version 4.1.6

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: propr
 Title: Calculating Proportionality Between Vectors of Compositional
         Data
-Version: 4.1.1
+Version: 4.1.6
 URL: http://github.com/tpq/propr
 BugReports: http://github.com/tpq/propr/issues
 Authors@R: c(
@@ -31,12 +31,12 @@ Suggests: ALDEx2, Biobase, cccrm, compositions, data.table, datasets,
         SDMTools, testthat, vegan
 LinkingTo: Rcpp
 NeedsCompilation: yes
-Packaged: 2018-11-18 23:46:53 UTC; thom
+Packaged: 2019-07-10 04:34:32 UTC; thom
 Author: Thomas Quinn [aut, cre],
   David Lovell [aut],
   Ionas Erb [aut],
   Anders Bilgrau [ctb],
   Greg Gloor [ctb]
 Maintainer: Thomas Quinn <contacttomquinn@gmail.com>
 Repository: CRAN
-Date/Publication: 2018-11-19 12:20:02 UTC
+Date/Publication: 2019-07-10 05:00:03 UTC

MD5

@@ -1,21 +1,21 @@
-e459d499cb2c743f2864cf4b351c0350 *DESCRIPTION
-e89a4a32e58b9e2b3ba5586aac16071f *NAMESPACE
-689268f3555256ce77ba58d6a14bc7e2 *NEWS.md
+a58a4c675547f1586c305d470741038c *DESCRIPTION
+44e572e6c0a8f171ee6899ed60c852f0 *NAMESPACE
+707712853d36e755c32428bea9700f75 *NEWS.md
 d0fd4cf23278f18b0e55178d3ea85df6 *R/0-params.R
-20084dc68a3b58f3791b15a444c94374 *R/1-propr.R
+dbe78bef7d84b577c06b81192ea89227 *R/1-propr.R
 5089d34f7ceddcf2c2e96c13409e9948 *R/2-proprCall.R
 4c07a6715abf529b667a7250b9426e40 *R/3-proprViz.R
-53d6ff2ab36d970c2136bbc36b3fbb6b *R/4-propd.R
-3e0bd3bdb8e1737a94d97c6aeb508e02 *R/5-propdCall.R
+428892dd0607a74dad957f398395573f *R/4-propd.R
+ca20236d720211900dcd0814269bc5ef *R/5-propdCall.R
 6b2ead4b32dd55250ed07f7970da7bfc *R/6-propdViz.R
 3e12e1e1c74fe94094f66cea545589d6 *R/7-aldex2propr.R
-38e8765fc47baa4ac1b6e47d7617985e *R/8-get.R
+0d23b0b530dc6b24ca79e7c3307414f2 *R/8-get.R
 436bcbf13363346f60df78265a49c552 *R/9-deprecated.R
 779bc8b2b75ed826d2358fe4ab1d1b0d *R/9-global.R
 36e3b5b20243244d591685587e19b69b *R/9-pra.R
-4ecc2ccb94e92baadd9ae806e61fa624 *R/RcppExports.R
+86d8c92a8ea22f9127776f11717050e9 *R/RcppExports.R
 0cb5f68d61c5e90d60547768394e7ab8 *README.md
-a9ce63628ecafd0379e96269116f8c13 *build/vignette.rds
+0f795b30a5583ddef912ad3ca9f05549 *build/vignette.rds
 85afe8e966882d64a79de4ad8f198689 *data/caneToad.counts.rda
 73203b36c5c9e855bd52d9beefaf5195 *data/caneToad.groups.rda
 f937a82f42500a3aec725965e09b3ac8 *data/datalist
@@ -28,22 +28,22 @@ ed6a318a02091045e6fd3b1064cd7929 *data/top.lr.rda
 214386d4fe680e9fd5f778370bbe1267 *inst/CITATION
 661d960e5a0e87abc9b2708cef811b8c *inst/doc/a_introduction.R
 13b356f0c37a5215a21c0d32ccbfe8c5 *inst/doc/a_introduction.Rmd
-e679fd293c7db759737d2d1b60e07b69 *inst/doc/a_introduction.html
+cba6be20cea5a5a4d86ea8d820d4e8db *inst/doc/a_introduction.html
 ff426c9901d9521d7a1506156911207a *inst/doc/b_visualization.R
 8338f7da4ae675b8053dd2c0adb12e05 *inst/doc/b_visualization.Rmd
-a6ac32a48fabf6c3618e8e4d88c56990 *inst/doc/b_visualization.html
+0ae6853bf774537eac012ef7fbd5c614 *inst/doc/b_visualization.html
 82911dccb62e943e0d63c93d1b7ea0af *inst/doc/d_advanced.R
 ba49707d6dbc812c59c47da5b232f8ba *inst/doc/d_advanced.Rmd
-73d10583650636539aa24b0f60093b43 *inst/doc/d_advanced.html
+3810f583534b5ba648cb1740f285d20f *inst/doc/d_advanced.html
 8ef6f7fa152bd982c5857746a92e111e *inst/doc/e_differential.R
 29c0446d35b4860cc32a2a27a5a35b0e *inst/doc/e_differential.Rmd
-3bb4943870fea1c02d74faf1d397e5be *inst/doc/e_differential.html
+904a31af121b42360148bd2396797881 *inst/doc/e_differential.html
 b4e9f79735763bf4a61c1e0ebd79728c *inst/doc/f_moderation.R
 9520b147409a3c4a92d4c4cb83625b54 *inst/doc/f_moderation.Rmd
-312dc7e9562b0c0c9519afa749458ea8 *inst/doc/f_moderation.html
+f31f0ada6c397a65eab961980211e126 *inst/doc/f_moderation.html
 e3ad967f3610e7ffa4e3a3252fad8fe4 *inst/doc/g_questions.R
 e4d96faab6b6070aa12aff451115e357 *inst/doc/g_questions.Rmd
-9f918445f2c58dc0b277e84ae181f393 *inst/doc/g_questions.html
+221f0d78bf65d1f024cfa7cf231e3d8f *inst/doc/g_questions.html
 c58d8af5df962f272ac64090a1db74a5 *man/aldex.cor.Rd
 e83d907ff4983e638b01c1abe25dab26 *man/aldex.glm.Rd
 c94404bec592ce30a5f70274e487a50e *man/aldex2propr.Rd
@@ -52,14 +52,15 @@ c94404bec592ce30a5f70274e487a50e *man/aldex2propr.Rd
 fcdbf28c33d8ad3f66727b47968d5c87 *man/alphaTheta_old.Rd
 28e003a8a265072a168a69d2a14736ea *man/calculateFDR.Rd
 ca7c74ff68a1daef20132551a77cbabf *man/calculateFDR_old.Rd
-7c1c3ef429a18f1983768a900a950037 *man/calculateTheta.Rd
+322344b184c1eaae02464220cc9652de *man/calculateTheta.Rd
 9f17b52c1566a993d582dfec9cc0e054 *man/calculateThetaW_old.Rd
 b7f65e07db69697cd2635c0fe8eaa352 *man/calculateTheta_old.Rd
 164a4f49b5717bee75efba4fda13fa29 *man/caneToad.counts.Rd
 b5a683db516b797f5da4257e58f9ea66 *man/caneToad.groups.Rd
 bd8828aab70a41d21048d4f0a211599b *man/dendroCheck.Rd
-554bd15af798e2792126116e0fcf9679 *man/getAdjacency.Rd
-8c0153cede35065472b04a343eda873e *man/getMatrix.Rd
+44d6f621cebf38326fbb1262f57d35ff *man/getAdj.Rd
+3646c212d58dc6d48bf017b3a1d523a5 *man/getAdjacency.Rd
+2da302c0688463043e3aec0727f0de4c *man/getMatrix.Rd
 c942bcdef8978b706f34c70306e8e5fb *man/getNetwork.Rd
 d4d57fd34a0599bedb080c025f9831db *man/getRatios.Rd
 14d3a4db2e72e400b2b9f7ed87457e63 *man/getReference.Rd
@@ -86,7 +87,7 @@ cb1890cb2af266c0621d097f18f75ca4 *man/permuteTheta_naive.Rd
 b064aa001e2f68bc9c0af48331ceda66 *man/progress.Rd
 ea8d79d44ece48a36ce68bec53ac29c7 *man/promptCheck.Rd
 f21bcb5ad8befdc789954eff3a4b3e28 *man/propd.Rd
-cdbe8e473f0b40815f2933e03e387fb7 *man/propr.Rd
+dddbee8268a552ea83fe5ad97baa9422 *man/propr.Rd
 d1c56c393eb511865d8e000b08c4b618 *man/proprALR.Rd
 5e4cab1de9281848136e63da1e9ebd98 *man/proprCLR.Rd
 24c7d0c015cba92079ae998cae4291fa *man/proprPairs.Rd
@@ -95,7 +96,7 @@ e4fa556de63e2d44d21957d6a63c4724 *man/proprPhit.Rd
 4bbee917d31bc028633ee3a448ab2a49 *man/proprSym.Rd
 e74113bb12a583411a0d6428a5139c16 *man/proprTri.Rd
 5c55a8316f4929eaac1541480e4dd9b5 *man/proprVLR.Rd
-1ee09e827ddc4fb2e87bd12e55e8b57e *man/qtheta.Rd
+e7ed79c9ea8295690def45120757dce9 *man/qtheta.Rd
 15ff584e7a89fc9eb6da44d0a6412344 *man/ratios.Rd
 5c48d73343cdf3ca94179534849550c5 *man/shale.Rd
 718bab977b5a22a76d6eb0e22b1731c9 *man/slate.Rd
@@ -104,19 +105,20 @@ ab271f0aa7ba9dbb705c6222d9cf5653 *man/top.lr.Rd
 e35e2692a61acb2c1d143cc72fe05828 *man/updateCutoffs.Rd
 bd975b07470fc9a358c5355998a97583 *man/visualize.Rd
 6f42842ad17082a9a54e4dd3f0c2287a *man/wide2long.Rd
-a5d78284f14701f20a81938162a0d91c *src/RcppExports.cpp
+8c99e4198c3d88c20c8136ffcbc21c7c *src/RcppExports.cpp
 fba12b82e88afc0026b7a18037010e40 *src/backend.cpp
 58f3b385b2823a4ef94f6aa0caa26903 *src/backend.h
 a14156d9f3f773e8a043a64fce798a7b *src/ctzRcpp.cpp
 2b9d3ee10265c37f47dd2080a094b1c1 *src/deprecated.cpp
 5f7a907ee2f7e4e5606491ce725a4619 *src/lr2propr.cpp
 f356448004caec64cdde60e0416ba523 *src/lrm.cpp
 cfb30e8074db2268bbb368e729f064a6 *src/lrv.cpp
-7c44bd42b9230745a232706537c28210 *src/omega.cpp
+35747f42c66aa149db50e4b187e5dc94 *src/omega.cpp
 38a416384180a93d31020bdffb37ccee *tests/testthat.R
-52a6c9253f0f5d4cad1f11d6b4d35ecb *tests/testthat/test-Fstat.R
+7cdb937930516b2bfd611e6a272a1835 *tests/testthat/test-Fstat.R
 cac5706ffb5cb340e4eeab7d616514f5 *tests/testthat/test-aldex2propr.R
 ac7887ecf849b1f187852d14150379af *tests/testthat/test-backend.R
+b2100842ca44549d7856cdfb656333aa *tests/testthat/test-getMatrix.R
 f3ab07de6e50fb777ee61bd72c22a20e *tests/testthat/test-getNetwork.R
 e8ea9d79a8def306f98c1b93f8addb15 *tests/testthat/test-getRatios.R
 9dbd69d7466a4f768aaa432210aa1260 *tests/testthat/test-half2mat.R
@@ -126,7 +128,7 @@ cbabe120dad75632dc4c8135a2920e57 *tests/testthat/test-lr2propr.R
 36c1e4852653ebd81030704d560c4e2b *tests/testthat/test-perb.R
 2c5b021d73e71e87715e7dbbfb57ea28 *tests/testthat/test-phis.R
 7329ca8ef8bde680bafc57cd14605088 *tests/testthat/test-phit.R
-c904db10363ed55674fcb2128e88b20a *tests/testthat/test-propd.R
+e3d7fc3856e7c73ecf3fa8354cf2eeaf *tests/testthat/test-propd.R
 fee153a618e9faee5adfde6530322eb1 *tests/testthat/test-simplify.R
 e8363c9012dd6461c783fe69cddc8f27 *tests/testthat/test-theta.R
 13b356f0c37a5215a21c0d32ccbfe8c5 *vignettes/a_introduction.Rmd

NAMESPACE

@@ -6,12 +6,12 @@ export(aldex2propr)
 export(bokeh)
 export(bowtie)
 export(bucket)
-export(calculateTheta)
 export(corr)
 export(cytescape)
 export(decomposed)
 export(dendrogram)
 export(gemini)
+export(getAdj)
 export(getAdjacency)
 export(getMatrix)
 export(getNetwork)

NEWS.md

@@ -1,3 +1,44 @@
+## propr 4.1.6
+---------------------
+* Update `propr` methods
+    * Fix error where `select` is used in presence of zeros
+* Update `propd` methods
+    * All methods now use `N + propd@dfz` degrees-of-freedom
+    * Omega no longer used for F-statistic by `updateF`
+    * Omega no longer used for cutoff by `qtheta`
+
+## propr 4.1.5
+---------------------
+* Update `qtheta` methods
+    * New `fdr` argument in `qtheta` method returns cutoff for FDR-adjusted p-value
+    * Remove `moderated` argument from `qtheta` method
+* Update `get` methods
+    * New `getAdj` offers a faster alternative to `getAdjacency`
+    * Have `getAdjacency` and `getMatrix` set diagonal to 0
+
+## propr 4.1.4
+---------------------
+* Update `propd` methods
+    * Return to using N-K degrees-of-freedom for `pf` and `qf` calls
+    * Have `qtheta` still use Omega (biased) to calculate theta from F-stat
+
+## propr 4.1.3
+---------------------
+* Update `propd` methods
+    * Now compute F-stat and F-mod using Omega (biased) for weighted thetas
+    * Now compute p-value from F-stat and F-mod using Omega (biased) degrees-of-freedom
+    * Update `qtheta` to use Omega (biased) degrees-of-freedom
+    * Remove superfluous `calculateTheta` input checks
+    * Stop export of `calculateTheta` function
+* Update C++ backend
+    * Add `Omega` function to compute population-level pre-factor
+    * Remove superfluous first argument to `omega` function
+
+## propr 4.1.2
+---------------------
+* New tests
+    * Add `getMatrix` test
+
 ## propr 4.1.1
 ---------------------
 * New `get` methods

R/1-propr.R

@@ -180,6 +180,8 @@ propr <- function(counts, metric = c("rho", "phi", "phs", "cor", "vlr"), ivar =
     if(!is.vector(select)) stop("Provide 'select' as vector.")
     if(is.character(select)) select <- match(select, colnames(counts))
     if(any(is.na(select))) stop("Some 'select' not in data.")
+
+    counts <- counts[, select]
     ct <- ct[, select]
     lr <- lr[, select]
   }

R/4-propd.R

@@ -93,18 +93,21 @@ setMethod("show", "propd",
 propd <- function(counts, group, alpha, p = 100, weighted = FALSE){
 
   # Clean "count matrix"
-  # if(any(apply(counts, 2, function(x) all(x == 0)))){
-  #   stop("Remove components with all zeros before proceeding.")}
   if(any(counts < 0)) stop("Data may not contain negative measurements.")
   if(any(is.na(counts))) stop("Remove NAs from 'counts' before proceeding.")
   if(class(counts) == "data.frame") counts <- as.matrix(counts)
   if(is.null(colnames(counts))) colnames(counts) <- as.character(1:ncol(counts))
   if(is.null(rownames(counts))) rownames(counts) <- as.character(1:nrow(counts))
-  if(missing(alpha)){ alpha <- NA
-  }else{ if(!is.na(alpha)) if(alpha == 0) alpha <- NA }
-  ct <- counts
+
+  # Clean group
+  if(length(unique(group)) != 2) stop("Please use exactly two unique groups.")
+  if(length(group) != nrow(counts)) stop("Too many or too few group labels.")
+  group <- as.character(group)
 
   # Replace zeros unless alpha is provided
+  if(missing(alpha)){ alpha <- as.numeric(NA)
+  }else{ if(!is.na(alpha)) if(alpha == 0) alpha <- as.numeric(NA) }
+  ct <- counts
   if(any(as.matrix(counts) == 0) & is.na(alpha)){
     message("Alert: Replacing 0s with next smallest value.")
     zeros <- ct == 0
@@ -132,8 +135,7 @@ propd <- function(counts, group, alpha, p = 100, weighted = FALSE){
   # Initialize @counts, @group, @alpha
   result@counts <- as.data.frame(ct)
   result@group <- as.character(group)
-  if(!missing(alpha)){ result@alpha <- as.numeric(alpha)
-  }else{ result@alpha <- as.numeric(NA) }
+  result@alpha <- as.numeric(alpha)
 
   # Initialize @permutes
   result@permutes <- data.frame()
@@ -151,6 +153,7 @@ propd <- function(counts, group, alpha, p = 100, weighted = FALSE){
                    weights = result@weights)
 
   # Initialize @results -- Tally frequency of 0 counts
+  # [note, use `counts` because `ct`` is already zero-replaced]
   if(any(as.matrix(counts) == 0)){
     message("Alert: Tabulating the presence of 0 counts.")
     result@results$Zeros <- ctzRcpp(as.matrix(counts)) # count 0s
@@ -160,8 +163,6 @@ propd <- function(counts, group, alpha, p = 100, weighted = FALSE){
   if(any(result@results$theta > 1)){
     message("Alert: Theta rounded to 14 decimal digits.")
     result@results$theta <- round(result@results$theta, 14)
-    result@results$theta_e <- round(result@results$theta_e, 14)
-    result@results$theta_f <- round(result@results$theta_f, 14)
   }
 
   message("Alert: Use 'setActive' to select a theta type.")