Hi,

Just a hint, the answer should look a lot like the chi-squared
gradient (http://www.nmr-relax.com/manual/chi_squared_gradient.html),
but probably without the sum and a few other differences.

Regards,

Edward



On 28 August 2014 15:41, Edward d'Auvergne <[email protected]> wrote:
> Hi,
>
> No, that's not correct.  Try performing the maths yourself and try to
> derive the chi-squared partial derivative.  You will see that it's a
> little different.
>
> Regards,
>
> Edward
>
>
>
> On 28 August 2014 15:38, Troels Emtekær Linnet <[email protected]> wrote:
>> Hi Edward.
>>
>> I is just target_functions/c_chi2.c where you dont sum the elements, but
>> return as array.
>>
>> Best
>> Troels
>>
>> 2014-08-28 15:30 GMT+02:00 Edward d'Auvergne <[email protected]>:
>>> Hi Troels,
>>>
>>> Could you derive the chi-squared Jacobian?  Maybe the Jacobian I have
>>> been using is not correct - this is the one required for the
>>> Levenberg-Marquardt optimisation algorithm.  Because the chi-squared
>>> is squared, its derivative will have a factor of 2 out the front, just
>>> like the gradient:
>>>
>>> http://www.nmr-relax.com/manual/chi_squared_gradient.html
>>>
>>> It might be useful to add a Jacobian section to this part of the
>>> manual with the equations.
>>>
>>> Cheers,
>>>
>>> Edward
>>>
>>>
>>>
>>> On 28 August 2014 15:14,  <[email protected]> wrote:
>>>> Author: tlinnet
>>>> Date: Thu Aug 28 15:14:16 2014
>>>> New Revision: 25379
>>>>
>>>> URL: http://svn.gna.org/viewcvs/relax?rev=25379&view=rev
>>>> Log:
>>>> Modified systemtest test Relax_disp.test_estimate_r2eff_err_methods() to 
>>>> show the difference between using the direct function Jacobian, or the 
>>>> chi2 function Jacobian.
>>>>
>>>> Added also the functionality to the estimate R2eff module, to switch 
>>>> between using the different Jacobians.
>>>>
>>>> The results show, that R2eff can be estimated better.
>>>>
>>>> ----------------------
>>>> The results are:
>>>>
>>>> R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 431.0.
>>>> r2eff=8.646/8.646 r2eff_err=0.0348/0.0692 i0=202664.191/202664.191 
>>>> i0_err=699.6443/712.4201
>>>>
>>>> R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 651.2.
>>>> r2eff=10.377/10.377 r2eff_err=0.0403/0.0810 i0=206049.558/206049.558 
>>>> i0_err=776.4215/782.1833
>>>>
>>>> R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 800.5.
>>>> r2eff=10.506/10.506 r2eff_err=0.0440/0.0853 i0=202586.332/202586.332 
>>>> i0_err=763.9678/758.7052
>>>>
>>>> R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 984.0.
>>>> r2eff=10.903/10.903 r2eff_err=0.0476/0.0922 i0=203455.021/203455.021 
>>>> i0_err=837.8779/828.7280
>>>>
>>>> R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 1341.1.
>>>> r2eff=10.684/10.684 r2eff_err=0.0446/0.0853 i0=218670.412/218670.412 
>>>> i0_err=850.0210/830.9558
>>>>
>>>> R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 1648.5.
>>>> r2eff=10.501/10.501 r2eff_err=0.0371/0.0742 i0=206502.512/206502.512 
>>>> i0_err=794.0523/772.9843
>>>>
>>>> R1rho at 799.8 MHz, for offset=124.247 ppm and dispersion point 1341.1.
>>>> r2eff=11.118/11.118 r2eff_err=0.0413/0.0827 i0=216447.241/216447.241 
>>>> i0_err=784.6562/788.0384
>>>>
>>>> R1rho at 799.8 MHz, for offset=130.416 ppm and dispersion point 800.5.
>>>> r2eff=7.866/7.866 r2eff_err=0.0347/0.0695 i0=211869.715/211869.715 
>>>> i0_err=749.2776/763.6930
>>>>
>>>> R1rho at 799.8 MHz, for offset=130.416 ppm and dispersion point 1341.1.
>>>> r2eff=9.259/9.259 r2eff_err=0.0331/0.0661 i0=217703.151/217703.151 
>>>> i0_err=682.2137/685.5838
>>>>
>>>> R1rho at 799.8 MHz, for offset=130.416 ppm and dispersion point 1648.5.
>>>> r2eff=9.565/9.565 r2eff_err=0.0373/0.0745 i0=211988.939/211988.939 
>>>> i0_err=839.0313/827.0373
>>>>
>>>> R1rho at 799.8 MHz, for offset=142.754 ppm and dispersion point 800.5.
>>>> r2eff=3.240/3.240 r2eff_err=0.0127/0.0253 i0=214417.382/214417.382 
>>>> i0_err=595.8865/613.4378
>>>>
>>>> R1rho at 799.8 MHz, for offset=142.754 ppm and dispersion point 1341.1.
>>>> r2eff=5.084/5.084 r2eff_err=0.0177/0.0352 i0=226358.691/226358.691 
>>>> i0_err=660.5314/655.7670
>>>>
>>>> R1rho at 799.8 MHz, for offset=179.768 ppm and dispersion point 1341.1.
>>>> r2eff=2.208/2.208 r2eff_err=0.0091/0.0178 i0=228620.553/228620.553 
>>>> i0_err=564.8353/560.0873
>>>>
>>>> R1rho at 799.8 MHz, for offset=241.459 ppm and dispersion point 1341.1.
>>>> r2eff=1.711/1.711 r2eff_err=0.0077/0.0155 i0=224087.486/224087.486 
>>>> i0_err=539.4300/546.4217
>>>>
>>>> Fitting with minfx to: 52V @N
>>>> -----------------------------
>>>>
>>>> min_algor='Newton', c_code=True, constraints=False, chi2_jacobian?=False
>>>> ------------------------------------------------------------------------
>>>>
>>>> R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 431.0, 
>>>> with 4 time points. r2eff=8.646 r2eff_err=0.0692, i0=202664.2, 
>>>> i0_err=712.4201, chi2=3.758.
>>>> R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 651.2, 
>>>> with 5 time points. r2eff=10.377 r2eff_err=0.0810, i0=206049.6, 
>>>> i0_err=782.1833, chi2=27.291.
>>>> R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 800.5, 
>>>> with 5 time points. r2eff=10.506 r2eff_err=0.0853, i0=202586.3, 
>>>> i0_err=758.7052, chi2=13.357.
>>>> R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 984.0, 
>>>> with 5 time points. r2eff=10.903 r2eff_err=0.0922, i0=203455.0, 
>>>> i0_err=828.7280, chi2=33.632.
>>>> R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 1341.1, 
>>>> with 5 time points. r2eff=10.684 r2eff_err=0.0853, i0=218670.4, 
>>>> i0_err=830.9558, chi2=35.818.
>>>> R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 1648.5, 
>>>> with 5 time points. r2eff=10.501 r2eff_err=0.0742, i0=206502.5, 
>>>> i0_err=772.9843, chi2=7.356.
>>>> R1rho at 799.8 MHz, for offset=124.247 ppm and dispersion point 1341.1, 
>>>> with 5 time points. r2eff=11.118 r2eff_err=0.0827, i0=216447.2, 
>>>> i0_err=788.0384, chi2=15.587.
>>>> R1rho at 799.8 MHz, for offset=130.416 ppm and dispersion point 800.5, 
>>>> with 5 time points. r2eff=7.866 r2eff_err=0.0695, i0=211869.7, 
>>>> i0_err=763.6930, chi2=14.585.
>>>> R1rho at 799.8 MHz, for offset=130.416 ppm and dispersion point 1341.1, 
>>>> with 5 time points. r2eff=9.259 r2eff_err=0.0661, i0=217703.2, 
>>>> i0_err=685.5838, chi2=79.498.
>>>> R1rho at 799.8 MHz, for offset=130.416 ppm and dispersion point 1648.5, 
>>>> with 5 time points. r2eff=9.565 r2eff_err=0.0745, i0=211988.9, 
>>>> i0_err=827.0373, chi2=0.447.
>>>> R1rho at 799.8 MHz, for offset=142.754 ppm and dispersion point 800.5, 
>>>> with 5 time points. r2eff=3.240 r2eff_err=0.0253, i0=214417.4, 
>>>> i0_err=613.4378, chi2=1.681.
>>>> R1rho at 799.8 MHz, for offset=142.754 ppm and dispersion point 1341.1, 
>>>> with 5 time points. r2eff=5.084 r2eff_err=0.0352, i0=226358.7, 
>>>> i0_err=655.7670, chi2=23.170.
>>>> R1rho at 799.8 MHz, for offset=179.768 ppm and dispersion point 1341.1, 
>>>> with 5 time points. r2eff=2.208 r2eff_err=0.0178, i0=228620.6, 
>>>> i0_err=560.0873, chi2=7.794.
>>>> R1rho at 799.8 MHz, for offset=241.459 ppm and dispersion point 1341.1, 
>>>> with 5 time points. r2eff=1.711 r2eff_err=0.0155, i0=224087.5, 
>>>> i0_err=546.4217, chi2=21.230.
>>>>
>>>> Fitting with minfx to: 52V @N
>>>> -----------------------------
>>>>
>>>> min_algor='BFGS', c_code=False, constraints=False, chi2_jacobian?=True
>>>> ----------------------------------------------------------------------
>>>>
>>>> R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 431.0, 
>>>> with 4 time points. r2eff=8.646 r2eff_err=0.0524, i0=202664.2, 
>>>> i0_err=1239.0827, chi2=3.758.
>>>> R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 651.2, 
>>>> with 5 time points. r2eff=10.377 r2eff_err=0.0228, i0=206049.6, 
>>>> i0_err=178.1907, chi2=27.291.
>>>> R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 800.5, 
>>>> with 5 time points. r2eff=10.506 r2eff_err=0.0345, i0=202586.3, 
>>>> i0_err=705.7630, chi2=13.357.
>>>> R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 984.0, 
>>>> with 5 time points. r2eff=10.903 r2eff_err=0.0206, i0=203455.0, 
>>>> i0_err=186.0857, chi2=33.632.
>>>> R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 1341.1, 
>>>> with 5 time points. r2eff=10.684 r2eff_err=0.0198, i0=218670.4, 
>>>> i0_err=165.0420, chi2=35.818.
>>>> R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 1648.5, 
>>>> with 5 time points. r2eff=10.501 r2eff_err=0.0407, i0=206502.5, 
>>>> i0_err=321.3685, chi2=7.356.
>>>> R1rho at 799.8 MHz, for offset=124.247 ppm and dispersion point 1341.1, 
>>>> with 5 time points. r2eff=11.118 r2eff_err=0.0301, i0=216447.2, 
>>>> i0_err=248.9394, chi2=15.587.
>>>> R1rho at 799.8 MHz, for offset=130.416 ppm and dispersion point 800.5, 
>>>> with 5 time points. r2eff=7.866 r2eff_err=0.0280, i0=211869.7, 
>>>> i0_err=259.8845, chi2=14.585.
>>>> R1rho at 799.8 MHz, for offset=130.416 ppm and dispersion point 1341.1, 
>>>> with 5 time points. r2eff=9.259 r2eff_err=0.0108, i0=217703.2, 
>>>> i0_err=88.1514, chi2=79.498.
>>>> R1rho at 799.8 MHz, for offset=130.416 ppm and dispersion point 1648.5, 
>>>> with 5 time points. r2eff=9.565 r2eff_err=0.1630, i0=211988.9, 
>>>> i0_err=2054.6615, chi2=0.447.
>>>> R1rho at 799.8 MHz, for offset=142.754 ppm and dispersion point 800.5, 
>>>> with 5 time points. r2eff=3.240 r2eff_err=0.0485, i0=214417.4, 
>>>> i0_err=611.7573, chi2=1.681.
>>>> R1rho at 799.8 MHz, for offset=142.754 ppm and dispersion point 1341.1, 
>>>> with 5 time points. r2eff=5.084 r2eff_err=0.0124, i0=226358.7, 
>>>> i0_err=122.7341, chi2=23.170.
>>>> R1rho at 799.8 MHz, for offset=179.768 ppm and dispersion point 1341.1, 
>>>> with 5 time points. r2eff=2.208 r2eff_err=0.0086, i0=228620.6, 
>>>> i0_err=219.4208, chi2=7.794.
>>>> R1rho at 799.8 MHz, for offset=241.459 ppm and dispersion point 1341.1, 
>>>> with 5 time points. r2eff=1.711 r2eff_err=0.0101, i0=224087.5, 
>>>> i0_err=166.9081, chi2=21.230.
>>>>
>>>> task #7822(https://gna.org/task/index.php?7822): Implement user function 
>>>> to estimate R2eff and associated errors for exponential curve fitting.
>>>>
>>>> Modified:
>>>>     trunk/specific_analyses/relax_disp/estimate_r2eff.py
>>>>     trunk/test_suite/system_tests/relax_disp.py
>>>>
>>>> Modified: trunk/specific_analyses/relax_disp/estimate_r2eff.py
>>>> URL: 
>>>> http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/estimate_r2eff.py?rev=25379&r1=25378&r2=25379&view=diff
>>>> ==============================================================================
>>>> --- trunk/specific_analyses/relax_disp/estimate_r2eff.py        (original)
>>>> +++ trunk/specific_analyses/relax_disp/estimate_r2eff.py        Thu Aug 28 
>>>> 15:14:16 2014
>>>> @@ -175,7 +175,7 @@
>>>>                      print(print_string),
>>>>
>>>>
>>>> -def multifit_covar(J=None, epsrel=0.0, errors=None):
>>>> +def multifit_covar(J=None, epsrel=0.0, errors=None, use_weights=True):
>>>>      """This is the implementation of the multifit covariance.
>>>>
>>>>      This is inspired from GNU Scientific Library (GSL).
>>>> @@ -184,9 +184,15 @@
>>>>
>>>>      The parameter 'epsrel' is used to remove linear-dependent columns 
>>>> when J is rank deficient.
>>>>
>>>> +    The weighting matrix 'W', is a square symmetric matrix. For 
>>>> independent measurements, this is a diagonal matrix. Larger values 
>>>> indicate greater significance.  It is formed by multiplying the supplied 
>>>> errors as 1./errors^2 with an Identity matrix::
>>>> +
>>>> +        W = I.(1/errors^2)
>>>> +
>>>> +    If 'use_weights' is set to 'False', the errors are set to 1.0.
>>>> +
>>>>      The covariance matrix is given by::
>>>>
>>>> -        covar = (J^T J)^{-1} ,
>>>> +        covar = (J^T.W.J)^{-1} ,
>>>>
>>>>      and is computed by QR decomposition of J with column-pivoting. Any 
>>>> columns of R which satisfy::
>>>>
>>>> @@ -224,6 +230,8 @@
>>>>      @type epsrel:           float
>>>>      @keyword errors:        The standard deviation of the measured 
>>>> intensity values per time point.
>>>>      @type errors:           numpy array
>>>> +    @keyword use_weights:   If the supplied weights should be used.
>>>> +    @type use_weights:      bool
>>>>      @return:                The co-variance matrix
>>>>      @rtype:                 square numpy array
>>>>      """
>>>> @@ -237,6 +245,10 @@
>>>>      # Now form the error matrix, with errors down the diagonal.
>>>>      weights = 1. / errors**2
>>>>
>>>> +    if use_weights == False:
>>>> +        weights[:] = 1.0
>>>> +
>>>> +    # Form weight matrix.
>>>>      W = multiply(weights, eye_mat)
>>>>
>>>>      # The covariance matrix (sometimes referred to as the 
>>>> variance-covariance matrix), Qxx, is defined as:
>>>> @@ -344,7 +356,7 @@
>>>>          self.factor = factor
>>>>
>>>>
>>>> -    def set_settings_minfx(self, scaling_matrix=None, 
>>>> min_algor='simplex', c_code=True, constraints=False, func_tol=1e-25, 
>>>> grad_tol=None, max_iterations=10000000):
>>>> +    def set_settings_minfx(self, scaling_matrix=None, 
>>>> min_algor='simplex', c_code=True, constraints=False, chi2_jacobian=False, 
>>>> func_tol=1e-25, grad_tol=None, max_iterations=10000000):
>>>>          """Setup options to minfx.
>>>>
>>>>          @keyword scaling_matrix:    The square and diagonal scaling 
>>>> matrix.
>>>> @@ -355,6 +367,8 @@
>>>>          @type c_code:               bool
>>>>          @keyword constraints:       If constraints should be used.
>>>>          @type constraints:          bool
>>>> +        @keyword chi2_jacobian:     If the chi2 Jacobian should be used.
>>>> +        @type chi2_jacobian:        bool
>>>>          @keyword func_tol:          The function tolerance which, when 
>>>> reached, terminates optimisation.  Setting this to None turns of the check.
>>>>          @type func_tol:             None or float
>>>>          @keyword grad_tol:          The gradient tolerance which, when 
>>>> reached, terminates optimisation.  Setting this to None turns of the check.
>>>> @@ -366,6 +380,7 @@
>>>>          # Store variables.
>>>>          self.scaling_matrix = scaling_matrix
>>>>          self.c_code = c_code
>>>> +        self.chi2_jacobian = chi2_jacobian
>>>>
>>>>          # Scaling initialisation.
>>>>          self.scaling_flag = False
>>>> @@ -561,7 +576,7 @@
>>>>          return 1. / self.errors * (self.func_exp(self.times, *params) - 
>>>> self.values)
>>>>
>>>>
>>>> -def estimate_r2eff(method='minfx', min_algor='simplex', c_code=True, 
>>>> constraints=False, spin_id=None, ftol=1e-15, xtol=1e-15, maxfev=10000000, 
>>>> factor=100.0, verbosity=1):
>>>> +def estimate_r2eff(method='minfx', min_algor='simplex', c_code=True, 
>>>> constraints=False, chi2_jacobian=False, spin_id=None, ftol=1e-15, 
>>>> xtol=1e-15, maxfev=10000000, factor=100.0, verbosity=1):
>>>>      """Estimate r2eff and errors by exponential curve fitting with 
>>>> scipy.optimize.leastsq or minfx.
>>>>
>>>>      THIS IS ONLY FOR TESTING.
>>>> @@ -583,10 +598,12 @@
>>>>      @type method:               string
>>>>      @keyword min_algor:         The minimisation algorithm
>>>>      @type min_algor:            string
>>>> +    @keyword c_code:            If optimise with C code.
>>>> +    @type c_code:               bool
>>>>      @keyword constraints:       If constraints should be used.
>>>>      @type constraints:          bool
>>>> -    @keyword c_code:            If optimise with C code.
>>>> -    @type c_code:               bool
>>>> +    @keyword chi2_jacobian:     If the chi2 Jacobian should be used.
>>>> +    @type chi2_jacobian:        bool
>>>>      @keyword spin_id:           The spin identification string.
>>>>      @type spin_id:              str
>>>>      @keyword ftol:              The function tolerance for the relative 
>>>> error desired in the sum of squares, parsed to leastsq.
>>>> @@ -661,7 +678,7 @@
>>>>                  top += 2
>>>>              subsection(file=sys.stdout, text="Fitting with %s to: 
>>>> %s"%(method, spin_string), prespace=top)
>>>>              if method == 'minfx':
>>>> -                subsection(file=sys.stdout, text="min_algor='%s', 
>>>> c_code=%s, constraints=%s"%(min_algor, c_code, constraints), prespace=0)
>>>> +                subsection(file=sys.stdout, text="min_algor='%s', 
>>>> c_code=%s, constraints=%s, chi2_jacobian?=%s"%(min_algor, c_code, 
>>>> constraints, chi2_jacobian), prespace=0)
>>>>
>>>>          # Loop over each spectrometer frequency and dispersion point.
>>>>          for exp_type, frq, offset, point, ei, mi, oi, di in 
>>>> loop_exp_frq_offset_point(return_indices=True):
>>>> @@ -692,7 +709,7 @@
>>>>
>>>>              elif method == 'minfx':
>>>>                  # Set settings.
>>>> -                E.set_settings_minfx(min_algor=min_algor, c_code=c_code, 
>>>> constraints=constraints)
>>>> +                E.set_settings_minfx(min_algor=min_algor, c_code=c_code, 
>>>> chi2_jacobian=chi2_jacobian, constraints=constraints)
>>>>
>>>>                  # Acquire results.
>>>>                  results = minimise_minfx(E=E)
>>>> @@ -737,7 +754,7 @@
>>>>                  point_info = "%s at %3.1f MHz, for offset=%3.3f ppm and 
>>>> dispersion point %-5.1f, with %i time points." % (exp_type, frq/1E6, 
>>>> offset, point, len(times))
>>>>                  print_strings.append(point_info)
>>>>
>>>> -                par_info = "r2eff=%3.3f r2eff_err=%3.3f, i0=%6.1f, 
>>>> i0_err=%3.3f, chi2=%3.3f.\n" % ( r2eff, r2eff_err, i0, i0_err, chi2)
>>>> +                par_info = "r2eff=%3.3f r2eff_err=%3.4f, i0=%6.1f, 
>>>> i0_err=%3.4f, chi2=%3.3f.\n" % ( r2eff, r2eff_err, i0, i0_err, chi2)
>>>>                  print_strings.append(par_info)
>>>>
>>>>                  if E.verbosity >= 2:
>>>> @@ -912,14 +929,24 @@
>>>>          #jacobian_matrix_exp2 = E.jacobian_matrix_exp
>>>>          #print jacobian_matrix_exp - jacobian_matrix_exp2
>>>>      else:
>>>> -        # Call class, to store value.
>>>> -        E.func_exp_grad(param_vector)
>>>> -        jacobian_matrix_exp = E.jacobian_matrix_exp
>>>> -        #E.func_exp_chi2_grad(param_vector)
>>>> -        #jacobian_matrix_exp = E.jacobian_matrix_exp_chi2
>>>> +        if E.chi2_jacobian:
>>>> +            # Call class, to store value.
>>>> +            E.func_exp_chi2_grad(param_vector)
>>>> +            jacobian_matrix_exp = E.jacobian_matrix_exp_chi2
>>>> +        else:
>>>> +            # Call class, to store value.
>>>> +            E.func_exp_grad(param_vector)
>>>> +            jacobian_matrix_exp = E.jacobian_matrix_exp
>>>> +            #E.func_exp_chi2_grad(param_vector)
>>>> +            #jacobian_matrix_exp = E.jacobian_matrix_exp_chi2
>>>>
>>>>      # Get the co-variance
>>>> -    pcov = multifit_covar(J=jacobian_matrix_exp, errors=E.errors)
>>>> +    if E.chi2_jacobian:
>>>> +        use_weights = False
>>>> +    else:
>>>> +        use_weights = True
>>>> +
>>>> +    pcov = multifit_covar(J=jacobian_matrix_exp, errors=E.errors, 
>>>> use_weights=use_weights)
>>>>
>>>>      # To compute one standard deviation errors on the parameters, take 
>>>> the square root of the diagonal covariance.
>>>>      param_vector_error = sqrt(diag(pcov))
>>>>
>>>> Modified: trunk/test_suite/system_tests/relax_disp.py
>>>> URL: 
>>>> http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/relax_disp.py?rev=25379&r1=25378&r2=25379&view=diff
>>>> ==============================================================================
>>>> --- trunk/test_suite/system_tests/relax_disp.py (original)
>>>> +++ trunk/test_suite/system_tests/relax_disp.py Thu Aug 28 15:14:16 2014
>>>> @@ -2946,12 +2946,13 @@
>>>>
>>>>
>>>>          # Now do it manually.
>>>> -        estimate_r2eff(method='scipy.optimize.leastsq')
>>>> -        estimate_r2eff(method='minfx', min_algor='simplex', c_code=True, 
>>>> constraints=False)
>>>> -        estimate_r2eff(method='minfx', min_algor='simplex', c_code=False, 
>>>> constraints=False)
>>>> -        estimate_r2eff(method='minfx', min_algor='BFGS', c_code=True, 
>>>> constraints=False)
>>>> -        estimate_r2eff(method='minfx', min_algor='BFGS', c_code=False, 
>>>> constraints=False)
>>>> +        #estimate_r2eff(method='scipy.optimize.leastsq')
>>>> +        #estimate_r2eff(method='minfx', min_algor='simplex', c_code=True, 
>>>> constraints=False)
>>>> +        #estimate_r2eff(method='minfx', min_algor='simplex', 
>>>> c_code=False, constraints=False)
>>>> +        #estimate_r2eff(method='minfx', min_algor='BFGS', c_code=True, 
>>>> constraints=False)
>>>> +        #estimate_r2eff(method='minfx', min_algor='BFGS', c_code=False, 
>>>> constraints=False)
>>>>          estimate_r2eff(method='minfx', min_algor='Newton', c_code=True, 
>>>> constraints=False)
>>>> +        estimate_r2eff(method='minfx', min_algor='BFGS', c_code=False, 
>>>> constraints=False, chi2_jacobian=True)
>>>>
>>>>
>>>>      def test_exp_fit(self):
>>>>
>>>>
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>>>>
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