added some diagnostics (vpd,z0,...)

NAMESPACE

@@ -15,6 +15,7 @@ export(calc_cov)
 export(calc_csi)
 export(calc_dshear)
 export(calc_ef)
+export(calc_evapotranspiration)
 export(calc_flux_footprint)
 export(calc_gustfactor)
 export(calc_iw)
@@ -27,10 +28,12 @@ export(calc_quadrant_analysis)
 export(calc_ri)
 export(calc_satvaporpressure)
 export(calc_spectrum)
+export(calc_spectrum1D)
 export(calc_ti)
 export(calc_tke)
 export(calc_ustar)
 export(calc_var)
+export(calc_vpd)
 export(calc_vtke)
 export(calc_windDirection)
 export(calc_windSpeed2D)
@@ -65,6 +68,7 @@ export(scale_phiu)
 export(scale_phiw)
 export(shift2maxccf)
 export(sos2Ts)
+export(ustar2z0)
 importFrom(MASS,kde2d)
 importFrom(RcppRoll,roll_mean)
 importFrom(RcppRoll,roll_sd)

R/auxilliary.R

@@ -37,7 +37,7 @@ binning=function(var1,var2,bins) {
 
 #' Shifting two timeseries to match maximum cross-correlation
 #'
-#'@description Shifts two timeseries to match their maximum cross-correlation
+#'@description Shifts two timeseries to match their maximum cross-correlation (can be used e.g. for lag-time correction)
 #'@param var1 vector, first timeseries
 #'@param var2 vector, second timeseries
 #'@param plot logical, should the cross-correlation be plotted? default \code{plot = TRUE}
@@ -61,7 +61,7 @@ shift2maxccf=function(var1,var2,plot=TRUE) {
 	n=max(n1,n2)
 	#calc cross-correlation
 	notna=(!is.na(var1) & !is.na(var2))
-    cc=ccf(var1[notna],var2[notna])
+	cc=ccf(var1[notna],var2[notna])
 	maxcc=max(cc$acf) #max positive cross-correlation
 	lag=cc$lag[which(cc$acf==max(cc$acf))] #respective time lag
 	if (plot == TRUE) {

R/constants.R

@@ -114,4 +114,12 @@ M_CO2 = function() {
 #' @keywords internal
 M_CH4 = function() {
 	return(0.01604)
+}
+
+#' Charnock constant (alpha)
+#'
+#' Charnock constant (alpha) used to convert friction velocity to surface roughness length
+#' @keywords internal
+alpha = function() {
+	return(0.016)
 }

R/diagnostics-meteorology.R

@@ -13,6 +13,27 @@ calc_satvaporpressure = function(temp) {
     return(a*exp(b*temp/(temp+c))*1000)
 }
 
+#' Vapor pressure deficit (VPD)
+#'
+#'@description Calculates vapor pressure deficit (VPD) from temperature and relative humidity using Arrhenius formula
+#'@param temp temperature [K]
+#'@param rh relative humidity [%]
+#'@return VPD, vapor pressure deficit [Pa]
+#'@export
+#'
+calc_vpd = function(temp,rh) {
+    #calculate saturation pressure here using Arrhenius formula
+    a=-1.0440397*10^4
+    b=-11.29465
+    c=-2.7022355*10^-2
+    d=1.289036*10^-5
+    e=-2.4780681*10^-9
+    f=6.5459673
+    temp=temp*5/9 #K to deg R (Rankine scale)
+    es=exp(a/temp+b+c*temp+d*temp^2+e*temp^3+f*log(temp))
+    return(es*(1-rh/100))
+}
+
 #' Potential temperature
 #'
 #'@description Calculates potential temperature for given temperature and pressure

R/diagnostics-turbulence.R

@@ -157,3 +157,32 @@ calc_br = function(sh,lh) {
 calc_ef = function(sh,lh) {
 	return(lh/(sh+lh))
 }
+
+#' Evapotranspiration
+#'
+#'@description Calculates evapotranspiration from latent heat flux
+#'@param lh latent heat flux [W/m^2]
+#'@param temp temperature [K] (optional), if provided, the latent heat of vaporization is calculated temperature-dependent
+#'
+#'@return evapotranspiration [kg/(s*m^2)]
+#'@export
+#'
+calc_evapotranspiration = function(lh,temp=NULL) {
+	lv=Lv(temp)
+	return(lh/lv)
+}
+
+
+### surface roughness and related concepts ###
+
+#' Calculates surface roughness length z0 from friction velocity using the simple estimate from Charnock, 1955
+#'
+#'@description Calculates surface roughness z0 from friction velocity using the simple estimate from Charnock, 1955: z0 = alpha*ustar^2/g with alpha=0.016 and g=9.81 m/s^2
+#'@param ustar friction velocity [m/s]
+#'
+#'@return surface roughness length [m]
+#'@export
+#'
+ustar2z0 = function(ustar) {
+	return(alpha()*ustar^2/g())
+}

R/ec-processing.R

@@ -387,6 +387,7 @@ cov2cf = function(cov_co2w,rho=NULL) {
 #'set.seed(5)
 #'x=rnorm(100)
 #'y=rnorm(100)
+#'y[1:10]=NA
 #'cov_xy=calc_cov(x,y)
 #'
 calc_cov = function(x,y) {

README.md

@@ -1,4 +1,4 @@
-# Reddy: An open-source package for analyzing eddy-covariance measurements
+# Reddy: A toolbox for analyzing eddy-covariance measurements
 <!-- badges: start --> 
 [![CRAN status](https://www.r-pkg.org/badges/version/Reddy)](https://cran.r-project.org/package=Reddy)
 [![Last Commit](https://img.shields.io/github/last-commit/noctiluc3nt/Reddy)](https://github.com/noctiluc3nt/Reddy)
@@ -31,7 +31,7 @@ The Reddy package provides functions for the post-processing, analysis and evalu
 - `spectrum.R`: wrapper for the rbase spectrum function to derive averaged FFT spectra and compare them with theoretical slopes
 - `surface-energy-balance.R`: visualization of surface energy balance, residual flux and closure ratio
 
-<image src="./inst/figures/schema.png">
+<image src="./inst/figures/schema2.png">
 
 
 ### Usage