Recent changes to FullSpace

FullSpace modified by A. Smith

A. Smith — Tue, 07 Nov 2017 14:17:37 -0000

--- v9
+++ v10
@@ -1,5 +1,5 @@
 ## Calculating a full space (get_space)
-When one plots a full space, each dimension gives possible values of the normalized rate constants. Then, ‘par’ must specify which rate constants are used. This is done using the field ‘par.rates’, and should be given as a cell of strings. Each string is of the form ‘experiment type’ ‘experiment index’, for example ‘R11’ would specify the first *R*₁ experiment (the first row of the ‘rates.R1’ field), or ‘R1p3’ would specify the third *R*1_*ρ* experiment. Then, this entry might look like
+When one plots a full space, each dimension gives possible values of the normalized rate constants. Then, ‘par’ must specify which rate constants are used. This is done using the field ‘par.rates’, and should be given as a cell of strings. Each string is of the form ‘experiment type’ ‘experiment index’, for example ‘R11’ would specify the first *R*₁ experiment (the first row of the ‘rates.R1’ field), or ‘R1p3’ would specify the third *R*_1*ρ* experiment. Then, this entry might look like

     par.rates={‘R11’,’R12’,’NOE1’};

FullSpace modified by A. Smith

A. Smith — Tue, 07 Nov 2017 14:17:02 -0000

--- v8
+++ v9
@@ -9,7 +9,7 @@

 If the standard deviation of an experiment was provided in the [info](/p/difrate/wiki/ExpSet/) variable before rate constant calculation, then we use a more general definition for the rate fraction:

-**R**_*ζ*^(*θ,S*)*R_ζ*^(*θ,S*)/*c_{ζ*
+**R**_*ζ*^(*θ,S*) = *R_ζ*^(*θ,S*) / *c_{ζ*

 where *c_ζ* is set to the standard deviation, otherwise it is given by the maximum of that rate constant. Alternatively, *c_ζ* may be user specified in the ‘par.norm’ field, which overrides the other two cases.}}

FullSpace modified by A. Smith

A. Smith — Tue, 07 Nov 2017 14:16:43 -0000

--- v7
+++ v8
@@ -9,7 +9,7 @@

 If the standard deviation of an experiment was provided in the [info](/p/difrate/wiki/ExpSet/) variable before rate constant calculation, then we use a more general definition for the rate fraction:

-*R_ζ*^(*θ,S*)/*c_{ζ*
+**R**_*ζ*^(*θ,S*)*R_ζ*^(*θ,S*)/*c_{ζ*

 where *c_ζ* is set to the standard deviation, otherwise it is given by the maximum of that rate constant. Alternatively, *c_ζ* may be user specified in the ‘par.norm’ field, which overrides the other two cases.}}

FullSpace modified by A. Smith

A. Smith — Tue, 07 Nov 2017 14:15:56 -0000

--- v6
+++ v7
@@ -9,7 +9,7 @@

 If the standard deviation of an experiment was provided in the [info](/p/difrate/wiki/ExpSet/) variable before rate constant calculation, then we use a more general definition for the rate fraction:

-*R_ζ^(*θ,S*)/c_{ζ*
+*R_ζ*^(*θ,S*)/*c_{ζ*

 where *c_ζ* is set to the standard deviation, otherwise it is given by the maximum of that rate constant. Alternatively, *c_ζ* may be user specified in the ‘par.norm’ field, which overrides the other two cases.}}

FullSpace modified by A. Smith

A. Smith — Tue, 07 Nov 2017 14:15:09 -0000

--- v5
+++ v6
@@ -9,7 +9,7 @@

 If the standard deviation of an experiment was provided in the [info](/p/difrate/wiki/ExpSet/) variable before rate constant calculation, then we use a more general definition for the rate fraction:

-*R_ζ/c_{ζ*
+*R_ζ^(*θ,S*)/c_{ζ*

 where *c_ζ* is set to the standard deviation, otherwise it is given by the maximum of that rate constant. Alternatively, *c_ζ* may be user specified in the ‘par.norm’ field, which overrides the other two cases.}}

FullSpace modified by A. Smith

A. Smith — Mon, 06 Nov 2017 20:09:48 -0000

--- v4
+++ v5
@@ -13,4 +13,5 @@

 where *c_ζ* is set to the standard deviation, otherwise it is given by the maximum of that rate constant. Alternatively, *c_ζ* may be user specified in the ‘par.norm’ field, which overrides the other two cases.

-    par.norm
+    par.norm=[1 1 1]
+Note that 'par.norm' needs one entry per dimension.

FullSpace modified by A. Smith

A. Smith — Mon, 06 Nov 2017 20:08:59 -0000

--- v3
+++ v4
@@ -10,3 +10,7 @@
 If the standard deviation of an experiment was provided in the [info](/p/difrate/wiki/ExpSet/) variable before rate constant calculation, then we use a more general definition for the rate fraction:

 *R_ζ/c_{ζ*
+
+where *c_ζ* is set to the standard deviation, otherwise it is given by the maximum of that rate constant. Alternatively, *c_ζ* may be user specified in the ‘par.norm’ field, which overrides the other two cases.
+
+    par.norm}

FullSpace modified by A. Smith

A. Smith — Mon, 06 Nov 2017 20:07:15 -0000

--- v2
+++ v3
@@ -7,4 +7,6 @@

     par.rates=[‘p1’,’p2’,’p3’];

-If the standard deviation of an experiment was provided in the ‘info’ variable before rate constant calculation (see section III.C), then we use a more general definition for the rate fraction,
+If the standard deviation of an experiment was provided in the [info](/p/difrate/wiki/ExpSet/) variable before rate constant calculation, then we use a more general definition for the rate fraction:
+
+*R_ζ/c_ζ*

FullSpace modified by A. Smith

A. Smith — Mon, 06 Nov 2017 20:05:34 -0000

--- v1
+++ v2
@@ -2,3 +2,9 @@
 When one plots a full space, each dimension gives possible values of the normalized rate constants. Then, ‘par’ must specify which rate constants are used. This is done using the field ‘par.rates’, and should be given as a cell of strings. Each string is of the form ‘experiment type’ ‘experiment index’, for example ‘R11’ would specify the first *R*₁ experiment (the first row of the ‘rates.R1’ field), or ‘R1p3’ would specify the third *R*1_*ρ* experiment. Then, this entry might look like

     par.rates={‘R11’,’R12’,’NOE1’};
+    
+Note that if one plots detector sensitivities, then the entries are abbreviated as ‘p1’, ’p2’, etc.
+
+    par.rates=[‘p1’,’p2’,’p3’];
+    
+If the standard deviation of an experiment was provided in the ‘info’ variable before rate constant calculation (see section III.C), then we use a more general definition for the rate fraction,

FullSpace modified by A. Smith

A. Smith — Mon, 06 Nov 2017 20:01:39 -0000

Calculating a full space (get_space)

When one plots a full space, each dimension gives possible values of the normalized rate constants. Then, ‘par’ must specify which rate constants are used. This is done using the field ‘par.rates’, and should be given as a cell of strings. Each string is of the form ‘experiment type’ ‘experiment index’, for example ‘R11’ would specify the first R₁ experiment (the first row of the ‘rates.R1’ field), or ‘R1p3’ would specify the third R1_ρ experiment. Then, this entry might look like

par.rates={‘R11’,’R12’,’NOE1’};