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Update analytic.py: raw string invalid escape sequences #105

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36 changes: 18 additions & 18 deletions EoN/analytic.py
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Original file line number Diff line number Diff line change
Expand Up @@ -485,7 +485,7 @@ def _dSIS_individual_based_(Y, t, G, nodelist, trans_rate_fxn, rec_rate_fxn):

def _dSIR_individual_based_(V, t, G, nodelist, index_of_node, trans_rate_fxn,
rec_rate_fxn):
''' <\dot{X}_i> = - tau sum_j g_{ij} <Xi><Yj>
r''' <\dot{X}_i> = - tau sum_j g_{ij} <Xi><Yj>
<\dot{Y}_i> = tau sum_j g_{ij} <Xi><Yj> - gamma_i <Y_i>
Z_i = 1-X_i-Y_i
'''
Expand Down Expand Up @@ -513,7 +513,7 @@ def SIS_individual_based(G, tau, gamma, rho = None, Y0=None, nodelist = None, tm
tmax = 100, tcount = 1001, transmission_weight=None,
recovery_weight=None, return_full_data = False):
#tested in test_SIS_individual_based
'''Encodes System (3.7) of Kiss, Miller, & Simon. Please cite the
r'''Encodes System (3.7) of Kiss, Miller, & Simon. Please cite the
book if using this algorithm.

See also:
Expand Down Expand Up @@ -770,7 +770,7 @@ def SIS_individual_based_pure_IC(G, tau, gamma, initial_infecteds, nodelist = No
transmission_weight=None,
recovery_weight=None,
return_full_data = False):
'''Encodes System (3.7) of Kiss, Miller, & Simon. Please cite the
r'''Encodes System (3.7) of Kiss, Miller, & Simon. Please cite the
book if using this algorithm.

The difference between this and SIS_individual_based is that this
Expand Down Expand Up @@ -858,7 +858,7 @@ def SIR_individual_based_pure_IC(G, tau, gamma, initial_infecteds,
transmission_weight=None,
recovery_weight=None,
return_full_data = False):
'''Encodes System (3.30) of Kiss, Miller, & Simon. Please cite the
r'''Encodes System (3.30) of Kiss, Miller, & Simon. Please cite the
book if using this algorithm.

The difference between this and SIR_individual_based is that this
Expand Down Expand Up @@ -936,7 +936,7 @@ def SIR_individual_based_pure_IC(G, tau, gamma, initial_infecteds,
######## PAIR BASED

def _dSIS_pair_based_(V, t, G, nodelist, index_of_node, trans_rate_fxn, rec_rate_fxn):
'''
r'''
<\dot{Y}_i> = tau \sum_j g_{ij} <XiYj> - gamma_i <Yi>
<\dot{XY}_ij> = tau sum_{k \neq i} g_{jk} <XiXj><XjYk>/<Xj>
- tau sum_{k neq j} g_{ik} <YkXi><XiYj>/<Xi>
Expand Down Expand Up @@ -1028,7 +1028,7 @@ def _dSIS_pair_based_(V, t, G, nodelist, index_of_node, trans_rate_fxn, rec_rate
return dV

def _dSIR_pair_based_(V, t, G, nodelist, index_of_node, trans_rate_fxn, rec_rate_fxn):
'''
r'''
<\dot{X}_i> = -tau sum_j g_{ij} <XiYj>
<\dot{Y}_i> = tau \sum_j g_{ij} <XiYj> - gamma_i <Y_i>
<\dot{XY}_ij> = tau sum_{k \neq i} g_{jk} <XiXj><XjYk>/<Xj>
Expand Down Expand Up @@ -1702,7 +1702,7 @@ def _dSIR_homogeneous_meanfield_(X, t, n_over_N, tau, gamma):

def SIS_homogeneous_meanfield(S0, I0, n, tau, gamma, tmin=0, tmax=100,
tcount=1001):
'''Encodes System (4.8) of Kiss, Miller, & Simon. Please cite the
r'''Encodes System (4.8) of Kiss, Miller, & Simon. Please cite the
book if using this algorithm.

In the text this is often referred to as the
Expand Down Expand Up @@ -1761,7 +1761,7 @@ def SIS_homogeneous_meanfield(S0, I0, n, tau, gamma, tmin=0, tmax=100,

def SIR_homogeneous_meanfield(S0, I0, R0, n, tau, gamma, tmin=0, tmax=100,
tcount=1001):
'''Encodes System (4.9) of Kiss, Miller, & Simon. Please cite the
r'''Encodes System (4.9) of Kiss, Miller, & Simon. Please cite the
book if using this algorithm.

In the text this is often referred to as the
Expand Down Expand Up @@ -2050,7 +2050,7 @@ def SIS_homogeneous_pairwise(S0, I0, SI0, SS0, n, tau, gamma, tmin = 0,
def SIR_homogeneous_pairwise(S0, I0, R0, SI0, SS0, n, tau, gamma, tmin = 0,
tmax=100, tcount=1001,
return_full_data=False):
'''Encodes System (4.11) of Kiss, Miller, & Simon. Please cite the
r'''Encodes System (4.11) of Kiss, Miller, & Simon. Please cite the
book if using this algorithm.

In the text this is often referred to as the
Expand Down Expand Up @@ -2356,7 +2356,7 @@ def _dSIR_heterogeneous_meanfield_(X, t, S0, Nk, tau, gamma):

def SIS_heterogeneous_meanfield(Sk0, Ik0, tau, gamma, tmin = 0, tmax=100,
tcount=1001, return_full_data=False):
'''Encodes System (5.10) of Kiss, Miller, & Simon. Please cite the
r'''Encodes System (5.10) of Kiss, Miller, & Simon. Please cite the
book if using this algorithm.

In the text this is often referred to as the
Expand Down Expand Up @@ -2450,7 +2450,7 @@ def SIS_heterogeneous_meanfield(Sk0, Ik0, tau, gamma, tmin = 0, tmax=100,

def SIR_heterogeneous_meanfield(Sk0, Ik0, Rk0, tau, gamma, tmin = 0, tmax=100,
tcount=1001, return_full_data=False):
'''
r'''
Encodes System (5.11) of Kiss, Miller, & Simon. Please cite the
book if using this algorithm.

Expand Down Expand Up @@ -2671,7 +2671,7 @@ def SIR_heterogeneous_meanfield_from_graph(G, tau, gamma, initial_infecteds=Non

####### HETEROGENEOUS PAIRWISE
def _dSIS_heterogeneous_pairwise_(X, t, Nk, NkNl, tau, gamma, Ks):
'''
r'''
Gives the derivatives


Expand Down Expand Up @@ -2939,7 +2939,7 @@ def SIS_heterogeneous_pairwise(Sk0, Ik0, SkSl0, SkIl0, IkIl0, tau, gamma,
def SIR_heterogeneous_pairwise(Sk0, Ik0, Rk0, SkSl0, SkIl0, tau, gamma,
tmin = 0, tmax=100, tcount=1001,
return_full_data=False, Ks = None):
'''Encodes System (5.15) of Kiss, Miller, & Simon. Please cite the
r'''Encodes System (5.15) of Kiss, Miller, & Simon. Please cite the
book if using this algorithm.

In the text this is often referred to as the
Expand Down Expand Up @@ -3556,7 +3556,7 @@ def SIR_compact_pairwise_from_graph(G, tau, gamma, initial_infecteds=None,

def _dSIS_super_compact_pairwise_(X, t, tau, gamma, N, k_ave, ksquare_ave,
kcube_ave):
'''
r'''
[\dot{I}] = tau [SI] - gamma [I]
[\dot{SS}] = 2 gamma [SI] - 2 tau [SI] [SS] Q
[\dot{SI}] = gamma ([II]-[SI]) + tau [SI] ([SS]-[SI])Q - tau [SI]
Expand Down Expand Up @@ -3676,7 +3676,7 @@ def SIR_super_compact_pairwise(R0, SS0, SI0, N, tau, gamma, psihat,
psihatPrime, psihatDPrime, tmin = 0,
tmax = 100, tcount = 1001,
return_full_data = False):
'''
r'''
Encodes system (5.22) of Kiss, Miller, & Simon. Please cite the
book if using this algorithm.

Expand Down Expand Up @@ -3881,7 +3881,7 @@ def psihatDPrime(x):


def _dSIS_effective_degree_(X, t, original_shape, tau, gamma):
'''
r'''
\dot{S}_{s,i} = - tau i S_{s,i} + gamma*I_{s,i}
+ gamma((i+1)S_{s-1,i+1}-iS_{s,i})
+ tau[ISS]((s+1)S_{s+1,i-1} - sS_{s,i})/[SS]
Expand Down Expand Up @@ -4054,7 +4054,7 @@ def SIS_effective_degree(Ssi0, Isi0, tau, gamma, tmin = 0, tmax=100,

def SIR_effective_degree(S_si0, I0, R0, tau, gamma, tmin=0, tmax=100,
tcount=1001, return_full_data=False):
'''Encodes system (5.38) of Kiss, Miller, & Simon. Please cite the
r'''Encodes system (5.38) of Kiss, Miller, & Simon. Please cite the
book if using this algorithm.

\dot{S}_{s,i} = - tau i S_{s,i} + gamma((i+1)S_{s,i+1} - i S_{s,i})
Expand Down Expand Up @@ -4360,7 +4360,7 @@ def _dSIR_compact_effective_degree_(X, t, N, tau, gamma):
def SIR_compact_effective_degree(Skappa0, I0, R0, SI0, tau, gamma, tmin=0,
tmax=100, tcount=1001,
return_full_data=False):
'''
r'''
Encodes system (5.43) of Kiss, Miller, & Simon. Please cite the
book if using this algorithm.

Expand Down