//' @rdname convert
//' @keywords internal manip
// [[Rcpp::export]]
Rcpp::List icd9ShortToPartsCpp(const Rcpp::CharacterVector icd9Short, const Rcpp::String minorEmpty) {
Rcpp::CharacterVector major(icd9Short.size());
Rcpp::CharacterVector minor(icd9Short.size());
for (int i = 0; i < icd9Short.size(); ++i) {
Rcpp::String thisShort = icd9Short[i];
if (thisShort == NA_STRING) { // .is_na() is private?
minor[i] = NA_STRING; // I think set_na() might be an alternative.
continue;
}
std::string s(thisShort.get_cstring()); // TODO maybe better to use as?
s = strimCpp(s); // in place or rewrite?
std::string::size_type sz = s.size();
if (icd9IsASingleE(s.c_str())) { // E code
switch (sz) {
case 2:
case 3:
case 4:
major[i] = s.substr(0, sz);
minor[i] = minorEmpty;
break;
case 5:
major[i] = s.substr(0, 4);
minor[i] = s.substr(4, 1);
break;
default:
major[i] = NA_STRING;
minor[i] = NA_STRING;
continue;
}
} else { // not an E code
switch (sz) {
case 1:
case 2:
case 3:
major[i] = s.substr(0, sz);
minor[minorEmpty];
continue;
case 4:
case 5:
major[i] = s.substr(0, 3);
minor[i] = s.substr(3, sz - 3);
continue;
default:
major[i] = NA_STRING;
minor[i] = NA_STRING;
continue;
}
}
} // for
return icd9MajMinToParts(icd9AddLeadingZeroesMajor(major), minor);
}
//' @rdname convert
//' @export
// [[Rcpp::export]]
Rcpp::CharacterVector icd9DecimalToShort(
const Rcpp::CharacterVector icd9Decimal) {
Rcpp::CharacterVector out = clone(icd9Decimal); // clone instead of pushing back thousands of times
size_t ilen = icd9Decimal.length();
if (ilen == 0)
return out;
for (size_t i = 0; i != ilen; ++i) {
Rcpp::String strna = icd9Decimal[i]; // need to copy here? does it copy?
if (strna == NA_STRING || strna == "")
continue;
// TODO: Rcpp::String doesn't implement many functions, so using STL. A FAST way
// might be to use Rcpp::String's function get_cstring, and recode the trim
// functions to take const char *. This would avoid the type change AND be
// faster trimming.
const char * thiscode_cstr = strna.get_cstring();
std::string thiscode(thiscode_cstr);
thiscode = trimLeftCpp(thiscode);
// TODO consider rejecting grossly invalid codes as NA:
std::size_t pos = thiscode.find_first_of(".");
if (pos != std::string::npos) {
#ifdef ICD9_DEBUG_TRACE
Rcpp::Rcout << "found .\n";
#endif
// now we assume that the major is snug against the left side, so we can add zero padding
thiscode.erase(pos, 1); // remove the decimal point
// could do fewer tests on the code by doing this last, but most codes are not V or E...
if (pos > 0 && pos < 4 && !icd9IsASingleVE(thiscode_cstr)) {
#ifdef ICD9_DEBUG_TRACE
Rcpp::Rcout << "found numeric\n";
#endif
thiscode.insert(0, 3 - pos, '0');
} else if (pos == 2 && icd9IsASingleV(thiscode_cstr)) {
#ifdef ICD9_DEBUG_TRACE
Rcpp::Rcout << "found V\n";
#endif
thiscode.insert(1, 1, '0');
out[i] = thiscode;
} else if ((pos == 2 || pos == 3) && icd9IsASingleE(thiscode_cstr)) {
#ifdef ICD9_DEBUG_TRACE
Rcpp::Rcout << "found E\n";
#endif
thiscode.insert(1, 4 - pos, '0');
}
// otherwise leave the code alone
out[i] = thiscode;
} else {
out[i] = Rcpp::String(icd9AddLeadingZeroesMajorSingleStd(thiscode));
}
}
return out;
}
// [[Rcpp::export]]
bool guessShortPlusFactorCpp(SEXP x_, int n) {
Rcpp::CharacterVector x;
switch(TYPEOF(x_)) {
case STRSXP: {
x = Rcpp::as<Rcpp::CharacterVector>(x_);
break;
}
case INTSXP: {
if (Rf_isFactor(x_))
x = Rf_getAttrib(x_, R_LevelsSymbol);
break;
}
case LGLSXP: {
// we will accept all logical values, if all are NA, which defauts to
// logical unless otherwise specified. And we obviously don't know whether
// these NAs would have been short or long, just default to short.
Rcpp::LogicalVector xl = Rcpp::LogicalVector(x_);
if (Rcpp::all(is_na(xl)))
return true;
// don't break, because if there were non-NA logicals, this is an error
}
default: {
Rcpp::stop("Character vectors and factors are accepted");
}
}
n = std::min((int)x.length(), n);
const char * b;
const char * ob;
Rcpp::String bs;
for (R_xlen_t i = 0; i != n; ++i) {
bs = x[i];
b = bs.get_cstring();
ob = b;
while (*b) {
if (*b == '.') return false;
++b;
}
// stop when we first get a five digit code. There are four digit major E codes.
if ((b - ob) == 5) return true;
}
return true;
}
// [[Rcpp::export]]
Rcpp::String icd9AddLeadingZeroesMajorSingle(Rcpp::String major) {
if (major == NA_STRING) {
return (NA_STRING);
}
std::string m(major);
if (!icd9IsASingleVE(major.get_cstring())) {
switch (strlen(major.get_cstring())) {
case 0:
return (NA_STRING);
case 1:
return ("00" + m);
case 2:
return ("0" + m);
case 3:
return (m);
}
} else {
switch (strlen(major.get_cstring())) {
case 1:
return (NA_STRING);
case 2:
if (icd9IsASingleV(m.c_str())) {
m.insert(1, "0");
return (m);
} else {
m.insert(1, "00");
return (m);
}
case 3:
if (icd9IsASingleV(m.c_str())) {
return (m);
} else {
m.insert(1, "0");
return (m);
}
case 4:
if (icd9IsASingleE(m.c_str()))
return (m);
}
}
return NA_STRING;
}
// [[Rcpp::export]]
Rcpp::CharacterVector icd9MajMinToCode(const Rcpp::CharacterVector major,
const Rcpp::CharacterVector minor, bool isShort) {
#ifdef ICD9_DEBUG_TRACE
Rcpp::Rcout << "icd9MajMinToCode: major.size() = " << major.size()
<< " and minor.size() = " << minor.size() << "\n";
#endif
if (major.size() != minor.size())
Rcpp::stop("major and minor lengths differ");
#ifdef ICD9_DEBUG_TRACE
Rcpp::Rcout << "major and minor are the same?\n";
#endif
Rcpp::CharacterVector out; // wish I could reserve space for this
Rcpp::CharacterVector::const_iterator j = major.begin();
Rcpp::CharacterVector::const_iterator n = minor.begin();
for (; j != major.end() && n != minor.end(); ++j, ++n) {
Rcpp::String mjrelem = *j;
if (mjrelem == NA_STRING) {
out.push_back(NA_STRING);
continue;
}
// work around Rcpp bug with push_front: convert to string just for this
// TODO: try to do this with C string instead
const char* smj_c = mjrelem.get_cstring();
std::string smj = std::string(smj_c);
switch (strlen(smj_c)) {
case 0:
out.push_back(NA_STRING);
continue;
case 1:
if (!icd9IsASingleVE(smj_c)) {
smj.insert(0, "00");
}
break;
case 2:
if (!icd9IsASingleVE(smj_c)) {
smj.insert(0, "0");
} else {
smj.insert(1, "0");
}
// default: // major is 3 (or more) chars already
}
Rcpp::String mnrelem = *n;
if (mnrelem == NA_STRING) {
//out.push_back(mjrelem);
out.push_back(smj);
continue;
}
// this can probably be done more quickly:
//std::string smj(mjrelem);
if (!isShort && mnrelem != "") {
smj.append(".");
}
smj.append(mnrelem);
out.push_back(smj);
}
// ?slow step somewhere around here, with use of Rcpp::String, maybe in the wrapping? Maybe in the multiple push_back calls
//return wrap(out);
return out;
}