microeco - microeco v1.15.0

• optimize calpreProcess function in transclassifier class • add byautoset parameter in calmanova function of transbeta class • fix get.edges namespace issue in transnetwork class • extend deletetaxonomylineage for nested usage in transabund class • set orderxmean default FALSE in transdiff class • optimize significance label position for error bar in transalpha class • use method param instead of calmethod in calcor function of trans_env class • update the help document

- R
Published by ChiLiubio about 1 year ago

microeco - microeco v1.14.0

• fix the otutable filtering bug for negative values in tidydataset of microtable (thank Fernando Puente-Sánchez for the finding) • fix asterisk usage issue in formula of linda method in transdiff • fix issue in parameter passing in plotdiffbar of transdiff • add fortaxaabund parameter in filtertaxa of microtable • extend pointsize to numerical variable in plotordination of transbeta and transenv • fix the significance label issue for barerrorbar in transdiff • add choices parameter in plotordination of transbeta • add NMDSmatrix parameter in calordination of transbeta • return a recreated microtable object in transnorm • add taxalevel parameter in calordination of transbeta • add loadingtextprefix and loadingtexttaxlevel parameter in plotordination of transbeta • add taxatextprefix parameter in plotordination of trans_env

- R
Published by ChiLiubio about 1 year ago

microeco - microeco v1.13.0

• apply calfeaturesel function to training data in transclassifier class • check data spliting for calfeaturesel function in transclassifier class • use ytextitalic parameter instead of ylabtypeitalic in plotcor function of transenv class • fix ylabitalic failing issue in plotcor function of transenv class • use ytextposition parameter instead of textyposition in plotcor function of transenv • add forcejaccardbinary parameter in calbetadiv function of microtable class • check node name attribute in transnetwork class • update help document in transabund class

- R
Published by ChiLiubio over 1 year ago

microeco - microeco v1.12.0

• return invisible self for method chaining in each class • add by and permutations parameters in calmanova function of transbeta class • use deprecate function of lifecycle package • replace deprecated functions of igraph package in transnetwork class • change default addlabelgroup argument in plottaxaroles function of transnetwork class • update the print function in each class • update the document in each class • delete biom and qiimer source package in extdata

- R
Published by ChiLiubio over 1 year ago

microeco - microeco v1.11.0

• set sample.size = NULL in rarefysamples in microtable class • check tbldf format for tidytaxonomy function and all input tables in microtable class • fix one sample error in filtertaxa of microtable class • fix transcomm issue for taxalevel not OTU in transnetwork class • add FlashWeavegml param in calnetwork of transnetwork class • allow factor for axis text in plotcor in transenv class • remove Env factor in result table of calcor in transenv class • delete pheatmap option in plotcor in transenv class • reassign resdiff table for customized use in plotdiff of transenv class • add facetswitch parameter in plotheatmap of transabund class • add y facet for highlevel in plotheatmap of transabund class • check whether highlevel and taxrank param same in transabund class • fix factor and names issue in plottern of transabund class • add anovavarequaltest param in caldiff of transalpha class • remove caltax4fun function in transfunc and delete tax4fun package in inst • fix partial taxonomic info issue in FUNGuild prediction of transfunc class • add lefsesubstrict and lefsesubalpha param in transdiff class • add stop message for wrong use of taxalevel in some methods of transdiff class • update document for transdiff, transalpha and transabund classes

- R
Published by ChiLiubio over 1 year ago

microeco - microeco v1.10.0

• restructure plotdiffabund function in transdiff class • add barerrorbar option in plottype parameter of plotalpha in transalpha class • update FAPROTAX to v1.2.10 • reconstruct calabund function in microtable class • add nodealledges and returnigraph parameter in subsetnetwork of transnetwork class • optimize edge parameter in subsetnetwork of transnetwork class • add checkedgetable and checknodetable in private of transnetwork • fix the issue for one factor in calmantel and plotcor of transenv class • check abnormal character for lefse method in transdiff class • add abundance summary for bygroup in transdiff class • fix inherit aes issue in label mapping of plotalpha and plotdiffabund functions • add OPLS-DA method in calordination of transbeta class • support DNAbin type for repfasta object in microtable and trans_func class • update the document

- R
Published by ChiLiubio over 1 year ago

microeco - microeco v1.9.1

Fix the issues in examples of last release.

- R
Published by ChiLiubio almost 2 years ago

microeco - microeco v1.9.0

• use plottype parameter instead of useboxplot in plotalpha of transalpha • more plot options in plottype parameter in plotalpha of transalpha • use add parameter instead of boxlotadd in plotalpha of transalpha • add partial parameter for partial correlation in calcor of transenv • set linealpha = 0.5 in plotscatterfit of transenv • add upbarwidth and leftbarwidth parameters in plotbar of transvenn • add leftbaralpha, bottomlinecolour, bottomlinewidth and bottombackgroundalpha parameters in plotbar of transvenn • add PLS-DA method in calordination of transbeta • add addsigtextsize parameter in plotdiffabund of transdiff • add rfimptype parameter for rf in transdiff • add parameter passing for rf in transdiff • delete rfntree parameter in transdiff • update the usage of lefsenorm param in transdiff • compare mean when medians are same across groups in lefse of transdiff • check the prefix in cladogram of transdiff • fix R2 issue for glmmbeta method in transdiff • restructure the R2 output format for lme and glmm methods in transalpha and transdiff • extend tidytaxonomy for microtable input • rename parameter usegroup to group in mergesamples function of microtable • stop when tbldf format data is found in microtable • fix parameter usenamerawtaxanotOTU NA issue in calnetwork of trans_network • import igraph >= 2.0.0

- R
Published by ChiLiubio almost 2 years ago

microeco - microeco v1.8.0

• rename ordination to method parameter in calordination of transbeta • fix inherit aes issue in plotordination function of transbeta • extend measure parameter to customized matrix input in transbeta$new • optimize output format of ANOSIM and perMANOVA for overall test in transbeta • fix feature name replace issue in transclassifier • extend calcaretList to no datatrain case in transclassifier • extend model training for all samples in transclassifier when the data is not splitted • add plotcaretListresamples function in transclassifier • add calcaretListresamples function in transclassifier • fix plotfeatureimp issue for regresssion in transclassifier • add rfsigshow and showsiggroup in plotfeatureimp of transclassifier • add rffeaturesig param in calfeatureimp of transclassifier • delete coordflip param in plotfeatureimp of transclassifier • add more definitions of metrics in calpredict of transclassifier • rename max.tree param to ntree in caltrain of transclassifier • opt trainControl usage in transclassifier • add metrics definations in calROC of transclassifier • fix R2 issue for glmmbeta method in transdiff when no random effect is provided • fix group factor issue for groupaggre in plotdiffbar of transdiff • fix coordflip FALSE feature order issue in plotdiffbar of transdiff • add groupaggre and grouptwosep params in plotdiffbar of transdiff • add addsig param in plotdiffbar func of transdiff • add documents in Return for Estimate in transalpha and transdiff • fix value scaling (< 1) minor issue in betareg in transdiff • fix group issue when no dataset in plotscatterplot function of transenv (customized usage) • use factor inside data when bygroup used in plotcor of transenv • check addabundtable input in calcor of transenv • unify Method name in statistics output of transalpha • add coefplot related parameters in plotalpha of transalpha • remove redundant spaces in factors of anova in transalpha • add FUNGuildconfidence param in calspefunc of transfunc • only tidy the first prefix in tidytaxonomy for multiple taxonomy names with same prefix (e.g., Kingdom level in Kraken) • fix abund NULL issue in calnetwork of transnetwork • add Std.Error for lm, lme, betareg and glmm models

- R
Published by ChiLiubio almost 2 years ago

microeco - microeco v1.7.1

• fix factor invalid issue for formula in trans_alpha

- R
Published by ChiLiubio about 2 years ago

microeco - microeco v1.7.0

• add calcaretList function in transclassifier • add lm and glmm method for caldiff in transenv • add edgeR method in transdiff • update FAPROTAX to v1.2.7 • add ytextsize parameter in plotcor of transenv • restructure rarefy function in microtable and transnorm • add rarefy, eBay, deseq2 and wrench method in transnorm • add Significance label for all methods in transalpha • extend bygroup for anova formula usage in transalpha • barfull instead of bartype param in plotbar of transabund • show all eigens in results of calordination of transbeta • add abundance checking and calculation in transclassifier • set same yaxis range for bygroup in plot of transalpha • fix factor issue for paired comparison in transdiff • fix group error in lme method of caldiff in transenv • fix metagenomeseq Group issue in transdiff • fix sampletable one column subsetting issue in transdiff • set factor for group and bygroup in transalpha • add detailed documentation for noderoles in transnetwork • fix repfasta load issue in new session • fix deletetaxonomylineage message issue in transabund • fix NA issue of COR method in trans_network

- R
Published by ChiLiubio about 2 years ago

microeco - microeco v1.6.0

• add transnorm class for data normalization and transformation • add bygroup param in calmanova and calanosim of transbeta class • fix kwdunn issue by space in groups for transalpha • filter index with NaN in transalpha • fix label issue in calsumlinks of transnetwork • skip error indexes for non-interger data in calalphadiv of microtable • fix colnames duplicate issue in plot of maaslin2 of transdiff • filter measure with same value for KWdunn in transdiff • check NA and name matching for othertaxa in calcor of transenv • add formula for FR in calspefuncperc function • optimize DESeq2 method in transdiff • add reference for rc-bray in transnullmodel • function stop if abundtable have very few features in plotdiffcladogram • Import ggplot2 >= 3.5.0

- R
Published by ChiLiubio about 2 years ago

microeco - microeco v1.5.0

• optimize ancombc2 method usage in transdiff class • support both group and formula input for linda method in transdiff class • design two output formats for linda in transdiff class • add scalespeciesratio parameter in calordination function of transbeta class • add loading arrow parameters for PCA in plotordination function of transbeta class • add lm method in transalpha and transdiff class • add messages for COR method in calnetwork of transnetwork class • fix plotfeatureimp error in transclassifier class • add group parameter in calprocess of transnullmodel class • fix the anova error in part of indexes with trycatch in transalpha class • skip the environmental variable with only one value in transenv class

- R
Published by ChiLiubio over 2 years ago

microeco - microeco v1.4.0

• add DCA method in calordination of transbeta • add glmmbeta option in method parameter of transdiff • add Pielou evenness index in calalphadiv function of microtable • add heatmap for formula usage in plotalpha of transalpha • fix the ordination axis text issue in transenv • use Machine double.eps in pseudo count of transdiff • change sortsamples parameter to default FALSE in plotbar of transvenn • fix tidytaxonomy function match issue in pattern parameter • add message for the transspefuncperc func in transfunc class • update the document of calalphadiv and cal_betadiv in microtable

- R
Published by ChiLiubio over 2 years ago

microeco - microeco v1.3.0

• fix bug of direction in transordination function of transenv class • add NMDSstresstextprefix parameter in plotordination function of transbeta class • add NMDSstresspos parameter in plotordination function of transbeta class • add modularity metric in calnetworkattr function of transnetwork class • add transspefuncperc function in transfunc class • force ggplot2 version >= 3.4.0 • fix textyorder for multiple groups in plotcor of transenv

- R
Published by ChiLiubio over 2 years ago

microeco - microeco v1.2.2

• fix error bar width issue in plotline of transabund • fix sample abund zero issue after feature filtering in tidydataset • update transalpha help document

- R
Published by ChiLiubio over 2 years ago

microeco - microeco v1.2.0

• add heatmap for formula usage in plotdiffbar of transdiff • add removeunknown parameter in transdiff • add line options for mean-se plot in transalpha class • add addsiglabelnumdec parameter in plotalpha of transalpha • add anovaposttest parameter in caldiff of transalpha • add closeness and eigenvector centrality in getnodetable of transnetwork class • add circlize method in plotsumlinks of transnetwork • add filterenv, trans and na.value parameters in plotcor of transenv • fix sample selection in transnullmodel • fix italic in plottaxaroles in transnetwork • fix calsumlinks tax extraction when taxalevel is not OTU • use deletetaxonomylineage & deletetaxonomyprefix params in transabund class • fix default zero removing issue of groups in KWdunn method of transalpha • fix relative abundance string bug in gexf file in transnetwork • fix relativeabundance null for Genus gexf file in transnetwork • rename simplifynames to keepfullname in plotdiffbar of trans_diff

- R
Published by ChiLiubio over 2 years ago

microeco - microeco v1.1.0

• fix the bug of node roles calculation in trans_network class

- R
Published by ChiLiubio almost 3 years ago

microeco - microeco v1.0.0

• add calanosim function in transbeta class • fix KWdunn bug when groups have hyphen in transalpha class • extend padjustmethod to KWdunn in transalpha class • add alpha param in caldiff of transalpha class • extend alpha param to anova letters in transdiff class • add ggpairs param in calautocor of transenv class • fix showtaxa select bug in transordination of transenv class • check usetaxanum in plotdiffcladogram func of transdiff class • optimize transvenn & delete redundant params • KWdunn letter ordered by medians from high to low • optimize filterthres parameter in transdiff class • fix group value NAN return NA bug in transalpha class • add standardize param in transenv class • extend filterthres param to more methods in transdiff class • add filterthres param in calcor of transenv class • add 'none' in plottype param of plotcor in transenv class • add xtextangle param in plotcor of transenv class • add Unassigned in pattern param of tidytaxonomy function • add checktaxaabund, checkmicrotable and checktaxlevel functions

- R
Published by ChiLiubio almost 3 years ago

microeco - microeco v0.20.0

• fix lefse lda result feature name bug in transdiff class • fix abs bug of lefse in transdiff class • optimize ystart and yincrease params in trans_alpha class

- R
Published by ChiLiubio almost 3 years ago

microeco - microeco v0.19.5

• fix funcaddgroups bug of FAPROTAX in calspefunc of transfunc class • update checkabund_table function in microtable class

- R
Published by ChiLiubio about 3 years ago

microeco - microeco v0.19.0

• add glmm method in transdiff and transalpha • restructure lme method in caldiff of transalpha • add maaslin2 method in transdiff and calcor of transenv • add transformation parameter in transdiff • add colorgroupmap param in plotdiffbar of transdiff • add SRS method in rarefysamples of microtable • add coordflip param in plotbar of transabund • add clusteringplot parameter in plotbar of transabund • allow petalcolor multiple values in plotvenn of transvenn • add returnmodel parameter in caldiff of transalpha • more data checking in plotcor of transenv • default character2numeric FALSE in transenv • add returnmodel parameter in caldiff of transalpha • update example dataset.RData

- R
Published by ChiLiubio about 3 years ago

microeco - microeco v0.17.0

• add savetable function in microtable class • add ggnested method for nested legend in plotbar of transabund • add plotradar function in transabund • add plotdonut function in transabund • create plottern function in transabund • add addlabel function in plotpie of transabund • add calNSTconvert function in transnullmodel • fix y axis bug in plotbar of transabund • create inner expandcolors function to expand more colors automatically • interpolate colors when not enough in transabund, transalpha and transbeta • add ggraphnodetext parameter in plotnetwork function • check input data format of microtable • set default colorvalues in plotsumlinks function • delete colorpalette20 variable • rename usecolors to colorvalues in plotclustering function of transbeta • reset default colorvalues in plotbar of transabund • fix addrownames2taxonomy for taxtable NULL in microtable • add Github and Issues link in microeco help document • rename all xtexttypehor parameters to xtextangle in transabund • delete ylabtitle parameter in plotbar of trans_abund • move igraph from 'Suggest' to 'Import'

- R
Published by ChiLiubio about 3 years ago

microeco - microeco v0.16.0

• add randomnetwork function in transnetwork • add linda method in transdiff • rename caltNST to calNST and add pNST method • fix plotgrouporder bug in plotgroupdistance function • add groupmorestats param in transabund • default clusterwalktrap for directed network in calmodule • parameters pass to bootstrapp in calpowerlaw • add stop message for only one biomarker in lefse • update document of each class • add more messages in plotdiffcladogram • fix group subset drop issue of data.frame in calmanova • more check on adddata in transenv • simplify padjustmethod in trans_diff • update example dataset, i.e. microtable object • add a help document of microeco

- R
Published by ChiLiubio about 3 years ago

microeco - microeco v0.15.0

• support regression in transclassifier • add plotfeatureimp func in transclassifier • KWdunn default letter instead of asterisk in transalpha and transdiff • mergeall param to support mpa format in saveabund of microtable • add lmequation param in plotscatterfit of transenv • fix coverage issue in microtable • more options in Upset plot in transvenn • add perc param in calspefuncperc of transfunc • add mergeby in calabund and sep in saveabund • fix group passing bug in transbeta • fix index checking in calordination of transenv • warning for NA in calspefunc • stop for no edge in calnetwork of transnetwork • adjust default padjusttype in calcor of transenv • support dataset NULL in transdiff • support dataset and networkmethod NULL in transnetwork • rename ANCOMBC to ancombc2 in transdiff • add DESeq2 method in transdiff • fix plotdiffabund issue for ancombc2 in trans_diff

- R
Published by ChiLiubio about 3 years ago

microeco - microeco v0.14.1

• fix plotcor of transenv for merging ggplot2 figures • fix Fisher index in cal_alphadiv of microtable

- R
Published by ChiLiubio over 3 years ago

microeco - microeco v0.14.0

• add lme and betareg models in transalpha and transdiff class • add byID param for transalpha and transdiff class • optimize calgroupdistancediff params of transbeta • xtextangle param in plotdiffabund of transdiff • fix calcor of transenv for only one feature • restructure facet param in transabund • rename calordinationenvfit in transenv • add calordinationanova function in transenv • add filtertaxa function in microtable • add orderedgroup and sep param in transbeta • add byID param in calgroupdistancediff of transbeta • update FAPROTAX to v1.2.6 in transfunc • optimize the ggplot in transabund

- R
Published by ChiLiubio over 3 years ago

microeco - microeco v0.13.0

1. add bygroup parameter in calgroupdistance of transbeta
2. create calgroupdistancediff function in transbeta
3. add bygroup param in calmantel of trans_env
4. multi-way anova table for transalpha and transdiff
5. opt inputtaxaname param in transabund
6. fix the abundance issue in getnodetable of trans_network
7. fix bug of pheatmap in plotheatmap of transabund
8. add scheirerRayHare test in transalpha and transdiff
9. ancombc2 instead of ancombc in trans_diff
10. use formula instead of anovaset in caldiff of trans_alpha

- R
Published by ChiLiubio over 3 years ago

microeco - microeco v0.12.0

1. add feature number checking in trans_network
2. fix cluster space issue in plotcor of transenv
3. optimize grouporder parameter in plotdiffcladogram in transdiff
4. add legendtitle param in plotheatmap of trans_abund
5. add spearman example in trans_env
6. add deleteunlinkednodes parameter in cal_network function
7. add facet3 parameter in plotbar and plotheatmap function of trans_abund
8. add more measure checking in trans_beta
9. auto calculate abundance in calcor of transenv if missing
10. add ANCOMBC method in trans_diff class
11. optimize trans_diff to plot abundance for all the methods
12. fix the bug in KWdunn of transdiff when all abund equal
13. add others abundance in alluvium of trans_abund
14. add ALDEx2t and ALDEx2kw methods in trans_diff
15. optimize calCscore of transnullmodel
16. opt plotdiffabund in trans_diff
17. add bygroup param in transalpha for sub-group test and plotting

- R
Published by ChiLiubio over 3 years ago

microeco - microeco v0.11.0

1. rename calcor to cormethod in trans_network$new
2. add 'bray', 'bicor', 'cclasso' and 'ccrepe' options in cormethod of transnetwork$new
3. add useWGCNApearsonspearman and useNetCoMipearsonspearman parameters in trans_network$new
4. add plotdiff function in transenv
5. fix the bug in getnodetable when tax_table is not available
6. move calsumlinks and plotsumlinks functions back to trans_network class
7. fix the bug from 'IncertaeSedis' in plotdiff_cladogram
8. check the diag of adjacency matrix in cal_network
9. add label related parameters in plottaxaroles of trans_network
10. rename selectsamples to orderx in plotspefunc_perc
11. fix the error when only one label in calsumlinks
12. create plotbar function in transvenn
13. change CORoptimizationlowhigh parameter in calnetwork

- R
Published by ChiLiubio almost 4 years ago

microeco - microeco v0.10.0

1.fix the bug for spieceasi glasso method in calnetwork 2.optimize the network construction of spieceasi method 3.change calcor NULL for non-cor methods in transnetwork 4.add errorbarwidth parameter in plotline of transabund 5.modify the print function in classes 6.change parameter names in plotdiff of transalpha 7.add labeltextsize parameter in plotdiff of transalpha 8.fix the bug of anova when one measure is used in caldiff of transalpha 9.check group names when addsig = T in plotdiff_abund

- R
Published by ChiLiubio about 4 years ago

microeco - microeco v0.9.0

1.fix the bug for wilcox test when method = "lefse" in transdiff 2.add plotline function for line chart in transabund 3.add addsig parameter for significance label for all the methods in plotdiffabund 4.reuse KW test for two groups in first step of lefse in transdiff 5.add addsig parameter in plotdiffabund of transdiff 6.fix the warning in caltax4fun 7.save reference profile and add KO names in caltax4fun2 8.correct the parameter in calmanova example 9.check julia software for networkmethod = FlashWeave in calnetwork function 10.add CORoptimizationlowhigh parameter in calnetwork function 11.rename yincreae parameter to yincrease in plotalpha of transalpha 12.optimize addtaxaname parameter in calnetwork of transnetwork

- R
Published by ChiLiubio about 4 years ago

microeco - microeco v0.8.0

1. optimize caldiff and plotalpha functions in trans_alpha class
2. add tNST method in trans_nullmodel class
3. add more differential test method in trans_diff class
4. restructure and optimize the return data and function name and structure of trans_diff class
5. optimize plotordination of transbeta class to make it flexible
6. add getadjacencymatrix function in trans_network
7. add transcomm function in transnetwork
8. use calpowerlaw function instead of previous two functions in transnetwork
9. add caldiff function in transenv class
10. add calautocor function in transenv class
11. reshape plotordination function of transbeta class
12. fix the bug in calmanova and reshape this function of transbeta class
13. optimize plotscatterfit function of transenv class for multiple groups
14. rename return data and optimize the code in trans_abund
15. rename transvenncom to transcomm function in transvenn class

- R
Published by ChiLiubio about 4 years ago

microeco - microeco v0.7.5

1. add more parameters for ordination plotting in trans_env
2. optimize p value adjustment of correlation network
3. add Recall-precision plot in plotROC of transclassifier
4. optimize FlashWeave network parameters input in trans_network
5. optimize network node roles plot
6. add tutorial wetsite hyperlink in the help document
7. add othertextshow and other parameter in plot_venn
8. add more checking blocks in microtable class
9. add more parameters in tidy_taxonomy function
10. add calpreProcess function in transclassifier
11. use getnodetable instead of calnodetype and optimize the function
12. add network plotting with igraph and networkD3 package
13. add network method based on the beemStatic package
14. optimize cal_manova and use adonis2 instead of adonis
15. add more null models in transsesbetampd and transsesbetamntd

- R
Published by ChiLiubio about 4 years ago

microeco - microeco v0.7.0

1. add trans_classifier class
2. add CCA method in trans_env class and rename functions associated with ordination.
3. optimize scaled-up methods and parameters in transordination of transenv class.
4. optimize the format of returned pathway files of caltax4fun2 in transfunc class.
5. optimize classes to accept null microtable object when created for external data analysis.
6. optimize text size adjustment parameters in plotlefsecladogram of trans_diff class
7. add taxa abundance filtering in transdiff and transclassifier object creating
8. add KWdunn for Dunn's Kruskal-Wallis Multiple Comparisons in transalpha$caldiff and transdiff$new.
9. optimize KW method in transalpha$caldiff and trans_diff$new.
10. add dendrogram option for clustering based on ggplot2 in plotcor of transenv class.
11. add colors instance
12. change useOTUsfrequency to usefrequency in transvenncom function of transvenn class.
13. fix the bug in transfunc$caltax4fun2_FRI()
14. fix the warnings in plotlefsecladogram of trans_diff class

- R
Published by ChiLiubio over 4 years ago

microeco - microeco v0.6.5

1. Add project url and lazydata in description.
2. Optimize plotgroupdistance function of trans_beta class.
3. Use lapply instead of sapply to avoid conflict in trans_nullmodel class.
4. Optimize color parameters in plotcor function of transenv class.
5. Add facet2 parameter in plotbar function of transabund class.
6. Add DNAStringSet class of rep_fasta in microtable used for tax4fun2.
7. Optimize calsesbetamntd function in trans_nullmodel class.

- R
Published by ChiLiubio over 4 years ago

microeco - microeco v0.6.0

1. Add getedgetable function in trans_network to get edges table easily.
2. Add more available methods in function calmodule of transnetwork.
3. Add the otutable checking in tidydataset function of microtable to remove taxa and samples with 0 abundance.
4. Add paircomparefiltermatch and paircomparefilterselect parameters and delete paircomparefilter in plotgroupdistance function in trans_beta.
5. Add the multi-factor analysis of variance in caldiff of transalpha class.
6. Add filterfeature parameter in plotcor of trans_env to filter taxa that are not required to show in the plot.
7. Use binary data for jaccard index in cal_betadiv of microtable class.
8. Add C-score calculation in trans_nullmodel class.
9. Add add_rownames2taxonomy function in microtable class.
10. Add the message in calnodetype of trans_network when NaN occur.
11. Add more available null model methods in calrcbray of transnullmodel class.
12. Add calpowerlawp and calpowerlawfit functions in trans_network class.
13. Add rename_taxa function in microtable to rename all taxa names easily.

- R
Published by ChiLiubio over 4 years ago

microeco - microeco v0.5.0

1. Remove the non-ASCII characters in fungifuncFungalTraits dataset to make it in line with the that in CRAN.
2. Remove the non-ASCII characters in author's name of FungalTraits in trans_func.R.
3. Modify tidy_taxonomy function to optimize the prefix with only one underline.
4. Add the betadisper analysis in trans_beta class.
5. Add NJC19 database in trans_func class.
6. Add function calrdaenvsquare() to get the contribution of each environmental variable in RDA.
7. Add function plotscatterfit() for the scatter fitting in transenv class.
8. Move funtions calsumlinks() and plotsumlinks() of microeco to package mecodev.
9. Fix the bug of taxa names mismatching in trans_network class
10. Add the parameter character2numeric to transform all the characters and factors to numeric of envdata in transenv class.
11. Add calordination function in transbeta class.
12. Rename plotcorr function to plotcor function in trans_env class.
13. Add more citations in messages.
14. Reshape codes to make them regularly.

- R
Published by ChiLiubio almost 5 years ago

microeco - microeco v0.4.0

1. Add the rep_fasta to store the representative sequences in the microtable object.
2. Add the tax4fun2 method for the functional prediction of prokaryotic community.
3. Filter the taxa in which the sum of abundance is zero in otu_table.
4. Check whether the phylogenetic tree is rooted in microtable class.
5. Add the R2 and significance test in calrda() of transenv class.
6. Move file reading and converting functions to package file2meco.
7. Optimize the calabund() to make it more flexible and compatible with the mixed user-defined data structure in taxtable.
8. Support the abundance calculation for multiple map correspondance of taxtable in calabund().
9. Add sub-network extracting by selecting edge label in subsetnetwork function of transnetwork class.
10. Add calmodule function in transnetwork class to support module classification in specialized sub-network.

- R
Published by ChiLiubio about 5 years ago

microeco - microeco v0.3.3

1. Sample names in dataset were modified to make them clear for users.
2. Add the library(ape) in README.
3. Fix the bug in orderx parameter in transabund class.
4. Update the tutorial.
5. Add the biomarker test method from metagenomeSeq package.
6. Update the prokaryotic trait database.
7. Add the FungalTraits database for fungi trait identification and analysis.

- R
Published by ChiLiubio about 5 years ago

microeco - microeco v0.3.2

1. Add the checking on whether the columns of otu_table of microtable object is numeric type.
2. Fix the bug of color assignment in plotlefsecladogram() of trans_diff class.
3. Add the SPIEC-EASI method in trans_network class.
4. Optimize the plotting in trans_alpha.
5. Optimize the help documents.
6. Compress the data size in data directory for the uploading to CRAN.
7. Add detailed citation information in inst/CITATION.
8. Add functions for the conversion between microtable and phyloseq objects.
9. Add function for transforming QIIME2 results to microtable object directly.
10. Fix all the example executable issues.
11. Add detailed references and author information in the corresponding functions.

- R
Published by ChiLiubio over 5 years ago

microeco - microeco v0.2.0

Modify the help documents style, now each class has one integral documentation. Add the fungi guild analysis from the FUNGuild database. Fix the bug of the error from the strong collinearity in linear discriminant analysis in Lefse of transdiff class, when sample number is small in groups. Fix the bug of showtaxa parameter of transrda in transenv class. Add another taxa roles plot in plottaxaroles function of transnetwork class. Change several function names in transfunc class. Add eigengenes analysis of modules in trans_network class.

- R
Published by ChiLiubio almost 6 years ago

microeco - microeco v0.1.4

Add the correlation plot for different groups in transenv Correct the wrong name in the help document of calabund Add the random seed parameter in the rarefy_samples in case of the R version problems

- R
Published by ChiLiubio about 6 years ago

microeco - microeco v0.1.3

Modify the names of functions identifying prokaryotic traits to make them more recognizable

- R
Published by ChiLiubio about 6 years ago

microeco - microeco v0.1.2

Add the alluvial plot in plot_bar Add the raw otu table file in the inst

- R
Published by ChiLiubio about 6 years ago

microeco - microeco v0.1.1

Add the LEfSe cladogram function

- R
Published by ChiLiubio about 6 years ago

microeco - microeco v0.1.0

• Plotting the taxonomic abundance
• Venn diagram
• Alpha diversity
• Beta diversity
• Differential abundance analysis
• Physicochemical data analysis
• Network analysis
• Null model analysis
• Functional analysis

- R
Published by ChiLiubio about 6 years ago