[Genabel-commits] r1512 - pkg/ProbABEL/checks/R-tests

[noreply at r-forge.r-project.org]

Author: lckarssen
Date: 2013-12-29 15:33:18 +0100 (Sun, 29 Dec 2013)
New Revision: 1512

Modified:
   pkg/ProbABEL/checks/R-tests/run_models_in_R_pacox.R
   pkg/ProbABEL/checks/R-tests/run_models_in_R_palinear.R
   pkg/ProbABEL/checks/R-tests/run_models_in_R_palogist.R
Log:
Harmonise variable names in ProbABEL's R-checks.


Modified: pkg/ProbABEL/checks/R-tests/run_models_in_R_pacox.R
===================================================================
--- pkg/ProbABEL/checks/R-tests/run_models_in_R_pacox.R	2013-12-29 14:01:50 UTC (rev 1511)
+++ pkg/ProbABEL/checks/R-tests/run_models_in_R_pacox.R	2013-12-29 14:33:18 UTC (rev 1512)
@@ -28,22 +28,22 @@
               intern=TRUE)
 cat("OK\n")
 
-resPaAddDose <- read.table(
+dose.add.PA <- read.table(
     paste0(tests.path, "coxph_dose_add.out.txt"),
     head=TRUE)[, colsAddDose]
-resPaAddProb <- read.table(
+prob.add.PA <- read.table(
     paste0(tests.path, "coxph_prob_add.out.txt"),
     head=TRUE)[, colsAddProb]
-resPaDom <- read.table(
+prob.dom.PA <- read.table(
     paste0(tests.path, "coxph_prob_domin.out.txt"),
     head=TRUE)[, colsDom]
-resPaRec <- read.table(
+prob.rec.PA <- read.table(
     paste0(tests.path, "coxph_prob_recess.out.txt"),
     head=TRUE)[, colsRec]
-resPaOdom <- read.table(
+prob.odom.PA <- read.table(
     paste0(tests.path, "coxph_prob_over_domin.out.txt"),
     head=TRUE)[, colsOdom]
-resPa2df <- read.table(
+prob.2df.PA <- read.table(
     paste0(tests.path, "coxph_prob_2df.out.txt"),
     head=TRUE)[, cols2df]
 
@@ -65,7 +65,7 @@
 dose.add.R <- run.model(model.fn.0, model.fn, snpdose)
 colnames(dose.add.R) <- colsAddDose
 rownames(dose.add.R) <- NULL
-stopifnot( all.equal(resPaAddDose, dose.add.R, tol=tol) )
+stopifnot( all.equal(dose.add.PA, dose.add.R, tol=tol) )
 cat("additive ")
 
 
@@ -74,7 +74,7 @@
 prob.add.R <- run.model(model.fn.0, model.fn, snpprob)
 colnames(prob.add.R) <- colsAddProb
 rownames(prob.add.R) <- NULL
-stopifnot( all.equal(resPaAddProb, prob.add.R, tol=tol) )
+stopifnot( all.equal(prob.add.PA, prob.add.R, tol=tol) )
 cat("additive ")
 
 ## dominant model
@@ -82,7 +82,7 @@
 prob.dom.R <- run.model(model.fn.0, model.fn, snpprob)
 colnames(prob.dom.R) <- colsDom
 rownames(prob.dom.R) <- NULL
-stopifnot( all.equal(resPaDom, prob.dom.R, tol=tol) )
+stopifnot( all.equal(prob.dom.PA, prob.dom.R, tol=tol) )
 cat("dominant ")
 
 ## recessive model
@@ -90,7 +90,7 @@
 prob.rec.R <- run.model(model.fn.0, model.fn, snpprob)
 colnames(prob.rec.R) <- colsRec
 rownames(prob.rec.R) <- NULL
-stopifnot( all.equal(resPaRec, prob.rec.R, tol=tol) )
+stopifnot( all.equal(prob.rec.PA, prob.rec.R, tol=tol) )
 cat("recessive ")
 
 ## over-dominant model
@@ -98,7 +98,7 @@
 prob.odom.R <- run.model(model.fn.0, model.fn, snpprob)
 colnames(prob.odom.R) <- colsOdom
 rownames(prob.odom.R) <- NULL
-stopifnot( all.equal(resPaOdom, prob.odom.R, tol=tol) )
+stopifnot( all.equal(prob.odom.PA, prob.odom.R, tol=tol) )
 cat("overdominant ")
 
 
@@ -110,7 +110,7 @@
 prob.2df.R <- run.model(model.fn.0, model.fn, snpd1, snpd2)
 colnames(prob.2df.R) <- cols2df
 rownames(prob.2df.R) <- NULL
-stopifnot( all.equal(resPa2df, prob.2df.R, tol=tol) )
+stopifnot( all.equal(prob.2df.PA, prob.2df.R, tol=tol) )
 cat("2df\n")
 
 cat("\t\t\t\t\t\tOK\n")

Modified: pkg/ProbABEL/checks/R-tests/run_models_in_R_palinear.R
===================================================================
--- pkg/ProbABEL/checks/R-tests/run_models_in_R_palinear.R	2013-12-29 14:01:50 UTC (rev 1511)
+++ pkg/ProbABEL/checks/R-tests/run_models_in_R_palinear.R	2013-12-29 14:33:18 UTC (rev 1512)
@@ -19,22 +19,22 @@
               intern=TRUE)
 cat("OK\n")
 
-resPaAddDose <- read.table(
+dose.add.PA <- read.table(
     paste0(tests.path, "linear_base_add.out.txt"),
     head=TRUE)[, colsAddDose]
-resPaAddProb <- read.table(
+prob.add.PA <- read.table(
     paste0(tests.path, "linear_ngp2_add.out.txt"),
     head=TRUE)[, colsAddProb]
-resPaDom <- read.table(
+prob.dom.PA <- read.table(
     paste0(tests.path, "linear_ngp2_domin.out.txt"),
     head=TRUE)[, colsDom]
-resPaRec <- read.table(
+prob.rec.PA <- read.table(
     paste0(tests.path, "linear_ngp2_recess.out.txt"),
     head=TRUE)[, colsRec]
-resPaOdom <- read.table(
+prob.odom.PA <- read.table(
     paste0(tests.path, "linear_ngp2_over_domin.out.txt"),
     head=TRUE)[, colsOdom]
-resPa2df <- read.table(
+prob.2df.PA <- read.table(
     paste0(tests.path, "linear_ngp2_2df.out.txt"),
     head=TRUE)[, cols2df]
 
@@ -55,7 +55,7 @@
 dose.add.R <- run.model(model.fn.0, model.fn, snpdose)
 colnames(dose.add.R) <- colsAddDose
 rownames(dose.add.R) <- NULL
-stopifnot( all.equal(resPaAddDose, dose.add.R, tol=tol) )
+stopifnot( all.equal(dose.add.PA, dose.add.R, tol=tol) )
 cat("additive ")
 
 
@@ -64,7 +64,7 @@
 prob.add.R <- run.model(model.fn.0, model.fn, snpprob)
 colnames(prob.add.R) <- colsAddProb
 rownames(prob.add.R) <- NULL
-stopifnot( all.equal(resPaAddProb, prob.add.R, tol=tol) )
+stopifnot( all.equal(prob.add.PA, prob.add.R, tol=tol) )
 cat("additive ")
 
 ## dominant model
@@ -72,7 +72,7 @@
 prob.dom.R <- run.model(model.fn.0, model.fn, snpprob)
 colnames(prob.dom.R) <- colsDom
 rownames(prob.dom.R) <- NULL
-stopifnot( all.equal(resPaDom, prob.dom.R, tol=tol) )
+stopifnot( all.equal(prob.dom.PA, prob.dom.R, tol=tol) )
 cat("dominant ")
 
 ## recessive model
@@ -80,7 +80,7 @@
 prob.rec.R <- run.model(model.fn.0, model.fn, snpprob)
 colnames(prob.rec.R) <- colsRec
 rownames(prob.rec.R) <- NULL
-stopifnot( all.equal(resPaRec, prob.rec.R, tol=tol) )
+stopifnot( all.equal(prob.rec.PA, prob.rec.R, tol=tol) )
 cat("recessive ")
 
 ## over-dominant model
@@ -88,7 +88,7 @@
 prob.odom.R <- run.model(model.fn.0, model.fn, snpprob)
 colnames(prob.odom.R) <- colsOdom
 rownames(prob.odom.R) <- NULL
-stopifnot( all.equal(resPaOdom, prob.odom.R, tol=tol) )
+stopifnot( all.equal(prob.odom.PA, prob.odom.R, tol=tol) )
 cat("overdominant ")
 
 ## 2df model
@@ -116,7 +116,7 @@
 }
 colnames(prob.2df.R) <- cols2df
 rownames(prob.2df.R) <- NULL
-stopifnot( all.equal(resPa2df, prob.2df.R, tol=tol) )
+stopifnot( all.equal(prob.2df.PA, prob.2df.R, tol=tol) )
 cat("2df\n")
 
 cat("\t\t\t\t\t\tOK\n")

Modified: pkg/ProbABEL/checks/R-tests/run_models_in_R_palogist.R
===================================================================
--- pkg/ProbABEL/checks/R-tests/run_models_in_R_palogist.R	2013-12-29 14:01:50 UTC (rev 1511)
+++ pkg/ProbABEL/checks/R-tests/run_models_in_R_palogist.R	2013-12-29 14:33:18 UTC (rev 1512)
@@ -19,22 +19,22 @@
               intern=TRUE)
 cat("OK\n")
 
-resPaAddDose <- read.table(
+dose.add.PA <- read.table(
     paste0(tests.path, "logist_add.out.txt"),
     head=TRUE)[, colsAddDose]
-resPaAddProb <- read.table(
+prob.add.PA <- read.table(
     paste0(tests.path, "logist_prob_add.out.txt"),
     head=TRUE)[, colsAddProb]
-resPaDom <- read.table(
+prob.dom.PA <- read.table(
     paste0(tests.path, "logist_prob_domin.out.txt"),
     head=TRUE)[, colsDom]
-resPaRec <- read.table(
+prob.rec.PA <- read.table(
     paste0(tests.path, "logist_prob_recess.out.txt"),
     head=TRUE)[, colsRec]
-resPaOdom <- read.table(
+prob.odom.PA <- read.table(
     paste0(tests.path, "logist_prob_over_domin.out.txt"),
     head=TRUE)[, colsOdom]
-resPa2df <- read.table(
+prob.2df.PA <- read.table(
     paste0(tests.path, "logist_prob_2df.out.txt"),
     head=TRUE)[, cols2df]
 
@@ -56,7 +56,7 @@
 dose.add.R <- run.model(model.fn.0, model.fn, snpdose)
 colnames(dose.add.R) <- colsAddDose
 rownames(dose.add.R) <- NULL
-stopifnot( all.equal(resPaAddDose, dose.add.R, tol=tol) )
+stopifnot( all.equal(dose.add.PA, dose.add.R, tol=tol) )
 cat("additive ")
 
 ## Additive model, probabilities
@@ -64,7 +64,7 @@
 prob.add.R <- run.model(model.fn.0, model.fn, snpprob)
 colnames(prob.add.R) <- colsAddProb
 rownames(prob.add.R) <- NULL
-stopifnot( all.equal(resPaAddProb, prob.add.R, tol=tol) )
+stopifnot( all.equal(prob.add.PA, prob.add.R, tol=tol) )
 cat("additive ")
 
 ## dominant model
@@ -72,7 +72,7 @@
 prob.dom.R <- run.model(model.fn.0, model.fn, snpprob)
 colnames(prob.dom.R) <- colsDom
 rownames(prob.dom.R) <- NULL
-stopifnot( all.equal(resPaDom, prob.dom.R, tol=tol) )
+stopifnot( all.equal(prob.dom.PA, prob.dom.R, tol=tol) )
 cat("dominant ")
 
 ## recessive model
@@ -80,7 +80,7 @@
 prob.rec.R <- run.model(model.fn.0, model.fn, snpprob)
 colnames(prob.rec.R) <- colsRec
 rownames(prob.rec.R) <- NULL
-stopifnot( all.equal(resPaRec, prob.rec.R, tol=tol) )
+stopifnot( all.equal(prob.rec.PA, prob.rec.R, tol=tol) )
 cat("recessive ")
 
 ## over-dominant model
@@ -88,7 +88,7 @@
 prob.odom.R <- run.model(model.fn.0, model.fn, snpprob)
 colnames(prob.odom.R) <- colsOdom
 rownames(prob.odom.R) <- NULL
-stopifnot( all.equal(resPaOdom, prob.odom.R, tol=tol) )
+stopifnot( all.equal(prob.odom.PA, prob.odom.R, tol=tol) )
 cat("overdominant ")
 
 
@@ -119,7 +119,7 @@
 }
 colnames(prob.2df.R) <- cols2df
 rownames(prob.2df.R) <- NULL
-stopifnot( all.equal(resPa2df, prob.2df.R, tol=tol) )
+stopifnot( all.equal(prob.2df.PA, prob.2df.R, tol=tol) )
 cat("2df\n")
 
 cat("\t\t\t\t\t\tOK\n")