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Combinatorics navigation #7

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844a135
commit for pr
hyunjimoon Jan 7, 2022
dbd92d5
Merge branch 'master' into combinatorics
Dashadower Jan 9, 2022
1ae4889
Find max hierarchy models for each subtree
Dashadower Jan 13, 2022
7cc22e8
Update n(signature)=1 case
Dashadower Jan 13, 2022
70233bd
Update highest model command and add apex search
Dashadower Jan 18, 2022
73a450d
Add chain search
Dashadower Jan 21, 2022
67fedf0
Update chain search
Dashadower Jan 21, 2022
80025a9
Update chain search code
Dashadower Jan 21, 2022
8733124
update search and add model df
Dashadower Jan 28, 2022
e80399d
Create model dataframe module and birthday model df
Dashadower Jan 30, 2022
d365077
update typing
Dashadower Jan 30, 2022
f65f1bc
Move files to directory, create mstan inferface and bayesian probabil…
Dashadower Jan 31, 2022
7b0577c
Update probability search and add score based algorithm
Dashadower Feb 4, 2022
883178b
Update bayesian probabilistic search to include plots
Dashadower Feb 5, 2022
3796258
remove pyc
Dashadower Feb 5, 2022
a76d53b
Upload full birthday DF
Dashadower Feb 13, 2022
ef62161
Remove redundant csv
Dashadower Feb 13, 2022
827e5af
full elpd for birthday
Dashadower Feb 13, 2022
9f514a4
Add roach model, score search, and notebook template
Dashadower Feb 15, 2022
64587d8
Upload roach csv
Dashadower Feb 16, 2022
3eacced
Update prob search
Dashadower Feb 18, 2022
876b4b4
Merge remote-tracking branch 'origin/master' into combinatorics
Dashadower Feb 18, 2022
72fdd62
Update notebook
Dashadower Feb 22, 2022
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Update chain algorithms and notebook
Dashadower Feb 22, 2022
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Dashadower Feb 22, 2022
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263 changes: 263 additions & 0 deletions examples/roach/roach.csv
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Open in desktop
Original file line number Diff line number Diff line change
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1 change: 1 addition & 0 deletions examples/roach/roach.json
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{"y":[153,127,7,7,0,0,73,24,2,2,0,21,0,179,136,104,2,5,1,203,32,1,135,59,29,120,44,1,2,193,13,37,2,0,3,0,0,15,11,19,0,19,4,122,48,0,0,3,0,9,0,0,0,12,0,357,11,60,0,159,50,48,178,4,6,0,33,127,4,63,88,5,0,0,62,4,150,38,0,3,1,14,77,42,21,1,45,0,0,0,0,0,183,28,49,1,0,0,3,0,0,0,0,18,0,0,5,0,19,5,0,27,0,0,77,1,3,2,0,0,22,102,0,0,0,0,0,0,0,4,12,2,0,0,1,0,40,0,1,2,27,0,2,0,0,0,0,3,1,20,0,0,0,0,0,0,0,0,0,53,69,15,0,2,4,6,8,0,0,0,18,38,0,2,18,34,1,109,5,15,0,64,0,1,0,1,3,5,7,18,1,0,0,3,3,0,19,0,8,26,50,15,0,19,5,17,121,1,0,0,0,0,4,1,14,1,25,0,14,0,59,243,80,69,14,9,38,37,48,293,7,10,19,24,91,1,0,0,0,0,148,3,26,12,77,0,7,0,1,0,17,0,7,11,6,50,1,0,0,0,171,8],"roach1":[308,331.25,1.67,3,2,0,70,64.56,1,14,138.25,16,97,98,44,450,36.67,75,2,342.5,22.5,4,94,132.13,80,95,34.13,19,25,57.5,3.11,10.5,47,2.63,204,0,0,246.25,76.22,15,14.88,51,15,52.5,13.75,1.17,1,2,0,2,2,30,7,18,2,266,174,252,0.88,372.5,42,19,263,34,1.75,213.5,13.13,154,21,220,38.32,352.5,7,4,59.5,7.5,112.88,172,13,18,0,27,148,32,28,0,28,0,14,5,0,104,27,132,258,1,2,6,3,3,0,0,0,1.25,0,16,68,1,18,123.67,2,82.5,0,1.25,171,91.88,5,7,0,4,53.75,138.06,1,1.25,28,15,0.88,0,33,136.25,127.5,2,2,0,3,46,68,0,49,27.13,45.5,0,4,0,1,0,0,10.5,0,3,0,0,0,3.75,0,0,0,0.88,2,81,31,10,10.23,0,13,1,33.25,0,53,5,157,23.33,6,10,100,55,0,16.25,7.78,53,2,73,0,0,0,3.18,5,3,0,10,1,0,1,12,17,16,2.5,0,21.88,173,111,35,0,3,2.1,0,49,1.25,1,1,0,0,54,4.2,51.25,30,196,0,2,1.5,96.25,241.5,140,18,3,0.54,82,19,18.75,51,0,1,0,5.44,0,3,0,0,0,0,28.75,0,3,2,135,0,68.25,1,0,0,0,1,1,2.5,51.25,13.13,0,0,0,0,0,0],"treatment":[1,1,1,1,1,1,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0,0,1,1,1,1,1,0,1,1,1,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],"senior":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1],"exposure2":[0.8,0.6,1,1,1.1429,1,0.8,1.1429,1,1.1429,1,1,1,0.8,1,0.8,0.8,1,1,1,1,1,1,0.8571,1,1,0.8,1,1,1,1,1,1,1,1,1,1,0.8,1.5714,1.4286,1,1,1,0.8,1,1,1,1,1,1,1.1429,1.1429,1,1,0.8,1,0.9143,1,1.2857,1,1,0.7714,1,1.4286,1,0.7714,1,1,1,1,1,0.6,1,1,1,1,1.2857,1,1,1,1,1,1,1.1429,1,1,1,0.8,0.8,1,1,0.6857,1,1,1,1,1,1,0.8,0.8571,1,1,1,1,1,1,0.4,0.8,1.1429,1,0.8,1,0.2,1,1,1,1,1,1,1,1,1.1429,1.1429,1,0.8,1,0.8,1,1,4.2857,0.8,0.8,0.8,1,1,1.2857,1,1,1,1,1,0.4571,1,2.4286,1.4286,1,1,1.1429,1,1.1429,1,1,1,0.8,1.1429,1,0.8,1.5714,1,1.1429,2.2857,1,0.5714,0.8,0.8571,0.8,0.8571,2.2857,0.8,1,0.8571,1,1.0286,0.6,0.8571,1,0.8,1,1.4857,1,1,1,0.8,0.8,1,1,0.8571,0.8,1,0.8,1,1,0.8,1,1,1,1.4286,1.7143,0.7714,0.8,1,1.8571,1,1,1,1,1,1,0.8,1,1,2.2857,0.8,1.4286,1.0286,1.7143,1.1429,1.1429,1,1,1.1429,0.8,1.4286,0.9143,1.1429,1.2857,0.6,1,0.8,1.1429,1,1.4286,1,1,1,1,1,1,1,1,1.1429,0.8571,1,1,1,1,1,1,1,0.6,1.0286,1,1,0.6857,0.8,1,0.8,1.4857,1,1,1,1],"N":[262]}
120 changes: 120 additions & 0 deletions examples/roach/roach.m.stan
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data {
# y roach1 treatment senior exposure2
int N;
int y[N];
real roach1[N];
int treatment[N];
int senior[N];
real exposure2[N];
}

transformed data {
vector[N] roach1_vec = to_vector(roach1);
#roach1_vec = roach1_vec ./ 100
vector[N] treatment_vec = to_vector(treatment);
vector[N] senior_vec = to_vector(senior);
vector[N] exposure2_vec = to_vector(exposure2);
}

model {
y ~ Regression();
}

module "glm" Regression() {
transformed parameters {
vector[N] offset = OffsetType();
vector[N] mu = Roach() + Treatment() + Senior();
}
Likelihood();
}

module "Poisson" Likelihood() {
generated quantities {
vector[N] log_lik;
for (n in 1:N) log_lik[n] = poisson_lpmf(y[n] | exp(mu + RandomEffects() + offset));
}
y ~ poisson(exp(mu + RandomEffects() + offset));
}

module "NegBinomial" Likelihood() {
parameters {
real<lower=0> phi;
}
generated quantities {
vector[N] log_lik;
for (n in 1:N) log_lik[n] = neg_binomial_2_log_lpmf(y[n] | mu + offset, phi);

}
PhiPrior();
y ~ neg_binomial_2_log(exp(mu + offset), phi);
}

module "normal" PhiPrior() {
phi ~ normal(0, 3);
}

module "cauchy" PhiPrior() {
phi ~ cauchy(0, 3);
}

module "log" OffsetType() {
return log(exposure2_vec);
}

module "identity" OffsetType() {
return exposure2_vec;
}

module "sqrt" Roach() {
parameters {
real roach_coeff;
}
return roach_coeff * sqrt(roach1_vec);
}

module "identity" Roach() {
parameters {
real roach_coeff;
}
return roach_coeff * roach1_vec;
}

module "no" Roach() {
return rep_vector(0, N);
}

module "yes" Treatment() {
parameters {
real treatment_coeff;
}
return treatment_coeff * treatment_vec;
}

module "no" Treatment() {
return rep_vector(0, N);
}

module "yes" Senior() {
parameters {
real senior_coeff;
}
return senior_coeff * senior_vec;
}

module "no" Senior() {
return rep_vector(0, N);
}

module "yes" RandomEffects() {
parameters {
vector[N] random_effect;
}
model {
random_effect ~ normal(0, 5);
}
return random_effect;
}

module "no" RandomEffects() {
return rep_vector(0, N) ;
}
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