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test_gp.R
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test_gp.R
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# simulate GP ideal and fit it
require(rstan)
require(dplyr)
require(ggplot2)
require(forcats)
# classic ARMA stan model:
num_person <- 25
num_bills <- 200
alpha_int <- rnorm(num_person)
sigma <- 0.1
adj_in <- runif(num_person,-.8,.8)
t <- 100
# simulate the GP
alpha_true <- runif(n = num_person,2,3)
rho_true <- runif(n=num_person,2.5,5.5)
sigma_true <- runif(n=num_person,0.5,3)
N_total = num_person
x_total <- 20 * (0:(t - 1)) / (t - 1) - 10
simu_data <- list(alpha=alpha_true, rho=rho_true, sigma=sigma_true,
N=N_total, x=x_total, T=t)
sim_gauss <- "data {
int<lower=1> N;
int<lower=1> T;
real x[T];
real<lower=0> rho[N];
real<lower=0> alpha[N];
real<lower=0> sigma[N];
}
transformed data {
//create one covariance matrix for each legislator
matrix[T, T] cov[N];
matrix[T, T] L_cov[N];
for(n in 1:N) {
cov[n] = cov_exp_quad(x, alpha[n], rho[n])
+ diag_matrix(rep_vector(1e-10, T));
L_cov[n] = cholesky_decompose(cov[n]);
}
}
parameters {}
model {}
generated quantities {
matrix[N,T] f;
for(n in 1:N) {
f[n,] = multi_normal_cholesky_rng(rep_vector(0, T), L_cov[n])';
}
}"
simu_fit <- stan(model_code = sim_gauss, data=simu_data, iter=1,
chains=1, seed=494838, algorithm="Fixed_param")
# more realistic
Y <- rstan::extract(simu_fit)$f[1,,]
require(tidyr)
require(stringr)
y_plot <- as_data_frame(Y) %>% mutate(person=1:n()) %>%
gather(key=time,value=estimate,-person) %>%
mutate(time=as.numeric(str_extract(time,'[0-9]+')))
y_plot %>%
ggplot(aes(y=estimate,x=time)) +
geom_line(aes(group=person),alpha=0.5) +
theme(panel.grid = element_blank(),
panel.background = element_blank())
# plot data
#relevel to consrain
person_points <- rep(1:num_person,times=num_bills)
bill_points <- rep(1:num_bills,each=num_person)
restrict_high <- sort.int(alpha_int,index.return = T,decreasing = T)$ix[1]
restrict_low <- sort.int(alpha_int,index.return = T,decreasing = F)$ix[1]
# generate time points
time_points <- rep(1:t,each=num_bills/t)
time_points <- time_points[bill_points]
absence_discrim <- rnorm(num_bills)
absence_diff <- rnorm(num_bills)
reg_discrim <- rnorm(num_bills)
reg_diff <- rnorm(num_bills)
pr_absence <- sapply(1:length(person_points),function(n) {
Y[person_points[n],time_points[n]]*absence_discrim[bill_points[n]] - absence_diff[bill_points[n]]
}) %>% plogis()
pr_vote <- sapply(1:length(person_points),function(n) {
Y[person_points[n],time_points[n]]*reg_discrim[bill_points[n]] - reg_diff[bill_points[n]]
}) %>% plogis()
absent <- as.numeric(runif(length(person_points))<pr_absence)
present <- as.numeric(runif(length(person_points))<pr_vote)
#outcome <- ifelse(absent==0,present,3)
outcome <- as.numeric(runif(length(person_points))<pr_vote)
person_points <- factor(person_points)
person_points <- fct_relevel(person_points,as.character(restrict_high),
after=num_person)
# need to adjust for full gaussian process inference.
# only non-missing for now
# now fit a model to the observed series
stan_code <- '
data {
int N;
int L;
int B;
int T;
int ll[N];
int bb[N];
int tt[N];
int outcome[N];
real id_diff;
real id_diff_high;
}
parameters {
vector[L-1] alpha_free;
vector<lower=-0.8,upper=0.8>[L-1] adj_in_free;
vector[L] Y_start;
vector[T-1] Y_var;
vector[B] discrim;
vector[B] diff;
real<lower=0> sigma;
vector[1] high;
vector<lower=-0.8,upper=0.8>[1] adj_high;
}
transformed parameters {
vector[L] alpha;
vector[L] adj_in;
vector[1] low;
vector[L] Y[T];
low = high - id_diff;
alpha=append_row(alpha_free,high);
adj_in=append_row(adj_in_free,adj_high);
for(t in 1:T) {
if(t==1) {
Y[1] = Y_start;
} else {
Y[t] = alpha + adj_in .* Y[t-1] + sigma*Y_var[t-1];
}
}
}
model {
diff ~ normal(0,3);
discrim ~ normal(0,3);
alpha_free ~ normal(0,1);
adj_in_free ~ normal(0,2);
adj_high ~ normal(0,1);
sigma ~ exponential(1/.1);
high ~ normal(id_diff_high,.01);
Y_var ~ normal(0,1);
Y_start ~ normal(0,1);
for(n in 1:N) {
outcome[n] ~ bernoulli_logit(discrim[bb[n]] * (Y[tt[n],ll[n]]) - diff[bb[n]]);
}
}
'
to_stan <- stan_model(model_code = stan_code)
run_ar1 <- sampling(to_stan,data=list(N=length(outcome),
L=nrow(Y),
B=num_bills,
T=t,
ll=as.numeric(person_points),
bb=bill_points,
tt=time_points,
outcome=outcome,
id_diff=sort.int(alpha_int,index.return = T,decreasing = T)$x[1] -
sort.int(alpha_int,index.return = T,decreasing = F)$x[1],
id_diff_high=sort.int(alpha_int,index.return = T,decreasing = T)$x[1]),
chains=4,cores=4)
print(run_ar1)
all_res <- summary(run_ar1)
alpha <- all_res$summary[grepl(x=row.names(all_res$summary),
pattern='alpha\\['),
'mean']
alpha <- alpha[c(1:(restrict_high-1),num_person,(restrict_high):(num_person-1))]
cor(alpha,alpha_int)
adj_in_est <- all_res$summary[grepl(x=row.names(all_res$summary),
pattern='adj_in\\['),
'mean']
adj_in_est <- adj_in_est[c(1:(restrict_high-1),num_person,(restrict_high):(num_person-1))]
cor(adj_in_est,adj_in)
Y_est <- all_res$summary[grepl(x=row.names(all_res$summary),
pattern='Y\\['),
'mean']
cor(Y_est,c(Y[c(1:(restrict_high-1),num_person,(restrict_high):(num_person-1)),]))
# now try a random walk model
alpha_int <- -1.25
sigma <- 0.1
adj_in <- 1
t <- 20
Y <- .gen_ts_data(t=t,
adj_in=adj_in,
alpha_int=alpha_int,
sigma=sigma,
init_sides=0)
to_stan <- stan_model(model_code = stan_code)
run_rw <- sampling(to_stan,data=list(N=length(Y$t_11),
Y=Y$t_11))