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

annotate maaslin-4450aa4ecc84/src/test-AnalysisModules/test-AnalysisModules.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
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	6 #Test Utilities
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	7 context("Test funcGetLMResults")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	8 context("Test funcGetStepPredictors")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	9
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	10 context("Test funcMakeContrasts")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	11 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	12 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	13 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	14 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	15 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	16 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	17 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	18 iTaxon = 6
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	19 #Add in updating QC errors
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	20 #Add in random covariates
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	21 strFormula = "adCur ~ Covariate1"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	22 strRandomFormula = NULL
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	23 lsSig = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	24 lsSig[[1]] = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	25 lsSig[[1]]$name = "Covariate1"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	26 lsSig[[1]]$orig = "Covariate1"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	27 lsSig[[1]]$taxon = "adCur"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	28 lsSig[[1]]$data = covY
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	29 lsSig[[1]]$factors = "Covariate1"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	30 lsSig[[1]]$metadata = covX1
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	31 vdCoef = c(Covariate1=0.6)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	32 lsSig[[1]]$value = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	33 lsSig[[1]]$std = sd(covX1)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	34 lsSig[[1]]$allCoefs = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	35 ret1 = funcMakeContrasts(strFormula=strFormula, strRandomFormula=strRandomFormula, frmeTmp=frmeTmp, iTaxon=iTaxon,
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	36 functionContrast=function(x,adCur,dfData)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	37 {
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	38 retList = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	39 ret = cor.test(as.formula(paste("~",x,"+ adCur")), data=dfData, method="spearman", na.action=c_strNA_Action)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	40 #Returning rho for the coef in a named vector
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	41 vdCoef = c()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	42 vdCoef[[x]]=ret$estimate
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	43 retList[[1]]=list(p.value=ret$p.value,SD=sd(dfData[[x]]),name=x,coef=vdCoef)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	44 return(retList)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	45 }, lsQCCounts=list())
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	46 ret1$adP = round(ret1$adP,5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	47 test_that("1. Test that the funcMakeContrasts works on a continuous variable.",{
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	48 expect_equal(ret1,list(adP=round(c(0.09679784),5),lsSig=lsSig,lsQCCounts=list()))})
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	49
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	50 strFormula = "adCur ~ Covariate1 + Covariate2"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	51 strRandomFormula = NULL
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	52 lsSig = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	53 lsSig[[1]] = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	54 lsSig[[1]]$name = "Covariate1"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	55 lsSig[[1]]$orig = "Covariate1"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	56 lsSig[[1]]$taxon = "adCur"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	57 lsSig[[1]]$data = covY
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	58 lsSig[[1]]$factors = "Covariate1"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	59 lsSig[[1]]$metadata = covX1
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	60 vdCoef = c(Covariate1=0.6)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	61 lsSig[[1]]$value = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	62 lsSig[[1]]$std = sd(covX1)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	63 lsSig[[1]]$allCoefs = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	64 lsSig[[2]] = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	65 lsSig[[2]]$name = "Covariate2"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	66 lsSig[[2]]$orig = "Covariate2"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	67 lsSig[[2]]$taxon = "adCur"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	68 lsSig[[2]]$data = covY
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	69 lsSig[[2]]$factors = "Covariate2"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	70 lsSig[[2]]$metadata = covX2
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	71 vdCoef = c(Covariate2=0.46666667)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	72 lsSig[[2]]$value = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	73 lsSig[[2]]$std = sd(covX2)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	74 lsSig[[2]]$allCoefs = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	75 ret1 = funcMakeContrasts(strFormula=strFormula, strRandomFormula=strRandomFormula, frmeTmp=frmeTmp, iTaxon=iTaxon,
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	76 functionContrast=function(x,adCur,dfData)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	77 {
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	78 retList = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	79 ret = cor.test(as.formula(paste("~",x,"+ adCur")), data=dfData, method="spearman", na.action=c_strNA_Action)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	80 #Returning rho for the coef in a named vector
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	81 vdCoef = c()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	82 vdCoef[[x]]=ret$estimate
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	83 retList[[1]]=list(p.value=ret$p.value,SD=sd(dfData[[x]]),name=x,coef=vdCoef)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	84 return(retList)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	85 }, lsQCCounts=list())
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	86 ret1$adP = round(ret1$adP,5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	87 test_that("Test that the funcMakeContrasts works on 2 continuous variables.",{
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	88 expect_equal(ret1,list(adP=round(c(0.09679784,0.21252205),5),lsSig=lsSig,lsQCCounts=list()))})
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	89
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	90 strFormula = "adCur ~ Covariate4"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	91 strRandomFormula = NULL
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	92 lsSig = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	93 lsSig[[1]] = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	94 lsSig[[1]]$name = "Covariate4"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	95 lsSig[[1]]$orig = "Covariate42"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	96 lsSig[[1]]$taxon = "adCur"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	97 lsSig[[1]]$data = covY
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	98 lsSig[[1]]$factors = "Covariate4"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	99 lsSig[[1]]$metadata = covX4 #update
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	100 vdCoef = c(Covariate42=NA)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	101 lsSig[[1]]$value = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	102 lsSig[[1]]$std = sd(covX4) #update
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	103 lsSig[[1]]$allCoefs = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	104 # Get return
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	105 rets = funcMakeContrasts(strFormula=strFormula, strRandomFormula=strRandomFormula, frmeTmp=frmeTmp, iTaxon=iTaxon,
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	106 functionContrast=function(x,adCur,dfData)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	107 {
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	108 retList = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	109 lmodKW = kruskal(adCur,dfData[[x]],group=FALSE,p.adj="holm")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	110 asLevels = levels(dfData[[x]])
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	111 # The names of the generated comparisons, sometimes the control is first sometimes it is not so
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	112 # We will just check which is in the names and use that
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	113 asComparisons = row.names(lmodKW$comparisons)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	114 #Get the comparison with the control
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	115 for(sLevel in asLevels[2:length(asLevels)])
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	116 {
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	117 sComparison = intersect(c(paste(asLevels[1],sLevel,sep=" - "),paste(sLevel,asLevels[1],sep=" - ")),asComparisons)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	118 #Returning NA for the coef in a named vector
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	119 vdCoef = c()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	120 vdCoef[[paste(x,sLevel,sep="")]]=NA
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	121 retList[[length(retList)+1]]=list(p.value=lmodKW$comparisons[sComparison,"p.value"],SD=NA,name=paste(x,sLevel,sep=""),coef=vdCoef)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	122 }
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	123 return(retList)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	124 }, lsQCCounts=list())
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	125 rets$adP=round(rets$adP,digits=5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	126 test_that("Test that the funcMakeContrasts works on 1 factor covariate with 2 levels.",{
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	127 expect_equal(rets,list(adP=round(c(0.24434),5),lsSig=lsSig,lsQCCounts=list()))})
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	128
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	129 strFormula = "adCur ~ Covariate3"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	130 strRandomFormula = NULL
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	131 lsSig = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	132 lsSig[[1]] = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	133 lsSig[[1]]$name = "Covariate3"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	134 lsSig[[1]]$orig = "Covariate32"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	135 lsSig[[1]]$taxon = "adCur"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	136 lsSig[[1]]$data = covY
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	137 lsSig[[1]]$factors = "Covariate3"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	138 lsSig[[1]]$metadata = covX3 #update
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	139 vdCoef = c(Covariate32=NA)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	140 lsSig[[1]]$value = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	141 lsSig[[1]]$std = sd(covX3) #update
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	142 lsSig[[1]]$allCoefs = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	143 lsSig[[2]] = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	144 lsSig[[2]]$name = "Covariate3"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	145 lsSig[[2]]$orig = "Covariate33"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	146 lsSig[[2]]$taxon = "adCur"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	147 lsSig[[2]]$data = covY
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	148 lsSig[[2]]$factors = "Covariate3"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	149 lsSig[[2]]$metadata = covX3 #update
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	150 vdCoef = c(Covariate33=NA)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	151 lsSig[[2]]$value = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	152 lsSig[[2]]$std = sd(covX3) #update
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	153 lsSig[[2]]$allCoefs = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	154 ret1 = funcMakeContrasts(strFormula=strFormula, strRandomFormula=strRandomFormula, frmeTmp=frmeTmp, iTaxon=iTaxon,
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	155 functionContrast=function(x,adCur,dfData)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	156 {
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	157 retList = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	158 lmodKW = kruskal(adCur,dfData[[x]],group=FALSE,p.adj="holm")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	159 asLevels = levels(dfData[[x]])
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	160 # The names of the generated comparisons, sometimes the control is first sometimes it is not so
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	161 # We will just check which is in the names and use that
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	162 asComparisons = row.names(lmodKW$comparisons)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	163 #Get the comparison with the control
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	164 for(sLevel in asLevels[2:length(asLevels)])
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	165 {
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	166 sComparison = intersect(c(paste(asLevels[1],sLevel,sep=" - "),paste(sLevel,asLevels[1],sep=" - ")),asComparisons)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	167 #Returning NA for the coef in a named vector
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	168 vdCoef = c()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	169 vdCoef[[paste(x,sLevel,sep="")]]=NA
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	170 retList[[length(retList)+1]]=list(p.value=lmodKW$comparisons[sComparison,"p.value"],SD=NA,name=paste(x,sLevel,sep=""),coef=vdCoef)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	171 }
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	172 return(retList)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	173 }, lsQCCounts=list())
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	174 ret1$adP = round(ret1$adP,5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	175 test_that("Test that the funcMakeContrasts works on 1 factor covariate with 3 levels.",{
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	176 expect_equal(ret1,list(adP=c(1.0,1.0),lsSig=lsSig,lsQCCounts=list()))})
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	177
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	178 strFormula = "adCur ~ Covariate4 + Covariate5"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	179 strRandomFormula = NULL
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	180 lsSig = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	181 lsSig[[1]] = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	182 lsSig[[1]]$name = "Covariate4"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	183 lsSig[[1]]$orig = "Covariate42"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	184 lsSig[[1]]$taxon = "adCur"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	185 lsSig[[1]]$data = covY
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	186 lsSig[[1]]$factors = "Covariate4"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	187 lsSig[[1]]$metadata = covX4 #update
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	188 vdCoef = c(Covariate42=NA)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	189 lsSig[[1]]$value = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	190 lsSig[[1]]$std = sd(covX4) #update
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	191 lsSig[[1]]$allCoefs = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	192 lsSig[[2]] = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	193 lsSig[[2]]$name = "Covariate5"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	194 lsSig[[2]]$orig = "Covariate52"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	195 lsSig[[2]]$taxon = "adCur"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	196 lsSig[[2]]$data = covY
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	197 lsSig[[2]]$factors = "Covariate5"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	198 lsSig[[2]]$metadata = covX5 #update
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	199 vdCoef = c(Covariate52=NA)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	200 lsSig[[2]]$value = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	201 lsSig[[2]]$std = sd(covX5) #update
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	202 lsSig[[2]]$allCoefs = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	203 ret1 = funcMakeContrasts(strFormula=strFormula, strRandomFormula=strRandomFormula, frmeTmp=frmeTmp, iTaxon=iTaxon,
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	204 functionContrast=function(x,adCur,dfData)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	205 {
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	206 retList = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	207 lmodKW = kruskal(adCur,dfData[[x]],group=FALSE,p.adj="holm")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	208 asLevels = levels(dfData[[x]])
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	209 # The names of the generated comparisons, sometimes the control is first sometimes it is not so
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	210 # We will just check which is in the names and use that
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	211 asComparisons = row.names(lmodKW$comparisons)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	212 #Get the comparison with the control
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	213 for(sLevel in asLevels[2:length(asLevels)])
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	214 {
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	215 sComparison = intersect(c(paste(asLevels[1],sLevel,sep=" - "),paste(sLevel,asLevels[1],sep=" - ")),asComparisons)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	216 #Returning NA for the coef in a named vector
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	217 vdCoef = c()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	218 vdCoef[[paste(x,sLevel,sep="")]]=NA
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	219 retList[[length(retList)+1]]=list(p.value=lmodKW$comparisons[sComparison,"p.value"],SD=NA,name=paste(x,sLevel,sep=""),coef=vdCoef)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	220 }
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	221 return(retList)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	222 }, lsQCCounts=list())
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	223 ret1$adP = round(ret1$adP,5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	224 test_that("1. Test that the funcMakeContrasts works on 2 factor covariate with 2 levels.",{
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	225 expect_equal(ret1,list(adP=round(c(0.24434,0.655852),5),lsSig=lsSig,lsQCCounts=list()))})
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	226
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	227
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	228 #Test Model selection
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
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	231 context("Test funcBoostModel")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	232 context("Test funcForwardModel")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	233 context("Test funcBackwardsModel")
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 #Test Univariates
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	237 context("Test funcSpearman")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	238 strFormula = "adCur ~ Covariate1"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	239 adCur = c(.26, .31, .25, .50, .36, .40, .52, .28, .38)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	240 x = 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	241 frmeTmp = data.frame(Covariate1=x, adCur=adCur)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	242 iTaxon = 2
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	243 lsQCCounts = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	244 lsSig = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	245 lsSig[[1]] = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	246 lsSig[[1]]$name = "Covariate1"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	247 lsSig[[1]]$orig = "Covariate1"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	248 lsSig[[1]]$taxon = "adCur"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	249 lsSig[[1]]$data = adCur
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	250 lsSig[[1]]$factors = "Covariate1"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	251 lsSig[[1]]$metadata = x
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	252 vdCoef = c(Covariate1=0.6)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	253 lsSig[[1]]$value = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	254 lsSig[[1]]$std = sd(x)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	255 lsSig[[1]]$allCoefs = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	256 ret1 = funcSpearman(strFormula=strFormula,frmeTmp=frmeTmp,iTaxon=iTaxon,lsQCCounts=lsQCCounts,strRandomFormula=NULL)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	257 ret1$adP = round(ret1$adP,5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	258 test_that("Test that the spearman test has the correct results for 1 covariate.",{
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	259 expect_equal(ret1,list(adP=round(c(0.09679784),5),lsSig=lsSig,lsQCCounts=list()))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	260 })
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	261
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	262 strFormula = "adCur ~ Covariate1 + Covariate2"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	263 frmeTmp = data.frame(Covariate1=x, Covariate2=x, adCur=adCur)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	264 iTaxon = 3
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	265 lsSig = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	266 lsSig[[1]] = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	267 lsSig[[1]]$name = "Covariate1"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	268 lsSig[[1]]$orig = "Covariate1"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	269 lsSig[[1]]$taxon = "adCur"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	270 lsSig[[1]]$data = adCur
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	271 lsSig[[1]]$factors = "Covariate1"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	272 lsSig[[1]]$metadata = x
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	273 vdCoef = c(Covariate1=0.6)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	274 lsSig[[1]]$value = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	275 lsSig[[1]]$std = sd(x)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	276 lsSig[[1]]$allCoefs = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	277 lsSig[[2]] = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	278 lsSig[[2]]$name = "Covariate2"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	279 lsSig[[2]]$orig = "Covariate2"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	280 lsSig[[2]]$taxon = "adCur"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	281 lsSig[[2]]$data = adCur
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	282 lsSig[[2]]$factors = "Covariate2"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	283 lsSig[[2]]$metadata = x
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	284 vdCoef = c(Covariate2=0.6)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	285 lsSig[[2]]$value = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	286 lsSig[[2]]$std = sd(x)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	287 lsSig[[2]]$allCoefs = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	288 lsQCCounts = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	289 ret1 = funcSpearman(strFormula=strFormula,frmeTmp=frmeTmp,iTaxon=iTaxon,lsQCCounts=lsQCCounts,strRandomFormula=NULL)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	290 ret1$adP = round(ret1$adP,5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	291 test_that("Test that the spearman test has the correct results for 2 covariates.",{
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	292 expect_equal(ret1,list(adP=round(c(0.09679784,0.09679784),5),lsSig=lsSig,lsQCCounts=list()))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	293 })
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	294
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	295
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	296 context("Test funcWilcoxon")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	297 strFormula = "adCur ~ Covariate1"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	298 x = c(TRUE,FALSE,TRUE,FALSE,TRUE,FALSE,TRUE,FALSE,FALSE)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	299 frmeTmp = data.frame(Covariate1=x, adCur=adCur)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	300 iTaxon = 2
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	301 lsSig = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	302 lsSig[[1]] = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	303 lsSig[[1]]$name = "Covariate1"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	304 lsSig[[1]]$orig = "Covariate1"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	305 lsSig[[1]]$taxon = "adCur"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	306 lsSig[[1]]$data = adCur
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	307 lsSig[[1]]$factors = "Covariate1"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	308 lsSig[[1]]$metadata = x
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	309 vdCoef = c(Covariate1=13)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	310 lsSig[[1]]$value = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	311 lsSig[[1]]$std = sd(x)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	312 lsSig[[1]]$allCoefs = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	313 lsQCCounts = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	314 ret1 = funcWilcoxon(strFormula=strFormula,frmeTmp=frmeTmp,iTaxon=iTaxon,lsQCCounts=lsQCCounts,strRandomFormula=NULL)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	315 ret1$adP = round(ret1$adP,5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	316 test_that("Test that the wilcoxon test has the correct results for 1 covariate.",{
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	317 expect_equal(ret1,list(adP=round(c(0.55555556),5),lsSig=lsSig,lsQCCounts=list()))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	318 })
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	319
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	320
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	321 context("Test funcKruskalWallis")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	322 strFormula = "adCur ~ Covariate1"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	323 x = as.factor(c("one","two","three","one","one","three","two","three","two"))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	324 frmeTmp = data.frame(Covariate1=x, adCur=adCur)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	325 iTaxon = 2
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	326 lsSig = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	327 lsSig[[1]] = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	328 lsSig[[1]]$name = "Covariate1"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	329 lsSig[[1]]$orig = "Covariate1three"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	330 lsSig[[1]]$taxon = "adCur"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	331 lsSig[[1]]$data = adCur
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	332 lsSig[[1]]$factors = "Covariate1"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	333 lsSig[[1]]$metadata = x
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	334 vdCoef = c(Covariate1three=NA)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	335 lsSig[[1]]$value = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	336 lsSig[[1]]$std = sd(x)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	337 lsSig[[1]]$allCoefs = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	338 lsSig[[2]] = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	339 lsSig[[2]]$name = "Covariate1"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	340 lsSig[[2]]$orig = "Covariate1two"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	341 lsSig[[2]]$taxon = "adCur"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	342 lsSig[[2]]$data = adCur
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	343 lsSig[[2]]$factors = "Covariate1"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	344 lsSig[[2]]$metadata = x
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	345 vdCoef = c(Covariate1two=NA)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	346 lsSig[[2]]$value = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	347 lsSig[[2]]$std = sd(x)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	348 lsSig[[2]]$allCoefs = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	349 lsQCCounts = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	350 ret1 = funcKruskalWallis(strFormula=strFormula,frmeTmp=frmeTmp,iTaxon=iTaxon,lsQCCounts=lsQCCounts,strRandomFormula=NULL)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	351 ret1$adP = round(ret1$adP,5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	352 test_that("Test that the Kruskal Wallis (Nonparameteric anova) has the correct results for 1 covariate.",{
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	353 expect_equal(ret1,list(adP=c(1.0,1.0),lsSig=lsSig,lsQCCounts=list()))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	354 })
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	355
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	356
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	357 context("test funcDoUnivariate")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	358 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	359 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	360 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	361 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	362 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	363 covX6 = as.factor(c("one","two","three","one","one","three","two","three","two"))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	364 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	365 frmeTmp = data.frame(Covariate1=covX1, Covariate2=covX2, Covariate3=covX3, Covariate4=covX4, Covariate5=covX5, Covariate6=covX6, adCur= covY)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	366 iTaxon = 7
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	367 # 1 cont answer
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	368 lsSig = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	369 lsSig[[1]] = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	370 lsSig[[1]]$name = "Covariate1"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	371 lsSig[[1]]$orig = "Covariate1"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	372 lsSig[[1]]$taxon = "adCur"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	373 lsSig[[1]]$data = adCur
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	374 lsSig[[1]]$factors = "Covariate1"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	375 lsSig[[1]]$metadata = frmeTmp[["Covariate1"]]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	376 vdCoef = c(Covariate1=0.6)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	377 lsSig[[1]]$value = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	378 lsSig[[1]]$std = sd(frmeTmp[["Covariate1"]])
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	379 lsSig[[1]]$allCoefs = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	380 lsHistory = list(adP=c(), lsSig=c(),lsQCCounts=list())
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	381 ret1 = funcDoUnivariate(strFormula="adCur ~ Covariate1",frmeTmp=frmeTmp,iTaxon=iTaxon, lsHistory=lsHistory, strRandomFormula=NULL)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	382 ret2 = funcDoUnivariate(strFormula=NULL,frmeTmp=frmeTmp,iTaxon=iTaxon, lsHistory=lsHistory, strRandomFormula="adCur ~ 1\|Covariate1")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	383 ret1$adP = round(ret1$adP,5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	384 ret2$adP = round(ret2$adP,5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	385 print("ret1")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	386 print(ret1)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	387 print("list(adP=round(c(0.09679784),5),lsSig=lsSig,lsQCCounts=list())")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	388 print(list(adP=round(c(0.09679784),5),lsSig=lsSig,lsQCCounts=list()))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	389 test_that("2. Test that the funcMakeContrasts works on a continuous variable.",{
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	390 expect_equal(ret1,list(adP=round(c(0.09679784),5),lsSig=lsSig,lsQCCounts=list()))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	391 expect_equal(ret2,list(adP=round(c(0.09679784),5),lsSig=lsSig,lsQCCounts=list()))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	392 })
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	393 lsSig[[2]] = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	394 lsSig[[2]]$name = "Covariate2"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	395 lsSig[[2]]$orig = "Covariate2"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	396 lsSig[[2]]$taxon = "adCur"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	397 lsSig[[2]]$data = adCur
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	398 lsSig[[2]]$factors = "Covariate2"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	399 lsSig[[2]]$metadata = frmeTmp[["Covariate2"]]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	400 vdCoef = c(Covariate2=0.46666667)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	401 lsSig[[2]]$value = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	402 lsSig[[2]]$std = sd(frmeTmp[["Covariate2"]])
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	403 lsSig[[2]]$allCoefs = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	404 ret1 = funcDoUnivariate(strFormula="adCur ~ Covariate1 + Covariate2",frmeTmp=frmeTmp,iTaxon=iTaxon, lsHistory=lsHistory,strRandomFormula=NULL)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	405 ret2 = funcDoUnivariate(strFormula=NULL,frmeTmp=frmeTmp,iTaxon=iTaxon, lsHistory=lsHistory, strRandomFormula="adCur ~ 1\|Covariate1 + 1\|Covariate2")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	406 ret1$adP = round(ret1$adP,5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	407 ret2$adP = round(ret2$adP,5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	408 test_that("Test that the funcMakeContrasts works on 2 continuous variables.",{
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	409 expect_equal(ret1,list(adP=round(c(0.09679784,0.21252205),5),lsSig=lsSig,lsQCCounts=list()))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	410 expect_equal(ret2,list(adP=round(c(0.09679784,0.21252205),5),lsSig=lsSig,lsQCCounts=list()))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	411 })
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	412 lsSig = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	413 lsSig[[1]] = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	414 lsSig[[1]]$name = "Covariate4"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	415 lsSig[[1]]$orig = "Covariate4"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	416 lsSig[[1]]$taxon = "adCur"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	417 lsSig[[1]]$data = adCur
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	418 lsSig[[1]]$factors = "Covariate4"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	419 lsSig[[1]]$metadata = frmeTmp[["Covariate4"]]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	420 vdCoef = c(Covariate4=5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	421 lsSig[[1]]$value = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	422 lsSig[[1]]$std = sd(frmeTmp[["Covariate4"]])
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	423 lsSig[[1]]$allCoefs = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	424 ret1 = funcDoUnivariate(strFormula="adCur ~ Covariate4",frmeTmp=frmeTmp,iTaxon=iTaxon, lsHistory=lsHistory,strRandomFormula=NULL)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	425 ret2 = funcDoUnivariate(strFormula=NULL,frmeTmp=frmeTmp,iTaxon=iTaxon, lsHistory=lsHistory, strRandomFormula="adCur ~ 1\|Covariate4")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	426 ret1$adP = round(ret1$adP,5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	427 ret2$adP = round(ret2$adP,5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	428 test_that("Test that the funcMakeContrasts works on 1 factor covariate with 2 levels.",{
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	429 expect_equal(ret1,list(adP=round(c(0.2857143),5),lsSig=lsSig,lsQCCounts=list()))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	430 expect_equal(ret2,list(adP=round(c(0.2857143),5),lsSig=lsSig,lsQCCounts=list()))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	431 })
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	432 lsSig[[2]] = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	433 lsSig[[2]]$name = "Covariate5"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	434 lsSig[[2]]$orig = "Covariate5"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	435 lsSig[[2]]$taxon = "adCur"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	436 lsSig[[2]]$data = adCur
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	437 lsSig[[2]]$factors = "Covariate5"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	438 lsSig[[2]]$metadata = frmeTmp[["Covariate5"]]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	439 vdCoef = c(Covariate5=8)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	440 lsSig[[2]]$value = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	441 lsSig[[2]]$std = sd(frmeTmp[["Covariate5"]])
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	442 lsSig[[2]]$allCoefs = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	443 ret1 = funcDoUnivariate(strFormula="adCur ~ Covariate4 + Covariate5",frmeTmp=frmeTmp,iTaxon=iTaxon, lsHistory=lsHistory, strRandomFormula=NULL)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	444 ret2 = funcDoUnivariate(strFormula=NULL,frmeTmp=frmeTmp,iTaxon=iTaxon, lsHistory=lsHistory, strRandomFormula="adCur ~ 1\|Covariate4 + 1\|Covariate5")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	445 ret3 = funcDoUnivariate(strFormula="adCur ~ Covariate4",frmeTmp=frmeTmp,iTaxon=iTaxon, lsHistory=lsHistory, strRandomFormula="adCur ~ 1\|Covariate5")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	446 ret1$adP = round(ret1$adP,5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	447 ret2$adP = round(ret2$adP,5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	448 ret3$adP = round(ret3$adP,5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	449 test_that("2. Test that the funcMakeContrasts works on 2 factor covariate with 2 levels.",{
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	450 expect_equal(ret1,list(adP=round(c(0.2857143,0.73016),5),lsSig=lsSig,lsQCCounts=list()))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	451 expect_equal(ret2,list(adP=round(c(0.2857143,0.73016),5),lsSig=lsSig,lsQCCounts=list()))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	452 expect_equal(ret3,list(adP=round(c(0.2857143,0.73016),5),lsSig=lsSig,lsQCCounts=list()))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	453 })
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	454 lsSig = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	455 lsSig[[1]] = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	456 lsSig[[1]]$name = "Covariate4"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	457 lsSig[[1]]$orig = "Covariate4"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	458 lsSig[[1]]$taxon = "adCur"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	459 lsSig[[1]]$data = adCur
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	460 lsSig[[1]]$factors = "Covariate4"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	461 lsSig[[1]]$metadata = frmeTmp[["Covariate4"]]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	462 vdCoef = c(Covariate4=5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	463 lsSig[[1]]$value = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	464 lsSig[[1]]$std = sd(frmeTmp[["Covariate4"]])
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	465 lsSig[[1]]$allCoefs = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	466 lsSig[[2]] = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	467 lsSig[[2]]$name = "Covariate1"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	468 lsSig[[2]]$orig = "Covariate1"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	469 lsSig[[2]]$taxon = "adCur"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	470 lsSig[[2]]$data = adCur
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	471 lsSig[[2]]$factors = "Covariate1"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	472 lsSig[[2]]$metadata = frmeTmp[["Covariate1"]]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	473 vdCoef = c(Covariate1=0.6)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	474 lsSig[[2]]$value = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	475 lsSig[[2]]$std = sd(frmeTmp[["Covariate1"]])
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	476 lsSig[[2]]$allCoefs = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	477 ret1 = funcDoUnivariate(strFormula="adCur ~ Covariate4 + Covariate1",frmeTmp=frmeTmp,iTaxon=iTaxon, lsHistory=lsHistory, strRandomFormula=NULL)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	478 ret2 = funcDoUnivariate(strFormula=NULL,frmeTmp=frmeTmp,iTaxon=iTaxon, lsHistory=lsHistory, strRandomFormula="adCur ~ 1\|Covariate4 + 1\|Covariate1")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	479 ret3 = funcDoUnivariate(strFormula="adCur ~ Covariate4",frmeTmp=frmeTmp,iTaxon=iTaxon, lsHistory=lsHistory, strRandomFormula="adCur ~ 1\|Covariate1")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	480 ret1$adP = round(ret1$adP,5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	481 ret2$adP = round(ret2$adP,5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	482 ret3$adP = round(ret3$adP,5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	483 test_that("Test that the funcMakeContrasts works on 1 factor covariate with 2 levels and a continuous variable.",{
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	484 expect_equal(ret1,list(adP=round(c(0.2857143,0.09679784),5),lsSig=lsSig,lsQCCounts=list()))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	485 expect_equal(ret2,list(adP=round(c(0.2857143,0.09679784),5),lsSig=lsSig,lsQCCounts=list()))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	486 expect_equal(ret3,list(adP=round(c(0.2857143,0.09679784),5),lsSig=lsSig,lsQCCounts=list()))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	487 })
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	488 lsSig = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	489 lsSig[[1]] = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	490 lsSig[[1]]$name = "Covariate3"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	491 lsSig[[1]]$orig = "Covariate32"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	492 lsSig[[1]]$taxon = "adCur"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	493 lsSig[[1]]$data = adCur
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	494 lsSig[[1]]$factors = "Covariate3"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	495 lsSig[[1]]$metadata = frmeTmp[["Covariate3"]]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	496 vdCoef = c(Covariate32=NA)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	497 lsSig[[1]]$value = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	498 lsSig[[1]]$std = sd(frmeTmp[["Covariate3"]])
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	499 lsSig[[1]]$allCoefs = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	500 lsSig[[2]] = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	501 lsSig[[2]]$name = "Covariate3"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	502 lsSig[[2]]$orig = "Covariate33"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	503 lsSig[[2]]$taxon = "adCur"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	504 lsSig[[2]]$data = adCur
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	505 lsSig[[2]]$factors = "Covariate3"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	506 lsSig[[2]]$metadata = frmeTmp[["Covariate3"]]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	507 vdCoef = c(Covariate33=NA)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	508 lsSig[[2]]$value = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	509 lsSig[[2]]$std = sd(frmeTmp[["Covariate3"]])
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	510 lsSig[[2]]$allCoefs = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	511 lsSig[[3]] = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	512 lsSig[[3]]$name = "Covariate1"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	513 lsSig[[3]]$orig = "Covariate1"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	514 lsSig[[3]]$taxon = "adCur"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	515 lsSig[[3]]$data = adCur
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	516 lsSig[[3]]$factors = "Covariate1"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	517 lsSig[[3]]$metadata = frmeTmp[["Covariate1"]]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	518 vdCoef = c(Covariate1=0.6)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	519 lsSig[[3]]$value = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	520 lsSig[[3]]$std = sd(frmeTmp[["Covariate1"]])
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	521 lsSig[[3]]$allCoefs = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	522 lsSig[[4]] = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	523 lsSig[[4]]$name = "Covariate2"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	524 lsSig[[4]]$orig = "Covariate2"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	525 lsSig[[4]]$taxon = "adCur"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	526 lsSig[[4]]$data = adCur
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	527 lsSig[[4]]$factors = "Covariate2"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	528 lsSig[[4]]$metadata = frmeTmp[["Covariate2"]]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	529 vdCoef = c(Covariate2=0.46666667)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	530 lsSig[[4]]$value = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	531 lsSig[[4]]$std = sd(frmeTmp[["Covariate2"]])
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	532 lsSig[[4]]$allCoefs = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	533 ret1 = funcDoUnivariate(strFormula="adCur ~ Covariate3 + Covariate1 + Covariate2",frmeTmp=frmeTmp,iTaxon=iTaxon, lsHistory=lsHistory, strRandomFormula=NULL)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	534 ret2 = funcDoUnivariate(strFormula=NULL,frmeTmp=frmeTmp,iTaxon=iTaxon, lsHistory=lsHistory, strRandomFormula="adCur ~ 1\|Covariate3 + 1\|Covariate1 + 1\|Covariate2")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	535 ret3 = funcDoUnivariate(strFormula="adCur ~ Covariate3 + Covariate1",frmeTmp=frmeTmp,iTaxon=iTaxon, lsHistory=lsHistory, strRandomFormula="adCur ~ 1\|Covariate2")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	536 ret1$adP = round(ret1$adP,5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	537 ret2$adP = round(ret2$adP,5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	538 ret3$adP = round(ret3$adP,5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	539 test_that("Test that the funcMakeContrasts works on 1 factor covariate with 3 levels and 2 continuous variables.",{
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	540 expect_equal(ret1,list(adP=round(c(1.0,1.0,0.09679784,0.21252205),5),lsSig=lsSig,lsQCCounts=list()))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	541 expect_equal(ret2,list(adP=round(c(1.0,1.0,0.09679784,0.21252205),5),lsSig=lsSig,lsQCCounts=list()))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	542 expect_equal(ret3,list(adP=round(c(1.0,1.0,0.09679784,0.21252205),5),lsSig=lsSig,lsQCCounts=list()))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	543 })
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	544 lsSig = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	545 lsSig[[1]] = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	546 lsSig[[1]]$name = "Covariate4"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	547 lsSig[[1]]$orig = "Covariate4"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	548 lsSig[[1]]$taxon = "adCur"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	549 lsSig[[1]]$data = adCur
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	550 lsSig[[1]]$factors = "Covariate4"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	551 lsSig[[1]]$metadata = frmeTmp[["Covariate4"]]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	552 vdCoef = c(Covariate4=5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	553 lsSig[[1]]$value = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	554 lsSig[[1]]$std = sd(frmeTmp[["Covariate4"]])
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	555 lsSig[[1]]$allCoefs = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	556 lsSig[[2]] = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	557 lsSig[[2]]$name = "Covariate2"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	558 lsSig[[2]]$orig = "Covariate2"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	559 lsSig[[2]]$taxon = "adCur"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	560 lsSig[[2]]$data = adCur
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	561 lsSig[[2]]$factors = "Covariate2"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	562 lsSig[[2]]$metadata = frmeTmp[["Covariate2"]]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	563 vdCoef = c(Covariate2=0.46666667)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	564 lsSig[[2]]$value = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	565 lsSig[[2]]$std = sd(frmeTmp[["Covariate2"]])
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	566 lsSig[[2]]$allCoefs = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	567 ret1 = funcDoUnivariate(strFormula="adCur ~ Covariate4 + Covariate2",frmeTmp=frmeTmp,iTaxon=iTaxon, lsHistory=lsHistory, strRandomFormula=NULL)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	568 ret2 = funcDoUnivariate(strFormula=NULL,frmeTmp=frmeTmp,iTaxon=iTaxon, lsHistory=lsHistory, strRandomFormula="adCur ~ 1\|Covariate4 + 1\|Covariate2")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	569 ret3 = funcDoUnivariate(strFormula= "adCur ~ Covariate4",frmeTmp=frmeTmp,iTaxon=iTaxon, lsHistory=lsHistory, strRandomFormula="adCur ~ 1\|Covariate2")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	570 ret1$adP = round(ret1$adP,5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	571 ret2$adP = round(ret2$adP,5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	572 ret3$adP = round(ret3$adP,5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	573 test_that("3. Test that the funcMakeContrasts works on 2 factor covariate with 2 levels and a continuous variable.",{
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	574 expect_equal(ret1,list(adP=round(c(0.2857143,0.21252205),5),lsSig=lsSig,lsQCCounts=list()))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	575 expect_equal(ret2,list(adP=round(c(0.2857143,0.21252205),5),lsSig=lsSig,lsQCCounts=list()))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	576 expect_equal(ret3,list(adP=round(c(0.2857143,0.21252205),5),lsSig=lsSig,lsQCCounts=list()))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	577 })
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	578 lsSig = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	579 lsSig[[1]] = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	580 lsSig[[1]]$name = "Covariate4"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	581 lsSig[[1]]$orig = "Covariate4"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	582 lsSig[[1]]$taxon = "adCur"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	583 lsSig[[1]]$data = adCur
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	584 lsSig[[1]]$factors = "Covariate4"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	585 lsSig[[1]]$metadata = frmeTmp[["Covariate4"]]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	586 vdCoef = c(Covariate4=5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	587 lsSig[[1]]$value = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	588 lsSig[[1]]$std = sd(frmeTmp[["Covariate4"]])
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	589 lsSig[[1]]$allCoefs = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	590 lsSig[[2]] = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	591 lsSig[[2]]$name = "Covariate3"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	592 lsSig[[2]]$orig = "Covariate32"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	593 lsSig[[2]]$taxon = "adCur"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	594 lsSig[[2]]$data = adCur
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	595 lsSig[[2]]$factors = "Covariate3"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	596 lsSig[[2]]$metadata = frmeTmp[["Covariate3"]]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	597 vdCoef = c(Covariate32=NA)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	598 lsSig[[2]]$value = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	599 lsSig[[2]]$std = sd(frmeTmp[["Covariate3"]])
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	600 lsSig[[2]]$allCoefs = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	601 lsSig[[3]] = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	602 lsSig[[3]]$name = "Covariate3"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	603 lsSig[[3]]$orig = "Covariate33"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	604 lsSig[[3]]$taxon = "adCur"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	605 lsSig[[3]]$data = adCur
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	606 lsSig[[3]]$factors = "Covariate3"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	607 lsSig[[3]]$metadata = frmeTmp[["Covariate3"]]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	608 vdCoef = c(Covariate33=NA)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	609 lsSig[[3]]$value = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	610 lsSig[[3]]$std = sd(frmeTmp[["Covariate3"]])
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	611 lsSig[[3]]$allCoefs = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	612 lsSig[[4]] = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	613 lsSig[[4]]$name = "Covariate2"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	614 lsSig[[4]]$orig = "Covariate2"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	615 lsSig[[4]]$taxon = "adCur"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	616 lsSig[[4]]$data = adCur
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	617 lsSig[[4]]$factors = "Covariate2"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	618 lsSig[[4]]$metadata = frmeTmp[["Covariate2"]]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	619 vdCoef = c(Covariate2=0.46666667)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	620 lsSig[[4]]$value = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	621 lsSig[[4]]$std = sd(frmeTmp[["Covariate2"]])
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	622 lsSig[[4]]$allCoefs = vdCoef
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	623 ret1 = funcDoUnivariate(strFormula="adCur ~ Covariate4 + Covariate3 + Covariate2",frmeTmp=frmeTmp,iTaxon=iTaxon, lsHistory=lsHistory, strRandomFormula=NULL)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	624 ret2 = funcDoUnivariate(strFormula=NULL,frmeTmp=frmeTmp,iTaxon=iTaxon, lsHistory=lsHistory, strRandomFormula="adCur ~ 1\|Covariate4 +1\|Covariate3 + 1\|Covariate2")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	625 ret1$adP = round(ret1$adP,5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	626 ret2$adP = round(ret2$adP,5)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	627 test_that("Test that the funcMakeContrasts works on 1 factor covariate with 2 levels , 1 factor with 3 levels, and a continuous variable.",{
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	628 expect_equal(ret1,list(adP=round(c(0.2857143,1.0,1.0,0.21252205),5),lsSig=lsSig,lsQCCounts=list()))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	629 expect_equal(ret2,list(adP=round(c(0.2857143,1.0,1.0,0.21252205),5),lsSig=lsSig,lsQCCounts=list()))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	630 })
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	631
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	632 #Test multivariates
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	633 context("Test funcLasso")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	634
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	635
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	636 context("Test funcLM")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	637 #This test just makes sure the statistical method is being called correctly for one covariate with the correct return
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	638 strFormula = "adCur ~ Covariate1"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	639 strRandomFormula = NULL
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	640 x = 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	641 x2 = c(34.2, 32.5, 22.4, 43, 3.25, 6.4, 7, 87, 9)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	642 xf1 = c(1,1,2,2,1,2,1,1,2)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	643 xf2 = c(1,1,1,1,2,2,2,2,2)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	644 frmeTmp = data.frame(Covariate1=x, Covariate2=x2, FCovariate3=xf1, FCovariate4=xf2, adCur=adCur)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	645 iTaxon = 5
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	646 lmRet = lm(as.formula(strFormula), data=frmeTmp, na.action = c_strNA_Action)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	647 test_that("Test that the lm has the correct results for 1 covariate.",{
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	648 expect_equal(funcLM(strFormula=strFormula,frmeTmp=frmeTmp,iTaxon=iTaxon,lsHistory=lsHistory,strRandomFormula=strRandomFormula),lmRet)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	649 })
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	650 #Test for correct call for 2 covariates
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	651 strFormula = "adCur ~ Covariate1 + Covariate2"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	652 lmRet = lm(as.formula(strFormula), data=frmeTmp, na.action = c_strNA_Action)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	653 test_that("Test that the lm has the correct results for 2 covariates.",{
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	654 expect_equal(funcLM(strFormula=strFormula,frmeTmp=frmeTmp,iTaxon=iTaxon,lsHistory=lsHistory,strRandomFormula=strRandomFormula),lmRet)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	655 })
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	656 ##Test for correct call with 1 random and one fixed covariate
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	657 #strFormula = "adCur ~ Covariate1"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	658 #strRandomFormula = "~1\|FCovariate3"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	659 #lmRet = glmmPQL(fixed=as.formula(strFormula), random=as.formula(strRandomFormula), family=gaussian(link="identity"), data=frmeTmp)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	660 #test_that("Test that the lm has the correct results for 1 random and one fixed covariate.",{
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	661 # expect_equal(funcLM(strFormula=strFormula,frmeTmp=frmeTmp,iTaxon=iTaxon,lsHistory=lsHistory,strRandomFormula=strRandomFormula),lmRet)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	662 #})
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	663 ##Test for correct call with 1 random and 2 fixed covariates
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	664 #strFormula = "adCur ~ Covariate1 + Covariate2"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	665 #strRandomFormula = "~1\|FCovariate3"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	666 #lmRet = glmmPQL(fixed=as.formula(strFormula), random=as.formula(strRandomFormula), family=gaussian(link="identity"), data=frmeTmp)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	667 #test_that("Test that the lm has the correct results for 1 random and 2 fixed covariates.",{
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	668 # expect_equal(funcLM(strFormula=strFormula,frmeTmp=frmeTmp,iTaxon=iTaxon,lsHistory=lsHistory,strRandomFormula=strRandomFormula),lmRet)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	669 #})
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	670 ##Test for correct call with 2 random and 1 fixed covariates
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	671 #strFormula = "adCur ~ Covariate1"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	672 #strRandomFormula = "~1\|FCovariate4+1\|FCovariate3"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	673 #lmRet = glmmPQL(fixed=as.formula(strFormula), random=as.formula(strRandomFormula), family=gaussian(link="identity"), data=frmeTmp)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	674 #test_that("Test that the lm has the correct results for 2 random and 1 fixed covariates.",{
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	675 # expect_equal(funcLM(strFormula=strFormula,frmeTmp=frmeTmp,iTaxon=iTaxon,lsHistory=lsHistory,strRandomFormula=strRandomFormula),lmRet)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	676 #})
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	677
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	678
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	679 context("Test funcBinomialMult")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	680 strFormula = "adCur ~ Covariate1"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	681 strRandomFormula = NULL
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	682 x = 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	683 x2 = c(34.2, 32.5, 22.4, 43, 3.25, 6.4, 7, 87, 9)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	684 xf1 = c(1,1,2,2,1,2,1,1,2)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	685 xf2 = c(1,1,1,1,2,2,2,2,2)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	686 frmeTmp = data.frame(Covariate1=x, Covariate2=x2, FCovariate3=xf1, FCovariate4=xf2, adCur=adCur)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	687 iTaxon = 5
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	688 lmRet = glm(as.formula(strFormula), family=binomial(link=logit), data=frmeTmp, na.action=c_strNA_Action)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	689 test_that("Test that the neg binomial regression has the correct results for 1 covariate.",{
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	690 expect_equal(funcBinomialMult(strFormula=strFormula,frmeTmp=frmeTmp,iTaxon=iTaxon,lsHistory=lsHistory,strRandomFormula=strRandomFormula),lmRet)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	691 })
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	692 #Test for correct call for 2 covariates
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	693 strFormula = "adCur ~ Covariate1 + Covariate2"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	694 iTaxon = 5
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	695 lmRet = glm(as.formula(strFormula), family=binomial(link=logit), data=frmeTmp, na.action=c_strNA_Action)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	696 test_that("Test that the neg binomial regression has the correct results for 2 covariates.",{
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	697 expect_equal(funcBinomialMult(strFormula=strFormula,frmeTmp=frmeTmp,iTaxon=iTaxon,lsHistory=lsHistory,strRandomFormula=strRandomFormula),lmRet)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	698 })
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	699 ##Test for correct call with 1 random and one fixed covariate
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	700 #strFormula = "adCur ~ Covariate1"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	701 #strRandomFormula = "~1\|FCovariate3"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	702 #lmRet = glmmPQL(fixed=as.formula(strFormula), random=as.formula(strRandomFormula), family=binomial(link=logit), data=frmeTmp)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	703 #test_that("Test that the lm has the correct results for 1 random and one fixed covariate.",{
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	704 # expect_equal(funcBinomialMult(strFormula=strFormula,frmeTmp=frmeTmp,iTaxon=iTaxon,lsHistory=lsHistory,strRandomFormula=strRandomFormula),lmRet)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	705 #})
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	706 ##Test for correct call with 1 random and 2 fixed covariates
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	707 #strFormula = "adCur ~ Covariate1 + Covariate2"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	708 #strRandomFormula = "~1\|FCovariate3"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	709 #lmRet = glmmPQL(fixed=as.formula(strFormula), random=as.formula(strRandomFormula), family=binomial(link=logit), data=frmeTmp)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	710 #test_that("Test that the lm has the correct results for 1 random and 2 fixed covariates.",{
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	711 # expect_equal(funcBinomialMult(strFormula=strFormula,frmeTmp=frmeTmp,iTaxon=iTaxon,lsHistory=lsHistory,strRandomFormula=strRandomFormula),lmRet)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	712 #})
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	713 ##Test for correct call with 2 random and 1 fixed covariates
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	714 #strFormula = "adCur ~ Covariate1"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	715 #strRandomFormula = "~1\|FCovariate4+1\|FCovariate3"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	716 #lmRet = glmmPQL(fixed=as.formula(strFormula), random=as.formula(strRandomFormula), family=binomial(link=logit), data=frmeTmp)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	717 #test_that("Test that the lm has the correct results for 2 random and 1 fixed covariates.",{
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	718 # expect_equal(funcBinomialMult(strFormula=strFormula,frmeTmp=frmeTmp,iTaxon=iTaxon,lsHistory=lsHistory,strRandomFormula=strRandomFormula),lmRet)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	719 #})
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	720
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	721
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	722 context("Test funcQuasiMult")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	723 strFormula = "adCur ~ Covariate1"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	724 strRandomFormula = NULL
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	725 x = c(44.4, 45.9, 41.9, 53.3, 44.7, 44.1, 50.7, 45.2, 60.1,44.4, 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	726 x2 = c(34.2, 32.5, 22.4, 43, 3.25, 6.4, 7, 87, 9,34.2, 32.5, 22.4, 43, 3.25, 6.4, 7, 87, 9)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	727 xf1 = c(1,1,2,2,1,1,2,2,2,1,1,2,2,1,1,2,2,2)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	728 xf2 = c(1,1,1,1,2,2,2,2,2,1,1,1,1,2,2,2,2,2)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	729 frmeTmp = data.frame(Covariate1=x, Covariate2=x2, FCovariate3=xf1, FCovariate4=xf2, adCur=adCur)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	730 iTaxon = 5
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	731 lmRet = glm(as.formula(strFormula), family=quasipoisson, data=frmeTmp, na.action=c_strNA_Action)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	732 test_that("Test that the quasi poisson has the correct results for 1 covariate.",{
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	733 expect_equal(funcQuasiMult(strFormula=strFormula,frmeTmp=frmeTmp,iTaxon=iTaxon,lsHistory=lsHistory,strRandomFormula=strRandomFormula),lmRet)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	734 })
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	735 #Test for correct call for 2 covariates
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	736 strFormula = "adCur ~ Covariate1 + Covariate2"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	737 iTaxon = 5
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	738 lmRet = glm(as.formula(strFormula), family=quasipoisson, data=frmeTmp, na.action=c_strNA_Action)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	739 test_that("Test that the quasi poisson has the correct results for 2 covariates.",{
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	740 expect_equal(funcQuasiMult(strFormula=strFormula,frmeTmp=frmeTmp,iTaxon=iTaxon,lsHistory=lsHistory,strRandomFormula=strRandomFormula),lmRet)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	741 })
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	742 ##Test for correct call with 1 random and one fixed covariate
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	743 #strFormula = "adCur ~ Covariate1"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	744 #strRandomFormula = "~1\|FCovariate3"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	745 #lmRet = glmmPQL(fixed=as.formula(strFormula), random=as.formula(strRandomFormula), family=quasipoisson, data=frmeTmp)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	746 #test_that("Test that the lm has the correct results for 1 random and one fixed covariate.",{
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	747 # expect_equal(funcQuasiMult(strFormula=strFormula,frmeTmp=frmeTmp,iTaxon=iTaxon,lsHistory=lsHistory,strRandomFormula=strRandomFormula),lmRet)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	748 #})
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	749 ##Test for correct call with 1 random and 2 fixed covariates
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	750 #strFormula = "adCur ~ Covariate1 + Covariate2"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	751 #strRandomFormula = "~1\|FCovariate3"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	752 #lmRet = glmmPQL(fixed=as.formula(strFormula), random=as.formula(strRandomFormula), family=quasipoisson, data=frmeTmp)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	753 #test_that("Test that the lm has the correct results for 1 random and 2 fixed covariates.",{
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	754 # expect_equal(funcQuasiMult(strFormula=strFormula,frmeTmp=frmeTmp,iTaxon=iTaxon,lsHistory=lsHistory,strRandomFormula=strRandomFormula),lmRet)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	755 #})
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	756 ##Test for correct call with 2 random and 1 fixed covariates
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	757 #strFormula = "adCur ~ Covariate1"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	758 #strRandomFormula = "~1\|FCovariate4+1\|FCovariate3"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	759 #lmRet = glmmPQL(fixed=as.formula(strFormula), random=as.formula(strRandomFormula), family=quasipoisson, data=frmeTmp)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	760 #test_that("Test that the lm has the correct results for 2 random and 1 fixed covariates.",{
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	761 # expect_equal(funcQuasiMult(strFormula=strFormula,frmeTmp=frmeTmp,iTaxon=iTaxon,lsHistory=lsHistory,strRandomFormula=strRandomFormula),lmRet)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	762 #})
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	763
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	764
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	765 #Test transforms
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	766 context("Test funcNoTransform")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	767 aTest1 = c(NA)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	768 aTest2 = c(NULL)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	769 aTest3 = c(0.5,1.4,2.4,3332.4,0.0,0.0000003)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	770 aTest4 = c(0.1)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	771 test_that("Test that no transform does not change the data.",{
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	772 expect_equal(funcNoTransform(aTest1), aTest1)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	773 expect_equal(funcNoTransform(aTest2), aTest2)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	774 expect_equal(funcNoTransform(aTest3), aTest3)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	775 expect_equal(funcNoTransform(aTest4), aTest4)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	776 })
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	777
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	778
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	779 context("Test funcArcsinSqrt")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	780 aTest1 = c(NA)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	781 aTest2 = c(0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,1.0)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	782 aTest3 = c(0.000001)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	783 test_that("Test that funcArcsinSqrt performs the transform correctly.",{
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	784 expect_equal(funcArcsinSqrt(NA), as.numeric(NA))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	785 expect_equal(funcArcsinSqrt(aTest1), asin(sqrt(aTest1)))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	786 expect_equal(funcArcsinSqrt(aTest2), asin(sqrt(aTest2)))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	787 expect_equal(funcArcsinSqrt(aTest3), asin(sqrt(aTest3)))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	788 })

Mercurial > repos > george-weingart > maaslin

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