'.$time_scale_file.' saved
';
mysqli_free_result($time_scale);
$n_int = count($int_name);
$base_ordovician = 488.3;
$study_max = max($int_bottom);
$study_min = min($int_top);
//////////////
//
// Column data saved as columns.csv
//
//////////////
$cols_file = "columns.csv";
$fh = fopen($cols_file, 'w') or die("can't open file");
chmod($cols_file, 0777);
$file_row = "col_id, lat, lng, sheet, col, col_area, project_id\n";
fwrite($fh, $file_row);
$q = "SELECT cols.id, lat, lng, project_id, col_group, col, col_area FROM cols
INNER JOIN col_groups ON col_groups.id=col_group_id
INNER JOIN projects ON projects.id=project_id
WHERE project = 'North America' AND col_group != 'Mexico' AND cols.id NOT IN (34, 111, 139, 218, 586, 587) AND status_code = 'active'"; //echo $q."
";
//(456,443,633,499)
$columns = mysqli_query($connect_macrostrat, $q);
while($row = mysqli_fetch_assoc($columns)) {
$file_row = $row['id'].",".$row['lat'].",".$row['lng'].",".$row['col_group'].",".$row['col'].",".$row['col_area'].",".$row['project_id']."\n";
fwrite($fh, $file_row);
$my_cols[] = $row['id'];
}
fclose($fh);
mysqli_free_result($columns);
echo 'File '.$cols_file.' saved
';
// get column polygons
$poly_file = "column_polygons.csv";
$fh = fopen($poly_file, 'w') or die("can't open file");
chmod($poly_file, 0777);
$file_row = "col_id, lat, lng\n";
fwrite($fh, $file_row);
$q = "SELECT col_id, AsText(col_area) coords FROM col_areas
WHERE col_id IN (".implode(",", $my_cols).")";
$columns = mysqli_query($connect_macrostrat, $q);
while($row = mysqli_fetch_assoc($columns)) {
$my_coord = ltrim($row['coords'], 'POLYGON((');
$my_coord = rtrim($my_coord, '))');
$my_coord = explode(",", $my_coord);
for($i=0; $i'.$poly_file.' saved
';
// get obselete columns to exclude
$obsolete_cols = array();
$q = "SELECT cols.id FROM cols
INNER JOIN col_groups ON col_groups.id=col_group_id
INNER JOIN projects ON projects.id=project_id
WHERE project = 'North America' AND status_code = 'obsolete'"; //echo $q."
";
$columns = mysqli_query($connect_macrostrat, $q);
while($row = mysqli_fetch_assoc($columns)) {
$obsolete_cols[] = $row['id'];
}
mysqli_free_result($columns);
//////////////
//
// get packages
//
//////////////
$counter = 0;
$temp_pkg = split_packages('marine');
// set package crossers
$pkg_file = "ordovician_packages.csv";
$fh = fopen($pkg_file, 'w') or die("can't open file");
chmod($pkg_file, 0777);
$file_row = "package_id, age_bottom, age_top, col_id\n";
fwrite($fh, $file_row);
for($i=0; $i$study_min && $row['top']<$study_max) {
$my_pkg[$counter] = $temp_pkg[$i];
$my_pkg_fo[$counter] = $row['bottom'];
$my_pkg_lo[$counter] = $row['top'];
$my_pkg_n_units[$counter] = $row['n_unit'];
$my_pkg_col_id[$counter] = $row['col_id'];
$temp_units = explode(",",$temp_pkg[$i]);
for($j=0; $j";
$lo_result = mysqli_query($connect_macrostrat, $q);
$lo_row = mysqli_fetch_assoc($lo_result);
$my_temp_lo = $lo_row['LO_h'];
mysqli_free_result($lo_result);
if($my_temp_fo==0) $my_pkg_fo_h[$counter] = $fo_row['age_bottom'];
else $my_pkg_fo_h[$counter] = $fo_row['age_bottom'] - $fo_row['half_duration'];
if($my_temp_lo==0) $my_pkg_lo_h[$counter] = $lo_row['age_top'];
else $my_pkg_lo_h[$counter] = $lo_row['age_top'] + $lo_row['half_duration'];
$file_row=$counter.",".$fo_row['age_bottom'].",".$lo_row['age_top'].",".$row['col_id']."\n";
// $file_row=$counter.",".$my_pkg_fo_h[$counter].",".$my_pkg_lo_h[$counter]."\n";
fwrite($fh, $file_row);
++$counter;
}
// get packages for testing gaps
if(in_array($row['col_id'], $my_cols)===TRUE) {
// get fo_h and lo_h for packages
$q = "SELECT units.id, FO_h, (b.age_bottom-b.age_top)/2 half_duration, b.age_bottom FROM units
INNER JOIN intervals b ON b.id=FO
INNER JOIN intervals t ON t.id=LO
WHERE units.id IN ($temp_pkg[$i])
ORDER BY b.age_bottom DESC, FO_h, t.age_top DESC, field(LO_h, 1,2,3,4,5,6,0)
LIMIT 1";
$fo_result = mysqli_query($connect_macrostrat, $q);
$fo_row = mysqli_fetch_assoc($fo_result);
if($fo_row['FO_h']==0) $my_gap_fo_h[] = $fo_row['age_bottom'];
else $my_gap_fo_h[] = $fo_row['age_bottom']-$fo_row['half_duration'];
if($fo_row['age_bottom']!=$row['bottom']) echo "bad base calc
";
mysqli_free_result($fo_result);
$my_gap_pkg[] = $temp_pkg[$i];
$my_gap_fo[] = $row['bottom'];
$my_gap_col_id[] = $row['col_id'];
}
mysqli_free_result($result);
}
$all_units = implode(",",$my_pkg);
$all_units_array = explode(",", $all_units);
$total_units = implode(",",$my_gap_pkg);
unset($temp_units, $temp_pkg, $counter);
echo "There are ".(count(explode(",",$total_units)))." units.
";
fclose($fh);
echo 'File '.$pkg_file.' saved
';
/*
// calculate package crossers
$crosser_file = 'package_crossers.csv';
$fh = fopen($crosser_file,'w');
chmod($crosser_file, 0666);
fclose($fh);
$file_name_r = 'temp.r';
$fh = fopen($file_name_r, 'w') or die("can't open file");
chmod($file_name_r, 0666);
$r_script = "
source('myFunctions.r')
time.scale <- read.csv(file='$time_scale_file', header=TRUE)
packages <- read.csv(file='$pkg_file', header=TRUE)
cross.temp <- crossers(packages[,2:3], time.scale[,2:3])
write.csv(cbind(time.scale[,c(4,1:3)],cross.temp), file='$crosser_file', quote=FALSE, row.names=FALSE)
";
fwrite($fh, $r_script);
fclose($fh);
$cmd = "echo 'rscript <- \"$file_name_r\"; source(rscript)' | " . "/usr/bin/R --slave 2>&1";
exec($cmd, $r_ran);
if(count($r_ran)>0) {
echo "R (Package Crossers): ";
print_r($r_ran); echo "
";
}
echo 'File '.$crosser_file.' saved
';
//////////////
//
// calculate environmental gaps for every unit
//
//////////////
$env_gap = array();
$env_unit_top = array();
$all_unit_array = explode(",",$all_units);
for($i=0; $i";
$result = mysqli_query($connect_macrostrat, $q);
if(mysqli_num_rows($result)==1) {
$test_unit = mysqli_fetch_assoc($result);
if($test_unit['FO_h'] == 0) {
$gap_top = $test_unit['age_bottom'];
} else {
$gap_top = $test_unit['age_bottom'] - ($test_unit['age_bottom']-$test_unit['bottom_top'])/2;
}
} else {
$gap_top = 0;
}
mysqli_free_result($result);
if(round($gap_bottom,5)==round($gap_top,5)) {
$env_gap[$all_unit_array[$i]]=0;
} else {
$env_gap[$all_unit_array[$i]] = log($gap_bottom-$gap_top);
}
if($gap_bottom<$gap_top) {
echo $focal_unit['id']." (".$test_unit['id']."): ".$gap_bottom." - ".$gap_top." = ".$env_gap[$all_unit_array[$i]]."
";
}
$env_unit_top[$all_unit_array[$i]] = $gap_bottom;
}
// echo "environmental gap:
";print_r($env_gap); echo "
";
//////////////
//
// get duration of gaps above packages
//
//////////////
for($i=0; $i= $my_gap_fo[$j] && $my_gap_fo[$j]>$temp_max) {
$temp_max = $my_gap_fo[$j];
}
if($my_gap_pkg[$j]!=$my_pkg[$i] && $my_pkg_col_id[$i]==$my_gap_col_id[$j] && $my_pkg_lo_h[$i] >= $my_gap_fo_h[$j] && $my_gap_fo_h[$j]>$temp_fo) {
$temp_fo = $my_gap_fo_h[$j];
}
}
if($my_pkg_lo[$i] != $temp_max) {
$my_pkg_gap[$i] = log($my_pkg_lo[$i] - $temp_max);
} else {
$my_pkg_gap[$i] = 0;
}
if(round($my_pkg_lo_h[$i],5) != round($temp_fo,5)) {
$my_pkg_gap2[$i] = log($my_pkg_lo_h[$i] - $temp_fo);
} else {
$my_pkg_gap2[$i] = 0;
}
}
*/
//////////////
//
// get matched ordovician genera and references
//
//////////////
// get all appropriate taxa
$my_genera = array();
$this_genus = array();
$my_genus_age = array();
$my_occurrences = array();
$q = "SELECT occurrences_temp2.taxon_no, genus_name, class, taxon_order, family, min(ta.top_age) pbdb_min,
occurrences_temp2.taxon_environment, occurrences_temp2.locomotion, occurrences_temp2.life_habit, occurrences_temp2.diet1, occurrences_temp2.diet2
FROM occurrences_temp2
INNER JOIN intervals b ON b.id=occurrences_temp2.FO
INNER JOIN intervals t ON t.id=occurrences_temp2.LO
INNER JOIN pbdb.interval_lookup ba ON ba.interval_no=occurrences_temp2.max_interval_no
INNER JOIN pbdb.interval_lookup ta ON ta.interval_no=occurrences_temp2.min_interval_no
LEFT OUTER JOIN pbdb.ecotaph ON ecotaph.taxon_no=occurrences_temp2.taxon_no
LEFT OUTER JOIN pbdb.authorities ON authorities.taxon_no=occurrences_temp2.taxon_no
WHERE occurrences_temp2.unit_id > 0 AND occurrences_temp2.unit_id IN (".$all_units.") AND (occurrences_temp2.extant = 'no' OR occurrences_temp2.extant IS NULL)
AND occurrences_temp2.col_id NOT IN (".implode(",",$obsolete_cols).")
AND ((b.age_bottom > ".$study_min." AND t.age_top < ".$study_max.") OR ((b.age_bottom IS NULL AND t.age_top IS NULL) AND (ba.base_age > ".$study_min." AND ta.top_age < ".$study_max.")))
AND (occurrences_temp2.release_date <= now() OR occurrences_temp2.release_date IS NULL)
AND (form_taxon = 'no' OR form_taxon IS NULL) AND (preservation != 'trace' OR preservation IS NULL)
GROUP BY occurrences_temp2.taxon_no"; //echo $q."
";
$result = mysqli_query($connect_macrostrat, $q);
echo "There are ".mysqli_num_rows($result)." queried genera
";
while($row=mysqli_fetch_assoc($result)) {
$my_genera[] = $row;
$this_genus[] = $row['taxon_no'];
$my_genus_age[$row['taxon_no']]['pbdb_min'] = $row['pbdb_min'];
}
mysqli_free_result($result);
// get global and NoAm ranges of taxa - even outside study interval
$q = "SELECT occurrence_no, taxon_no, ba.base_age, ta.top_age, FO_h, LO_h, unit_id,
b.age_bottom-((b.age_bottom-b.age_top)/2*LEAST(1,FO_h)) bottom, t.age_bottom+((t.age_bottom-t.age_top)/2*LEAST(1,LO_h)) top,
unit_id, col_id, occurrences_temp2.collection_no,
original_taxon_no, original_taxon_rank, paleolat, paleolng
FROM occurrences_temp2
INNER JOIN pbdb.interval_lookup ba ON ba.interval_no=occurrences_temp2.max_interval_no
INNER JOIN pbdb.interval_lookup ta ON ta.interval_no=occurrences_temp2.min_interval_no
LEFT OUTER JOIN intervals b ON b.id=FO
LEFT OUTER JOIN intervals t ON t.id=LO
WHERE taxon_no IN (".implode(",", $this_genus).")
AND (occurrences_temp2.unit_id=0 OR occurrences_temp2.unit_id IN (".$all_units."))
AND (occurrences_temp2.col_id IS NULL OR occurrences_temp2.col_id NOT IN (".implode(",",$obsolete_cols)."))"; //echo $q."
";
$result = mysqli_query($connect_macrostrat, $q);
echo "There are ".mysqli_num_rows($result)." queried occurrences
";
$counter = 0;
$int_occurrences = array();
$int_paleolat = array();
while($row=mysqli_fetch_assoc($result)) {
if($row['unit_id']==0 || in_array($row['unit_id'], $all_units_array)===FALSE) { // not matched to north america
$occurrence_bottom = $row['base_age'];
$occurrence_top = $row['top_age'];
} else {
if($row['base_age']>$row['top'] && $row['top_age']<$row['bottom']) {// pbdb and unit ages overlap: use youngest bottom and oldest top
$occurrence_bottom = min($row['base_age'], $row['bottom']);
$occurrence_top = max($row['top_age'], $row['top']);
} else { // pbdb and unit ages DO NOT overlap: use macrostrat
$occurrence_bottom = $row['bottom'];
$occurrence_top = $row['top'];
}
}
$my_occurrences[] = array(
"occurrence_no" => $row['occurrence_no'],
"taxon_no" => $row['taxon_no'],
"bottom" => $occurrence_bottom,
"top" => $occurrence_top,
"unit_id" => $row['unit_id'],
"col_id" => $row['col_id'],
"collection_no" => $row['collection_no'],
"original_taxon_no" => $row['original_taxon_no'],
"original_taxon_rank" => $row['original_taxon_rank'],
"paleolat" => $row['paleolat'],
"paleolng" => $row['paleolng']
);
// get occurrence interval combinations
for($i=0; $i<$n_int; ++$i) {
if($occurrence_bottom>$int_top[$i] && $occurrence_top<$int_bottom[$i]) $int_occurrences[$i][] = $counter;
if($occurrence_bottom>$int_top[$i] && $occurrence_top<$study_max && is_numeric($row['paleolat'])) $int_paleolat[$i][$row['taxon_no']][] = $row['paleolat'];
}
++$counter;
if(isset($my_genus_age[$row['taxon_no']]['global_max'])===FALSE) $my_genus_age[$row['taxon_no']]['global_max'] = $occurrence_bottom;
else if($my_genus_age[$row['taxon_no']]['global_max'] < $row['base_age']) $my_genus_age[$row['taxon_no']]['global_max'] = $occurrence_bottom;
if(isset($my_genus_age[$row['taxon_no']]['global_min'])===FALSE) $my_genus_age[$row['taxon_no']]['global_min'] = $occurrence_top;
else if($my_genus_age[$row['taxon_no']]['global_min'] > $row['top_age']) $my_genus_age[$row['taxon_no']]['global_min'] = $occurrence_top;
if($row['unit_id']>0 && in_array($row['unit_id'], $all_units_array) && (($row['top'] < 443.7 && $my_genus_age[$row['taxon_no']]['pbdb_min'] < 443.7) || $row['top'] >= 443.7)) {
if(isset($my_genus_age[$row['taxon_no']]['noam_max'])===FALSE) $my_genus_age[$row['taxon_no']]['noam_max'] = $occurrence_bottom;
else if($my_genus_age[$row['taxon_no']]['noam_max'] < $row['base_age']) $my_genus_age[$row['taxon_no']]['noam_max'] = $occurrence_bottom;
if(isset($my_genus_age[$row['taxon_no']]['noam_min'])===FALSE) $my_genus_age[$row['taxon_no']]['noam_min'] = $occurrence_top;
else if($my_genus_age[$row['taxon_no']]['noam_min'] > $row['top_age']) $my_genus_age[$row['taxon_no']]['noam_min'] = $occurrence_top;
}
}
mysqli_free_result($result);
// $pbdb_file = "ordovician_genera.csv";
$pbdb_file = "ordovician_genera_culled.csv";
$fh = fopen($pbdb_file, 'w') or die("can't open file");
chmod($pbdb_file, 0666);
$file_row = "interval_id, interval_name, age_bottom, age_top, taxon_no, genus, class, order, family, life_habit, locomotion, taxon_environment, diet1, diet2, n_species_NoAm, n_species_global, n_collections_NoAm, n_occur_NoAm, global_endemic_to_interval, NoAm_FAD, NoAm_LAD, global_FAD, global_LAD, max_N_paleolat_during_prior, max_S_paleolat_during_prior, n_matched_units_greater_n_45, n_matched_units_greater_s_45, max_great_circle_NoAm, max_great_circle_Global, n_packages_occupied, n_packages_total, n_units_occupied, n_units_total,n_carb_units, n_carb_units_occupied, n_siliciclastic_units, n_siliciclastic_units_occupied, n_truncating_packages_total, n_truncating_packages_occupied, n_env_truncation, n_env_truncation_double, n_units_entirely_within_interval, min_gap, max_gap, mean_gap, median_gap, min_env_gap, max_env_gap, mean_env_gap, median_env_gap, n_env_gap, n_columns_occupied, n_columns_total, n_trunc_columns_occupied\n";
fwrite($fh, $file_row);
$my_collections = array();
for($i=0; $i < 1; ++$i) {
// for($i=0; $i<$n_int; ++$i) {
// get total units and packages
$my_packages = array();
$my_columns = array();
$my_carb = array();
$my_clast = array();
$q = "SELECT units.id, color, col_id FROM units
INNER JOIN intervals b ON b.id=FO
INNER JOIN intervals t ON t.id=LO
WHERE units.id IN (".$all_units.") AND b.age_bottom>$int_top[$i] AND t.age_top<$int_bottom[$i]";
$result = mysqli_query($connect_macrostrat, $q);
while($row = mysqli_fetch_assoc($result)) {
$my_packages[] = $unit_packages[$row['id']];
if(in_array($row['color'], $carb_colors)) $my_carb[] = $row['id'];
if(in_array($row['color'], $clast_colors)) $my_clast[] = $row['id'];
$my_columns[] = $row['col_id'];
}
$n_units_total = mysqli_num_rows($result);
$n_packages_total = count(array_unique($my_packages));
$n_columns_total = count(array_unique($my_columns));
mysqli_free_result($result);
unset($my_packages, $my_columns);
// loop through each package and count truncations
$truncating_packages = array();
$spanning_packages = array();
for($k=0; $k=$int_top[$i]) {
$truncating_packages[] = $k;
// non-truncating packages
} else if($my_pkg_lo[$k]<$int_bottom[$i] && $my_pkg_fo[$k]>$int_top[$i]) {
$spanning_packages[] = $k;
}
}
// loop through each occurrence in this interval and get those that occur in this interval
$interval_genus = array();
for($k=0; $k$int_top[$i]) $global_endemic_to_interval = 1;
else $global_endemic_to_interval = 0;
for($k=0; $k0 && ($my_genus_age[$row['taxon_no']]['pbdb_min'] < 443.7 && $row['top'] < 443.7) || $row['top'] >= 443.7)) {
$global_occurrences[] = $row['occurrence_no'];
$global_collections[] = $row['collection_no'];
if(is_numeric($row['paleolat']) && is_numeric($row['paleolng'])) {
$global_paleolat[] = $row['paleolat'];
$global_paleolng[] = $row['paleolng'];
}
$my_collections[] = $row['collection_no'];
if($row['original_taxon_rank']=='species') $global_species[] = $row['original_taxon_no'];
if($row['unit_id']>0 && in_array($row['unit_id'], $all_units_array)) {
$noam_occurrences[] = $row['occurrence_no'];
$noam_collections[] = $row['collection_no'];
$noam_units[] = $row['unit_id'];
$noam_columns[] = $row['col_id'];
if($row['original_taxon_rank']=='species') $noam_species[] = $row['original_taxon_no'];
$noam_paleolat[] = $row['paleolat'];
$noam_paleolng[] = $row['paleolng'];
if($row['paleolat']>= 45) $matched_unit_n_45[] = $row['unit_id'];
if($row['paleolat']<= -45) $matched_unit_s_45[] = $row['unit_id'];
if(is_numeric($row['paleolat']) && is_numeric($row['paleolng'])) {
$unit_paleolat[$row['unit_id']][] = $row['paleolat']; //echo $row['paleolat']."
";
$unit_paleolng[$row['unit_id']][] = $row['paleolng'];
}
$noam_packages[] = $unit_packages[$row['unit_id']];
}
}
}
$n_occur = count(array_unique($noam_occurrences));
$n_coll = count(array_unique($noam_collections));
$noam_units = array_unique($noam_units);
$n_units = count($noam_units);
if($n_units>0) {
$noam_units = array_combine(range(0,$n_units-1,1), $noam_units);
$n_cols = count(array_unique($noam_columns));
$n_species = count(array_unique($noam_species));
$n_packages = count(array_unique($noam_packages));
// print_r($noam_columns); echo " - $n_cols
";
if(count($my_carb)>0) $n_carb_units_occupied = count(array_unique(array_intersect($my_carb, $noam_units)));
else $n_carb_units_occupied = 0;
if(count($my_clast)>0) $n_siliciclastic_units_occupied = count(array_unique(array_intersect($my_clast, $noam_units)));
$n_siliciclastic_units_occupied = 0;
$n_occur_global = count(array_unique($global_occurrences));
$n_coll_global = count(array_unique($global_collections));
$n_species_global = count(array_unique($global_species));
$n_matched_units_greater_n_45 = count(array_unique($matched_unit_n_45));
$n_matched_units_greater_s_45 = count(array_unique($matched_unit_s_45));
$temp_taxon_no = array_keys($int_paleolat[$i]);
$max_paleolat_N = 'NA';
max_paleolat_S = 'NA';
for($k=0; $k";
}
}
fclose($fh2);
if($n_units>1) {
$file_name_r = 'temp.r';
$fh3 = fopen($file_name_r, 'w') or die("can't open file");
chmod($file_name_r, 0666);
$r_script = "
source('myFunctions.r')
coords <- read.csv(file='$circle_file', header=TRUE)
if(nrow(unique(coords[,1:2]))>1) {
max.dist <- max(great.circle2(coords[,1:2]), na.rm=TRUE)
} else {
max.dist <- 'NA'
}
write.table(max.dist, file='temp_dist.csv', quote=FALSE, row.names=FALSE, col.names=FALSE, sep=',')
";
fwrite($fh3, $r_script);
fclose($fh3);
$cmd = "echo 'rscript <- \"$file_name_r\"; source(rscript)' | " . "/usr/bin/R --slave 2>&1";
exec($cmd, $r_ran);
if(count($r_ran)>0) {
echo "R (Matched great circle): ";
print_r($r_ran); echo "
";
}
$handle = fopen("temp_dist.csv", "r");
while ($row = fgetcsv($handle, 1000, ",")) $max_dist_noam = $row[0];
fclose($handle);
if($max_dist_noam=='NA') {
$handle = fopen($circle_file, "r");
echo $max_dist_noam."
";
while ($file_row = fgetcsv($handle, 1000, ",")) {
print_r($file_row); echo "
";
}
print_r($noam_units);echo "
";
print_r($noam_collections);echo "
";
fclose($handle);
}
} else {
$max_dist_noam='NA';
}
// get global great circle distance
if(count($global_paleolat)>1 && count($global_paleolng)==count($global_paleolat)) {
// set up file for sending to R for great circle analysis
$circle_file = "global_great_circle.csv";
$fh2 = fopen($circle_file, 'w') or die("can't open file");
chmod($circle_file, 0666);
$file_row = "plat, plng\n";
fwrite($fh2, $file_row);
for($k=0; $k&1";
exec($cmd, $r_ran);
if(count($r_ran)>0) {
echo "R (Global great circle): ";
print_r($r_ran); echo "
";
}
$handle = fopen("temp_dist.csv", "r");
while ($row = fgetcsv($handle, 1000, ",")) $max_dist_global = $row[0];
fclose($handle);
} else {
$max_dist_global = 'NA';
}
$n_env_temp = array();
$n_env_temp2 = array();
// get stratigraphic gap duration
if($n_packages>0) {
$pkg_occupied = array_combine(range(0,$n_packages-1), array_unique($noam_packages));
$trunc_temp = array_intersect($truncating_packages, array_unique($noam_packages));
$n_trunc_packages_occupied = count($trunc_temp);
if($n_trunc_packages_occupied>0) {
$trunc_temp = array_combine(range(0,$n_trunc_packages_occupied-1,1), $trunc_temp);
// get n truncating columns
$trunc_temp_columns = array();
for($k=0; $k<$n_trunc_packages_occupied; ++$k) {
$trunc_temp_columns[] = $my_pkg_col_id[$trunc_temp[$k]];
}
$n_trunc_columns_occupied = count(array_unique($trunc_temp_columns));
} else {
$n_trunc_columns_occupied = 0;
}
if($n_trunc_packages_occupied>1) {
$trunc_packages_occupied = array_combine(range(0,($n_trunc_packages_occupied-1),1), $trunc_temp);
//print_r($trunc_temp); echo "
";
//print_r($trunc_packages_occupied); echo "
";
$temp_gap = array();
for($zz=0; $zz<$n_trunc_packages_occupied; ++$zz) {
$temp_gap[] = $my_pkg_gap2[$trunc_packages_occupied[$zz]];
}
sort($temp_gap);
//print_r($temp_gap); echo "
";
$max_gap = max($temp_gap);
$min_gap = min($temp_gap);
$mean_gap = array_sum($temp_gap)/$n_trunc_packages_occupied;
$h = intval($n_trunc_packages_occupied/2);
if($n_trunc_packages_occupied % 2 == 0) {
$median_gap = ($temp_gap[$h] + $temp_gap[$h-1])/2;
} else {
$median_gap = $temp_gap[$h];
}
} else if($n_trunc_packages_occupied==1) {
$trunc_packages_occupied = array_combine(range(0,($n_trunc_packages_occupied-1),1), $trunc_temp); // returns package keys
$max_gap = $my_pkg_gap2[$trunc_packages_occupied[0]];
$min_gap = $max_gap;
$mean_gap = $max_gap;
$median_gap = $max_gap;
} else {
$max_gap = NULL;
$min_gap = NULL;
$mean_gap = NULL;
$median_gap = NULL;
}
// get environmental truncation
for($k=0; $k<$n_packages; ++$k) {
// get unit of oldest occurrence in interval
$q = "SELECT units.id, b.age_bottom, t.age_top, color FROM occurrences_temp2
INNER JOIN units ON units.id=occurrences_temp2.unit_id
INNER JOIN intervals b ON b.id=units.FO
INNER JOIN intervals t ON t.id=units.LO
WHERE taxon_no=".$this_genus[$j]." AND (occurrences_temp2.release_date <= now() OR occurrences_temp2.release_date IS NULL)
AND units.id IN (".$my_pkg[$pkg_occupied[$k]].")
AND b.age_bottom > ".$int_top[$i]." AND t.age_top < ".$int_bottom[$i]."
GROUP BY units.id
ORDER BY b.age_bottom DESC, units.FO_h, t.age_top DESC, field(units.LO_h, 1,2,3,4,5,0)
LIMIT 1"; //echo $q."
";
$result = mysqli_query($connect_macrostrat, $q);
if(mysqli_num_rows($result)==1) {
$max_unit = mysqli_fetch_assoc($result);
$occupied_unit = $max_unit['id'];
$occupied_bottom = $max_unit['age_bottom'];
$occupied_top = $max_unit['age_top'];
$occupied_color = $max_unit['color'];
$next_unit_temp = NULL;
// get oldest unit in overlying intervals - may span into focal interval
if($i==0) {
$previous_top = 418.7;
$previous_bottom = $study_max;
} else {
$previous_top = $int_top[$i-1];
$previous_bottom = $int_bottom[$i-1];
}
$q = "SELECT units.id, color, LO_h, FO_h, b.age_bottom, t.age_top FROM units
INNER JOIN intervals b ON b.id=FO
INNER JOIN intervals t ON t.id=LO
WHERE units.id IN (".$my_pkg[$pkg_occupied[$k]].") AND b.age_bottom>".$previous_top." AND t.age_top<".$previous_bottom."
ORDER BY b.age_bottom DESC, FO_h, t.age_top DESC, field(LO_h, 1,2,3,4,5,0)
LIMIT 1";
$temp_pkg_result = mysqli_query($connect_macrostrat, $q);
if(mysqli_num_rows($temp_pkg_result)>0) {
$next_int_unit = mysqli_fetch_assoc($temp_pkg_result);
$next_unit_temp = $next_int_unit['id'];
if($next_int_unit['color'] != $occupied_color) {
$n_env_temp[] = $pkg_occupied[$k];
// echo $occupied_unit.' '.$occupied_color.' - '.$next_int_unit['id'].' '.$next_int_unit['color']."
";
}
}
mysqli_free_result($temp_pkg_result);
// loop through the units within the focal interval - may not span into overlying interval
if(is_null($next_unit_temp)) $temp_exclude = $occupied_unit;
else $temp_exclude = $occupied_unit.",".$next_unit_temp;
$q = "SELECT units.id, color, LO_h, FO_h, b.age_bottom, t.age_top FROM units
INNER JOIN intervals b ON b.id=FO
INNER JOIN intervals t ON t.id=LO
WHERE units.id IN (".$my_pkg[$pkg_occupied[$k]].") AND b.age_bottom > ".$int_top[$i]." AND t.age_top >= ".$int_top[$i]."
AND b.age_bottom<=".$occupied_top." AND units.id NOT IN (".$temp_exclude.")
ORDER BY b.age_bottom DESC, FO_h, t.age_top DESC, field(LO_h, 1,2,3,4,5,0)"; //echo $q."
";
$temp_pkg_result = mysqli_query($connect_macrostrat, $q); //if(mysqli_num_rows($temp_pkg_result)>2) echo $q."
";
while($pkg_row=mysqli_fetch_assoc($temp_pkg_result)) {
if($pkg_row['color']!=$occupied_color && $pkg_row['age_top']<$occupied_top) {
// echo $occupied_unit.' '.$occupied_color.' - '.$pkg_row['id'].' '.$pkg_row['color']."
";
if($pkg_row['age_top']>=$int_top[$i]) { // unit is contained entirely within the interval
$n_env_temp[] = $pkg_occupied[$k]; //echo $n_env_truncation."
";
} else if ($pkg_row['age_top']<$int_top[$i] && $pkg_row['age_bottom']>$int_top[$i]) { // units spans interval boundary
$n_env_temp[] = $pkg_occupied[$k]; //echo $n_env_truncation."
";
}
}
if($pkg_row['age_top']>=$int_top[$i] && $pkg_row['age_bottom']<=$int_bottom[$i]) $n_env_temp2[] = $pkg_occupied[$k];
}
mysqli_free_result($temp_pkg_result);
if($occupied_top>=$int_top[$i] && $occupied_bottom<=$int_bottom[$i]) $n_env_temp2[] = $pkg_occupied[$k];
}
mysqli_free_result($result);
}
}
$n_env_truncation = count(array_unique($n_env_temp));
$n_env_truncation2 = count($n_env_temp);
$n_env_truncation3 = count(array_unique($n_env_temp2));
// if($n_env_truncation>0) {print_r($n_env_temp); echo "
";}
// tabulate environmental gap length
$env_gap_count = array();
if($n_units>1) {
$my_occupied_units = array_combine(range(0,$n_units-1,1), array_unique($noam_units));
for($zzz=0; $zzz<$n_units; ++$zzz) {
if($env_unit_top[$my_occupied_units[$zzz]] >= $int_top[$i] && $env_unit_top[$my_occupied_units[$zzz]] < $int_bottom[$i]) {
$env_gap_count[] = $env_gap[$my_occupied_units[$zzz]];
}
}
unset($my_occupied_units);
} else if($n_units==1) {
$my_occupied_units = array_combine(array(0), array_unique($noam_units));
if($env_unit_top[$my_occupied_units[0]] >= $int_top[$i] && $env_unit_top[$my_occupied_units[0]] < $int_bottom[$i]) {
$env_gap_count[] = $env_gap[$my_occupied_units[0]];
}
unset($my_occupied_units);
}
// tabulate stats
$n_env_gap = count($env_gap_count);
if($n_env_gap>1) {
$min_env_gap=min($env_gap_count);
$max_env_gap=max($env_gap_count);
$mean_env_gap=array_sum($env_gap_count)/$n_env_gap;
$h = intval($n_env_gap/2);
if($n_env_gap % 2 == 0) {
$median_env_gap = ($env_gap_count[$h] + $env_gap_count[$h-1])/2;
} else {
$median_env_gap = $env_gap_count[$h];
}
} else if($n_env_gap==1) {
$min_env_gap=$env_gap_count[0];
$max_env_gap=$env_gap_count[0];
$mean_env_gap=$env_gap_count[0];
$median_env_gap=$env_gap_count[0];
} else {
$min_env_gap=NULL;
$max_env_gap=NULL;
$mean_env_gap=NULL;
$median_env_gap=NULL;
}
unset($env_gap_count);
if(isset($file_row)) unset($file_row);
$file_row = $int_id[$i].",".$int_name[$i].",".$int_bottom[$i].",".$int_top[$i].",".
$my_genera[$j]['taxon_no'].",".$my_genera[$j]['genus_name'].",".$my_genera[$j]['class'].",".$my_genera[$j]['taxon_order'].",".$my_genera[$j]['family'].",".
$my_genera[$j]['life_habit'].",".$my_genera[$j]['locomotion'].",".$my_genera[$j]['taxon_environment'].",".$my_genera[$j]['diet1'].",".$my_genera[$j]['diet2'].",".
$n_species.",".$n_species_global.",".$n_coll.",".$n_occur.",".$global_endemic_to_interval.",".
$my_genus_age[$this_genus[$j]]['noam_max'].",".$my_genus_age[$this_genus[$j]]['noam_min'].",".
$my_genus_age[$this_genus[$j]]['global_max'].",".$my_genus_age[$this_genus[$j]]['global_min'].",".
$max_paleolat_N.",".$max_paleolat_S.",".$n_matched_units_greater_n_45.",".$n_matched_units_greater_s_45.",".
$max_dist_noam.",".$max_dist_global.",".
$n_packages.",".$n_packages_total.",".$n_units.",".$n_units_total.",".
count($my_carb).",".count(array_intersect($noam_units, $my_carb)).",".count($my_clast).",".count(array_intersect($noam_units, $my_clast)).",".
count($truncating_packages).",".count(array_intersect($noam_packages, $truncating_packages)).",".
$n_env_truncation.",".$n_env_truncation2.",".$n_env_truncation3.",".
$min_gap.",".$max_gap.",".$mean_gap.",".$median_gap.",".
$min_env_gap.",".$max_env_gap.",".$mean_env_gap.",".$median_env_gap.",".$n_env_gap.",".
$n_cols.",".$n_columns_total.",".$n_trunc_columns_occupied."\n";
fwrite($fh, $file_row);
unset($file_row);
}
}
}
fclose($fh);
$my_collections = implode(",",array_unique($my_collections));
// get references and authorizers & enterers
$q = "SELECT occurrences_temp2.collection_no, collections.reference_no, collections.authorizer, collections.enterer, collections.modifier,
refs.author1init, refs.author1last, refs.author2init, refs.author2last, refs.otherauthors, refs.pubyr, refs.reftitle, refs.pubtitle,
refs.editors, refs.pubvol, refs.firstpage, refs.lastpage, refs.publication_type
FROM occurrences_temp2
INNER JOIN pbdb.collections ON occurrences_temp2.collection_no=collections.collection_no
INNER JOIN pbdb.refs ON refs.reference_no=collections.reference_no
WHERE collections.collection_no IN (".$my_collections.")
GROUP BY occurrences_temp2.collection_no
ORDER BY occurrences_temp2.collection_no"; //echo $q."
";
$result = mysqli_query($connect_macrostrat, $q);
$data_credits = array();
$ref_credits = array();
while($row=mysqli_fetch_assoc($result)) {
if(isset($data_credits[$row['authorizer']])) ++$data_credits[$row['authorizer']]['auth'];
else $data_credits[$row['authorizer']] = array('auth'=> 1, 'enter' => 0, 'modify' => 0);
if(isset($data_credits[$row['enterer']])) ++$data_credits[$row['enterer']]['enter'];
else $data_credits[$row['enterer']] = array('auth'=> 0, 'enter' => 1, 'modify' => 0);
if(isset($data_credits[$row['modifier']])) ++$data_credits[$row['modifier']]['modify'];
else $data_credits[$row['modifier']] = array('auth'=> 0, 'enter' => 0, 'modify' => 1);
if(isset($ref_credits[$row['reference_no']])) {
++$ref_credits[$row['reference_no']]['count'];
} else {
$author_temp = $row['author1last'].", ".$row['author1init'];
if(is_null($row['otherauthors'])===FALSE) {
$author_temp = $author_temp.' ,'.$row['author2init']." ".$row['author2last'].", ".$row['otherauthors'].".";
} else if(is_null($row['author2last'])===FALSE) {
$author_temp = $author_temp.' and '.$row['author2init']." ".$row['author2last'].".";
}
if($row['publication_type']=='journal article' || $row['publication_type']=='serial monograph' || $row['publication_type']=='abstract') {
$full_ref = $author_temp." ".$row['pubyr'].". ".$row['reftitle'].". ".$row['pubtitle']." ".$row['pubvol'].":".$row['firstpage']."-".$row['lastpage'];
} else if ($row['publication_type']=='guidebook' || $row['publication_type']=='book/book chapter' || $row['publication_type']=='Ph.D. thesis' || $row['publication_type']=='M.S. thesis') {
if(is_null($row['editors'])) $editor_temp = '';
else $editor_temp = $row['editors']." (eds.) ";
$full_ref = $author_temp." ".$row['pubyr'].". ".$row['reftitle'].". In ".$editor_temp.". ".$row['pubtitle']." ".$row['firstpage']."-".$row['lastpage'];
} else {
if(is_null($row['reftitle']) || $row['reftitle']=='') $temp_pubtitle = '';
else $temp_pubtitle = $row['reftitle'].". ";
$full_ref = $author_temp." ".$row['pubyr'].". ".$temp_pubtitle." Unpublished data";
}
$ref_credits[$row['reference_no']] = array('count'=> 1, 'full' => $full_ref, 'type' => $row['publication_type']);
}
}
mysqli_free_result($result);
// write text files
$credit_file = 'collection_credits.txt';
$fh = fopen($credit_file,'w');
chmod($credit_file, 0777);
$file_row = "name\tauthorized\tentered\tmodified\n";
fwrite($fh, $file_row);
$my_people = array_keys($data_credits);
for($i=0; $i'.$credit_file.' saved
';
$ref_file = 'references.txt';
$fh = fopen($ref_file,'w');
chmod($ref_file, 0777);
$file_row = "reference_no\tcitation\tn_collections\n";
fwrite($fh, $file_row);
$my_refs = array_keys($ref_credits);
for($i=0; $i'.$ref_file.' saved
';
$coll_file = 'collections.csv';
$fh = fopen($coll_file,'w');
chmod($coll_file, 0777);
fwrite($fh, $my_collections);
fclose($fh);
echo 'File '.$coll_file.' saved
';
}
//////////////
//
// stuff at the end
//
//////////////
if(isset($_POST['submit'])) {
$t1 = microtime(true);
$time_diff = $t1 - $t0;
if ($time_diff/60 < 1) {
$diff_seconds = round($time_diff, 3);
echo "
This process took ".$diff_seconds." seconds";
} else if ($time_diff>=1 & $time_diff<3600) {
$diff_min = round($time_diff/60, 3);
echo "
This process took ".$diff_min." minutes";
} else {
$diff_hour = round($time_diff/3600, 3);
echo "
This process took ".$diff_hour." hours";
}
}
?>