R-packages – /branches/cluster-2.1/src/pam.c

Rev 8500 – create cluster-2.1 branch

maechler — Tue, 11 Mar 2025 21:41:39 +0000

maechler – 1 file(s) modified
create cluster-2.1 branch

+ /branches/cluster-2.1 (copied from /trunk/cluster@8468)

Rev 8465 – tweaks from mv Fortran -> C: dysta() returns; dysta, dysta3 ...

maechler — Fri, 06 Dec 2024 10:49:50 +0000

maechler – 11 file(s) modified
tweaks from mv Fortran -> C: dysta() *returns*; dysta, dysta3 no longer exported

~ /trunk/cluster/.Rbuildignore
~ /trunk/cluster/DESCRIPTION
~ /trunk/cluster/inst/NEWS.Rd
~ /trunk/cluster/src/clara.c
~ /trunk/cluster/src/cluster.h
~ /trunk/cluster/src/dysta.c
~ /trunk/cluster/src/fanny.c
~ /trunk/cluster/src/init.c
~ /trunk/cluster/src/pam.c
~ /trunk/cluster/src/twins.c
~ /trunk/cluster/tests/dysta-ex.R

Rev 8457 – translate last remaining Fortran dysta.f and daisy.f to *.c adapting ...

maechler — Fri, 04 Oct 2024 15:42:51 +0000

maechler – 14 file(s) modified
translate last remaining Fortran dysta.f and daisy.f to *.c adapting calls,headers

~ /trunk/cluster/DESCRIPTION
~ /trunk/cluster/inst/NEWS.Rd
~ /trunk/cluster/R/agnes.q
~ /trunk/cluster/R/daisy.q
~ /trunk/cluster/R/mona.q
~ /trunk/cluster/src/cluster.h
+ /trunk/cluster/src/daisy.c
x /trunk/cluster/src/daisy.f
+ /trunk/cluster/src/dysta.c
x /trunk/cluster/src/dysta.f
~ /trunk/cluster/src/init.c
~ /trunk/cluster/src/mona.c
~ /trunk/cluster/src/pam.c
~ /trunk/cluster/src/twins.c

Rev 8308 – remove old unused code for .C(..)

maechler — Thu, 30 Nov 2023 10:41:39 +0000

maechler – 1 file(s) modified
remove old unused code for .C(..)

~ /trunk/cluster/src/pam.c

Rev 8061 – tweaks + as.data.frame()

maechler — Fri, 25 Mar 2022 22:06:34 +0000

maechler – 12 file(s) modified
tweaks + as.data.frame(<silhouette>)

~ /trunk/cluster/.Rbuildignore
~ /trunk/cluster/DESCRIPTION
~ /trunk/cluster/inst/NEWS.Rd
~ /trunk/cluster/inst/po/en@quot/LC_MESSAGES/cluster.mo
~ /trunk/cluster/inst/po/en@quot/LC_MESSAGES/R-cluster.mo
~ /trunk/cluster/man/clusGap.Rd
~ /trunk/cluster/man/silhouette.Rd
~ /trunk/cluster/NAMESPACE
~ /trunk/cluster/po/cluster.pot
~ /trunk/cluster/po/R-cluster.pot
~ /trunk/cluster/R/silhouette.R
~ /trunk/cluster/src/pam.c

Rev 7920 – pam(, medoids="random", nstart=, variant = "faster"): `fasterPAM` et al. from ...

maechler — Sat, 30 Jan 2021 21:27:20 +0000

maechler – 8 file(s) modified
pam(*, medoids="random", nstart=*, variant = "faster"): `fasterPAM` et al. from Erich Schubert

~ /trunk/cluster/DESCRIPTION
~ /trunk/cluster/inst/NEWS.Rd
~ /trunk/cluster/man/pam.Rd
~ /trunk/cluster/R/pam.q
~ /trunk/cluster/src/pam.c
~ /trunk/cluster/tests/agnes-ex.Rout.save
~ /trunk/cluster/tests/pam.R
~ /trunk/cluster/tests/pam.Rout.save

Rev 7640 – pam(*, pamonce = 4 or 5): do { .. } ...

maechler — Mon, 01 Apr 2019 16:09:16 +0000

maechler – 4 file(s) modified
pam(*, pamonce = 4 or 5): do { .. } instead of `goto ..`

~ /trunk/cluster/DESCRIPTION
~ /trunk/cluster/inst/NEWS.Rd
~ /trunk/cluster/man/pam.Rd
~ /trunk/cluster/src/pam.c

Rev 7639 – pam(*, pamonce = {3,4,5}) "FASTPAM{1,2,3}" algorithms from Erich Schubert

maechler — Mon, 01 Apr 2019 15:51:00 +0000

maechler – 6 file(s) modified
pam(*, pamonce = {3,4,5}) "FASTPAM{1,2,3}" algorithms from Erich Schubert

~ /trunk/cluster/DESCRIPTION
~ /trunk/cluster/inst/NEWS.Rd
~ /trunk/cluster/man/pam.Rd
~ /trunk/cluster/src/pam.c
~ /trunk/cluster/tests/pam.R
~ /trunk/cluster/tests/pam.Rout.save

Rev 7509 – (from a year ago:) clara() with Jaccard metric, pam() ...

maechler — Thu, 29 Mar 2018 14:44:04 +0000

maechler – 20 file(s) modified
(from a year ago:) clara() with Jaccard metric, pam() to follow, not quiet yet; + small things

~ /trunk/cluster/DESCRIPTION
~ /trunk/cluster/inst/NEWS.Rd
+ /trunk/cluster/inst/test-tools.R
~ /trunk/cluster/man/clara.Rd
~ /trunk/cluster/man/clusGap.Rd
~ /trunk/cluster/man/mona.Rd
~ /trunk/cluster/man/pam.Rd
~ /trunk/cluster/man/xclara.Rd
~ /trunk/cluster/NAMESPACE
~ /trunk/cluster/R/0aaa.R
~ /trunk/cluster/R/clara.q
~ /trunk/cluster/R/clusGapGen.R
~ /trunk/cluster/R/daisy.q
~ /trunk/cluster/R/pam.q
~ /trunk/cluster/src/clara.c
~ /trunk/cluster/src/cluster.h
~ /trunk/cluster/src/daisy.f
~ /trunk/cluster/src/init.c
~ /trunk/cluster/src/pam.c
~ /trunk/cluster/TODO-MM

Rev 7331 – switch (again!) mona to use C version; catch p=1 as ...

maechler — Fri, 10 Mar 2017 08:04:00 +0000

maechler – 12 file(s) modified
switch (again!) mona to use C version; catch p=1 as error; cosmetic

~ /trunk/cluster/DESCRIPTION
~ /trunk/cluster/inst/NEWS.Rd
~ /trunk/cluster/man/pam.Rd
~ /trunk/cluster/R/mona.q
~ /trunk/cluster/R/pam.q
~ /trunk/cluster/src/cluster.h
~ /trunk/cluster/src/init.c
~ /trunk/cluster/src/mona.c
x /trunk/cluster/src/mona.f
~ /trunk/cluster/src/pam.c
~ /trunk/cluster/tests/mona.R
~ /trunk/cluster/tests/mona.Rout.save

Rev 7274 – checking for too large `n`; thanks to Mikko Korpela

maechler — Sat, 24 Sep 2016 09:42:33 +0000

maechler – 5 file(s) modified
checking for too large `n`; thanks to Mikko Korpela

~ /trunk/cluster/DESCRIPTION
~ /trunk/cluster/inst/NEWS.Rd
~ /trunk/cluster/man/pam.Rd
~ /trunk/cluster/R/pam.q
~ /trunk/cluster/src/pam.c

Rev 6994 – add missing UNPROTECT(.) before (error!) return() {which we have ...

maechler — Wed, 29 Jul 2015 19:30:34 +0000

maechler – 1 file(s) modified
add missing UNPROTECT(.) before (error!) return() {which we have not seen}

~ /trunk/cluster/src/pam.c

Rev 6879 – initialize nisol["1"] also for k = 1

maechler — Sun, 01 Feb 2015 20:03:15 +0000

maechler – 1 file(s) modified
initialize nisol["1"] also for k = 1

~ /trunk/cluster/src/pam.c

Rev 6877 – fix pam(*, k=1) returning nonsensical `silinfo`

maechler — Sat, 31 Jan 2015 19:19:18 +0000

maechler – 7 file(s) modified
fix pam(*, k=1) returning nonsensical `silinfo`

~ /trunk/cluster/DESCRIPTION
~ /trunk/cluster/po/cluster.pot
~ /trunk/cluster/po/R-cluster.pot
~ /trunk/cluster/po/update-me.sh
~ /trunk/cluster/src/pam.c
~ /trunk/cluster/tests/pam.R
~ /trunk/cluster/tests/pam.Rout.save

Rev 6873 – C cl_Pam() - build `ans` list such that components are ...

maechler — Tue, 27 Jan 2015 08:42:52 +0000

maechler – 3 file(s) modified
C cl_Pam() - build `ans` list such that components are PROTECT()ed

~ /trunk/cluster/DESCRIPTION
~ /trunk/cluster/src/pam.c
~ /trunk/cluster/tests/pam.Rout.save

Rev 6872 – basically revert r6871: do pass `n` for now

maechler — Mon, 26 Jan 2015 18:21:15 +0000

maechler – 4 file(s) modified
basically revert r6871: do pass `n` for now

~ /trunk/cluster/R/pam.q
~ /trunk/cluster/src/cluster.h
~ /trunk/cluster/src/init.c
~ /trunk/cluster/src/pam.c

Rev 6871 – cl_Pam() no need to pass `n`; can get it from ...

maechler — Mon, 26 Jan 2015 17:46:41 +0000

maechler – 3 file(s) modified
cl_Pam() no need to pass `n`; can get it from the object

~ /trunk/cluster/src/cluster.h
~ /trunk/cluster/src/init.c
~ /trunk/cluster/src/pam.c

Rev 6869 – pam() now uses .Call() instead of .C() -- (kept old ...

maechler — Mon, 26 Jan 2015 13:30:42 +0000

maechler – 16 file(s) modified
pam() now uses .Call() instead of .C() -- (kept old code for now)

~ /trunk/cluster/DESCRIPTION
~ /trunk/cluster/man/pam.object.Rd
~ /trunk/cluster/R/agnes.q
~ /trunk/cluster/R/clara.q
~ /trunk/cluster/R/daisy.q
~ /trunk/cluster/R/diana.q
~ /trunk/cluster/R/fanny.q
~ /trunk/cluster/R/internal.R
~ /trunk/cluster/R/pam.q
~ /trunk/cluster/src/cluster.h
~ /trunk/cluster/src/dysta.f
~ /trunk/cluster/src/fanny.c
~ /trunk/cluster/src/init.c
~ /trunk/cluster/src/pam.c
~ /trunk/cluster/tests/pam.R
~ /trunk/cluster/tests/pam.Rout.save

Rev 6712 – use error(_(..)) instead of REprintf() for errors, and add ...

maechler — Thu, 27 Mar 2014 11:02:14 +0000

maechler – 6 file(s) modified
use error(_(..)) instead of REprintf() for errors, and
add po/cluster.pot for future translations of (the few) C level error messages

+ /trunk/cluster/inst/po/en@quot/LC_MESSAGES/cluster.mo
+ /trunk/cluster/po/cluster.pot
~ /trunk/cluster/po/translators.txt
~ /trunk/cluster/src/clara.c
~ /trunk/cluster/src/pam.c
~ /trunk/cluster/src/twins.c

Rev 6057 – pam(*, pamonce=.) incorporate the faster SWAP algorithms provided by Matthias ...

maechler — Wed, 01 Feb 2012 08:42:19 +0000

maechler – 10 file(s) modified
pam(*, pamonce=.) incorporate the faster SWAP algorithms provided by Matthias Studer

~ /trunk/cluster/DESCRIPTION
~ /trunk/cluster/DONE-MM
~ /trunk/cluster/man/pam.Rd
~ /trunk/cluster/R/pam.q
~ /trunk/cluster/src/cluster.h
~ /trunk/cluster/src/init.c
~ /trunk/cluster/src/pam.c
~ /trunk/cluster/tests/pam.R
~ /trunk/cluster/tests/pam.Rout.save
~ /trunk/cluster/TODO-MM

Rev 5779 – we returned too early instead of signalling an error, when ...

maechler — Fri, 20 May 2011 20:58:50 +0000

maechler – 3 file(s) modified
we returned too early instead of signalling an error, when cluster.only=TRUE and some computed dissimilarities where NA

~ /trunk/cluster/ChangeLog
~ /trunk/cluster/R/pam.q
~ /trunk/cluster/src/pam.c

Rev 5758 – make clara() more pam()-like on C level --- notably allow ...

maechler — Sat, 16 Apr 2011 18:09:23 +0000

maechler – 11 file(s) modified
make clara() more pam()-like on C level --- notably allow "pamLike=TRUE" argument

~ /trunk/cluster/DESCRIPTION
~ /trunk/cluster/R/clara.q
~ /trunk/cluster/src/clara.c
~ /trunk/cluster/src/cluster.h
~ /trunk/cluster/src/init.c
~ /trunk/cluster/src/pam.c
~ /trunk/cluster/tests/clara-2.R
~ /trunk/cluster/tests/clara.Rout.save
~ /trunk/cluster/tests/diana-ex.Rout.save
~ /trunk/cluster/tests/ellipsoid-ex.Rout.save
~ /trunk/cluster/tests/pam.Rout.save

Rev 5592 – rename some compiled routines, in order to allow registration of ...

maechler — Sat, 19 Jun 2010 16:37:03 +0000

maechler – 19 file(s) modified
rename some compiled routines, in order to allow registration of those names

~ /trunk/cluster/ChangeLog
~ /trunk/cluster/DESCRIPTION
~ /trunk/cluster/NAMESPACE
~ /trunk/cluster/R/clara.q
~ /trunk/cluster/R/fanny.q
~ /trunk/cluster/R/mona.q
~ /trunk/cluster/R/pam.q
~ /trunk/cluster/R/zzz.R
~ /trunk/cluster/src/clara.c
~ /trunk/cluster/src/cluster.h
~ /trunk/cluster/src/fanny.c
~ /trunk/cluster/src/init.c
~ /trunk/cluster/src/mona.f
~ /trunk/cluster/src/pam.c
~ /trunk/cluster/src/spannel.c
~ /trunk/cluster/tests/clara-NAs.Rout.save
~ /trunk/cluster/tests/clara.Rout.save
~ /trunk/cluster/tests/fanny-ex.Rout.save
~ /trunk/cluster/tests/sweep-ex.R

Rev 4967 – misc. updates since September; notably pam(, do.swap)

maechler — Fri, 29 Feb 2008 11:13:02 +0000

maechler – 20 file(s) modified
misc. updates since September; notably pam(<large>, do.swap)

~ /trunk/cluster/ChangeLog
~ /trunk/cluster/DESCRIPTION
~ /trunk/cluster/man/clara.Rd
~ /trunk/cluster/man/pam.Rd
~ /trunk/cluster/R/clara.q
~ /trunk/cluster/R/pam.q
~ /trunk/cluster/src/cluster.h
~ /trunk/cluster/src/ind_2.h
~ /trunk/cluster/src/pam.c
~ /trunk/cluster/tests/clara-2.Rout.save
~ /trunk/cluster/tests/clara-ex.Rout.save
~ /trunk/cluster/tests/clara-NAs.Rout.save
~ /trunk/cluster/tests/clusplot-out.R
~ /trunk/cluster/tests/clusplot-out.Rout.save
~ /trunk/cluster/tests/daisy-ex.Rout.save
~ /trunk/cluster/tests/ellipsoid-ex.Rout.save
~ /trunk/cluster/tests/fanny-ex.Rout.save
~ /trunk/cluster/tests/mona.Rout.save
~ /trunk/cluster/tests/pam.R
~ /trunk/cluster/tests/pam.Rout.save

Rev 3083 – many more fanny extensions

maechler — Wed, 19 Apr 2006 14:36:37 +0000

maechler – 14 file(s) modified
many more fanny extensions

~ /trunk/cluster/ChangeLog
~ /trunk/cluster/DESCRIPTION
~ /trunk/cluster/man/fanny.object.Rd
~ /trunk/cluster/man/fanny.Rd
~ /trunk/cluster/R/fanny.q
~ /trunk/cluster/R/pam.q
~ /trunk/cluster/R/plotpart.q
~ /trunk/cluster/src/clara.c
~ /trunk/cluster/src/cluster.h
~ /trunk/cluster/src/dysta.f
~ /trunk/cluster/src/fanny.c
~ /trunk/cluster/src/init.c
~ /trunk/cluster/src/pam.c
~ /trunk/cluster/tests/fanny-ex.R

Rev 2953 – comment "logical"

maechler — Sat, 07 Jan 2006 15:58:54 +0000

maechler – 2 file(s) modified
comment "logical"

~ /trunk/cluster/src/clara.c
~ /trunk/cluster/src/pam.c

Rev 2922 – bswap() calling and coding more in parallel with ./clara.c 's ...

maechler — Sat, 06 Aug 2005 10:06:36 +0000

maechler – 1 file(s) modified
bswap() calling and coding more in parallel with ./clara.c 's bswap2()

~ /trunk/cluster/src/pam.c

Rev 2895 – introduce 'trace_lev'; fixing 'ntt= 0/1' checks

maechler — Thu, 09 Jun 2005 11:38:57 +0000

maechler – 1 file(s) modified
introduce 'trace_lev'; fixing 'ntt= 0/1' checks

~ /trunk/cluster/src/pam.c

Rev 2889 – + some comments; silinfo : ntt = 0/1 checks (partially ...

maechler — Wed, 08 Jun 2005 21:45:59 +0000

maechler – 1 file(s) modified
+ some comments; silinfo : ntt = 0/1 checks (partially wrong?)

~ /trunk/cluster/src/pam.c

Rev 2844 – new 'med_given' option {+ more comments; cosmetic: not using 'l'}

maechler — Sat, 03 Jul 2004 00:04:07 +0000

maechler – 1 file(s) modified
new 'med_given' option {+ more comments; cosmetic: not using 'l'}

~ /trunk/cluster/src/pam.c

Rev 2841 – bswap(): declare some vars only inside the first for(k ..) ...

maechler — Thu, 01 Jul 2004 21:22:00 +0000

maechler – 1 file(s) modified
bswap(): declare some vars only *inside* the first for(k ..) loop

~ /trunk/cluster/src/pam.c

Rev 2840 – speedup computing ammax in first for(i. ) loop; dont need ...

maechler — Tue, 29 Jun 2004 18:18:16 +0000

maechler – 1 file(s) modified
speedup computing ammax in first for(i. ) loop; dont need 2nd; + comments

~ /trunk/cluster/src/pam.c

Rev 2818 – compute (s*1.1 + 1) only once

maechler — Mon, 26 Apr 2004 16:38:21 +0000

maechler – 1 file(s) modified
compute (s*1.1 + 1) only once

~ /trunk/cluster/src/pam.c

Rev 2796 – use ind_2() instead of F77_CALL(meet)()

maechler — Wed, 10 Mar 2004 10:36:56 +0000

maechler – 1 file(s) modified
use ind_2(*) instead of F77_CALL(meet)(*)

~ /trunk/cluster/src/pam.c

Rev 2783 – + 2 simple comments

maechler — Mon, 05 Jan 2004 23:55:51 +0000

maechler – 1 file(s) modified
+ 2 simple comments

~ /trunk/cluster/src/pam.c

Rev 2778 – in dark(): get rid of two "--foo" (1-indexing); use ...

maechler — Tue, 02 Dec 2003 09:16:14 +0000

maechler – 1 file(s) modified
in dark(): get rid of two "--foo" (1-indexing);
use pointer to sylinf[] columns for increased readability

~ /trunk/cluster/src/pam.c

Rev 2777 – bswap(): cosmetic; cstat(): use [k], not [numcl]; dark(): use ...

maechler — Mon, 01 Dec 2003 17:51:03 +0000

maechler – 1 file(s) modified
bswap(): cosmetic; cstat(): use [k], not [numcl];
dark(): use [k] as in cstat(); further get rid of --syl, --negbr, --nelem

~ /trunk/cluster/src/pam.c

Rev 2774 – introduce 'all_stats': option not to compute silhouette stats, etc s/i__/i/ ...

maechler — Sun, 30 Nov 2003 00:18:57 +0000

maechler – 1 file(s) modified
introduce 'all_stats': option *not* to compute silhouette stats, etc
s/i__/i/ etc; cstat(): Rboolean 'kand';
many cosmetic, incl. dark(): "< +/-1" instead of "<="

~ /trunk/cluster/src/pam.c

Rev 2773 – version of 2003.11.29.23.15.00 (now is 06 Aug 2005).

maechler — Sat, 29 Nov 2003 23:15:00 +0000

maechler – 1 file(s) modified
version of 2003.11.29.23.15.00 (now is 06 Aug 2005).

~ /trunk/cluster/src/pam.c

Rev 2771 – version of 2003.11.29.15.40.05 (now is 06 Aug 2005).

maechler — Sat, 29 Nov 2003 15:40:05 +0000

maechler – 1 file(s) modified
version of 2003.11.29.15.40.05 (now is 06 Aug 2005).

~ /trunk/cluster/src/pam.c

R-packages – /branches/cluster-2.1/src/pam.c

Rev 8500 – create cluster-2.1 branch

Rev 8465 – tweaks from mv Fortran -> C: dysta() *returns*; dysta, dysta3 ...

Rev 8457 – translate last remaining Fortran dysta.f and daisy.f to *.c adapting ...

Rev 8308 – remove old unused code for .C(..)

Rev 8061 – tweaks + as.data.frame()

Rev 7920 – pam(*, medoids="random", nstart=*, variant = "faster"): `fasterPAM` et al. from ...

Rev 7640 – pam(*, pamonce = 4 or 5): do { .. } ...

Rev 7639 – pam(*, pamonce = {3,4,5}) "FASTPAM{1,2,3}" algorithms from Erich Schubert

Rev 7509 – (from a year ago:) clara() with Jaccard metric, pam() ...

Rev 7331 – switch (again!) mona to use C version; catch p=1 as ...

Rev 7274 – checking for too large `n`; thanks to Mikko Korpela

Rev 6994 – add missing UNPROTECT(.) before (error!) return() {which we have ...

Rev 6879 – initialize nisol["1"] also for k = 1

Rev 6877 – fix pam(*, k=1) returning nonsensical `silinfo`

Rev 6873 – C cl_Pam() - build `ans` list such that components are ...

Rev 6872 – basically revert r6871: do pass `n` for now

Rev 6871 – cl_Pam() no need to pass `n`; can get it from ...

Rev 6869 – pam() now uses .Call() instead of .C() -- (kept old ...

Rev 6712 – use error(_(..)) instead of REprintf() for errors, and add ...

Rev 6057 – pam(*, pamonce=.) incorporate the faster SWAP algorithms provided by Matthias ...

Rev 5779 – we returned too early instead of signalling an error, when ...

Rev 5758 – make clara() more pam()-like on C level --- notably allow ...

Rev 5592 – rename some compiled routines, in order to allow registration of ...

Rev 4967 – misc. updates since September; notably pam(, do.swap)

Rev 3083 – many more fanny extensions

Rev 2953 – comment "logical"

Rev 2922 – bswap() calling and coding more in parallel with ./clara.c 's ...

Rev 2895 – introduce 'trace_lev'; fixing 'ntt= 0/1' checks

Rev 2889 – + some comments; silinfo : ntt = 0/1 checks (partially ...

Rev 2844 – new 'med_given' option {+ more comments; cosmetic: not using 'l'}

Rev 2841 – bswap(): declare some vars only *inside* the first for(k ..) ...

Rev 2840 – speedup computing ammax in first for(i. ) loop; dont need ...

Rev 2818 – compute (s*1.1 + 1) only once

Rev 2796 – use ind_2(*) instead of F77_CALL(meet)(*)

Rev 2783 – + 2 simple comments

Rev 2778 – in dark(): get rid of two "--foo" (1-indexing); use ...

Rev 2777 – bswap(): cosmetic; cstat(): use [k], not [numcl]; dark(): use ...

Rev 2774 – introduce 'all_stats': option *not* to compute silhouette stats, etc s/i__/i/ ...

Rev 2773 – version of 2003.11.29.23.15.00 (now is 06 Aug 2005).

Rev 2771 – version of 2003.11.29.15.40.05 (now is 06 Aug 2005).

Rev 8465 – tweaks from mv Fortran -> C: dysta() returns; dysta, dysta3 ...

Rev 7920 – pam(, medoids="random", nstart=, variant = "faster"): `fasterPAM` et al. from ...

Rev 2841 – bswap(): declare some vars only inside the first for(k ..) ...

Rev 2796 – use ind_2() instead of F77_CALL(meet)()

Rev 2774 – introduce 'all_stats': option not to compute silhouette stats, etc s/i__/i/ ...