Add k.klaus

NAMESPACE

@@ -15,6 +15,8 @@ export(k.crusius)
 export(k.crusius.base)
 export(k.heiskanen)
 export(k.heiskanen.base)
+export(k.klaus)
+export(k.klaus.base)
 export(k.macIntyre)
 export(k.macIntyre.base)
 export(k.read)

R/k.klaus.R

@@ -0,0 +1,64 @@
+# ---Author: Bennett McAfee, 2026-06-08 --- 
+# Last update: 2026-06-08 
+
+#'@export
+k.klaus = function(ts.data, wnd.z, lake.area, spatial.int, method = c("linear", "power")){
+
+  if(!has.vars(ts.data, 'wnd')){
+    stop('k.klaus requires a "wnd" (wind speed) column in the supplied data')
+  }
+
+  wind = get.vars(ts.data, 'wnd')
+
+  k600 = k.klaus.base(wind[,2], wnd.z, lake.area, spatial.int, method = method)
+
+  return(data.frame(datetime=ts.data$datetime, k600=k600))
+}
+
+
+#'@export
+k.klaus.base <- function(wnd, wnd.z, lake.area, spatial.int, method = c("linear", "power")) {
+
+  method <- match.arg(method)
+
+  # converting m2 to km2
+  lake.area <- lake.area / 1e6 
+
+  # Converting uz to u10
+  if (wnd.z != 10){
+    wnd <- wind.scale.base(wnd = wnd, wnd.z = wnd.z)
+  }
+
+  # helper logit function
+  logit.custom <- function(x){
+    return(log(x / (1 - x)))
+  }
+
+  # sanity checks
+  if (any(spatial.int <= 0 | spatial.int >= 1)) {
+    stop("spatial.int must be between 0 and 1 (exclusive)")
+  }
+
+  if (method == "linear") {
+    k600 <- (0.328 * log10(lake.area) + 1.581) * wnd - 0.066 * logit.custom(spatial.int) + 1.266
+  } else if (method == "power") {
+    k600 <- (0.281 * log10(lake.area) + 1.361) * (wnd ^ 1.097) - 0.072 * logit.custom(spatial.int) + 1.401
+  } else if (method == "exp") {
+    # if (is.null(sdi)) {
+    #   stop("sdi must be provided for exponential model")
+    # }
+    # k600 <- (-0.057 * logit.custom(spatial.int) + 2.366) * exp(wnd * (0.144 * log10(sdi) + 0.156))
+    stop('The exponential model was removed per Klaus and Vachon (2020): "...[We] do not recommend using our
+models that include SDI."')
+  }
+
+  k600 <- k600 * (24/100) # convert cm/hr to m/day
+
+  return(k600)
+}
+
+
+# -- References
+# Klaus, Marcus, and Dominic Vachon. 2020. 
+# Challenges of Predicting Gas Transfer Velocity from Wind Measurements over Global Lakes. 
+# Aquatic Sciences 82 (3): 53. https://doi.org/10.1007/s00027-020-00729-9

R/k.read.R

@@ -7,6 +7,7 @@
 #'k.crusius
 #'k.vachon
 #'k.heiskanen
+#'k.klaus
 #'@title Returns a timeseries of gas exchange velocity
 #'@description
 #'Returns the gas exchange velocity based on the chosen model in units of m/day
@@ -24,13 +25,19 @@
 #'k.vachon(ts.data, lake.area, params=c(2.51,1.48,0.39))
 #'
 #'k.heiskanen(ts.data, wnd.z, Kd, atm.press)
+#'
+#'k.klaus(ts.data, wnd.z, lake.area, spatial.int, method = c("linear", "power"))
 #'@param ts.data vector of datetime in POSIXct format
-#'@param method Only for \link{k.crusius}. String of valid method . Either "linear", "bilinear", or "power"
+#'@param method Only for \link{k.crusius} and \link{k.klaus}. String of valid method. For k.crusius either "linear", "bilinear", or "power". For k.klaus either "linear" or "power"
 #'@param wnd.z height of wind measurement, m
 #'@param Kd Light attenuation coefficient (Units:m^-1)
 #'@param atm.press atmospheric pressure in mb
 #'@param lat Latitude, degrees north
 #'@param lake.area Lake area, m^2
+#'@param spatial.int Only for \link{k.klaus}. Numeric scale of spatial integration, expressed relative
+#'to total lake surface area: from near 0 (a point-scale measurement, e.g. 1 m^2 / lake.area)
+#'up to but not including 1 (whole-lake integration). Must satisfy 0 < spatial.int < 1; the value 1 is
+#'not supported because the model uses logit(spatial.int).
 #'@param params Only for \link{k.vachon.base} and \link{k.macIntyre}. See details.
 #'
 #'@details Can change default parameters of MacIntyre and Vachon models. Default for Vachon is
@@ -70,14 +77,18 @@
 #'\emph{An approach to estimation of near-surface turbulence and CO2 transfer
 #'velocity from remote sensing data}. Journal of Marine Systems 66, (2007): 182-194.
 #'
+#'Marcus Klaus and Dominic Vachon. \emph{Challenges of Predicting Gas Transfer Velocity from Wind Measurements over Global Lakes}. 
+#'Aquatic Sciences 82 (3): 53. (2020).
+#'
 #'@author
-#'Hilary Dugan, Jake Zwart, Luke Winslow, R. Iestyn. Woolway, Jordan S. Read
+#'Hilary Dugan, Jake Zwart, Luke Winslow, R. Iestyn. Woolway, Jordan S. Read, Bennett McAfee
 #'@seealso
 #'\link{k.cole}
 #'\link{k.crusius}
 #'\link{k.macIntyre}
 #'\link{k.vachon}
 #'\link{k.heiskanen}
+#'\link{k.klaus}
 #'@examples
 #'data.path = system.file('extdata', package="LakeMetabolizer")
 #'
@@ -101,6 +112,7 @@
 #'atm.press  = 1018
 #'lat       = tb.data$metadata$latitude
 #'lake.area = tb.data$metadata$lakearea
+#'spatial.int        = 1/lake.area
 #'
 #'#for k.read and k.macIntyre, we need LW_net.
 #'#Calculate from the observations we have available.
@@ -116,6 +128,8 @@
 #'
 #'k600_macIntyre = k.macIntyre(ts.data, wnd.z=wnd.z, Kd=kd, atm.press=atm.press)
 #'
+#'k600_klaus = k.klaus(ts.data, wnd.z=wnd.z, lake.area=lake.area, spatial.int=spatial.int)
+#'
 #'@export
 k.read = function(ts.data, wnd.z, Kd, atm.press, lat, lake.area){
 
@@ -178,6 +192,7 @@ k.read = function(ts.data, wnd.z, Kd, atm.press, lat, lake.area){
 #'k.crusius.base
 #'k.vachon.base
 #'k.heiskanen.base
+#'k.klaus.base
 #'@title Returns a timeseries of gas exchange velocity
 #'@description
 #'Returns the gas exchange velocity based on the chosen model in units of m/day
@@ -199,8 +214,9 @@ k.read = function(ts.data, wnd.z, Kd, atm.press, lat, lake.area){
 #'
 #'k.heiskanen.base(wnd.z, Kd, atm.press, dateTime, Ts, z.aml, airT, wnd, RH, sw, lwnet)
 #'
+#'k.klaus.base(wnd, wnd.z, lake.area, spatial.int, method = c("linear", "power"))
 #'@param wnd Numeric value of wind speed, (Units:m/s)
-#'@param method Only for \link{k.crusius.base}. String of valid method . Either "constant", "bilinear", or "power"
+#'@param method Only for \link{k.crusius.base} and \link{k.klaus.base}. String of valid method. For k.crusius.base either "constant", "bilinear", or "power". For k.klaus.base either "linear" or "power"
 #'@param wnd.z Height of wind measurement, (Units: m)
 #'@param Kd Light attenuation coefficient (Units: m^-1)
 #'@param lat Latitude, degrees north
@@ -213,10 +229,15 @@ k.read = function(ts.data, wnd.z, Kd, atm.press, lat, lake.area){
 #'@param RH Numeric value of relative humidity, \%
 #'@param sw Numeric value of short wave radiation, W m^-2
 #'@param lwnet Numeric value net long wave radiation, W m^-2
+#'@param spatial.int Only for \link{k.klaus}. Numeric scale of spatial integration, expressed relative
+#'to total lake surface area: from near 0 (a point-scale measurement, e.g. 1 m^2 / lake.area)
+#'up to but not including 1 (whole-lake integration). Must satisfy 0 < spatial.int < 1; the value 1 is
+#'not supported because the model uses logit(spatial.int).
 #'@param params Optional parameter input, only for \link{k.vachon.base} and \link{k.macIntyre.base}. See details.
 #'@details Can change default parameters of MacIntyre and Vachon models. Default for Vachon is
 #'c(2.51,1.48,0.39). Default for MacIntyre is c(1.2,0.4872,1.4784). Heiskanen et al. (2014) uses MacIntyre
 #'model with c(0.5,0.77,0.3) and z.aml constant at 0.15.
+#'
 #'@return Numeric value of gas exchange velocity (k600) in units of m/day. Before use,
 #'should be converted to appropriate gas using \link{k600.2.kGAS}.
 #'@keywords methods math
@@ -248,15 +269,19 @@ k.read = function(ts.data, wnd.z, Kd, atm.press, lat, lake.area){
 #'\emph{An approach to estimation of near-surface turbulence and CO2 transfer
 #'velocity from remote sensing data}. Journal of Marine Systems 66, (2007): 182-194.
 #'
+#'Marcus Klaus and Dominic Vachon. \emph{Challenges of Predicting Gas Transfer Velocity from Wind Measurements over Global Lakes}. 
+#'Aquatic Sciences 82 (3): 53. (2020).
+#'
 #'@author
-#'R. Iestyn. Woolway, Hilary Dugan, Luke Winslow, Jordan S Read, GLEON fellows
+#'R. Iestyn. Woolway, Hilary Dugan, Luke Winslow, Jordan S Read, Bennett McAfee, GLEON fellows
 #'@seealso
 #'\link{k.cole}
 #'\link{k.read}
 #'\link{k.crusius}
 #'\link{k.macIntyre}
 #'\link{k.vachon}
 #'\link{k.heiskanen}
+#'\link{k.klaus}
 #'@examples
 #'wnd.z <- 2
 #'Kd <- 2
@@ -271,6 +296,7 @@ k.read = function(ts.data, wnd.z, Kd, atm.press, lat, lake.area){
 #'RH <- 90
 #'sw <- 800
 #'lwnet <- -55
+#'spatial.int <- 1/lake.area
 #'timeStep <- 30
 #'
 #'U10 <- wind.scale.base(wnd, wnd.z)
@@ -288,6 +314,8 @@ k.read = function(ts.data, wnd.z, Kd, atm.press, lat, lake.area){
 #'k600_macInytre <- k.macIntyre.base(wnd.z, Kd, atm.press,
 #'dateTime, Ts, z.aml, airT, wnd, RH, sw, lwnet)
 #'
+#'k600_klaus <- k.klaus.base(wnd, wnd.z, lake.area, spatial.int)
+#'
 #'@export
 k.read.base <- function(wnd.z, Kd, lat, lake.area, atm.press, dateTime, Ts, z.aml, airT, wnd, RH, sw, lwnet){