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ChangeLog
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2023-09-03: Ver. 0.1-34
* Remove the meta table from the doc.
* Modify CITATION.
* Replace "sprintf()" in C.
* Fix use of unary operator that may be intended as compound assignment (-=).
2022-10-24: Ver. 0.1-32
* Fix more "(theta^(mut.step - ss)) %*% diag(poolPI)" errors in the
haplo.post.prob() function.
2022-10-01: Ver. 0.1-31
* Fix empty while() and for() warnings caught by clang.
* Fix \_ and \# warnings caught by checkRd.
* Change "http" to "https" in some Rd files.
* Use "is()" to replace "class()" inside the "if()" in some R code.
* Fix "stric-prototypes" warnings by adding "void" to functions
without arguments.
* Fix "deprecated-non-prototype" warnings.
* Fix "(theta^(mut.step - ss)) %*% diag(poolPI)" error in the
haplo.post.prob() function.
2021-02-09: Ver. 0.1-30
* Change http to https.
* Change \A, \G, \C, and \T in vignettes to avoid conflicts.
2020-05-10: Ver. 0.1-29
* Fix warning '__builtin_strncpy' output truncated due to
"-Wstringop-truncation" by gcc10.
2019-12-01: Ver. 0.1-28
* Fix multiple definition warnings due to "-fno-common" as default in gcc-10.
2019-11-28: Ver. 0.1-27
* Fix a compiler warning.
2019-09-10: Ver. 0.1-26
* Fix a bug in "get.rooted.tree.height", see "https://github.com/snoweye/phyclust/issues/5" for details.
2019-08-23: Ver. 0.1-25
* Fix illegal character encoding in string literal.
* Minors.
2019-03-20: Ver. 0.1-24
* Push some PROTECT and UNPROTECT back within the call.
2019-03-07: Ver. 0.1-23
* Move PROTECT to the caller functions.
2017-11-18: Ver. 0.1-21
* Fix a warning from CRAN as
phyclust/phyclust_optim_nmmin.c:260:21: warning: ‘%5d’ directive writing
between 5 and 10 bytes into a region of size 6 [-Wformat-overflow=]
2017-08-05: Ver. 0.1-20
* Fix call stack unbalance.
2017-04-07: Ver. 0.1-19
* Add UNPROTECT() to several C files.
2016-12-10: Ver. 0.1-18
* Migrate all documents to the new website.
2016-07-14: Ver. 0.1-17
* Fix a read.table bug.
2015-11-25: Ver. 0.1-16
* Change "gasdev(m,v)" in "src/msdir/ms.c" to avoid different outcomes from
the same seed. (static int is not supposed to act like that)
Bug is found by Paul Staab.
* Modify "ms()" by adding "tbs" to "opts", and "tbs.matrix" for assigning
values of "tbs".
This is suggested by Mark Beaumont.
2015-01-02: Ver. 0.1-16
* Fix Update_Eta_given_Z_ADJUST renormalizing problems.
2014-12-26: Ver. 0.1-16
* Fix phyclust_qmatrix_array.c line 102 and 125.
2014-12-16: Ver. 0.1-16
* Fix *total_sum potential overflow problem.
2014-12-11: Ver. 0.1-16
* Fix R_phyclust_e_step to manually copy Z_modifiled to Z_normalized for
storing back to R.
2014-10-03: Ver. 0.1-16
* Fix inst/doc/*.html to fit HTML5.
* Get rid of jss.*
2014-01-31: Ver. 0.1-16
* Add opts = -u to seqgen() man page.
2013-12-14: Ver. 0.1-15
* Move vignettes.
2013-01-07: Ver. 0.1-14
* add temp.file to ms() and seq.gen().
* replace scan() by readLines() in ms() and seq.gen().
2012-12-23: Ver. 0.1-13
* fix .GlobalEnv problem.
* fix .Last.load problem.
* drop unvisible functions.
2012-04-29: Ver. 0.1-12
* fix a bug in ms().
* fix more F0, stdout, putchar, ...etc in baseml() for CRAN.
* fix fprintf(stderr, ...) bugs everywhere replacing by REprintf(...).
* check demo examples and vignettes.
* add missing to C and R code.
* add an update function to phyclust.
* fix memory overwrite problems in sequencing error probability.
2012-03-01: Ver. 0.1-11
* add sequencing error models in C and R, phyclust.se(), phyclust.se.update().
* fix stdout, stderr, fprintf, printf, puts, ...etc for CRAN.
* add PAML C function baseml to find tree using maximum likelihood.
* modify PAML functions for baseml and fix bugs.
* fix the fclose() problem in baseml.
* generate the R function paml.baseml() to call PAML baseml.
* generate utility functions such write.paml(), write.paml.format(), ... etc.
* rename some C functions of seq-gen borrowed from PAML with conflicts.
* fix the fclose() problem in seq-gen.
2011-10-31: Ver. 0.1-10
* modify some warnings in C code due to the R CRAN's checking report.
2011-10-24: Ver. 0.1-9
* modify for new release of R-2.14.x.
2011-07-03: Ver. 0.1-9
* modify read.fasta.format().
* add some minor tools.
2010-11-16: Ver. 0.1-9
* fix a bug in missing_flag.
* add .amino.acid, .codon, and .genetic.code, and translated functions.
* modified plotdots().
* Add a few arguments for reading, writing and translating unaligned
sequences.
2010-09-15: Ver. 0.1-8
* semi-supervised clustering.
* remove any X_unique and replace by X.
2010-04-26: Ver. 0.1-7
* fix a bug in the initialization NJ and randomNJ using neighbor-joining,
* modify the EM algorithm for missing data or gaps of sequences in C,
* add a C function for finding a consensus sequence,
* modify plotdots() based on the consensus sequence,
* add an R function plotclass() and plotstruct() for structure plots, and
* move the manuals of ms and seq-gen from the package to this website to
reduce the package size.
======================== Log Before Release ===================================
2009-12-24:
* Add seq.gen() for SNP.
* Modified seq-gen.c allowing dynamical tree sizes with argument -u.
2009-11-08:
* Add logL, em.step, e.step, and m.step to R/.
* Adjust some fprintf() to printf().
* A bug which does not update count_Mu_X when Mu is updated, and it causes
the negative values of count_Mu_X and positive huge logL.
* Rewrite logL with scaled exponent to avoid overflow and underflow.
2009-10-06:
* Add logPt and Q_matrix to R/.
* Add seq-gen.
* Add R's random number generation to seq-gen.
* Fix more bugs in ms including memory leaks and missed allocations.
* Fix more bugs in seq-gen including memory leaks and missed allocations.
* Add manualMu.
* Remove seq-gen's stdin.
2009-10-03:
* Add ms.
2009-10-01:
* Finish ECM, AECM methods.
* Fix a big bug in logpL and delete X_org_summarized.
2009-09-23:
* Add function pointers to deal unique sequences.
* Add ECM, AECM methods.
2009-09-12:
* Add count_Mu_X in empcs to speed up.
* Remove all NN.
* Add empirical version for F81 and HKY85.
* Add est_non_seg_site = FALSE to speed up.
* Add unique_seq_id to speed up.
2009-09-01:
* Rewrite Q to QA in C and add EE, EV, VE, VV.
* Add SNP.
* Add F81 model.
2009-08-21:
* Rebuild R code.
2009-07-28:
* Rewrite in C.
* Rename to phyclust.
2009-07-01:
* Add functions to output file in PHYLIP and FASTA format.
2009-06-01:
* Update and add several functions.
2009-03-09:
* Package initialized.