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: ā€˜%5dā€™ 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.