const char *memcached_load(const char *library_name){
if(!memcached_linked){
memcached_linked=true;
memcached_status=dlink(library_name);
}
return memcached_status;
}
void _check_prerequisits()
{
_check_prereqs_xplatform();
uid_t euid = geteuid();
if (euid == 0)
fatal("Please run as a standard user, not as root.");
#if defined(__APPLE__)
// Docker Community Edition application on Mac does not require groups as below
#else
std::string user = getUSER();
if (0 != bashcommand("groups $USER | grep docker"))
fatal("Please add the current user to the docker group. As root: " + utils::kCODE_S + "adduser " + user + " docker" + utils::kCODE_E);
if (0 != bashcommand("groups | grep docker"))
fatal(user + " hasn't picked up group docker yet. Log out then in again, or run " + utils::kCODE_S + "exec su -l " + user + utils::kCODE_E);
#endif
if (!commandexists("docker"))
fatal("Please install Docker before using dRunner.\n(e.g. use https://raw.githubusercontent.com/j842/scripts/master/install_docker.sh )");
if (!commandexists("curl"))
fatal("Please install curl before using dRunner.");
// check ~/.drunner/bin is in ~/.profile.
_ensure_line(Poco::Path::home() + ".profile", "PATH=\"$HOME/.drunner/bin:$PATH\"");
// check symbolic link
std::string ddir = Poco::Path::home() + ".drunner";
Poco::File dlink(ddir);
if (dlink.exists())
{
if (dlink.isLink())
dlink.remove();
else
dlink.renameTo(ddir + "09");
}
drunner_assert(!dlink.exists(), ".drunner folder still exists. :/ \n" + ddir);
int r = symlink((ddir + getVersionNice()).c_str(), ddir.c_str());
if (r != 0)
fatal("Failed to create symlink at " + ddir);
}
int glm_fit(int family, int link, int N, int M, int S,
const double *y, const double *prior, const double * offset, const double *X,
const int *stratum, int maxit, double conv, int init,
int *rank, double *Xb,
double *fitted, double *resid, double *weights,
double *scale, int *df_resid, double theta) {
const double eta = 1.e-8; /* Singularity threshold */
int i = 0, j=0;
int Nu, dfr, irls;
int empty = 0;
//TO DO
//need to add condition to ensure theta>0
//trim code, remove unneeded if statements
//add way to handle intercept only models well in R entry
/* Is iteration necessary? */
irls = ( ((offset) || (M>0)) && !((family==GAUSSIAN) && (link==IDENTITY)));
// if (family == BINOMIAL) cout<<"M "<<M<<endl;
// for (int i = 0; i != 1000; i++) {cout<<i<<"\t"<<prior[i]<<endl;}
if (!init || !irls) {
/* Fit intercept and/or strata part of model */
empty = wcenter(y, N, prior, stratum, S, 0, fitted);
}
Nu = 0;
int invalid = 0;
for (i=0; i<N; i++) {
double mu = fitted[i];
double ri, wi;
double pi = prior? prior[i] : 1.0;
if (!muvalid(family, mu, theta)) {
invalid = 1;
pi = 0.0;
}
if (!(pi)) {wi = ri = 0.0;}
else {
Nu ++;
double Vmu = varfun(family, mu, theta);
if (link == family) {
ri = (y[i] - mu)/Vmu;
wi = pi*Vmu;
}
else {
double D = dlink(link, mu);
ri = D*(y[i] - mu);
wi = pi/(D*D*Vmu);
}
}
weights[i] = wi;
resid[i] = ri;
if (weights[i] <= 0.) weights[i] = 0.;
}
/* If M>0, include covariates */
int x_rank = 0, convg = 0, iter = 0;
if ((M == 0) && !offset) convg = 1;
if (M> 0 || offset) { //maybe also where there is an offset?
convg = 0;
double wss_last = 0.0;
if (irls) {
/* IRLS algorithm */
double *yw = (double *) Calloc(N, double); //working y
while(iter<maxit && !convg) {
for (i=0; i<N; i++) {
yw[i] = resid[i] + linkfun(link, fitted[i]); //current estimate of eta + (y-mu)/gradient
}
if (offset) {for (i=0; i<N; i++) {yw[i] -= offset[i];}}
empty = wcenter(yw, N, weights, stratum, S, 1, resid); //removes the mean from yw
//////////// now it tries to fit the regression line (no intercept) to the residuals
const double *xi = X;
double *xbi = Xb;
x_rank = 0;
for (i=0; i<M; i++, xi+=N) {
double ssx = wssq(xi, N, weights);
wcenter(xi, N, weights, stratum, S, 1, xbi);
double *xbj = Xb;
for (j=0; j<x_rank; j++, xbj+=N) wresid(xbi, N, weights, xbj, xbi);
double ssr = wssq(xbi, N, weights);
if (ssr/ssx > eta) {
wresid(resid, N, weights, xbi, resid); //takes the residuals after fitting the regression line (no intercept) to the mean value per stratum
x_rank++;
xbi+=N;
}
}
double wss=0.0;
Nu = 0;
for (i=0; i<N; i++) {
double D, Vmu, ri, wi;
double mu = invlink(link, yw[i] - resid[i]); //ie. (yw - (yw - mean(yw))) = mean(yw)
if (offset) {mu = invlink(link, yw[i] + offset[i] - resid[i]);}
fitted[i] = mu;
double pi = prior? prior[i] : 1.0;
if (!(pi && (weights[i]>0.0))) {wi = ri = 0.0;} else {
if (!(muvalid(family, mu, theta))) {
if ((family == 4) && (mu > 5.0)) {mu = fitted[i] = 5.0;}
if ((family == 4) && (mu < 0.001)) {mu = fitted[i] = 0.001;}
}
Vmu = varfun(family, mu, theta);
Nu ++;
if (link == family) {
ri = (y[i] - mu)/Vmu;
wi = pi*Vmu;
}
else {
D = dlink(link, mu);
ri = D*(y[i] - mu);
wi = pi/(D*D*Vmu);
}
wss += wi*ri*ri;
weights[i] = wi;
resid[i] = ri;
if (weights[i] <= 0.) weights[i] = 0.;
}
}
convg =/* (family==2) ||*/ (Nu<=0) || (iter && (fabs(wss-wss_last)/wss_last < conv));
wss_last = wss;
iter ++;
}
Free(yw);
} else {
