A little code cleanup

Author: marknovak

ExpPatch-Scripts/ExpPatch_MiscFunctions.r

@@ -1,52 +1,67 @@
 ##############################################################
-# Miscallaneous functions that are useful in multiple contexts
+# Miscellaneous functions that are useful in multiple contexts
 ##############################################################
 
 # minDiff is Minimum assumed difference between survey sets
-ConvertDate2SurveyDate<-function(dat,minDiff=9){
-	dat$Date<-as.Date(dat$Date)
-	SDates<-sort(unique(dat$Date))
-	Dates<-data.frame(SurveyDate=SDates,Date=SDates)
-	Dates$difDates<-c(0,diff(Dates$Date))
-	for(i in 2:nrow(Dates)){ if(Dates$difDates[i]<minDiff){Dates$SurveyDate[i]<-Dates$SurveyDate[i-1]}	}
-	dat<-merge(dat,Dates[,-3],by='Date',all.x=TRUE)
-	# Switch names (in order to use 'Date' subsequently)
-	colnames(dat)[which(colnames(dat)=='Date')]<-'TrueDate'
-	colnames(dat)[which(colnames(dat)=='SurveyDate')]<-'Date'
-	dat<-dat[,c(length(dat),1:(length(dat)-1))]
-	return(dat)
+ConvertDate2SurveyDate <- function(dat, minDiff = 9) {
+  dat$Date <- as.Date(dat$Date)
+  SDates <- sort(unique(dat$Date))
+  Dates <- data.frame(SurveyDate = SDates, Date = SDates)
+  Dates$difDates <- c(0, diff(Dates$Date))
+  for (i in 2:nrow(Dates)) {
+    if (Dates$difDates[i] < minDiff) {
+      Dates$SurveyDate[i] <- Dates$SurveyDate[i - 1]
+    }
+  }
+  dat <- merge(dat, Dates[, -3], by = 'Date', all.x = TRUE)
+  # Switch names (in order to use 'Date' subsequently)
+  colnames(dat)[which(colnames(dat) == 'Date')] <- 'TrueDate'
+  colnames(dat)[which(colnames(dat) == 'SurveyDate')] <- 'Date'
+  dat <- dat[, c(length(dat), 1:(length(dat) - 1))]
+  return(dat)
 }
 
 
 # Match-up and rename Survey dates in two datasets
 # (e.g., abundance dynamics and feeding observations)
 # Spits out only the 2nd dataset (i.e. it conforms the dates in the 2nd dataset
 # to match up with those of the 1st dataset.
-MatchDates<-function(datA,datB,minDiff=9){
-	datA$Date<-as.Date(datA$Date)
-	datB$Date<-as.Date(datB$Date)
-	SDatesA<-sort(unique(datA$Date))
-	SDatesB<-sort(unique(datB$Date))
-	for(i in 1:length(SDatesA)){
-		tDate<-SDatesA[i]
-		tDateSeq<-seq(tDate-minDiff,tDate+minDiff,1)
-		Match<-which(datB$Date%in%tDateSeq)
-		if(length(Match)!=0){datB$Date[Match]<-tDate}
-		if(length(Match)==0){warning(paste0('No date match found for ',tDate))}
-	}
-	return(datB)
+MatchDates <- function(datA, datB, minDiff = 9) {
+  datA$Date <- as.Date(datA$Date)
+  datB$Date <- as.Date(datB$Date)
+  SDatesA <- sort(unique(datA$Date))
+  SDatesB <- sort(unique(datB$Date))
+  for (i in 1:length(SDatesA)) {
+    tDate <- SDatesA[i]
+    tDateSeq <- seq(tDate - minDiff, tDate + minDiff, 1)
+    Match <- which(datB$Date %in% tDateSeq)
+    if (length(Match) != 0) {
+      datB$Date[Match] <- tDate
+    }
+    if (length(Match) == 0) {
+      warning(paste0('No date match found for ', tDate))
+    }
+  }
+  return(datB)
 }
 
 # Scale the points of a graph by their x-value
-ptscale<-function(x,Scale=1,base=4){return(Scale*log(x,exp(base)))}
+ptscale <- function(x, Scale = 1, base = 4) {
+  return(Scale * log(x, exp(base)))
+}
 
 
-# Computes the variance of a weighted mean following Cochran 1977 
-var.wtd.mean.cochran <- function(x,w,na.rm=TRUE){
-	if(na.rm){	x<-x[!is.na(x)]; w<-w[!is.na(x)] }
-	n = length(w)
-	xWbar = weighted.mean(x,w)
-	wbar = mean(w)
-	out = n/((n-1)*sum(w)^2)*(sum((w*x-wbar*xWbar)^2)-2*xWbar* sum((w-wbar)*(w*x-wbar*xWbar))+xWbar^2*sum((w-wbar)^2))
-	return(out)
+# Computes the variance of a weighted mean following Cochran 1977
+var.wtd.mean.cochran <- function(x, w, na.rm = TRUE) {
+  if (na.rm) {
+    x <- x[!is.na(x)]
+    w <- w[!is.na(x)]
+  }
+  n = length(w)
+  xWbar = weighted.mean(x, w)
+  wbar = mean(w)
+  out = n / ((n - 1) * sum(w) ^ 2) * (sum((w * x - wbar * xWbar) ^ 2) - 2 *
+                                        xWbar * sum((w - wbar) * (w * x - wbar * xWbar)) + xWbar ^ 2 * sum((w -
+                                                                                                              wbar) ^ 2))
+  return(out)
 }