Merge pull request #60 from lawinslow/master

Fixing edge-case issues in meta.depths
GLEON · May 28, 2015 · e9a4197 · e9a4197
2 parents 2d7be6c + 8a3c2bd
commit e9a4197
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Showing 6 changed files with 12 additions and 16 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: rLakeAnalyzer
 Title: Package for the Analysis of Lake Physics
 Maintainer: Luke Winslow <[email protected]>
-Version: 1.7.3
+Version: 1.7.6
 Author: Luke Winslow, Jordan Read, Richard Woolway, Jennifer Brentrup, Taylor
     Leach, Jake Zwart
 Description: Standardized methods for calculating common important derived

diff --git a/R/meta.depths.R b/R/meta.depths.R
@@ -95,20 +95,16 @@ meta.depths = function(wtr, depths, slope=0.1, seasonal=TRUE, mixed.cutoff=1){
 		Tdepth[i] = mean(depths[ i:(i+1) ]);
 	}
 
-	tmp = sort.int(c(Tdepth, thermoD+1e-6), index.return = TRUE)
+	tmp = sort.int(unique(c(Tdepth, thermoD)), index.return = TRUE)
 	sortDepth = tmp$x
 	sortInd = tmp$ix
+	numDepths = length(sortDepth) #set numDepths again, it could have changed above
 	drho_dz = approx(Tdepth, drho_dz, sortDepth)
 	drho_dz = drho_dz$y
 
-	thermo_index = 1
-	thermoId = numDepths;
-	for(i in 1:numDepths){
-		if(thermoId == sortInd[i]){
-			thermo_index = i
-			break;
-		}
-	}
+	#find the thermocline index
+	# this is where we will start our search for meta depths
+	thermo_index = which(sortDepth == thermoD)
 
 	for (i in thermo_index:numDepths){ # moving down from thermocline index
 		if (!is.na(drho_dz[i]) && drho_dz[i] < slope){ #top of metalimnion
@@ -117,7 +113,7 @@ meta.depths = function(wtr, depths, slope=0.1, seasonal=TRUE, mixed.cutoff=1){
 		}
 	}
 
-	if (i-thermo_index > 1 && (!is.na(drho_dz[thermo_index]) && drho_dz[thermo_index] > slope)){
+	if (i-thermo_index >= 1 && (!is.na(drho_dz[thermo_index]) && drho_dz[thermo_index] > slope)){
 		metaBot_depth = approx(drho_dz[thermo_index:i],
 			sortDepth[thermo_index:i],slope)
 		metaBot_depth = metaBot_depth$y
@@ -134,7 +130,7 @@ meta.depths = function(wtr, depths, slope=0.1, seasonal=TRUE, mixed.cutoff=1){
 		}
 	}
 
-	if(thermo_index - i > 1 && (!is.na(drho_dz[thermo_index]) && drho_dz[thermo_index] > slope)){
+	if(thermo_index - i >= 1 && (!is.na(drho_dz[thermo_index]) && drho_dz[thermo_index] > slope)){
 		metaTop_depth = approx(drho_dz[i:thermo_index], sortDepth[i:thermo_index], slope);
 		metaTop_depth = metaTop_depth$y
 	}

diff --git a/man/internal.energy.Rd b/man/internal.energy.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/internal.energy.R
 \name{internal.energy}
 \alias{internal.energy}

diff --git a/man/meta.depths.Rd b/man/meta.depths.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/meta.depths.R
 \name{meta.depths}
 \alias{meta.depths}

diff --git a/man/thermo.depth.Rd b/man/thermo.depth.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/thermo.depth.R
 \name{thermo.depth}
 \alias{thermo.depth}

diff --git a/man/wtr.plot.temp.Rd b/man/wtr.plot.temp.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/wtr.plot.temp.R
 \name{wtr.plot.temp}
 \alias{wtr.plot.temp}