 ###_ + Subsetting
 setMethod("[", signature(x="TDR", i="numeric", j="missing", drop="missing"),
           function(x, i, j, ..., drop) {
-    new(class(x), file=getFileName(x), dtime=getDtime(x), time=getTime(x)[i],
-        depth=getDepth(x)[i],
-        concurrentData=tryCatch(getCCData(x)[i, , drop=FALSE],
-          error=function(k) data.frame()))
-})
+              new(class(x), file=getFileName(x), dtime=getDtime(x),
+                  time=getTime(x)[i], depth=getDepth(x)[i],
+                  concurrentData=tryCatch(getCCData(x)[i, , drop=FALSE],
+                                          error=function(k) data.frame()))
+          })
 
 
 ###_ + Generators and Summaries
@@ -1516,11 +1516,11 @@ setMethod("[", signature(x="TDR", i="numeric", j="missing", drop="missing"),
 ##'           file=srcfn, speed=TRUE)
 "createTDR" <- function(time, depth,
                         concurrentData=data.frame(matrix(ncol=0,
-                          nrow=length(time))),
+                                                         nrow=length(time))),
                         speed=FALSE, dtime, file)
 {
     if (missing(dtime)) dtime <- .getInterval(time)
-    if(speed) {
+    if (speed) {
         new("TDRspeed", time=time, depth=depth, concurrentData=concurrentData,
             dtime=dtime, file=file)
     } else {
@@ -1562,7 +1562,7 @@ setMethod("extractDive", signature(obj="TDR", diveNo="numeric",
                                    id="numeric"), # for TDR object
           function(obj, diveNo, id) {
               if (length(id) != length(getTime(obj))) {
-                  stop ("id and obj must have equal number of rows")
+                  stop("id and obj must have equal number of rows")
               }
               okpts <- .diveIndices(id, unique(diveNo))
               if (is(obj, "TDRspeed")) {

R/austFilter.R

@@ -166,8 +166,8 @@
     ## --------------------------------------------------------------------
     ## Author: Sebastian Luque
     ## --------------------------------------------------------------------
-    if (!window %% 2) stop ("window size must be an odd number")
-    if (nrow(x) < window) stop ("there are fewer rows than window size")
+    if (!window %% 2) stop("window size must be an odd number")
+    if (nrow(x) < window) stop("there are fewer rows than window size")
     tpos <- window %/% 2                # test subscript - 1
     testfun <- function(k) {            # k=matrix with group to test
         mid <- tpos + 1                 # subscript of pt to test
@@ -205,9 +205,9 @@
     ## --------------------------------------------------------------------
     ## Author: Sebastian Luque
     ## --------------------------------------------------------------------
-    if (!window %% 2) stop ("window size must be an odd number")
+    if (!window %% 2) stop("window size must be an odd number")
     wdw.errmess <- "there are fewer rows than window size"
-    if (nrow(x) < window) stop (wdw.errmess)
+    if (nrow(x) < window) stop(wdw.errmess)
     tpos <- window %/% 2                      # test subscript - 1
     ref <- c(-seq(tpos), seq(tpos))           # reference points for test
     travel.fun <- function(k) {           # k=subscripts
@@ -222,7 +222,7 @@
 
     while (any(rmsSwitch)) {           # stop when switch is all FALSE
         switchidx <- which(rmsSwitch)
-        if ((length(switchidx) + (tpos * 2)) < window) stop (wdw.errmess)
+        if ((length(switchidx) + (tpos * 2)) < window) stop(wdw.errmess)
         testrows.new <- testrows[rmsSwitch]
         idx <- seq_along(testrows.new)  # index the above
         testidx.mtx <- testidx <- c(idx, sapply(ref, "+", idx))

R/calibrate.R

@@ -287,7 +287,7 @@
                               smooth.par=0.1, knot.factor=3,
                               descent.crit.q=0, ascent.crit.q=0)
 {
-    if (!is(x, "TDR")) stop ("x is not a TDR object")
+    if (!is(x, "TDR")) stop("x is not a TDR object")
     mCall <- match.call()
     depth <- getDepth(x)
     time <- getTime(x)

R/detPhase.R

@@ -107,14 +107,14 @@
     ## Final run to determine times with all corrected activities
     finacts <- .rleActivity(time, act, interval)
     nphase <- length(levels(finacts[[1]]))
-    if(act[1] == "L" & act[length(act)] == "L") {
+    if (act[1] == "L" & act[length(act)] == "L") {
         message("Record is complete\n", nphase, " phases detected")
     } else {
-        if(act[1] != "L" & act[length(act)] != "L") {
+        if (act[1] != "L" & act[length(act)] != "L") {
             message("Record is truncated at the beginning and at the end\n",
                     nphase, " phases detected")
         } else {
-            if(act[1] != "L") {
+            if (act[1] != "L") {
                 message("Record is truncated at the beginning\n", nphase,
                         " phases detected")
             } else {

R/diveMove-deprecated.R

@@ -25,33 +25,33 @@ NULL
 ##' @section \code{bouts2.nls}:
 ##' For \code{bouts2.nls}, use \code{\link{fitNLSbouts}}.
 "bouts2.nls" <- function(lnfreq, start, maxiter) {
-   .Deprecated("fitNLSbouts", package="diveMove",
+    .Deprecated("fitNLSbouts", package="diveMove",
                 msg=paste("'bouts2.nls' is now deprecated in favor of",
                           "the new method 'fitNLSbouts'.",
                           "Please see help(fitNLSbouts)"))
-   fitNLSbouts(lnfreq, start=start, maxiter=maxiter)
+    fitNLSbouts(lnfreq, start=start, maxiter=maxiter)
 }
 
 ##' @rdname diveMove-deprecated
 ##' @section \code{bec2}:
 ##' For \code{bec2}, use \code{\link{bec}}.
 "bec2" <- function(fit) {
-   .Deprecated("bec", package="diveMove",
+    .Deprecated("bec", package="diveMove",
                 msg=paste("'bec2' is now deprecated in favor of",
                           "the new generalized method 'bec'.",
                           "Please see help(bec)"))
-   bec(fit)
+    bec(fit)
 }
 
 ##' @rdname diveMove-deprecated
 ##' @section \code{bec3}:
 ##' For \code{bec3}, use \code{\link{bec}}.
 "bec3" <- function(fit) {
-   .Deprecated("bec", package="diveMove",
+    .Deprecated("bec", package="diveMove",
                 msg=paste("'bec3' is now deprecated in favor of",
                           "the new generalized method 'bec'.",
                           "Please see help(bec)"))
-   bec(fit)
+    bec(fit)
 }
 
 ##' @rdname diveMove-deprecated
@@ -69,11 +69,11 @@ NULL
 ##' @section \code{bouts3.nls}:
 ##' For \code{bouts3.nls}, use \code{\link{fitNLSbouts}}.
 "bouts3.nls" <- function(lnfreq, start, maxiter) {
-   .Deprecated("fitNLSbouts", package="diveMove",
+    .Deprecated("fitNLSbouts", package="diveMove",
                 msg=paste("'bouts3.nls' is now deprecated in favor of",
                           "the new method 'fitNLSbouts'.",
                           "Please see help(fitNLSbouts)"))
-   fitNLSbouts(lnfreq, start=start, maxiter=maxiter)
+    fitNLSbouts(lnfreq, start=start, maxiter=maxiter)
 }
 
 ##' @rdname diveMove-deprecated

R/plotTDR.R

@@ -50,16 +50,16 @@
     nights <- .night(time, sunrise.time, sunset.time)
     nconcurVars <- ifelse(is.null(concurVars), 0, ncol(concurVars))
     plotrows <- nconcurVars + 1
-    ncheight <- 1.35 * (1/plotrows)
-    lheights <- c(rep((1 - ncheight)/nconcurVars, nconcurVars), ncheight)
+    ncheight <- 1.35 * (1 / plotrows)
+    lheights <- c(rep((1 - ncheight) / nconcurVars, nconcurVars), ncheight)
     mardepthonly <- c(4, 4, 1, 1) + 0.1    # for depth plot only
     mardepthmore <- c(4, 4, -0.1, 1) + 0.1 # for depth plot and more vars
     martop <- c(-0.1, 4, 1, 1) + 0.1       # for top plot
     marnontop <- c(-0.1, 4, -0.1, 1) + 0.1 # for plots between depth and top one
     orig <- structure(0, class=class(time), tzone=attr(time, "tzone"))
     "plot.fun" <- function(xlim, ylim) {
         xticks <- orig + seq(from=xlim[1], to=xlim[2], length=20)
-        if(is.null(concurVars)) {
+        if (is.null(concurVars)) {
             par(las=1, bty="n", mar=mardepthonly, ...)
         } else {
             par(las=1, bty="n", mar=mardepthmore, ...)
@@ -118,7 +118,7 @@
     }
     if (!interact) {
         rx <- range(as.numeric(time))   # max and min of dates
-        xlim <- if(is.null(xlim)) rx else as.numeric(xlim)
+        xlim <- if (is.null(xlim)) rx else as.numeric(xlim)
         ylim <- if (is.null(depth.lim)) {
             rev(range(depth, na.rm=TRUE))
         } else rev(depth.lim)
@@ -128,7 +128,7 @@
             stop("tcltk support is absent")
         rx <- range(as.numeric(time))   # max and min of dates
         diffrx <- diff(rx)
-        xlim <- x10 <- if(is.null(xlim)) { # define xlim if not there already
+        xlim <- x10 <- if (is.null(xlim)) { # define xlim if not there already
             rx + (diffrx * 0.01)           # add 1% to each side
         } else as.numeric(xlim)
         xlmid <- xm0 <- mean(xlim)     # two vars with date range midpoint
@@ -145,16 +145,16 @@
         replot <- function(...) {
             xZ <<- as.numeric(tcltk::tclvalue(xZoom))
             xM <<- as.numeric(tcltk::tclvalue(xlmid))
-            xr.half <- (xr0/2) * 100/xZ
+            xr.half <- (xr0 / 2) * 100 / xZ
             xlim <- xM + c(-xr.half, xr.half)
             yTop <<- as.numeric(tcltk::tclvalue(yMax))
             ylim <- c(yTop, ylim[2])
             plot.fun(xlim=xlim, ylim=ylim)
         }
         replot.maybe <- function(...) {
-            if(as.numeric(tcltk::tclvalue(xZoom)) != xZ ||
-               as.numeric(tcltk::tclvalue(xlmid)) != xM ||
-               as.numeric(tcltk::tclvalue(yMax)) != yTop) replot()
+            if (as.numeric(tcltk::tclvalue(xZoom)) != xZ ||
+                as.numeric(tcltk::tclvalue(xlmid)) != xM ||
+                as.numeric(tcltk::tclvalue(yMax)) != yTop) replot()
         }
         coords <- list()
         zocrange <- function() {
@@ -193,7 +193,7 @@
         tpan.s <- tcltk::tkscale(xmid.frame, command=replot.maybe,
                                  from=xm0 - xr0, to=xm0 + xr0,
                                  showvalue=FALSE, variable=xlmid,
-                                 resolution=xr0/2000, length=200,
+                                 resolution=xr0 / 2000, length=200,
                                  orient="horiz")
         ## Maximum depth selection
         maxdep.l <- tcltk::tklabel(dep.frame, text="Max. Depth (m)")

R/plotZOC.R

@@ -15,11 +15,11 @@
     ## --------------------------------------------------------------------
     ## Author: Sebastian P. Luque
     ## --------------------------------------------------------------------
-    if (!is(x, "TDR")) stop ("x is not a TDR object")
+    if (!is(x, "TDR")) stop("x is not a TDR object")
     time <- getTime(x)
     depth <- getDepth(x)
     if (length(time) != nrow(zoc.filter)) {
-        stop ("x and zoc.filter must have the same number of records")
+        stop("x and zoc.filter must have the same number of records")
     }
     nfilters <- ncol(zoc.filter)
     if (missing(xlim)) xlim <- range(time)
@@ -85,8 +85,8 @@
     ## --------------------------------------------------------------------
     ## Author: Sebastian P. Luque
     ## --------------------------------------------------------------------
-    if (!is(x, "TDR")) stop ("x is not a TDR object")
-    if (!is(y, "TDRcalibrate")) stop ("y is not a TDRcalibrate object")
+    if (!is(x, "TDR")) stop("x is not a TDR object")
+    if (!is(y, "TDRcalibrate")) stop("y is not a TDRcalibrate object")
     time.in <- getTime(x)
     depth.in <- getDepth(x)
     time.out <- getTime(getTDR(y))

R/readLocs.R

@@ -60,7 +60,7 @@
         inLocs <- read.csv(locations, ...)
     } else {
         if (! is.data.frame(locations)) {
-            stop ("'locations' must be a data.frame, path to a file, or a connection")
+            stop("'locations' must be a data.frame, path to a file, or a connection")
         } else {inLocs <- locations}
     }
     if (missing(loc.idCol)) {

R/readTDR.R

@@ -39,15 +39,15 @@
                           basename(summary(file)$description),
                           basename(file))
     } else {
-        stop ("'file' must be a path to a file, or a connection")
+        stop("'file' must be a path to a file, or a connection")
     }
     rawdat <- read.csv(file, ...)
     names(rawdat) <- tolower(names(rawdat))
     rawdat.ncol <- seq(ncol(rawdat))
     dtpasted <- paste(rawdat[, dateCol], rawdat[, timeCol])
     datetime <- as.POSIXct(strptime(dtpasted, format=dtformat), tz=tz)
     origint <- .getInterval(datetime)
-    if(!identical(all.equal(origint, subsamp), TRUE)) {
+    if (!identical(all.equal(origint, subsamp), TRUE)) {
         steptim <- as.numeric((subsamp) / origint)
         stepind <- seq(from=1, to=length(datetime), by=round(steptim))
         datetime <- datetime[stepind]

R/runquantile.R

@@ -198,7 +198,7 @@
     np <- length(probs)
     k <- as.integer(k)
     type <- as.integer(type)
-    if (k <= 1) return (rep(x, n, np))
+    if (k <= 1) return(rep(x, n, np))
     if (k > n) k <- n
     if (is.na(type) || (type < 1 | type > 9))
         warning("'type' outside allowed range [1,9]; changing 'type' to ",

R/speedStats.R

@@ -17,7 +17,7 @@
         mspeed <- mean(speed, na.rm=TRUE)
         tdist <- sum(difft * speed, na.rm=TRUE)
         if (!missing(vdist)) {
-            angle <- asin(ifelse(vdist < tdist, vdist/tdist, NA)) * (180 / pi)
+            angle <- asin(ifelse(vdist < tdist, vdist / tdist, NA)) * (180 / pi)
             cbind(tdist=tdist, mean.speed=mspeed, angle=angle)
         } else {
             cbind(tdist=tdist, mean.speed=mspeed, angle=NA)

R/stampDive.R

@@ -15,7 +15,7 @@
     ## --------------------------------------------------------------------
     ## Author: Sebastian Luque
     ## --------------------------------------------------------------------
-    if (!is(x, "TDRcalibrate")) stop ("x needs to be a TDRcalibrate object")
+    if (!is(x, "TDRcalibrate")) stop("x needs to be a TDRcalibrate object")
     act <- getGAct(x, "activity")
     diveid <- getDAct(x, "dive.id")
 
@@ -36,7 +36,7 @@
     phaseid[act == "L"] <- 0             # dry phase.id should be 0
     ## make a sequence for phase.id > 0 from 1:number of such phases
     phase.no[act != "L"] <- rep(seq(along=table(phaseid[phaseid > 0])),
-                table(phaseid[phaseid > 0]))
+                                table(phaseid[phaseid > 0]))
     ok <- match(unique(diveid[diveid > 0]), diveid) # required subscripts
     phase.no <-  phase.no[ok]
     activity <- act[ok]