From 30c387396412e2b4f19b577378d09ab51db38dd9 Mon Sep 17 00:00:00 2001 From: TuomasBorman Date: Tue, 5 Nov 2024 21:51:54 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20microbio?= =?UTF-8?q?me/mia@0dc4943b403fae05b1f78c9d5aac1bce9de7395e=20=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- 404.html | 2 +- CONTRIBUTING.html | 2 +- LICENSE-text.html | 2 +- articles/index.html | 2 +- articles/mia.html | 6 +- authors.html | 8 +- index.html | 2 +- pkgdown.yml | 2 +- reference/GlobalPatterns.html | 4 +- reference/HintikkaXOData.html | 4 +- reference/Tengeler2020.html | 4 +- reference/Tito2024QMP.html | 4 +- reference/addAlpha.html | 4 +- reference/addCluster.html | 4 +- reference/addDivergence.html | 4 +- reference/addLDA-1.png | Bin 17716 -> 17731 bytes reference/addLDA.html | 16 +- reference/addNMF.html | 4 +- reference/agglomerate-methods.html | 4 +- reference/agglomerateByPrevalence.html | 4 +- reference/calculateDMN.html | 4 +- reference/convertFromDADA2.html | 4 +- reference/convertFromPhyloseq.html | 4 +- reference/deprecate.html | 4 +- reference/dmn_se.html | 4 +- reference/enterotype.html | 4 +- reference/esophagus.html | 4 +- reference/getCrossAssociation.html | 4 +- reference/getDissimilarity.html | 4 +- reference/getDominant.html | 4 +- reference/getMediation.html | 4 +- reference/getPERMANOVA.html | 244 +++++++++++++++++++++++++ reference/getPrevalence.html | 4 +- reference/hierarchy-tree.html | 4 +- reference/importBIOM.html | 4 +- reference/importHUMAnN.html | 4 +- reference/importMetaPhlAn.html | 4 +- reference/importMothur.html | 4 +- reference/importQIIME2.html | 4 +- reference/importTaxpasta.html | 4 +- reference/index.html | 6 +- reference/isContaminant.html | 4 +- reference/meltSE.html | 4 +- reference/mergeSEs.html | 4 +- reference/mia-datasets.html | 4 +- reference/mia-package.html | 4 +- reference/peerj13075.html | 4 +- reference/rarefyAssay.html | 4 +- reference/runCCA.html | 33 ++-- reference/runDPCoA.html | 4 +- reference/runNMDS.html | 4 +- reference/splitOn.html | 4 +- reference/summaries.html | 4 +- reference/taxonomy-methods.html | 4 +- reference/transformAssay.html | 4 +- sitemap.xml | 1 + 56 files changed, 373 insertions(+), 121 deletions(-) create mode 100644 reference/getPERMANOVA.html diff --git a/404.html b/404.html index 43887393b..ddc2d6713 100644 --- a/404.html +++ b/404.html @@ -32,7 +32,7 @@ mia - 1.15.4 + 1.15.5 diff --git a/CONTRIBUTING.html b/CONTRIBUTING.html index ff0888ba8..1edcdbaa5 100644 --- a/CONTRIBUTING.html +++ b/CONTRIBUTING.html @@ -17,7 +17,7 @@ mia - 1.15.4 + 1.15.5 diff --git a/LICENSE-text.html b/LICENSE-text.html index 609040780..783432e58 100644 --- a/LICENSE-text.html +++ b/LICENSE-text.html @@ -17,7 +17,7 @@ mia - 1.15.4 + 1.15.5 diff --git a/articles/index.html b/articles/index.html index dae0dae2d..ad8b6d06b 100644 --- a/articles/index.html +++ b/articles/index.html @@ -17,7 +17,7 @@ mia - 1.15.4 + 1.15.5 diff --git a/articles/mia.html b/articles/mia.html index 9fe6804ad..c45300543 100644 --- a/articles/mia.html +++ b/articles/mia.html @@ -32,7 +32,7 @@ mia - 1.15.4 + 1.15.5 @@ -69,7 +69,7 @@

mia: Microbiome analysis tools

2024-11-05

- Source: vignettes/mia.Rmd + Source: vignettes/mia.Rmd @@ -600,7 +600,7 @@

Session info## other attached packages: ## [1] phyloseq_1.50.0 scater_1.34.0 ## [3] ggplot2_3.5.1 scuttle_1.16.0 -## [5] mia_1.15.4 TreeSummarizedExperiment_2.14.0 +## [5] mia_1.15.5 TreeSummarizedExperiment_2.14.0 ## [7] Biostrings_2.74.0 XVector_0.46.0 ## [9] SingleCellExperiment_1.28.0 MultiAssayExperiment_1.32.0 ## [11] SummarizedExperiment_1.36.0 Biobase_2.66.0 diff --git a/authors.html b/authors.html index f94ba48dc..32538cc8e 100644 --- a/authors.html +++ b/authors.html @@ -17,7 +17,7 @@ mia - 1.15.4 + 1.15.5 @@ -168,20 +168,20 @@

Authors and Citation

Citation

- Source: DESCRIPTION + Source: DESCRIPTION

Borman T, Ernst F, Shetty S, Lahti L (2024). mia: Microbiome analysis. -R package version 1.15.4, https://github.com/microbiome/mia. +R package version 1.15.5, https://github.com/microbiome/mia. 

@Manual{,
   title = {mia: Microbiome analysis},
   author = {Tuomas Borman and Felix G.M. Ernst and Sudarshan A. Shetty and Leo Lahti},
   year = {2024},
-  note = {R package version 1.15.4},
+  note = {R package version 1.15.5},
   url = {https://github.com/microbiome/mia},
 }
diff --git a/index.html b/index.html index 22a7dd385..0ce75504b 100644 --- a/index.html +++ b/index.html @@ -33,7 +33,7 @@ mia - 1.15.4 + 1.15.5 diff --git a/pkgdown.yml b/pkgdown.yml index 8cf6c9127..1cba84b00 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -3,4 +3,4 @@ pkgdown: 2.1.1 pkgdown_sha: ~ articles: mia: mia.html -last_built: 2024-11-05T08:39Z +last_built: 2024-11-05T21:48Z diff --git a/reference/GlobalPatterns.html b/reference/GlobalPatterns.html index 7a0b5aeb4..f9c42c26b 100644 --- a/reference/GlobalPatterns.html +++ b/reference/GlobalPatterns.html @@ -24,7 +24,7 @@ mia - 1.15.4 + 1.15.5 @@ -51,7 +51,7 @@

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample.

- Source: R/mia.R + Source: R/mia.R
diff --git a/reference/HintikkaXOData.html b/reference/HintikkaXOData.html index e4f058522..86dd3fea3 100644 --- a/reference/HintikkaXOData.html +++ b/reference/HintikkaXOData.html @@ -23,7 +23,7 @@ mia - 1.15.4 + 1.15.5
@@ -50,7 +50,7 @@

Multiomics dataset from 40 rat samples

- Source: R/mia.R + Source: R/mia.R
diff --git a/reference/Tengeler2020.html b/reference/Tengeler2020.html index 1e59cda0f..448ac8353 100644 --- a/reference/Tengeler2020.html +++ b/reference/Tengeler2020.html @@ -22,7 +22,7 @@ mia - 1.15.4 + 1.15.5
@@ -49,7 +49,7 @@

Gut microbiota profiles of 27 individuals with ADHD and healthy controls

- Source: R/mia.R + Source: R/mia.R
diff --git a/reference/Tito2024QMP.html b/reference/Tito2024QMP.html index cfaed2608..747d03af3 100644 --- a/reference/Tito2024QMP.html +++ b/reference/Tito2024QMP.html @@ -23,7 +23,7 @@ mia - 1.15.4 + 1.15.5
@@ -50,7 +50,7 @@

Fecal microbiota samples from 589 patients across different colorectal cancer stages

- Source: R/mia.R + Source: R/mia.R
diff --git a/reference/addAlpha.html b/reference/addAlpha.html index f38aebf92..43ac830f3 100644 --- a/reference/addAlpha.html +++ b/reference/addAlpha.html @@ -18,7 +18,7 @@ mia - 1.15.4 + 1.15.5
@@ -45,7 +45,7 @@

Estimate alpha diversity indices

- Source: R/addAlpha.R + Source: R/addAlpha.R
diff --git a/reference/addCluster.html b/reference/addCluster.html index 309b86ce1..7207d19ad 100644 --- a/reference/addCluster.html +++ b/reference/addCluster.html @@ -18,7 +18,7 @@ mia - 1.15.4 + 1.15.5
@@ -45,7 +45,7 @@

Clustering wrapper

- Source: R/cluster.R + Source: R/cluster.R
diff --git a/reference/addDivergence.html b/reference/addDivergence.html index 55296293d..360151c0d 100644 --- a/reference/addDivergence.html +++ b/reference/addDivergence.html @@ -17,7 +17,7 @@ mia - 1.15.4 + 1.15.5
@@ -44,7 +44,7 @@

Estimate divergence

- Source: R/addDivergence.R + Source: R/addDivergence.R
diff --git a/reference/addLDA-1.png b/reference/addLDA-1.png index 0fe75d7fd4662716042e04334c5a12dfd6f7cb97..6dba3786338118883d7406903d5dacec55150483 100644 GIT binary patch literal 17731 zcmeHv2~<;8_ir2!tqo{Vsf@L@4xb1pN(2P7XsJ~JB?Ds!BBBBT#E=jSi4#<1sKtWH z$M6?>_zdC@twCAh3?-p;!`e>QZdAlY0#7NF9b&hx}7GGLD)vJon8<3G3#k>D(zuh_G zJP@c`;lKX+7YF{uf&T*>ur+kb3`F#GZaIv;6yY+i8zRmg=YcV&XisnSNDbyUlLejRB1#p;A&o?%tUu9&4&SWG>6xz2D zo?$x|bImS?z_aK+?mzODYroifFT`t~j9XugFVuc%zrirpJ_(N&bG1)|-S>lf+UL#9 z3v9Gc-XU|&*g}GlVmdlw4tom-#Mh`a`9U!m~9F2jswd8S8NqzlY77Dev9;l0zyARiTqRG9#yw$eXY;vM(9NZA@HP;X4J7TYzOOvLf0b_c;p+xNIh+AXqQFtC{oN7 zmB!%5@SMr5paPS?boKGlol>;VLVOLU4G^H6fVn`LB)D~;hAO0}v%#=6*tJ@+W=RZV zXaJLi4a3s0xiP=S7#3^p)q9d+RQ5F+!#Wl#jIZL>bUx&Uo+`a=na{QGbcq-Wlks$~%(nM`yW zsR-}6+mb1TQb)s7sD?mv#y ze);dn)iR215hs5BUl+~)M`_( zovJ8D~a?aL^rRzaFLe5223bm9S;XdlM!_#Y(n$vto z!E{ZGRFIlZ5C83%b~K|$dmIr)0^A%|*^(4kOMmg=paKN*aapP9P5seEHN!w3dccd8 zAP)fpam9)%=vnIKc|I_c(fQ#^W76MEpOIfQ#mlSk-Qx|rVWX!dT!t3gzuU*j41Ah% z>SbBE$Tt_OK16!rI6`Amsib5`vBpbhDsA2Tc0_PZnOSLk2{Qpz6;vDUrb;pgjZGI0 zZecc+umb-&_zi=BtZ+b)rmrQ>t3UZt`}`-{{pwyYJ`T+

V@|bxT0BZ5+(aO2An9 zPEhzuXhMI?0Jy`cQD&cqV#aC5c2_Ls7C(u?a5ms4kAP8!xEr)@BepEWcfBQnMPSFW zE@cPw0BW5-0Y>Cuo|8=$hKzqKptVsB1(Qi9NG}NhHyfA&d(q_(9~etNF%tBSx~K1eX4~jP7B_FI-^nfV1LUXjrZXRsz|$wPcd~1(cbDZ%pr*_d<;4 z2YH-xiqmtd@q@{06EG^(wC2U*zs(EpUbu-I7^8lZ_yl z`e(Cb>_EfY2?Y*y*!LUl3T$1q3Vn5v#X$YgiBkhUG;cX0X;9IAvE7xpJ80m=ykR*@gt98CV&-;Z)rK+D=6Ns2?XZ~I{>0j#3?N$UcgccDj!_fpFc4EH|-0?VcAXC zfoVUy>ns0*Xnjx}2xC07=h}Q72qSz8lkhAg20GU$ zGgf!fz2(oKUg$A&9b9IVr~{6S$Wsu$E~r@K<6K-HD1QL8Y{Anh@)1ax^g?ldd7*Az zg1^u4TBRZA0J<`z0nQEe=gvijx%DL}Faq>kc|CvO{DKJ!6~%e4qu19o=$ly<<#m;* zvPw>oTM}rRisf25grbhfr&r>(a(;F2|1sgxK_Cm=;wP^-$*H znxA=`kF&=}`;!ewp8n$7o#x_!9f7y3Zs~#?##iGWZ@ZTXsCZKURlYIKhABeRprwL- zhdkGFtLBd<;sDI;oreoKuMRQ=Xn{xB8l5f5+#bqP$w7<}3rBkY$GkI(Sj#_D+Z6^F zrIjTaDW6U0064;|^~M63G1CT9z={>A`SF%F=SeWOMm=LFP6`uxbY>sX{^#|n!3Hn=BxW|yR7%|a*iYA`=HYrI#T8|-MfhsPI368H z+p%BA_-Kl|$vA5yj4x+pM?aT9mmngz87bM~f~Un?k?V$Lzks(Bb-1<*8>>3)UR|J^ zUDuj>RLzDq(@6Ap1EqPsYT>tE=#2eHSY`k5NPttJJS0zYOR0;JUx7}QXc~93>Wh1K z#_PgWo|XBZ1|k85pDu7k3#*<@xw9X`` zm^_&kr~}9cNklh~cSfV`LqElhCswJOrO&*kE}E+iM3N7G`FO+aQV6;WZUiy_{@D+i zy1u-*ZNnXBXC(ingPS^-PKKhbEuU75}>N!K$s)>i$IAPSaeWNA7T3g!b(=u&o()kZC;MD6a zi9G2ro&lz{q`1~OM&(q>x|vhz2v$j6koqS%52}J{p|J_M0_S8{-oa+ig~^}lb#Z>; zm_n}f{{Uc@Uew3ps$3c8!bs5GR?Qxg@M?J$S|MbZWQ7Lt63T|5)qu?g6HC;=@3U0Tx|SE9jX(cBG-BuUnFW>%Ze(U*>7sEv2XwdU zC1#{a#n?7bKmD8Wd|F};90pYDqqAyUf92kx9wVu*ibei3b;TC}75+Fyp#@frcAHk^ zC5@A-8Hxs^Yvm|xW$u_5@7KXi?dXOOK>QhWLMzao(s5@h8z}XCUl$a<^eHYOk~p8) zxWOQQb!}{z>MhR#vzSJ>-E$f!HByqzG*30f#!JO0t~ODNAiQ=uv3E4@)rz-`57+fK zG*Ttgy%$Z0UrkMqz13;%u4C7hQaXuCqb;3X5<^Jhq?#}13hVE!`%I&ef=S7GZxFWC z{utNp7j~)(N%re)m=<94#RFOa_T{+A>AeHt3guKXcZ>PJieHPz{!|V3Jm;)&GD%ES zr8&I1m{r$v#JNO?4ib8w8e(~JN#-!k z)W_AV$hd0GXqjs-)P(Nwg#(@8T~ljKvD!GPJ=>gXbn}e9%%5oqxNy=Of{OEea=q2k zOVzd|`KOo0lRe71=%vylv@;i~3D+B|;pp>Gk_(4^?$;O;&ZdZUy8DSLh&jn@L*3D0 zSjORD`!;LBk~l2cFQ)yv1-Jc)Y{x8HIXZf?Qie*m!T+=$?p0RZ-Mrim&a4=C6tcpn zqvWH4ZL;E+j@5NB-@(mhX$Qca&mw$aZsVO&!{{AElr9I4(B62T_| z;}0)krIHM!r~pW8qH)z?ux?w}_Zwpd0&_79uv9dL><-!;yfyoIfoY<3(-C!qoCK1w zp5fCU6wTZR>js@mso;h1#RgIZ6NMe{cIMvQIJFg=14J*!4_xv$a5RNU5|$*E2ebRc zro`JdubQdjdA4Z-eJ`$&ohWD(-69J+K>4Ly)#@C&2vZPR5>x{BJ<6ebT47U-DI(|$qypFP4%}hc?2O7_7$$e=!Hw2D%x}t+eOh#^TUQ)jl{v^GXPFJ9rIOQ>|K|1D4tSY0wj-KOmq6yr^nmh({)n zDE~fx+Jn1nv5VghE%`Fcsh76rHB0^Pgan;|CO{e( z*fnma0~EU+?3d)w+(}tbHlUADlzJ4gwC=ofycrtNqp9oaxI>l)y>0i8pHOEcD#HJBHOHWA$d19?YlvB9#mVT!>|Yf4gO6d zU+ZhuxoVz?`2n8Fb3>`FGlS%G;_nzO`uJZ-ang5NO}b9Ilc=ymbpay*Q|3XYA=;8f z#1GEH_wH9~R*p*xJ6L$XTw$tLO)qT0Mx6!p_(^PKGd1PhgHcitQ&cT(h#=b8P_Lq1KM>vt4OOzBT9Rcnt!yZR;ECf7Vm z*tVrxbQ&M>(J>V<8eNdY5lKoq{DyN>tedf&df=0h3eJ$)8B>9yKjKqbP)Cj{IA8|F^jMvP%$o}Vx*NAVJB z052MpPw6wAjkajRCY1kN*+1Z8dQ@s;0@OmI-udckmmSNu?&8ik#@fI$8$D zV0^DPJo643-58)tVK6X<){Zwa9izC3r0Uqm)$=OCg8{V&3c_{*jcjU^ocE~Vy4F%4 z5cfB?2vqiqxhRY!(7_a;8mH!%;exW(TSi?veJy)+<-l|d-CzA_;c0Cf0u~wr zNAi{g z++AhrgmUa3QUkYjnsr76iMa|hTT5+!#?G7D2c3z#2PjXE1W7U%jm-0QiPrR|iYvPu zWH5+-V)XYQ>^;o###6iJ(4@B};v6q^--L4OziWe$J-VT$w=Sua*0HM*!u)e%Vm)<= zLW`5%g;dNw*4MGe-0r9b;oa6UvoKj6f2m2;eQHcK*_^KjmbY!neAq1M8*%9+#M|>m0**6}IE4)yfn(|s zXfLP+yqTlSYo@(+=gR8i_Xg>BKxp$n9)76-3`*Cf9uP*^_4{>fK$srC?nEJ@3vhrq6ez%z77=~-m?O%Lctm|b(fc6iG+C}V zSfUNR(s(hT9#Tz){fkd-S;{frt3sqqHPdFjcyN=sxB8@8=?thzObC(}CIy{?P476^ z5jm}R%?dSsoG7lEv#dd3I!mOu+&3#UB4#~Vehn!xnM$R#Y`+@1c`=uVh10)VC36X5 zx1qzx{Ga3f;b=vG|2^n9OsW{pJN}vTQbTXY|3_o_18;e|a029*XskH(%JRng_b&x# zR~#+IOi@4f4o3L9er1p|;!mksdYxD?9TJl`rL+X!c&ENQ0G_npxoN1gd<&Cfd18!> z3HqAv8riJ15bde(pt`CdWV{4MFSY79uM?w2;|pV_NRolyRYJJd_ead^#@9@^E8+VE zvc+k)qD!38#jbcUmz*Yky`fkSv1TX+DKQpd)jcL+E=!pWd4O(f&{{*%_Xai@?}uk< zNgaJCkpUiI&(Tj8%g=o=lnH~ik{oTkngL6-T0Jof_euCnX(YgrKVjt*t@qvVXb!oD z()jx9L%0{OYJqI->(2B-ol(ZR?#4Hr)b(uKk>?p8=K80KZRQ2@kjXgS*ZCATk?i(@ z^KS+@DZ6R`??jDE#*Fe8b7@V}+%a9nlaTvAYoFcUZUtWhmL++DUJcQ)n%YiLcjYFi$rW>~C2NYY1a~Y$B;NNyw$61Hm$X*r7cKy_r!gO@yx=Jibgm zzrO5Irm;@%B6d0be_sLpU(I~aH8nUHW{p{W*sYPA4O{o!rNEx+`}G#<`Cf`yym(2p zPv}Zp#=_Ri`@ePk+b^|4zg&&ytv24X)OORiPLG%VyvjZK@cm8KmV9k=eQWW$2d@uz zS{6uSw;WakzEX4*#mdB!yTuL|w#a*y!pzTL1~ten5H~mJX`?9wZ{OzmL)mb8pnE}K z(mnN6a9O2FpLy*>g0`Kpe)~nTSpnLx2=7O$aP*-O<5U@781o>|+0nY2>qxrsK-&$0 zCY_VNMqZZQJxtUGDw!E;@~GhroT0f+pw&PtOuWJl;)g39mQGJ^_}&YS@hH+fs(&9$ zpQE^aj8AN_5;<3v3-VGMG!gwVUvM-RgNgev;@L5g$ffJ8=G#>ov-P#u3ADb!0!#8>~ zkGE1-o$XTv#O7EX#4vg^7?`4HpCb2M5ZB8i<}_O=u!6!G_jnce+C)WW-48Y466|Np*tzBj&wJG3$OGGT!z-pz%?Vkxg|G|A zO!BQQ4fi>y&;tk1;^)$!SJ5kLjF_*Pqd0bHV?n*Nf6|$y{BZ1^j!|ADF;t2CUi!Yr zy2zqx{Eh#p5IGlw-x;TiBYq^sxp|&dcJF=E{uT0?yaob*jc9Sy+uFI}JapiFWk%%F zc~1QLy~!HcTL=}_hXJzft(u~RN$*Xk&_NNK7@eh}puk-}AJwh1XfuUR3YL>A=Py2Z zTm8Lkd*qAxD>qjv_O(=v6{Y2Kn&`#fXov8oS8-pT$$%EcDil^9=w#29{ev~fS{2Lu z$92)qo-gqBBMzVud)lG2{7I+IS##1ZWTj5?AvaJ2^B=%%#LZRcb?R1XyEXv`e;(<5 z7E3C0j2+WWkphh+<$d^Ee(}()weVbJ$`9S^v{N(Qm#sE_u9ZXtVevmL@QjmIs9XWf zsdu`XF7LM^FMT2L{(jO1cv5b-wM&!iXH(ShWfm( zAl>}QO-kg_XmT4 zE;grcK2K=w-m9DPeNEID!tA9!(-gh2T`IHOwj5CwAB4-r3m*@Ayp3DhvNg6BjS++0&Ub=qq?bVJg+tw(Z*euzsed0A5y{6>Ld)dxk>Qk*-$(qMnu^l{f1WucnWv4%%5)8bH!A1Cp zhT6c5>>aRmDGT2O+w!#M`pix=s+d@FWmpQ9Rkb)V7x`PlkzO})6?_i-kynuC2{xU2 zkv|6H*>lvNwtB*XF=hf&XM`x0gWto~3izdVQ?+nWybII=Cu>k}@K~0iwWMjnWWX{< zs7dXKt6ra?x()pf8kwBXxD+ejF8l;<$>~jFIn0u=6*h$)%*2M^HL?(Zy`%Ugr?fs) z9t1RiVv}dWCX4Sk!>1qM5r#=-+VNrc(D$wj%-=bykd8}U!6_Q!<1qJy(y=7PpE?bCD_(#054%I!n#7IueSfNLr3T9 z>W6N?{Dwb-ds;rgAESr!8vbAV!k_08CI26jm_I0<^_do^5qu78!Q~fi1afs}Gs zG5)3n2N6x9=%%C2vzyZCMM^mo23%XS`U?c(qc_Y>-V|JT?S%lQ8U%nQrb}QTpo{{A zfF&S3A}pvU=upAvF2E6;>j1kShF{fpgU!J&ka>V{DaHN4hNxb0l+R%IPKP@duxWzj-YsxfUl1*WUy{-k{rt$-cL_{? zG`R?N1Enqj4R!T|Dl~%komTG%2|4~k&fTg6`Gz#kWW-#$zxgi@&nn=gR%F_zX@Chc zxT$O(OfjjF=?3a7dH0EdSL2Q1*C588(jFPc4+sc6m3^k%3@&sC#;KM}mzU9d8}o0g z)gW@tzyK3eXkqJd2+@rVL(Q_Ku#ZESYOPD$HD}P@M5N+Y$V=%l521$2iOycpNvrdg zQIrxxtY;}J`qDN56K`)yJ_S^A77z-&#vd<+nZXdg3kN!PaOdJlr04fjIKFbj${1OR zN8nG6t!DtJ4OyzV*tM2Z04iRH$?v}X8u18bmC*z3l-W)wtJl$m%5(Ar@IIiz3n?%AkoyfUq^^?|XQO`#TZRf-zB*BrR3nP$vHiv$N4Fp3t=7N+Z4^SM^)Q`t}>>9`{ zeYPVor*fj+q92vt>*-z&m|A^j&g=3XC!UwH-ociY*EQ20LGRs=?$j8(M4V-M6(5(k zWyhgkih?CV@y;6-?w=k)2>=R>E6S^rd_?&8X{D6$Bz`V}KAQA6?!L6!Hhc0SveKz1 z-ohu4?Z~D|m$X_ITLcCAIp3=vncBaIa7!z^h&AF6aA4=`ADRSIO#g70N%#>GlP-3+Csbc16rB2M?ocHBLaXeE>n?(6{>POChC(F5Zxy zAc&yf-`f6o$Ji;Kd&5^@aM7wWi9W?ROzEjwpI(2!$t<)#4|)k63{%jVj`Y6Q+cGmw zsB9uX)!KASW&3`*_z}JhT|xD338x3Q)c0EgnzDK!yWo536#y*yQPXSzH@w=QF#Q>PfY{Fm)(%YMDDw? zCO8Lik7la}OFhS#Huep#Rj0_&$K(Jl)WNQac8@ydv%t5oz@9r|Bl=?-4Bgt(R3nn5 zPhQoA!u1`2vISfV?mUq$DI((4XGjwf?LpO!Tg)5ME+8#VYC0Bo5k(j|F%}QE~@fw`Ss}Td{MI=U&^79E+En@+pn~VinhR zukM)EJ3Rzd7dU2UM3U;hY%<5=Wk9@nRBASnxdpYhmKr-SxhsCu=MY(Uve1*fg zdN%;|g+ubW<1NK9cZ}-CgEjX5Sj7j{k=)miW4mQ3K2RMj7niWgsfE*@-tWjXt7Mq9t{;{ZPNqFrqUC-))N~SE4gGA-+op#eN-M8p5jzKghM1VJ$J5Z zYWv~u#szsXA z&J@ljSEzYtA9uI9l$p1kqrL}=(9v2&#N6YgwPmIgQOIzLtVG&~y!G`J9g-l#tIxrq zs|wrH-TS=^1K^%dMU{xEBp<(SOAS+zVMf8xA*%PWRm!3HDY({!jhx`j5l?hfA@OzS zHIWfB87pHpK2$2|Lb`8x+?Lq%z5Mb?%NIqw$N~&g%#S^rN-<{y zep~|n8Is)1umfZO9<6@))R*y|{3EFeQZRApIeI>cp2bpM^$B_F^-4sWY%>@L1OXyP z?Q)!}>%HNB74m$2SkEuZf%H_EV*6m|mzHatcuQ!fYv@68<+h86jOg?pO@3?#qKiD& zqv?m2BX^FdnN#V$oTzba0)viLUYt4bH7qFqls@{u1)0r+8x8sv6+dxU)cvLS%YU%% zrbCf(3Yvy7QbzP;hy^z4zCB5bZ58RhohD@+dbQAgqzdX|I?qSd+Wq{e_{80`W9FAm zrI{}#tQ9^`-hyPzPOLFTR;&q=R}Vi~xZ#}%Qk<>^f)-7@qk>&x|OD6Z~YZH!Zx zZu!Qxo?kU{L1B#)r`^xRiSW7g;NAsmPI=0eSkDN3rWj)gSZw1o(4`Zuoyj(XPdlKB zs2i)ed%)F9MKzU3(cZDA%EzGJ>iBu~M}H)o<71-2<>#VhOqY3hPflHW2Z>B>Mr^+7u>u9)KDu_Ey$GoxfwaBW}C6CxymH5<7^@IR2EGe zt>XKkue@+RVPlmh*1W0pedb^I{5;w8w}7_8Bdwb8xa5UD%2SfA@j9cn*quQg9nV9V zD(brO9>lTh#OJ2V_b>6``d3YPZZK4QsGArlORZykoR%cTK8^>k1Ww)4{{r7FoU&iV zNoHoHXbnkzxLmL&ypEKac2OAdev(hsll?AkRVy7k<1g2h)2sB>`hMeTldSwf9$qPl zf+1#WEZdc{^$KHiJVCw)%rb41Hy-cb#rv%;*zHe$dD6;Q#OrbWO7%{_iM35y6w97F zrh1DoLN$q`L2$z1Ep(wrl0ft{W4w?4LH=h_RFzAv%>e?Ng9q#;N9e7`m)MjY(}>g9 z`D)1svhrj{__VG3e2+THZ2dQ7Xb+Z4cXUVXgCX^kXMWrS6Hx-U3Y>iQ+WqO$l&Jf5 z6qzeZ8fQuo;W|?XI2}HW1CFfVRMGDl!r|7`MJZ#Ku&xaA#zgi7W1oqq)|{%>u_IE; zQ>x*lhj@l?^g&W=^K9MFV6ei5Ww8Uhhj7+(D<$6+C4Cg0;y>XZJ1nS2I3GL#XV3}X zvasq>NLs0iD#~-kn-P}HCbsB#bO4P}@2q&A>PPw|Sy*<&rql4f2{?u%_LU`#{0Uw( zwSKECK^|;Ea5^7?LH0R@STjvqvmth_s&EhQcwmflD$CwhGa1Vka44p{;{kV-AFWlX zGvR0MT@*?=rXBkF%u&ms7(2@O)vhl?!-VR?q~F)4IMpd9>tfP_(0d3)IerZsFt#}e zU4T0GF_xWFO?GuqOdGXcS(Xw3vxk0;*iS-@bDMUfG$#C;D+y;40C!XXBT^IQl^)@v z`l7pm_y)>yF?4wLwVqAcTX%nF%X9U2pE}>p@TbXwOX%ISG(hwk`t3`y)3e%PAghW> zbm&#BB#7&GAKcMTNsZYul67*|E8|y)j2HkK@N+IQFU;%ewS3AD4%I^Ik>Vs*pAZ;K z_)K(TJM~@5&reL+h2^*s$aS8k`A?eIpyIpywoli}`XZ_ZX@mW>Q6k=C;~C=Ygm$s3 z66(jSvfV%%49>)E6)X&66+xOY*Jp9#n}!o3Ca#~qE(E~IW_A=|)@`J9AjULyL7P}F zk~q?z0slOw{TX&&PbLw!I!7<+_tX63Lv?*PQST<6!NmExK60VvY-%|l zW#x{OCq*9oqh@@s(Gta}>VDc@ISpwyjuaw+eap7G^a4rK1*y`ep-zfAk7FD~!-DlU9UwzD;n z5;qrZcr&3fXrSVTRZ7$hK_2FX@dPZ`S3)dtfmPKpa8hQ(8~g~iF-rj#Kj$Xu!4|($ zYwjQri`%sSFMxg#oP98?K2r^a;lx%h8*D2s!YGG+dQ$}cm2HMXVbV3}@=)28^!^_9 zi(C|Hl{3P9@-h^Rv^yL1qHOV-^c}MoW~$(rc5P+3F?ufKQVN1U=IN(?bh@$+*LS5osX?jtkwrMrezxVtU;aJ6faO&eQJvwyHLvOsD#T4TP%dV;v4tX&z2It zvi~%4pm}*j(govPw*j0hzTy6m_%~xzdzW)%wLq*Fm*ou7ixPpmXB}SHE|--c?PRQ- z_#K300eKhLa2hRa$LDY0v@N!@)Z(U1%6|$J^8dgh)(pNmJr|Mi;;Ap3^g9oi&EPf1 z)xvp^;U5pf^?5kj+|x{T6&ME78*r(gff>6yBqh;je64F&g17zJ3^D%gV5fB%;03_8T7(^Q+_bSnJW#e`AWvSjBtVIAKE zn_JthO^hzqC0DOal($IpgVb-vrgj4P_y}Fq4bipT^`Zja?d){YJ#uJ!>KbDtf|1Mn z5>8Tm4Z9=qb0IzcuNqEDL<21Nnv=x-7UN&x)Cs%?5^Rwh&XE3$=-*#C45!xvGvNst u6SPOl^F5LbVBl-Gs`IbUzvn<1YtE4VQzCMx!`?&Na$vv5KGqL}3;zW)jU0#o literal 17716 zcmeIa2~<Hf05`?m< z6qHUx1+vp25FjBWih?Cb>^6O9L_jx?fEWS^fwvN>&aH9pc;mhIzdQc_jPak0A$w#s zbFDq+TyuVN&J}+;e8?63h4B|C6bilXhdoD8sCfw})SP1r=7W~@n|UMPG5?sG>mKj~ zpGg-%5_l|(`N2C5g)+OM{im1KH+lkv`U4oRNp6jyU)GwbWgIVm(t<+XQNseZyOgV@xL&|ePHHqO# z%EWl$`rK&+X}NBj|NirD4*Z(~{|y{ysNtP365ouIAOldecf6&R?8WBlx*; zdr0d%Zr{{7MR>inKIo#Md!HkZPZ({&>l2#VJF^8wcsb#inQm6|BuwfHAa_~n6K?iN z(d}|Q(A;vnF>FCX<(yQXcsNZYW{L!Y31(r*22M7tEK z;WwI*_8ItKZk6_l+Cpr2xQK@S(15IiSHb?!Aj1%AgtPEI=CA8^Q#=fFS4^ESI*sZg z2+Q)SFPa(Qls>rg+TP4(jr6KM(78D@e&liYb=U&C79UV#UDzq*Qj}4!A

-hM1+E zKt7%LyVh8uxZjz?8px?oxCufIcez9PO39oaaFCb4n5KLO&`&$~d~xT(glEQYlfqgm z)v3rn*vN3RJPz(`09+bP_$cO~U*8MM8%5QKqAwjjwcH zZ-Ugg*+TbfppY+Ay+S@?*=G|JEny^u^9oNL$4zh2(pfSFQUnougy+pFENXF` zOOv)8^?#se-*oGkl(FvrxvKt)lRz>~811y3JG|DjE|n9_iZXW9vWPb4;YHFmnO`yiM4GsIHbJ9XaQIoLrk4M`&K6 zs%CCad}OOTzFYFXuTfRTDW;JiwQ%Ng7+!IU?qAhjTd6c1=%i$kJQZ$m8mmxUyk;+m}6 zVgEs}pt)lzXXsgtR7h}4?V=dSwaSZX$fA*`9cN8Bx!nZ&lwSWe6}oe=F&NN`opf*_ zU!Y`fOSQ=E)>$lZ%EE-^y1}~9R+!XrUY&JVb7gc&B+a|3B}HppHo{J8#tG`i4Ds%T zJl3fBOnb$6ZVD%f^vmZO~~7FI*<*ErFq5*D-;II-=jT62b|Q2n-8J9Q_#4Nf=N-LZOGR8eAt6v}C;H?B?}un{cL_TCH&bvblq z`r)EmTda(mnkftqD4@`(gig%m<#Y zT4srwKA?DosP22}PHDtR{mwpqHUG>GEp=4Wo@6bC{HwuUfgXFvYO8*ykeyhrBmG^j zS=HF-8RX`21MN`m<<>{_VO3mm?3<~}VxR?>M?!6Tpxd&MhsNztzKPGC1AT;LojQ-e z``XI5zt024;7teno}w+~o0gfTrzxjit8N%-XJ!7XCGJa9{7q!1{mwn#^5{RglGk^G zg158z(PjDkVwDUVzJGH0D<6tWDs}(vvMKtIJgNh;MCkKq283@Fo?= zCb)!=4=rMZGf1qYTUuHuUx^HOr__snGs00-4q|U|p+l2>R5R=_P>+5jHysX}Ft_&k z!~epK^sHwhFVURRlU~)m&_K$75#ELw{3#!6CuiRb4~spc2Rf z%7=1IIHF_csD+Aw)PWi5u30<4eJl%;Sf+;Kvt}Cgnk@V=kx!{?cB*#*oLmg`P%2Kg zUe@l4>*;86`tDe||Ff(YwqIvu=5ovl+1}Y$GeMW)S1|XbUX!SR{Pt?Idtp@e!=2hG zfr)dg277O)g-&@rL8p{O=3W@4<9Mq(dvyat=2q3mdMJuUC*Ek- z(vPUIE?*6f7(^U9=B9g<{@r51sOh(2O&^h?)7zGj{}#aVFYX2Y_mS7XU*tbf=)Wj0 z4z3z8ckI!bQx;dRTSP?$kc9g1ht|$lEx{EEt@C=s9QhfA_rb}K2x2pHFx5K4BHr`h%Y@t`*@rRr$;zur3ojvqUroji=pTtnx9B*Fs(F#IiPF zSDAq)C!z&b*TG6=^eG*wvEm#(xfIG}Oh2>~Ycxp9^5&Tbs=?))B(7=<>4SMh#!~G- z+AAR=m*w=@zC5_a!~Y1ToL_g>l~9{GwV9LsqawY=n{&sOco!#-Ohyp*h*u9sJX z%JO9Av%IKLesLc!gq_gL#xURN$?0Pd9J>8XAq6p(Pri%Qu-@GG{g;3Cew})2gkV#| z<0MeOSL8y@45y?^${l1==W_Kcd`8wE-9ye zUF|pPy1$A1Z3WsMC-IHfu@4n@`krF~2`BH63q`C{c48r1ezFi?#xn}VYNif92fA&4 zO;gtQ7QY@w>&dS$!sS04(QU%C^ZNWMgHOr5n(ECxm|6Y&5xi+v_J|Hpp-gM{o_#i} zK;dV;c1#EeFmudt7V;G+xkZtM;NqZtaxX)Tb7Yu6B2G2`30X^)cJLUfEObXI=9$`+ z9D)0bcZVaXW0L;INV}0&FS!*S(fE}P?bc55Vq~MYy_&4IKHivm+(2H}ZZyRH@`Q~% zRo*RSve`U*x@Vf>vn&IAk~g(}7u%V*V_HHFNYqXZOm_T*rnEFTJ0p<)VCmaYK7Or7 zX2igI;EktZs!_x9#)jYuxm$c_qw9{cpapB`3M zYTAPO2_C}O9Z9Ok>t}&o&~uv79;#=&X{wN20r{ec1pk4Q`3 z3EiM*U)=e@2vUvm993Zgr{P2K1-N!-tai|Xnd+UCycbL z5FZ5rvNUf1OxXnz|y zbnLoi4+|Y>QjIecz0(-tqEAhX@UG@YC!nOaU~jls?eBc{>7=1qpoU^hHkB(b(Q|c4 z4(?^E_1)4Vnr38Q?_egw9xGv*w{qtwyy2wq@VP=xhg`7`ZRjR&SBU91SA^Qm6&pOH znnp7kBU|RpqOZy^MrM2S>F&G8lhL+SZ~@*=-HSxI6~?X>ywU4aE76z~!!walr6;v= zyaT{!jI3!%iwqqd9oDtD^F}I*&}l#ZUQ@)wxp%S-=rS!k7be(eWwsf$5&WowLH*8* z=yMeJJPn5Mxw2($IZp3Biwvffh`5jaR_-#!SpR=QeBChqAyyX$O5PlPX`rW zWK`c*bv~F}bY5^E#?XuIYWsQ7%p;@}8AmJ_B%CO~zq;zR_N6i|8kBNEM{|f%e4`;H zvB1IFzfRSY>QKbz*329dJ?OD<0i$T}tBWLk4_Pk9f}Me5f_xni{t~$C)LQ6 z*ABiZ(VADgEqd~~skcW6l9LOzMnz8y{N8L9GL43V8JugxiLXShV^9FwoIkWXFuBsb zjHOC&@e=sV9QOB>R`%#c0s^Q-wkO2u&#~wHiHh~j9W5_w^N^~A;jP~hd^7@NX}$Ga zUPf=-Xt*mkUVhv0pr=-;#k&Ah$=Q~g&Wx2BjQbjLBXUjZ)I6T^TKB?3W)i&GNaw0t zhcbW;QcXqGwZw9HdEyp6zQ$QefP{};lROK|x>cd6760fy?BwAOzhv|rfhqV(*(f@R zO=!D5JgxOVUbltrSu^DZ74dhjFozZIM%((5H$;9MPn_|vhJ`FFfKbQ4( zL|lr2laQAzV_v!3d4F!$M2R--;II`i^+Cj|k=sa@C#h)q4tX!J-Ll^T>%Xy)LsncW zi`c5sc=Yn#akqvWu_s;6KBO}k;7)eJkTvZ=(RnwpCFJ$K3 zsCfaWVau5Tx@hvv*Nv{yF*jd){K#heG*;9HlbHyLhoT<|-q0!Ht8%`9wc%nM@PG45St=VA>xKB~ zLBX#H`IKYo3+?W9JDz+DoLj}+)REs~b9eFEs6G|ag(dm>5W%dC?m+j3k~mJyc^9P| zPsz|rs+B!N!Q$57GuFUkp<*KBs40=luAu_2g=wj>Uxe7Le>sb?%t#n>26740!MQ;7E~vljFy;Z(&_`XlFkH7^u;!Nu7WSz| zp3ThDFBI^G+Oax!FP%3NKd?U`rbuF^-q^A!5{I1aK{_6yGCP0MlVf`;sMiL^8)q8+ zid>`3>k8Ph(qC&w-~B;95G{K(@>YO>y&=D`?&aaK@;m$%uXx*YokmvwIqy}njx<8> z$HeVO3aD{u=9wLv&WA)RB}w;H@Bg_--GKzoFgkJt!Bbd4rYL?wu<#W|5>s{*!z3S4 z+=-ReL2i(%`Mb_^tY9ruSAL`|ZwwC*TrNs`(=@6MEdHnS&3N*gmDa2R+vDoNJDETs zsxB#gKaMTp>qIV&&>FtOQa|ZYYV2dRPDx@=VBmz8;v@3QLis}NRPinlkrB3}DlPDX+?Q5!Zgir<>fz?Hj$D>oWz_oRnXot}>V4kdKIt}>-R5Q|Xq4vWU zJG33Bl?PW8R?}y(a1oq}Odt=D zrg=#Rbt9~TjyNVr3Olh>7RbT5zy`(_IvJsOPSK%&m(8;%@AHbKBh`0Q5Ypk&u-FCL6WXv$k~bm~9=hk(OW@*_oOElfCg%^+g5hOOHk&DNnfPbABsqm=KL zH^-;Rb05AFn!yHj%INlJr_5$HT{87wkYJo$-{Q_tPmoZ<4|x9J_l#Aa&2Jd~O}p*D zgW3StDU}1U34OOspc#jpT>HN&?5*B}-;JB8fg*)=IEwigh-o}_N@W>JEooQ!8fqKG z>w!=bPnt@6diiqmx(#doh>YH30`}&|PPHNvSoSuy>i+0d$G|HNlr`H^r^(KxfG zqGEf48?bcomLyjNenV4M>|Ec-|QD4Jhmfg>Yw%mgxgBfI%iO=Q>OG5{Z*(0+thYl z6;5*CFZNK~AA1flZpNH4waJ;K53I2{+FjW0kzMxO){s!#pSXyTeC@>l+!n*|mbx*e z?T#~%0B1P!Rmr1Mc!v9-KNlf2TvE1mz6|O49^`n+@wtTrEVWQohgicki~&zWpu<)C zQu2FC8P&Ut^4LcwNw1!&@iN~Gl|!VN$Z&<*Y^EO+UG^Ply{j8QBW^vBOfSb5xF?8i zIEn7enzM!`a0u|ms*gJ3#$7yX8d3l6RMNC%6p*x+3dy?_FM*P^ftu4eLjR@-AP(`0 zue#^aR>$oJA!8gP-!Mkg572+Qr#&lJi#8)b(Hi9?xZ)Yjl6go8LYAro;UjO64kQb~ zLv=WJrjuZ{__d}KYV+{d<_}U|7QqE3)87e7$uD>HQ%Q=^*v>w9;owm-u-v(!h>4^J zx^%WSlfiref^dcspT=hIcvj^G$%~whV5(FK#kau!(pcYvzzkB}L2~iso|2OvN+{np zm&v2=CKa_6S7?KvmaCuy&Lz8>)j2b#gKmUdM}Ck{3Xs_3Z$V*(#&Xk5_wSvk3->E0 zO_R({YxR_=jbCx{-(shxjGKqElb&0K0?CPuK~^eIQN1;FEhkpmIoUjGSr&jswA1F) z0RYOCX}!y5^;XN2i^;X4YkjDK%K)eON^!zSU0s?>)RBqDrhBf%iMo1b9LWWUD0PhB z?O*Z|0jr}{MBvK`sDf@(fB!UEn4t8G{@Cq!R_>vhbdYbmiu zwhu~4lY12J=`qTE=$_$5M8X&Zv0NOKL@@KE^2zTKv>qq0X{dXiU9uV<9X+vSIIwPz zA+UjV0ydxl-aqdOtM?rm<$7hn`6vg+kz}1LvYSqB8|I;X-L?ePrkE;#K{!A)=`$x%n&us1xwdT(p{gFRzNBs21 z?T7<^-j4V$BnpMW_S)JmzA!agQzhcZ@U(~<#4cnxTnV2?l1tPBxB-yi zGHM7jKb-Bbzd$<*GafUNLY9$%gGMKB*;kmvRQSGT%vUAz?pre0vFB3QMp`MihaXIOePKElIo$f&A^Y6rRa)}DEw4K8EYf#zXl~n*3G-{}28;w__n_?Z zGTo(+!yw$~`A2y2=*!k|7dY5tIwq|)7bnS;I`=-b)4k?_Od4sEY;(I4C*P2iUX{Sp zG}ce-&{7sZS(sqdd#QE23Z1|n3vFL!-(9I~r!8DIVqL2aX>X4d$5GoO)WzroU4lFC z@!YE9(dVt>mhh?cp0n)37;5~CyS0a_j@o-IwWn}(tH#jN`S7sMK-@WXL>DAUOl+i| z(Y^11rp{uM7E5cU%tv#uW_^dfUBheY5k(`yY?T<<`&}At0Y+*&Yz2Y1{T8MA3O3j0 zz$|X}l=Ap@ET3R*w?Bo2MxBaUa&*m1{a|g>TLZL(-?=?gp!4`IsawH_td=e_r!$93-%K)(nl8+Y)y%7!D>h@sB?!D#YokW?K+n6 zw(7|%8lg^GfzGlslb7m{9qK=na<%b;6L?}nheTZ)rriQ+WiE~6!w$&arW|9>(~v}E z9;L>-*X5CER(r*QGEF@301+fXv@^Sx?41Q92Y{X>$Fjnjj|`Rn zU7U-{KAlk~*@mQQ2ho1lDul>B#mB)XEmyjjxHWH+ww-%$3RD+gAZ=m? zXt2bRR!J@^k<})8o|x3K} z#y!m(94IfE6ow%vq!eIIQ{)85Mt=;p-+W^4*6$jpkt13l?`gfg@?w{@%-aST__we~5Y z6-R5zwHo3EgYssU(+-HL zc|Zb3z&CwWm5KO^&QT$sPf*Cw8cMO=G{%?SINO1&j|o zcqlv4`KbTHR83=)*D&RnH4p6A^gb}2;-Ku-k&w}rR*8D=&^(k^>+8w4)A=o=Qx*fq z0ppI0h8!E*e%OC2P)0GM@m6GX%gAschaD?|@c5{eZ$3{R`~WuBqL*?K9E6BQ#&pT{ zN>vVVh?LtpF885)3(|uz>wrGe>iYu~?^-nlo^{Ni+zt4&OzBMi!4Dt`Y_Zh(g>>l~ z$Q@tK&Uy3PQoaukXM|(rY=ZEk6dcp`o4~nuKNQ>nS+N~b3(j;N-#^`{c{`6!Qsf}x zaHvV`)|C<VTJl{4U?PBo8@t%;CIurp0Djl^E$iTCgo2E}uxc*0H(MH}7& zU<5aIx|n}Nk%81PJWQ;sdG9ZxSDWVe4*Q+~*MY_3t3j;S;uXNm@zeMy&>*oojVyzc zt~G(Mm}{kVS$1`gfO!Kt8R$_lTfq_kU%0aW25nau4DGWvXn=!Uqj=g>Tuwfw=%Y7lV#;RQ%+>?J!T;|VKJw@Wo5*v|Q@ElbeER1lUc{##&4lz?#Me!sa zcK28F7*hBJWO2&t5j7Wid&E({#p}=MzYepi1>5t3Y7rMk^ggcOS3ef8*RjNR+s6gL zHD^B?*ypd~Wd%d7*qPQI=f9KjHOvrN(Xx>!8ZgH|@f@E`)8WjSjq$5f`q!Y(Ppggh zZe_yl1LIvDW-Z;-E!){gG~Pt0RWjf?(-O0^HXK*Zit-j#lH(O|=(yW@EqPkWqmtuZ zN2o6oWu#a|A99I)Lo^V5+#_NYo;l4>)gsQuxY6poAY%J3^>}9w&0d8E8lp-Z?#-u} zJ%P^xo4aD5qcvV=9Q*47p2ni1r`$E z(@stZDkE#cqEIbotRK!ti4T>Rt{)>cd5Hu;^9LUxM)uIUy~<1U=83eXVo4``mC(Qh zH}y~>Wva&L+d8fg&dD#(d!J+X4yLj|0=H^>UCeb`o%~UbQY+)epA0>_%IT_rTsY}L z(1AJaZ+wjj0~Ai2XrOUiU5S?e$m(BfQd?@86*dGYdaM|YzPWt`(XiHe%H=O_yIlG|gDi51ha7F_yxoa~k-yB=l1s*b#8 zj{nCWnlIiM-;>0fs#QBPLUCz~#Jr&IJLi?uS+f(5XW4n*A=y=Rb_p9biE+HHU+t<^ z^RAlMo?Cf_OP*L?R)^(e!qv_tw@4T6XY~cvEVv_w4u!3J6*EjXG?(1T&)iaY{fun#P`ebNpG6`VxQJh_SJ+>XTV<=j;5Dr&Mn|lg%5jd6CW85x}ThQ z`5}-v^CIl3RZkw8Glpka5b|Ud^vOe0$;0( zxO!QTR71IM$Qw^yo!zuCS+SG&3D}Pc_F@0GBjv?8hh^7GsD$!W2aCV)D-NoaJwoc5 z4udOjW6bHNnN6^2VM5RaomK}7Rv^pJ^7O=5w1VP85USrD9K2dg#n*&SRRdiQt2b&r zMp69)^ko`&D2Xrj?nf9dbAu)5|LeN7`*6{UXjX!umm4!*U&z7n#e)2Hr+m9X`L0x;Wlbg!zUcunm5*7 z93CK-3{!vwe;qdR2AJ@@Jkk)rV<_5;{1m8*Y%vMh(xqBJlt(W}axT47y|S(@v^~?F z$=|`P)l>)bFi;sscHGC>zMW9j2yT_Mo0p##Zrr?Kc1LHiHAs~!Hc86et*l1}NiFao z__!WJTI*0^`CjNlR1$}j+}81fCY|8bl3wtdeT$KBD^`c*?fh~5p^e%@2%Mkt4O*Tr z3Ck!F+;+5W=#r*$dZI(!qb39ikG79*tKJ^X>q6V-7372XbmJ~vxZx!ThLl^Y(i7c@ z&%Y=m6+j6gq+0W_pdKgo?LLr5J&2GU)|*L#~B3BTHvEl-E`@w zkyCMw3h5?RZSXAkw5TJt{7vn^g&*nGp{O7cMQYO-hHfmMx2DJza zC?K+L6dmEd7N690`dJb|aT9^jNk-}cbIR_r@GQGDpwzlE4?MF21-jyC@i81v3^*z* zQjNdj``)6F=9uy$bajc0R1Lf+w0sb6&o~t3CDn8yQ=>k?OLeM?;$o)ShiVre`=GnP z`+ox!wOJ2ws-gu+DbDnIx({v!&iUeMrG5lez`$$^L525b=rQYFZwj7ixrX|cE9j|+ zjW3ISPr${oK#;z8Zq;{ft|9HehL*46zBcnRtot$$W4eW=aEKq8PusUGa%g_j2ME3u zY`^J*pf-wT_VFz;0T#OG3a+IH?~xVHgec#xRj?Eqz;Y}qjRFVNw?KZigkhi7v52bx zl@v9iWQfePJrqAhHb{*`n^mTlIdD`BEe8+WT3(gXGgNHil`oO-ELfdeLspBw?l{ZS z#H6kgBeG5HiC=*Y5tX@-UAe*Yx%?{)yn)iGgJHZ)0Sk5ctBn7zVeaMC>JCd^+6{*g z)L;+b^cAp8^VC(SE$NW#u-TS)@IHRkd}c59j z82$htfrIuh^NH9J>M1%hyh^Z?#`>Uwe}za`BTploylC2$STowDzvlgWdT(7d(xz22 zj6F1cN7annZ5>~=O@gu>UITkTO53Wn+sZ-q@n_@`z>l@0bHtc<$9OZfe;)WPP$atU zh6HQFioy@KwXD#q1;}w%y}|FRr36p2El1PDP2~mT==!=8kGe>MmffkG&X>;zR*7!d zdvV{G`3fK2NLy}%C0Rhb0?!zp(&)*DjZ@8Bx3jDAx5wt2%=5bE4`=!~afdk|>nI|3 z4^3BB*3E2>uBO#c_NF@>0caAN&T(q{RNNzk^Px9T0p3W08K1aLo?BZkP^oXG84TDm z-(iI01O?xknq&F?a`u3U;PcrUAN|huGarNN7D3>`7nT|*Q(8Q~U>EpU*8E9tcn*wR z>=Ab#k;V}X{k=$H&yF&V=4(IkB2OWsulMoA#bXmU7-$JFvS7Tsr zA2kuCc)h=~9)N(rFW2JiBPZ?*#B|N|vFaB3DK2{tUxv|(&z{38GUFu5K@-?Pd^cMf z^Hn=OyL7j7x$pG7p(?t2i(c4*;G3z2x%bzAL@+erFA{ zVfEzb%`_tt0kkC$UO!*$i(8Z+$$*4)OT*&Jc7(`w?zKfNJ9FcvVSG|4T{X!G2nb)M z)_)KjUDJGPF^==$^;(dL?Y?i7M&nPdFB3^)^mug<@gCqZ>q@cBrH_DADZ^JD=?$6dRmYUx_fE$&xZQ~3k31? z8^-!Ywa4e#aF0(9rj}=EWDn5L$;PmREyVtzf#_BFy8_*|RjZom!L?7(14eEo2_)Mr zO4Z%I-sj6)KP+9@<%1vT3}(w5n?|ZQxlmWhek<|U!%-Qp1ZTLEmWpB2YDZq5ec+Ww z`HB&JH}kjmT^%*k9g-^o@Vl5oqrd^aUrlk~bW2S4&$%`X83uPz{GrKs#OX9!Hh;rg ztFz;Nn*Bz1LX%q^8df1V{0TktzD3tSqeNiPly(!viwWT~$B* zPXBVaok4}m?HgY1sOG!ZeD5cMf<7eKWrG5L7g|`S5P*UC!wYt2BGiGsonK;7j3rAt#mzou71EgL{rmP zA|MCUuU;ifxWo@;q?ezI*!Fr7fL5~?Khg(Ths%#A?y2c<`gwjvN+#AKdh!lWL_W7c zWH~3EE`?jsb#x=<;kAJ9j?%u~M;vBeVq#xPuffoFr0`*ALRot5(5I&<0hh8vSbB2I z01{P9AD|BVX*Q)7yV8yfA+Mo`#W;5s+aUy;h|_-Q(<7l>OQQ@@4=a7<>9bW{VM5!L;ob_W4OM%_CKA$**9-IgC2VZn^b(ttax43t4oihK8r~Ko|-*1U+kcrRhv{t32#$8 zNx9Ob{WWWQu=3WF2Q;f;CjHKM2GR&;;)_JX9h#&rCTRT_06D&p1yrg!)+@%KcxS;n zGd&MdqT+YN2TtRCswj-k7R(G}w*Fll(jtxdbcWk=waogYz8@}RM1L$%0Q7{zN4_B9 zZ^5P!6)*qBE$Jxh8@sZWeUuVWFAu8Ddg{x4!zAu;f!$xgou@DJn_s}IunP|~l1k4l zaeRFvOizpW8U$fA_Nc`;3)Ug0123=)!_sp@6FHZO1`*3C#(SSwnHiY3+^^$(w=Iuc z?Eun|G;1bMsJT_z{};gS{B^U!r~oS0 zl6&@S&Hl~-+lDcxJQc`E9C16}=xcJpoVI%MG;xN$oL^v^`|r^Z(L(xs?Ckk$ zP{h!p+`Rf}IyNDxo%=~<+*>w3LeF*C2#)HnfY95XO@qApK^QZ3URUh;m%$?cx*HMe zXL${0N@bYSHXvE&GMkL#RR)K&OY^~RzQw%vU+aoC|BG5@pdW={@2L(cH@MagYU1F7 zU5hgaEmxcOk7D4#fiQDkMU$@G>-YV7@*JcrE-kmX<74acR<^ z-(KmQT%VP)4OygEdg#+h#ZQK*~w?>~Rx0HjK?NV@jJ%eI9Zw5|KT MKeUIvJMhB)08*ADp#T5? diff --git a/reference/addLDA.html b/reference/addLDA.html index 51cde7678..ddcc18f0f 100644 --- a/reference/addLDA.html +++ b/reference/addLDA.html @@ -19,7 +19,7 @@ mia - 1.15.4 + 1.15.5

@@ -46,7 +46,7 @@

Latent Dirichlet Allocation

- Source: R/addLDA.R + Source: R/addLDA.R
@@ -137,12 +137,12 @@

Examples

loadings <- attr(reducedDim(tse, "LDA"), "loadings") head(loadings) #> 1 2 -#> AD3 9.169111e-04 3.116696e-07 -#> Acidobacteria 3.402166e-02 2.882915e-05 -#> Actinobacteria 1.107907e-01 3.892977e-02 -#> Armatimonadetes 4.938193e-04 2.348346e-07 -#> BRC1 6.631669e-05 1.103271e-07 -#> Bacteroidetes 9.712131e-02 4.088929e-01 +#> AD3 1.002653e-03 3.804851e-07 +#> Acidobacteria 3.719581e-02 3.985709e-05 +#> Actinobacteria 1.102707e-01 4.975727e-02 +#> Armatimonadetes 5.400106e-04 2.425910e-07 +#> BRC1 7.245526e-05 1.969087e-07 +#> Bacteroidetes 9.502497e-02 3.684216e-01 # Estimate models with number of topics from 2 to 10 tse <- addLDA(tse, k = c(2, 3, 4, 5, 6, 7, 8, 9, 10), name = "LDA_10") diff --git a/reference/addNMF.html b/reference/addNMF.html index 9d646fb40..bb948e3d4 100644 --- a/reference/addNMF.html +++ b/reference/addNMF.html @@ -19,7 +19,7 @@ mia - 1.15.4 + 1.15.5
@@ -46,7 +46,7 @@

Non-negative Matrix Factorization

- Source: R/addNMF.R + Source: R/addNMF.R
diff --git a/reference/agglomerate-methods.html b/reference/agglomerate-methods.html index 493edbd6d..5c5c9ff61 100644 --- a/reference/agglomerate-methods.html +++ b/reference/agglomerate-methods.html @@ -24,7 +24,7 @@ mia - 1.15.4 + 1.15.5
@@ -51,7 +51,7 @@

Agglomerate or merge data using taxonomic information

- Source: R/agglomerate.R, R/splitByRanks.R + Source: R/agglomerate.R, R/splitByRanks.R
diff --git a/reference/agglomerateByPrevalence.html b/reference/agglomerateByPrevalence.html index f61d1e6f8..4a0ea49cd 100644 --- a/reference/agglomerateByPrevalence.html +++ b/reference/agglomerateByPrevalence.html @@ -17,7 +17,7 @@ mia - 1.15.4 + 1.15.5
@@ -44,7 +44,7 @@

Agglomerate data based on population prevalence

- Source: R/getPrevalence.R + Source: R/getPrevalence.R
diff --git a/reference/calculateDMN.html b/reference/calculateDMN.html index 5e01847cf..d6e972973 100644 --- a/reference/calculateDMN.html +++ b/reference/calculateDMN.html @@ -19,7 +19,7 @@ mia - 1.15.4 + 1.15.5
@@ -46,7 +46,7 @@

Dirichlet-Multinomial Mixture Model: Machine Learning for Microbiome Data

- Source: R/calculateDMM.R + Source: R/calculateDMM.R
diff --git a/reference/convertFromDADA2.html b/reference/convertFromDADA2.html index f52c8a78e..5d5b0d952 100644 --- a/reference/convertFromDADA2.html +++ b/reference/convertFromDADA2.html @@ -17,7 +17,7 @@ mia - 1.15.4 + 1.15.5
@@ -44,7 +44,7 @@

Create a TreeSummarizedExperiment object from ‘DADA2’ results

- Source: R/convertFromDADA2.R + Source: R/convertFromDADA2.R
diff --git a/reference/convertFromPhyloseq.html b/reference/convertFromPhyloseq.html index 440529b4a..17bf05d77 100644 --- a/reference/convertFromPhyloseq.html +++ b/reference/convertFromPhyloseq.html @@ -18,7 +18,7 @@ mia - 1.15.4 + 1.15.5
@@ -45,7 +45,7 @@

Create a TreeSummarizedExperiment object from a phyloseq object

- Source: R/convertFromPhyloseq.R, R/convertToPhyloseq.R + Source: R/convertFromPhyloseq.R, R/convertToPhyloseq.R
diff --git a/reference/deprecate.html b/reference/deprecate.html index 5052ecad9..e455c73d7 100644 --- a/reference/deprecate.html +++ b/reference/deprecate.html @@ -17,7 +17,7 @@ mia - 1.15.4 + 1.15.5
@@ -44,7 +44,7 @@

These functions will be deprecated. Please use other functions instead.

- Source: R/deprecate.R + Source: R/deprecate.R
diff --git a/reference/dmn_se.html b/reference/dmn_se.html index 1099a880d..0e31fed22 100644 --- a/reference/dmn_se.html +++ b/reference/dmn_se.html @@ -19,7 +19,7 @@ mia - 1.15.4 + 1.15.5
@@ -46,7 +46,7 @@

Twins' microbiome data from 278 individuals

- Source: R/mia.R + Source: R/mia.R
diff --git a/reference/enterotype.html b/reference/enterotype.html index 2741272ee..5babf797a 100644 --- a/reference/enterotype.html +++ b/reference/enterotype.html @@ -24,7 +24,7 @@ mia - 1.15.4 + 1.15.5
@@ -51,7 +51,7 @@

Human gut microbiome dataset from 22 subjects based on shotgun DNA sequencing

- Source: R/mia.R + Source: R/mia.R
diff --git a/reference/esophagus.html b/reference/esophagus.html index 74551a52b..e6e279dd9 100644 --- a/reference/esophagus.html +++ b/reference/esophagus.html @@ -20,7 +20,7 @@ mia - 1.15.4 + 1.15.5
@@ -47,7 +47,7 @@

Human esophageal community from 3 individuals

- Source: R/mia.R + Source: R/mia.R
diff --git a/reference/getCrossAssociation.html b/reference/getCrossAssociation.html index 409540a39..e6c5403a6 100644 --- a/reference/getCrossAssociation.html +++ b/reference/getCrossAssociation.html @@ -17,7 +17,7 @@ mia - 1.15.4 + 1.15.5
@@ -44,7 +44,7 @@

Calculate correlations between features of two experiments.

- Source: R/getCrossAssociation.R + Source: R/getCrossAssociation.R
diff --git a/reference/getDissimilarity.html b/reference/getDissimilarity.html index 724f8f6a9..d7e6950ed 100644 --- a/reference/getDissimilarity.html +++ b/reference/getDissimilarity.html @@ -23,7 +23,7 @@ mia - 1.15.4 + 1.15.5
@@ -50,7 +50,7 @@

Calculate dissimilarities

- Source: R/addDissimilarity.R + Source: R/addDissimilarity.R
diff --git a/reference/getDominant.html b/reference/getDominant.html index e18c34f93..2b62357a3 100644 --- a/reference/getDominant.html +++ b/reference/getDominant.html @@ -19,7 +19,7 @@ mia - 1.15.4 + 1.15.5
@@ -46,7 +46,7 @@

Get dominant taxa

- Source: R/getDominant.R + Source: R/getDominant.R
diff --git a/reference/getMediation.html b/reference/getMediation.html index f316ea3b0..80a749b5c 100644 --- a/reference/getMediation.html +++ b/reference/getMediation.html @@ -19,7 +19,7 @@ mia - 1.15.4 + 1.15.5
@@ -46,7 +46,7 @@

Perform mediation analysis

- Source: R/mediate.R + Source: R/mediate.R
diff --git a/reference/getPERMANOVA.html b/reference/getPERMANOVA.html new file mode 100644 index 000000000..c8a9c101d --- /dev/null +++ b/reference/getPERMANOVA.html @@ -0,0 +1,244 @@ + +Calculate PERMANOVA (Permutational Multivariate Analysis of Variance) — getPERMANOVA • mia + + +
+
+ + + +
+
+
+

Calculate PERMANOVA (Permutational Multivariate Analysis of Variance)

+ Source: R/getPERMANOVA.R + +
+ +
+

These functions perform PERMANOVA to assess the significance of group +differences based on a specified dissimilarity matrix. The results can be +returned directly or added to metadata in an object of class +TreeSummarizedExperiment.

+
+ +
+ 
getPERMANOVA(x, ...)
+
+addPERMANOVA(x, ...)
+
+# S4 method for class 'SingleCellExperiment'
+getPERMANOVA(x, ...)
+
+# S4 method for class 'SummarizedExperiment'
+getPERMANOVA(x, assay.type = "counts", formula = NULL, col.var = NULL, ...)
+
+# S4 method for class 'ANY'
+getPERMANOVA(x, formula, data, method = "bray", test.homogeneity = TRUE, ...)
+
+# S4 method for class 'SummarizedExperiment'
+addPERMANOVA(x, name = "permanova", ...)
+
+ +
+

Arguments

+ + +
x
+

TreeSummarizedExperiment.

+ + +
...
+

additional arguments passed to vegan::adonis2.

  • by: Character scalar. Specifies how significance is +calculated. (Default: "margin")

    • +

  • na.action: function. Action to take when missing +values for any of the variables in formula are encountered. +(Default: na.fail)

    • +

  • full Logical scalar. should all the results from the +homogeneity calculations be returned. When FALSE, only +summary tables are returned. (Default: FALSE)

    • +

  • homogeneity.test: Character scalar. Specifies +the significance test used to analyse +vegan::betadisper results. +Options include 'permanova' +(vegan::permutest), 'anova' +(stats::anova) and 'tukeyhsd' +(stats::TukeyHSD). +(Default: "permanova")

    • +
+ + +
assay.type
+

Character scalar. Specifies which assay to use for +calculation. (Default: "counts")

+ + +
formula
+

formula. If x is a +SummarizedExperiment +a formula can be supplied. Based on the right-hand side of the given formula +colData is subset to col.var.

+

col.var and formula can be missing, which turns the CCA +analysis into a CA analysis and dbRDA into PCoA/MDS.

+ + +
col.var
+

Character scalar. When x is a +SummarizedExperiment,col.var can be used to specify variables +from colData.

+ + +
data
+

data.frame or coarcible to one. The covariance table +including covariates defined by formula.

+ + +
method
+

Character scalar. A dissimilarity metric used in +PERMANOVA and group dispersion calculation. (Default: "bray")

+ + +
test.homogeneity
+

Logical scalar. Should the homogeneity of +group dispersions be evaluated? (Default: TRUE)

+ + +
name
+

Character scalar. A name for the results that will be +stored to metadata. (Default: "permanova")

+ +
+
+

Value

+

getPERMANOVA returns the PERMANOVA results or a list containing the +PERMANOVA results and homogeneity test results if +test.homogeneity = TRUE. addPERMANOVA adds these results to +metadata of x.

+
+
+

Details

+

PERMANOVA is a non-parametric method used to test whether the centroids of +different groups (as defined by the formula or covariates) are significantly +different in terms of multivariate space.

+

PERMANOVA relies on the assumption of group homogeneity, meaning the groups +should be distinct and have similar variances within each group. This +assumption is essential as PERMANOVA is sensitive to differences in +within-group dispersion, which can otherwise confound results. +This is why the functions return homogeneity test results by default.

+

The functions utilize vegan::adonis2 to compute +PERMANOVA. For homogeneity testing, +vegan::betadisper along +with vegan::permutest are utilized by default, +which allow testing for equal dispersion across groups and validate the +homogeneity assumption.

+
+
+

See also

+

For more details on the actual implementation see +vegan::adonis2, +vegan::betadisper, and +vegan::permutest. See also +addCCA and addRDA

+
+ +
+

Examples

+ 

+data(GlobalPatterns)
+tse <- GlobalPatterns
+
+# Apply relative transformation
+tse <- transformAssay(tse, method = "relabundance")
+# Perform PERMANOVA
+tse <- addPERMANOVA(
+    tse,
+    assay.type = "relabundance",
+    method = "bray",
+    formula = x ~ SampleType,
+    permutations = 99
+    )
+# The results are stored to metadata
+metadata(tse)[["permanova"]]
+#> $permanova
+#> Permutation test for adonis under reduced model
+#> Marginal effects of terms
+#> Permutation: free
+#> Number of permutations: 99
+#> 
+#> adonis2(formula = formula, data = data, permutations = 99, method = ..1, by = by, na.action = na.action)
+#>            Df SumOfSqs      R2      F Pr(>F)   
+#> SampleType  8   8.2466 0.73109 5.7773   0.01 **
+#> Residual   17   3.0332 0.26891                 
+#> Total      25  11.2798 1.00000                 
+#> ---
+#> Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
+#> 
+#> $homogeneity
+#>            Df    Sum Sq    Mean Sq        F N.Perm Pr(>F) Total variance
+#> SampleType  8 0.4996524 0.06245655 5.807135     99   0.01      0.6824898
+#>            Explained variance
+#> SampleType          0.7321024
+#> 
+
+
+
+
+ +
+ + +
+

Developed by Tuomas Borman, Felix G.M. Ernst, Sudarshan A. Shetty, Leo Lahti.

+
+ +
+

Site built with pkgdown 2.1.1.

+
+ +
+ + + + + + + + diff --git a/reference/getPrevalence.html b/reference/getPrevalence.html index 50f30e0e8..651d420a7 100644 --- a/reference/getPrevalence.html +++ b/reference/getPrevalence.html @@ -18,7 +18,7 @@ mia - 1.15.4 + 1.15.5
@@ -45,7 +45,7 @@

Calculation prevalence information for features across samples

- Source: R/getPrevalence.R + Source: R/getPrevalence.R
diff --git a/reference/hierarchy-tree.html b/reference/hierarchy-tree.html index 56ce7e35b..06e9ecdaf 100644 --- a/reference/hierarchy-tree.html +++ b/reference/hierarchy-tree.html @@ -19,7 +19,7 @@ mia - 1.15.4 + 1.15.5
@@ -46,7 +46,7 @@

Calculate hierarchy tree

- Source: R/taxonomy.R + Source: R/taxonomy.R
diff --git a/reference/importBIOM.html b/reference/importBIOM.html index 89c09633c..c13aeeca7 100644 --- a/reference/importBIOM.html +++ b/reference/importBIOM.html @@ -22,7 +22,7 @@ mia - 1.15.4 + 1.15.5
@@ -49,7 +49,7 @@

Convert a TreeSummarizedExperiment object to/from ‘BIOM’ results

- Source: R/convertFromBIOM.R + Source: R/convertFromBIOM.R
diff --git a/reference/importHUMAnN.html b/reference/importHUMAnN.html index 0a55ee1e0..e481f74e6 100644 --- a/reference/importHUMAnN.html +++ b/reference/importHUMAnN.html @@ -17,7 +17,7 @@ mia - 1.15.4 + 1.15.5
@@ -44,7 +44,7 @@

Import HUMAnN results to TreeSummarizedExperiment

- Source: R/importHumann.R + Source: R/importHumann.R
diff --git a/reference/importMetaPhlAn.html b/reference/importMetaPhlAn.html index dceaec480..74ecf57e0 100644 --- a/reference/importMetaPhlAn.html +++ b/reference/importMetaPhlAn.html @@ -17,7 +17,7 @@ mia - 1.15.4 + 1.15.5
@@ -44,7 +44,7 @@

Import Metaphlan results to TreeSummarizedExperiment

- Source: R/importMetaphlan.R + Source: R/importMetaphlan.R
diff --git a/reference/importMothur.html b/reference/importMothur.html index 15394fb40..e0fe3cee8 100644 --- a/reference/importMothur.html +++ b/reference/importMothur.html @@ -18,7 +18,7 @@ mia - 1.15.4 + 1.15.5
@@ -45,7 +45,7 @@

Import Mothur results as a TreeSummarizedExperiment

- Source: R/importMothur.R + Source: R/importMothur.R
diff --git a/reference/importQIIME2.html b/reference/importQIIME2.html index 249803584..0dc5a0371 100644 --- a/reference/importQIIME2.html +++ b/reference/importQIIME2.html @@ -22,7 +22,7 @@ mia - 1.15.4 + 1.15.5
@@ -49,7 +49,7 @@

Import QIIME2 results to TreeSummarizedExperiment

- Source: R/importQIIME2.R + Source: R/importQIIME2.R
diff --git a/reference/importTaxpasta.html b/reference/importTaxpasta.html index a6b8c0a74..3d214ca93 100644 --- a/reference/importTaxpasta.html +++ b/reference/importTaxpasta.html @@ -18,7 +18,7 @@ mia - 1.15.4 + 1.15.5
@@ -45,7 +45,7 @@

Import taxpasta-specific BIOM results to TreeSummarizedExperiment

- Source: R/importTaxpasta.R + Source: R/importTaxpasta.R
diff --git a/reference/index.html b/reference/index.html index 4c3463410..1941d749d 100644 --- a/reference/index.html +++ b/reference/index.html @@ -17,7 +17,7 @@ mia - 1.15.4 + 1.15.5
@@ -58,6 +58,10 @@

Association addMediation() getMediation()

Perform mediation analysis

+ +

getPERMANOVA() addPERMANOVA()

+ +

Calculate PERMANOVA (Permutational Multivariate Analysis of Variance)

Clustering

diff --git a/reference/isContaminant.html b/reference/isContaminant.html index 7ffea3ac2..c9ebd9cac 100644 --- a/reference/isContaminant.html +++ b/reference/isContaminant.html @@ -20,7 +20,7 @@ mia - 1.15.4 + 1.15.5 @@ -47,7 +47,7 @@

decontam functions

- Source: R/decontam.R + Source: R/decontam.R
diff --git a/reference/meltSE.html b/reference/meltSE.html index 357ab3e59..dcfb77331 100644 --- a/reference/meltSE.html +++ b/reference/meltSE.html @@ -19,7 +19,7 @@ mia - 1.15.4 + 1.15.5
@@ -46,7 +46,7 @@

Converting a SummarizedExperiment object into a long data.frame

- Source: R/meltAssay.R + Source: R/meltAssay.R
diff --git a/reference/mergeSEs.html b/reference/mergeSEs.html index 6493c881b..1e740a68b 100644 --- a/reference/mergeSEs.html +++ b/reference/mergeSEs.html @@ -17,7 +17,7 @@ mia - 1.15.4 + 1.15.5
@@ -44,7 +44,7 @@

Merge SE objects into single SE object.

- Source: R/mergeSEs.R + Source: R/mergeSEs.R
diff --git a/reference/mia-datasets.html b/reference/mia-datasets.html index 1b3a2253d..fd7beec3e 100644 --- a/reference/mia-datasets.html +++ b/reference/mia-datasets.html @@ -20,7 +20,7 @@ mia - 1.15.4 + 1.15.5
@@ -47,7 +47,7 @@

mia datasets

- Source: R/mia.R + Source: R/mia.R
diff --git a/reference/mia-package.html b/reference/mia-package.html index 7c419a93e..4e51c6b40 100644 --- a/reference/mia-package.html +++ b/reference/mia-package.html @@ -22,7 +22,7 @@ mia - 1.15.4 + 1.15.5
@@ -49,7 +49,7 @@

mia Package.

- Source: R/mia.R + Source: R/mia.R
diff --git a/reference/peerj13075.html b/reference/peerj13075.html index 53a876f53..77cf583ac 100644 --- a/reference/peerj13075.html +++ b/reference/peerj13075.html @@ -22,7 +22,7 @@ mia - 1.15.4 + 1.15.5
@@ -49,7 +49,7 @@

Skin microbial profiles 58 genetically unrelated individuals

- Source: R/mia.R + Source: R/mia.R
diff --git a/reference/rarefyAssay.html b/reference/rarefyAssay.html index d77fff150..a9f134e5e 100644 --- a/reference/rarefyAssay.html +++ b/reference/rarefyAssay.html @@ -20,7 +20,7 @@ mia - 1.15.4 + 1.15.5
@@ -47,7 +47,7 @@

Subsample Counts

- Source: R/rarefyAssay.R + Source: R/rarefyAssay.R
diff --git a/reference/runCCA.html b/reference/runCCA.html index 40fde6249..614179ac8 100644 --- a/reference/runCCA.html +++ b/reference/runCCA.html @@ -18,7 +18,7 @@ mia - 1.15.4 + 1.15.5
@@ -45,7 +45,7 @@

Canonical Correspondence Analysis and Redundancy Analysis

- Source: R/runCCA.R + Source: R/runCCA.R
@@ -121,25 +121,27 @@

Arguments

...

additional arguments passed to vegan::cca or vegan::dbrda and other internal functions.

  • method a dissimilarity measure to be applied in dbRDA and -possible following homogeneity test. (By default: -method="euclidean")

    • +possible following homogeneity test. (Default: "euclidean")

  • scale: Logical scalar. Should the expression values be standardized? scale is disabled when using *RDA functions. Please scale before performing RDA. (Default: TRUE)

  • na.action: function. Action to take when missing values for any of the variables in formula are encountered. (Default: na.fail)

    • -

  • full Logical scalar. should all the results from the -significance calculations be returned. When full=FALSE, only +

  • full Logical scalar. Should all the results from the +significance calculations be returned. When FALSE, only summary tables are returned. (Default: FALSE)

  • homogeneity.test: Character scalar. Specifies -the significance test used to analyse vegan::betadisper results. -Options include 'permanova' (vegan::permutest), 'anova' -(stats::anova) and 'tukeyhsd' (stats::TukeyHSD). -(By default: homogeneity.test="permanova")

    • +the significance test used to analyse +vegan::betadisper results. +Options include 'permanova' +(vegan::permutest), 'anova' +(stats::anova) and 'tukeyhsd' +(stats::TukeyHSD). +(Default: "permanova")

  • permutations a numeric value specifying the number of permutations for significance testing in vegan::anova.cca. -(By default: permutations=999)

    • +(Default: 999)

@@ -164,7 +166,7 @@

Arguments

variables
-

Deprecated. Use "col.var" instead.

+

Deprecated. Use col.var instead.

test.signif
@@ -192,8 +194,8 @@

Arguments

name
-

Character scalar. A name for the column of the -colData where results will be stored. (Default: "CCA")

+

Character scalar. A name for the reducedDim() +where results will be stored. (Default: "CCA")

@@ -213,7 +215,8 @@

Details

which turns the CCA analysis into a CA analysis and dbRDA into PCoA/MDS.

Significance tests are done with vegan:anova.cca (PERMANOVA). Group dispersion, i.e., homogeneity within groups is analyzed with -vegan:betadisper (multivariate homogeneity of groups dispersions +vegan::betadisper +(multivariate homogeneity of groups dispersions (variances)) and statistical significance of homogeneity is tested with a test specified by homogeneity.test parameter.

diff --git a/reference/runDPCoA.html b/reference/runDPCoA.html index cf8de91f5..f3dee7c1e 100644 --- a/reference/runDPCoA.html +++ b/reference/runDPCoA.html @@ -19,7 +19,7 @@ mia - 1.15.4 + 1.15.5 @@ -46,7 +46,7 @@

Calculation of Double Principal Correspondance analysis

- Source: R/runDPCoA.R + Source: R/runDPCoA.R
diff --git a/reference/runNMDS.html b/reference/runNMDS.html index 9f3c3dc27..d7aa08c53 100644 --- a/reference/runNMDS.html +++ b/reference/runNMDS.html @@ -18,7 +18,7 @@ mia - 1.15.4 + 1.15.5
@@ -45,7 +45,7 @@

Perform non-metric MDS on sample-level data

- Source: R/runNMDS.R + Source: R/runNMDS.R
diff --git a/reference/splitOn.html b/reference/splitOn.html index 26583daa9..d3d85925b 100644 --- a/reference/splitOn.html +++ b/reference/splitOn.html @@ -18,7 +18,7 @@ mia - 1.15.4 + 1.15.5
@@ -45,7 +45,7 @@

Split TreeSummarizedExperiment column-wise or row-wise based on grouping variable

- Source: R/splitOn.R + Source: R/splitOn.R
diff --git a/reference/summaries.html b/reference/summaries.html index 6631a1291..b33e8fa39 100644 --- a/reference/summaries.html +++ b/reference/summaries.html @@ -18,7 +18,7 @@ mia - 1.15.4 + 1.15.5
@@ -45,7 +45,7 @@

Summarizing microbiome data

- Source: R/summaries.R + Source: R/summaries.R
diff --git a/reference/taxonomy-methods.html b/reference/taxonomy-methods.html index 68d81f518..7e9ecfa95 100644 --- a/reference/taxonomy-methods.html +++ b/reference/taxonomy-methods.html @@ -19,7 +19,7 @@ mia - 1.15.4 + 1.15.5
@@ -46,7 +46,7 @@

Functions for accessing taxonomic data stored in rowData.

- Source: R/taxonomy.R + Source: R/taxonomy.R
diff --git a/reference/transformAssay.html b/reference/transformAssay.html index 4e92e77a0..0965037bc 100644 --- a/reference/transformAssay.html +++ b/reference/transformAssay.html @@ -18,7 +18,7 @@ mia - 1.15.4 + 1.15.5
@@ -45,7 +45,7 @@

Transform assay

- Source: R/transformCounts.R + Source: R/transformCounts.R
diff --git a/sitemap.xml b/sitemap.xml index 81dc8d321..f06933779 100644 --- a/sitemap.xml +++ b/sitemap.xml @@ -28,6 +28,7 @@ /reference/getDissimilarity.html /reference/getDominant.html /reference/getMediation.html +/reference/getPERMANOVA.html /reference/getPrevalence.html /reference/hierarchy-tree.html /reference/importBIOM.html