eofunc
Computes empirical orthogonal functions (EOFs, aka: Principal Component Analysis).
Prototype
function eofunc ( data : numeric, neval : integer, optEOF : logical ) return_val : numeric
Arguments
dataA multi-dimensional array in which the rightmost dimension is the number of observations. Generally, this is the time dimension.
If your rightmost dimension is not time, then see eofunc_n.
Commonly, the data array contains anomalies from some base climatology, however, this is not required.
nevalA scalar integer that specifies the number of eigenvalues and eigenvectors to be returned. This is usually less than or equal to the minimum number of observations or number of variables.
optEOFA logical variable to which various optional arguments may be assigned as attributes. These optional arguments alter the default behavior of the function. optEOF must be set to True, and then you can attach the following attributes:
- optEOF@jopt - an integer that indicates whether to use the covariance matrix (optEOF@jopt=0) or the correlation matrix (optEOF@jopt=1) to compute EOFs. The default is to use a covariance matrix (optEOF@jopt = 0).
- optEOF@pcrit - a float value between 0 and 100 that indicates the percentage of non-missing points that must exist at any single point in order to be calculated. The default is 50%. Points that contain all missing values will automatically be set to missing.
Return value
A multi-dimensional array containing normalized EOFs. The returned array will be of the same size as data with the rightmost dimension removed and an additional leftmost dimension of the same size as neval added. Double if data is double, float otherwise.
The return variable will have associated with it the following attributes:
- eval: a one-dimensional array of size neval that contains the eigenvalues.
- pcvar: a one-dimensional float array of size neval equal to the percent variance associated with each eigenvalue.
- pcrit: The same value and type of optEOF@pcrit if the user changed the default.
- matrix: A string indicating the type of matrix used, "correlation" or "covariance".
- method: A string indicating if the input array, data, was/was-not transposed for the purpose of computing the eigenvalues and eigenvectors. The string can have two values: "transpose" or "no transpose"
- eval_transpose: This attribute is returned only if method="transpose". eval_transpose will contain the eigenvalues of the transposed covariance matrix. These eigenvalues are then scaled such that they are consistent with the original input data.
print(return_val@pcvar) print(return_val@pcrit)
Description
This function computes Empirical Orthogonal Functions (EOFs) via a covariance matrix or, optionally, via a correlation matrix. This is also known as Principal Component Analysis or Eigen Analysis. The EOFs are calculated using LAPACK's "dspevx" routine. Missing values are ignored when computing the covariance or correlation matrix. The returned values are normalized such that the sum of squares for each EOF pattern equals one. To denormalize the returned EOFs multiply by the square root of the associated eigenvalue (aka, the singular value).
If data does NOT have time as the rightmost dimension, then use eofunc_n to avoid having to reorder the data.
Use the eofunc_Wrap function if metadata retention is desired. The interface is identical.
Most commonly, the input data consists of anomalies.
This function differs from the deprecated eofcov and eofcor functions in that it may transpose the input data array prior to computing the EOFs. If data is transposed, a linear transformation is applied to the EOFs of the transposed array prior to returning. The reason for using this approach is computational efficiency.
Comments on weighting observations
Generally, when performing and EOF analysis on observations over the globe or a portion of the globe, the values are weighted prior to calculating. This is usually required to account for the convergence of the meridions (area weighting) which lessens the impact of high-latitude grid points that represent a small area of the globe. Most frequently, the square root of the cosine of the latitude is used to compute the area weight. The square root is used to create a covariance matrix that reflects the area of each matrix element. If weighted in this manner, the resulting covariance values will include quantities calculated via:
[x*sqrt(cos(lat(x)))]*[y*sqrt(cos(lat(y)))] = x*y*sqrt(cos(lat(x)))*sqrt(cos(lat(y)))Note that the covariance of a grid point with itself yields standard cosine weighting:
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[x*sqrt(cos(lat(x)))]*[x*sqrt(cos(lat(x)))] = x^2 * cos(lat(x)).Note on standard EOF analysis
Conventional EOF analysis yields patterns and time series which are both orthogonal. The derived patterns are a function of the domain. However, the EOF procedure is strictly mathematical (not statistical) and is not based upon physics. The results may produce patterns that are similar to physical modes within the the system. However, physical meaning is dependent on your interpretation of the mathematical result.
Note on signs of EOF analysis (conributed by Andrew Dawson, UEA)
EOFs are eigenvectors of the covariance matrix formed from the input data. Since an eigenvector can be multiplied by any scalar and still remain an eigenvector, the sign is arbitrary. In a mathematical sense the sign of an eigenvector is rather unimportant. This is why the EOF analysis may yield different signed EOFs for slightly different inputs. Sign only becomes an issue when you wish to interpret the physical meaning (if any) of an eigenvector.
You should approach the interpretation of EOFs by looking at both the EOF pattern and the associated time series together. For example, consider an EOF of sea surface temperature. If your EOF has a positive centre and the associated time series is increasing, then you will interpret this centre as a warming signal. If your EOF had come out the other sign (ie. a negative centre), then the associated time series would also be the opposite sign and you would still interpret the centre as a warming signal.
In essence, the sign flip does not change the physical interpretation of the result. Hence, it is up to you to choose which sign to associate with your EOF patterns for visualisation (remembering that any sign change to an EOF must be applied to the associated time series also). Usually you would simply adjust the sign so that all your EOF patterns with the same physical interpretation also look the same.
If desired, EOF spatial patterns may be tested for orthogonality by using the dot product:
d01 = sum(eof(0,:,:)*eof(1,:,:)) d12 = sum(eof(1,:,:)*eof(2,:,:)) d02 = sum(eof(0,:,:)*eof(2,:,:)) print("d01="+d01+" d12="+d12+" d02="+d02) ; may be +/- 1e-8
References:
Quadrelli, Roberta, Christopher S. Bretherton, John M. Wallace, 2005: On Sampling Errors in Empirical Orthogonal Functions. J. Climate, 18, 3704-3710 North, G. R., T. L. Bell, R. F. Cahalan, and F. J. Moeng, Sampling errors in the estimation of empirical orthogonal functions, Mon. Wea. Rev., 110, 699-706, 1982. Dawson, A.: EOF Analysis
Acknowledgement: The code used is a modified version of David Pierce's fortran code.
See Also
eofunc_Wrap, eofunc_north, eofunc_n, eofunc_n_Wrap, eofunc_ts, eofunc_ts_n, eofunc_ts_Wrap, eofunc_ts_n_Wrap, eofunc_varimax, eof2data, eof2data_n
Examples
In the following, the attribute pcvar can be output via:
print(ev@pcvar) ; 1D vector of length "neval"
This attribute could also be used in graphics. For example, it could be used in a title.
title = "%=" + ev@pcvar(1)
sprintf can be used to format the title more precisely:
title = "%=" + sprintf("%5.2f", ev@pcvar(1) )Example 1
Let x be two-dimensional with dimensions "variables" (size = nvar) and "time". Commonly, 'x' contains anomalies.
neval = 3 ; calculate 3 EOFs out of 7 ev = eofunc(x,neval,False) ; ev(neval,nvar) ; Use eofunc_Wrap if metadata retention is desired ; ev = eofunc_Wrap(x,neval,False) ; ev(neval,nvar) ; print the percent-variance explained print("% var="+ ev@pcvar) option = True option@jopt = 1 ; use correlation matrix ev_cor = eofunc(x,neval,option) ; ev_cor(neval,nvar) ; Use eofunc_Wrap if metadata retention is desired ; ev_cor = eofunc_Wrap(x,neval,option) ; ev_cor(neval,nvar) ; print the percent-variance explained print("% var="+ ev_cor@pcvar)Example 2
Let x be three-dimensional with dimensions of time, lat, lon.
With NCL versions 6.3.0 and earlier, you need to reorder x so that time is the rightmost dimension. With NCL versions 6.4.0 and later, use eofunc_n to avoid having to reorder.
y!0 = "time" ; name dimensions if not already done y!1 = "lat" ; must be named to reorder y!2 = "lon" neval = nvar ; calculate all EOFs ev = eofunc(y(lat|:,lon|:,time|:),neval,False) ; Use eofunc_Wrap if metadata retention is desired ; ev = eofunc_Wrap(y(lat|:,lon|:,time|:),neval,False) ;;ev = eofunc_n(y,neval,False,0) ; NCL V6.4.0 and later ; ev(neval,nlat,nlon) ; Use eofunc_n_Wrap if metadata retention is desired ; ev = eofunc_n_Wrap(y,neval,False,0) ; denormalize the EOFs [units same as data] do ne=0,neval-1 ev(ne,:,:) = ev(ne,:,:)*sqrt( ev@eval(ne) ) end do
Example 3
Let z be four-dimensional with dimensions time, lev, lat, and lon:
neval = 3 ; calculate 3 EOFs out of klev*nlat*mlon ev = eofunc(z(lat|:,lon|:,time|:),neval,False) ; Use eofunc_Wrap if metadata retention is desired ; ev = eofunc_Wrap(z(lat|:,lon|:,time|:),neval,False) ;;ev = eofunc_n(z,neval,False,0) ; NCL V6.4.0 and later ; ev will be dimensioned neval, level, lat, lon ; Use eofunc_n_Wrap if metadata retention is desired ; ev = eofunc_n_Wrap(z,neval,False,0)Example 4
Calculate the EOFs at every other lat/lon point. Use of a temporary array is NOT necessary but it avoids having to reorder the array twice in this example:
neval = 5 ; calculate 5 EOFs out of nlat*mlon zTemp = z(lat|::2,lon|::2,time|:) ; reorder and use temporary array ev = eofunc(zTemp,neval,False) ; ev(neval,nlat/2,mlon/2) ; Use eofunc_Wrap if metadata retention is desired ; ev = eofunc_Wrap(zTemp,neval,False) ; ev(neval,nlat/2,mlon/2) ;;ev = eofunc_n(z(:,::2,::2),neval,False,0) ; NCL V6.4.0 and later, no reordering ; Use eofunc_n_Wrap if metadata retention is desired ; ev = eofunc_n_Wrap(z(:,::2,::2),neval,False,0)Example 5
Let z be four-dimensional with dimensions level, lat, lon, time. Calculate the EOFs at one specified level:
kl = 3 ; specify level neval = 8 ; calculate 8 EOFs out of nlat*mlon ev = eofunc(z(kl,:,:,:),neval,False) ; ev will be dimensioned neval, lat, lon ; Use eofunc_Wrap if metadata retention is desired ; ev = eofunc_Wrap(z(kl,:,:,:),neval,False)Example 6
Let z be four-dimensional with dimensions time, lev, lat, lon. Reorder x so that time is the rightmost dimension and calculate on one specified level:
kl = 3 ; specify level neval = 8 ; calculate 8 EOFs out of nlat*mlon zTemp = z(lev|kl,lat|:,lon|:,time|:) ev = eofunc(zTemp,neval,False) ; Use eofunc_Wrap if metadata retention is desired ; ev = eofunc_Wrap(zTemp,neval,False) ;;ev = eofunc_n(z,neval,False,0) ; no reordering needed ; ev will be dimensioned neval, lat, lon ; Use eofunc_n_Wrap if metadata retention is desired ; ev = eofunc_n_Wrap(z,neval,False,0) ; no reordering neededExample 7
Area-weight the data prior to calculation. Let p be three-dimensional with dimensions time, lat, lon. The array "lat" contains the latitudes. See example 7 in the eofunc_n documentation for how to do this without reordering.
; calculate the weights using the square root of the cosine of the latitude and ; also convert degrees to radians wgt = sqrt(cos(lat*0.01745329)) ; reorder data so time is fastest varying pt = p(lat|:,lon|:,time|:) ; (lat,lon,time) ptw = pt ; create an array with metadata ; weight each point prior to calculation. ; conform is used to make wgt the same size as pt ptw = pt*conform(pt, wgt, 0) optEOF = True optEOF@pcrit = 80 evec= eofunc(ptw,neval,optEOF) ; Use eofunc_Wrap if metadata retention is desired ; evec= eofunc_Wrap(ptw,neval,optEOF) ; denormalize the EOFs ; print the % variance explained do ne=0,neval-1 evec(ne,:,:) = evec(ne,:,:)*sqrt( evec@eval(ne) ) ; units same as data print("% var="+ evec@pcvar(ne) ) end do