maaslin: maaslin-4450aa4ecc84/src/test-BoostGLM/test-BoostGLM.R annotate

annotate maaslin-4450aa4ecc84/src/test-BoostGLM/test-BoostGLM.R @ 1:a87d5a5f2776

Uploaded the version running on the prod server

author	george-weingart
date	Sun, 08 Feb 2015 23:08:38 -0500
parents
children

rev	line source
1 a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	1 c_strDir <- file.path(getwd( ),"..")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	2
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	3 source(file.path(c_strDir,"lib","Constants.R"))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	4 source(file.path(c_strDir,"lib","Utility.R"))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	5 source(file.path(c_strDir,"lib","AnalysisModules.R"))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	6
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	7 # General setup
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	8 covX1 = c(44.4, 45.9, 41.9, 53.3, 44.7, 44.1, 50.7, 45.2, 60.1)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	9 covX2 = c(144.4, 245.9, 141.9, 253.3, 144.7, 244.1, 150.7, 245.2, 160.1)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	10 covX3 = as.factor(c(1,2,3,1,2,3,1,2,3))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	11 covX4 = as.factor(c(1,1,1,1,2,2,2,2,2))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	12 covX5 = as.factor(c(1,2,1,2,1,2,1,2,1))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	13 covY = c(.26, .31, .25, .50, .36, .40, .52, .28, .38)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	14 frmeTmp = data.frame(Covariate1=covX1, Covariate2=covX2, Covariate3=covX3, Covariate4=covX4, Covariate5=covX5, adCur= covY)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	15 iTaxon = 6
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	16
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	17 lsCov1 = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	18 lsCov1$name = "Covariate1"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	19 lsCov1$orig = "Covariate1"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	20 lsCov1$taxon = "adCur"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	21 lsCov1$data = covY
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	22 lsCov1$factors = "Covariate1"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	23 lsCov1$metadata = covX1
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	24 vdCoef = c()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	25 vdCoef["(Intercept)"]=round(0.0345077486,5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	26 vdCoef["Covariate1"]= round(0.0052097355,5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	27 vdCoef["Covariate2"]= round(0.0005806568,5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	28 vdCoef["Covariate32"]=round(-0.1333421874,5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	29 vdCoef["Covariate33"]=round(-0.1072006419,5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	30 vdCoef["Covariate42"]=round(0.0849198280,5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	31 lsCov1$value = c(Covariate1=round(0.005209736,5))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	32 lsCov1$std = round(0.0063781728,5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	33 lsCov1$allCoefs = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	34 lsCov2 = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	35 lsCov2$name = "Covariate2"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	36 lsCov2$orig = "Covariate2"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	37 lsCov2$taxon = "adCur"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	38 lsCov2$data = covY
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	39 lsCov2$factors = "Covariate2"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	40 lsCov2$metadata = covX2
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	41 lsCov2$value = c(Covariate2=round(0.0005806568,5))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	42 lsCov2$std = round(0.0006598436,5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	43 lsCov2$allCoefs = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	44 lsCov3 = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	45 lsCov3$name = "Covariate3"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	46 lsCov3$orig = "Covariate32"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	47 lsCov3$taxon = "adCur"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	48 lsCov3$data = covY
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	49 lsCov3$factors = "Covariate3"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	50 lsCov3$metadata = covX3
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	51 lsCov3$value = c(Covariate32=round(-0.1333422,5))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	52 lsCov3$std = round(0.0895657826,5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	53 lsCov3$allCoefs = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	54 lsCov4 = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	55 lsCov4$name = "Covariate3"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	56 lsCov4$orig = "Covariate33"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	57 lsCov4$taxon = "adCur"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	58 lsCov4$data = covY
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	59 lsCov4$factors = "Covariate3"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	60 lsCov4$metadata = covX3
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	61 lsCov4$value = c(Covariate33=round(-0.1072006,5))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	62 lsCov4$std = round(0.0792209541,5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	63 lsCov4$allCoefs = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	64 lsCov5 = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	65 lsCov5$name = "Covariate4"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	66 lsCov5$orig = "Covariate42"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	67 lsCov5$taxon = "adCur"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	68 lsCov5$data = covY
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	69 lsCov5$factors = "Covariate4"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	70 lsCov5$metadata = covX4
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	71 lsCov5$value = c(Covariate42=round(0.08491983,5))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	72 lsCov5$std = round(0.0701018621,5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	73 lsCov5$allCoefs = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	74
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	75 context("Test funcClean")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	76
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	77 context("Test funcBugHybrid")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	78 # multiple covariates, one call lm
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	79 aiMetadata = c(1:5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	80 aiData = c(iTaxon)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	81 dFreq = 0.5 / length( aiMetadata )
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	82 dSig = 0.25
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	83 dMinSamp = 0.1
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	84 adP = c()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	85 lsSig = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	86 funcReg = NA
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	87 funcAnalysis = funcLM
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	88 funcGetResult = funcGetLMResults
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	89 lsData = list(frmeData=frmeTmp, aiMetadata=aiMetadata, aiData=aiData, lsQCCounts=list())
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	90 lsData$astrMetadata = names(frmeTmp)[aiMetadata]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	91
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	92 adPExpected = round(c(0.4738687,0.4436566,0.4665972,0.5378693,0.3124672),5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	93 QCExpected = list(iLms=numeric(0))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	94 lsSigExpected = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	95 lsSigExpected[[1]] = lsCov1
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	96 lsSigExpected[[2]] = lsCov2
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	97 lsSigExpected[[3]] = lsCov3
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	98 lsSigExpected[[4]] = lsCov4
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	99 lsSigExpected[[5]] = lsCov5
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	100 expectedReturn = list(adP=adPExpected,lsSig=lsSigExpected,lsQCCounts=QCExpected)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	101 receivedReturn = funcBugHybrid(iTaxon=iTaxon,frmeData=frmeTmp,lsData=lsData,aiMetadata=aiMetadata,dFreq=dFreq,dSig=dSig,dMinSamp=dMinSamp,adP=adP,lsSig=lsSig, strLog=NA,funcReg=funcReg,lsNonPenalizedPredictors=NULL,funcAnalysis=funcAnalysis,lsRandomCovariates=NULL,funcGetResult=funcGetResult)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	102 receivedReturn$adP = round(receivedReturn$adP,5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	103
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	104 vCoefs=receivedReturn$lsSig[[1]]$allCoefs
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	105 vCoefs[1]=round(vCoefs[1],5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	106 vCoefs[2]=round(vCoefs[2],5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	107 vCoefs[3]=round(vCoefs[3],5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	108 vCoefs[4]=round(vCoefs[4],5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	109 vCoefs[5]=round(vCoefs[5],5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	110 vCoefs[6]=round(vCoefs[6],5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	111 receivedReturn$lsSig[[1]]$allCoefs=vCoefs
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	112 receivedReturn$lsSig[[2]]$allCoefs=vCoefs
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	113 receivedReturn$lsSig[[3]]$allCoefs=vCoefs
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	114 receivedReturn$lsSig[[4]]$allCoefs=vCoefs
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	115 receivedReturn$lsSig[[5]]$allCoefs=vCoefs
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	116 vValue=c()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	117 vValue[receivedReturn$lsSig[[1]]$orig]=round(receivedReturn$lsSig[[1]]$value[[1]],5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	118 receivedReturn$lsSig[[1]]$value=vValue
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	119 vValue=c()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	120 vValue[receivedReturn$lsSig[[2]]$orig]=round(receivedReturn$lsSig[[2]]$value[[1]],5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	121 receivedReturn$lsSig[[2]]$value=vValue
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	122 vValue=c()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	123 vValue[receivedReturn$lsSig[[3]]$orig]=round(receivedReturn$lsSig[[3]]$value[[1]],5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	124 receivedReturn$lsSig[[3]]$value=vValue
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	125 vValue=c()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	126 vValue[receivedReturn$lsSig[[4]]$orig]=round(receivedReturn$lsSig[[4]]$value[[1]],5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	127 receivedReturn$lsSig[[4]]$value=vValue
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	128 vValue=c()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	129 vValue[receivedReturn$lsSig[[5]]$orig]=round(receivedReturn$lsSig[[5]]$value[[1]],5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	130 receivedReturn$lsSig[[5]]$value=vValue
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	131 receivedReturn$lsSig[[1]]$std=round(receivedReturn$lsSig[[1]]$std,5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	132 receivedReturn$lsSig[[2]]$std=round(receivedReturn$lsSig[[2]]$std,5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	133 receivedReturn$lsSig[[3]]$std=round(receivedReturn$lsSig[[3]]$std,5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	134 receivedReturn$lsSig[[4]]$std=round(receivedReturn$lsSig[[4]]$std,5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	135 receivedReturn$lsSig[[5]]$std=round(receivedReturn$lsSig[[5]]$std,5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	136 test_that("funcBugHybrid works with the lm option with multiple covariates.",{expect_equal(receivedReturn,expectedReturn)})
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	137
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	138
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	139 # single covariate, single call lm
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	140 aiMetadata = c(1)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	141 dFreq = 0.5 / length( aiMetadata )
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	142 lsData$astrMetadata = names(frmeTmp)[aiMetadata]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	143 adPExpected = round(c(0.1081731),5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	144 QCExpected = list(iLms=numeric(0))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	145 lsSigExpected = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	146 lsSigExpected[[1]] = lsCov1
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	147 lsSigExpected[[1]]$std=round(0.005278468,5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	148 vdCoef = c()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	149 vdCoef["(Intercept)"]=round(-0.102410716,5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	150 vdCoef["Covariate1"]= round(0.009718095,5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	151 lsSigExpected[[1]]$allCoefs= vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	152 lsSigExpected[[1]]$value = c(Covariate1=round(0.009718095,5))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	153
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	154 expectedReturn = list(adP=adPExpected,lsSig=lsSigExpected,lsQCCounts=QCExpected)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	155 receivedReturn = funcBugHybrid(iTaxon=iTaxon,frmeData=frmeTmp,lsData=lsData,aiMetadata=aiMetadata,dFreq=dFreq,dSig=dSig,dMinSamp=dMinSamp,adP=adP,lsSig=lsSig, strLog=NA,funcReg=funcReg,lsNonPenalizedPredictors=NULL,funcAnalysis=funcAnalysis,lsRandomCovariates=NULL,funcGetResult=funcGetResult)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	156 receivedReturn$adP = round(receivedReturn$adP,5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	157
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	158 vCoefs=receivedReturn$lsSig[[1]]$allCoefs
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	159 vCoefs[1]=round(vCoefs[1],5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	160 vCoefs[2]=round(vCoefs[2],5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	161 receivedReturn$lsSig[[1]]$allCoefs=vCoefs
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	162 vValue=c()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	163 vValue[receivedReturn$lsSig[[1]]$orig]=round(receivedReturn$lsSig[[1]]$value[[1]],5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	164 receivedReturn$lsSig[[1]]$value=vValue
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	165 receivedReturn$lsSig[[1]]$std=round(0.005278468,5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	166 test_that("funcBugHybrid works with the lm option with 1 covariates.",{expect_equal(receivedReturn,expectedReturn)})
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	167
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	168
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	169 # multiple covariate, single call univariate
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	170 funcReg = NA
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	171 funcAnalysis = funcDoUnivariate
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	172 funcGetResult = NA
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	173 aiMetadata = c(3,1,2)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	174 dFreq = 0.5 / length( aiMetadata )
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	175 lsData$astrMetadata = names(frmeTmp)[aiMetadata]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	176 adPExpected = round(c(1.0,1.0,0.09679784,0.21252205),5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	177 QCExpected = list(iLms=numeric(0))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	178 lsSigExpected = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	179 lsCov1 = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	180 lsCov1$name = "Covariate3"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	181 lsCov1$orig = "Covariate32"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	182 lsCov1$taxon = "adCur"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	183 lsCov1$data = covY
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	184 lsCov1$factors = "Covariate3"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	185 lsCov1$metadata = frmeTmp[["Covariate3"]]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	186 vdCoef = c(Covariate32=NA)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	187 lsCov1$value = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	188 lsCov1$std = sd(frmeTmp[["Covariate3"]])
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	189 lsCov1$allCoefs = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	190 lsCov2 = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	191 lsCov2$name = "Covariate3"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	192 lsCov2$orig = "Covariate33"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	193 lsCov2$taxon = "adCur"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	194 lsCov2$data = covY
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	195 lsCov2$factors = "Covariate3"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	196 lsCov2$metadata = frmeTmp[["Covariate3"]]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	197 vdCoef = c(Covariate33=NA)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	198 lsCov2$value = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	199 lsCov2$std = sd(frmeTmp[["Covariate3"]])
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	200 lsCov2$allCoefs = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	201 lsCov3 = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	202 lsCov3$name = "Covariate1"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	203 lsCov3$orig = "Covariate1"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	204 lsCov3$taxon = "adCur"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	205 lsCov3$data = covY
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	206 lsCov3$factors = "Covariate1"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	207 lsCov3$metadata = frmeTmp[["Covariate1"]]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	208 vdCoef = c(Covariate1=0.6)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	209 lsCov3$value = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	210 lsCov3$std = sd(frmeTmp[["Covariate1"]])
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	211 lsCov3$allCoefs = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	212 lsCov4 = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	213 lsCov4$name = "Covariate2"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	214 lsCov4$orig = "Covariate2"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	215 lsCov4$taxon = "adCur"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	216 lsCov4$data = covY
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	217 lsCov4$factors = "Covariate2"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	218 lsCov4$metadata = frmeTmp[["Covariate2"]]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	219 vdCoef = c(Covariate2=0.46666667)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	220 lsCov4$value = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	221 lsCov4$std = sd(frmeTmp[["Covariate2"]])
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	222 lsCov4$allCoefs = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	223
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	224 lsSigExpected = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	225 lsSigExpected[[1]] = lsCov1
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	226 lsSigExpected[[2]] = lsCov2
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	227 lsSigExpected[[3]] = lsCov3
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	228 lsSigExpected[[4]] = lsCov4
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	229
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	230 expectedReturn = list(adP=adPExpected,lsSig=lsSigExpected,lsQCCounts=QCExpected)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	231 receivedReturn = funcBugHybrid(iTaxon=iTaxon,frmeData=frmeTmp,lsData=lsData,aiMetadata=aiMetadata,dFreq=dFreq,dSig=dSig,dMinSamp=dMinSamp,adP=adP,lsSig=lsSig, strLog=NA,funcReg=funcReg,lsNonPenalizedPredictors=NULL,funcAnalysis=funcAnalysis,lsRandomCovariates=NULL,funcGetResult=funcGetResult)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	232 receivedReturn$adP = round(receivedReturn$adP,5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	233 test_that("funcBugHybrid works with the univariate option with 3 covariates.",{expect_equal(receivedReturn,expectedReturn)})
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	234
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	235
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	236 # single covariate, single call univariate
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	237 funcReg = NA
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	238 funcAnalysis = funcDoUnivariate
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	239 funcGetResult = NA
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	240 aiMetadata = c(1)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	241 dFreq = 0.5 / length( aiMetadata )
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	242 lsData$astrMetadata = names(frmeTmp)[aiMetadata]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	243 adPExpected = round(c(0.09679784),5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	244 QCExpected = list(iLms=numeric(0))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	245 lsSigExpected = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	246 lsSigExpected[[1]] = lsCov3
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	247
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	248 expectedReturn = list(adP=adPExpected,lsSig=lsSigExpected,lsQCCounts=QCExpected)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	249 receivedReturn = funcBugHybrid(iTaxon=iTaxon,frmeData=frmeTmp,lsData=lsData,aiMetadata=aiMetadata,dFreq=dFreq,dSig=dSig,dMinSamp=dMinSamp,adP=adP,lsSig=lsSig, strLog=NA,funcReg=funcReg,lsNonPenalizedPredictors=NULL,funcAnalysis=funcAnalysis,lsRandomCovariates=NULL,funcGetResult=funcGetResult)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	250 receivedReturn$adP = round(receivedReturn$adP,5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	251 test_that("funcBugHybrid works with the univariate option with 1 covariates.",{expect_equal(receivedReturn,expectedReturn)})
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	252
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	253
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	254 context("Test funcBugs")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	255 #One LM run
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	256 frmeData=frmeTmp
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	257 aiMetadata=c(1)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	258 aiData=c(iTaxon)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	259 strData=NA
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	260 dFreq= 0.5 / length( aiMetadata )
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	261 dSig=0.25
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	262 dMinSamp=0.1
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	263 strDirOut=NA
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	264 funcReg=NA
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	265 lsNonPenalizedPredictors=NULL
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	266 lsRandomCovariates=NULL
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	267 funcAnalysis=funcLM
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	268 funcGetResults=funcGetLMResults
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	269 fDoRPlot=FALSE
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	270 lsData = list(frmeData=frmeData, aiMetadata=aiMetadata, aiData=aiData, lsQCCounts=list())
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	271 lsData$astrMetadata = names(frmeTmp)[aiMetadata]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	272 QCExpected = list(iLms=numeric(0))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	273
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	274 expectedReturn = list(aiReturnBugs=aiData,lsQCCounts=QCExpected)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	275 receivedReturn = funcBugs(frmeData=frmeData, lsData=lsData, aiMetadata=aiMetadata, aiData=aiData, strData=strData, dFreq=dFreq, dSig=dSig, dMinSamp=dMinSamp,strDirOut=strDirOut, funcReg=funcReg,lsNonPenalizedPredictors=lsNonPenalizedPredictors,funcAnalysis=funcAnalysis,lsRandomCovariates=lsRandomCovariates,funcGetResults=funcGetResults,fDoRPlot=fDoRPlot)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	276
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	277 test_that("funcBugs works with the lm option with 1 covariate.",{expect_equal(receivedReturn,expectedReturn)})
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	278
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	279 #multiple LM run
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	280 frmeData=frmeTmp
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	281 aiMetadata=c(1:5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	282 aiData=c(iTaxon)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	283 strData=NA
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	284 dFreq= 0.5 / length( aiMetadata )
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	285 dSig=0.25
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	286 dMinSamp=0.1
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	287 strDirOut=NA
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	288 funcReg=NA
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	289 lsNonPenalizedPredictors=NULL
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	290 lsRandomCovariates=NULL
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	291 funcAnalysis=funcLM
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	292 funcGetResults=funcGetLMResults
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	293 fDoRPlot=FALSE
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	294 lsData = list(frmeData=frmeData, aiMetadata=aiMetadata, aiData=aiData, lsQCCounts=list())
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	295 lsData$astrMetadata = names(frmeTmp)[aiMetadata]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	296 QCExpected = list(iLms=numeric(0))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	297
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	298 expectedReturn = list(aiReturnBugs=aiData,lsQCCounts=QCExpected)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	299 receivedReturn = funcBugs(frmeData=frmeData, lsData=lsData, aiMetadata=aiMetadata, aiData=aiData, strData=strData, dFreq=dFreq, dSig=dSig, dMinSamp=dMinSamp,strDirOut=strDirOut, funcReg=funcReg,lsNonPenalizedPredictors=lsNonPenalizedPredictors,funcAnalysis=funcAnalysis,lsRandomCovariates=lsRandomCovariates,funcGetResults=funcGetResults,fDoRPlot=fDoRPlot)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	300
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	301 print("START START")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	302 print(expectedReturn)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	303 print("RECEIVED")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	304 print(receivedReturn)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	305 print("STOP STOP")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	306
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	307 test_that("funcBugs works with the lm option with multiple covariates.",{expect_equal(receivedReturn,expectedReturn)})

Mercurial > repos > george-weingart > maaslin

annotate maaslin-4450aa4ecc84/src/test-BoostGLM/test-BoostGLM.R @ 1:a87d5a5f2776