[Power-commits] r33 - in pkg/sse: . R inst/slowTests/testthat tests/testthat
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Aug 19 15:45:58 CEST 2019
Author: thofab
Date: 2019-08-19 15:45:57 +0200 (Mon, 19 Aug 2019)
New Revision: 33
Modified:
pkg/sse/ChangeLog
pkg/sse/DESCRIPTION
pkg/sse/R/power.R
pkg/sse/inst/slowTests/testthat/test-advanced.R
pkg/sse/tests/testthat/test-standard.R
Log:
All minor changes see ChangeLog for details
Modified: pkg/sse/ChangeLog
===================================================================
--- pkg/sse/ChangeLog 2019-08-16 20:37:45 UTC (rev 32)
+++ pkg/sse/ChangeLog 2019-08-19 13:45:57 UTC (rev 33)
@@ -1,9 +1,14 @@
version 0.7-12 2019/08/13
+ splitting of tests into tests at tests/ and inst/slowTests to
+ reduce the time used for R CMD check
correcting some spelling errors in man pages
correcting some spelling in warning/error messages
+ changing the sequence of asserting that arguments are fine for
+ (argument 'smooth' in plot() and of 'lm.range' in powEx())
+ some resolving of lintr issues (line length etc.)
version 0.7-11 2019/07/19
removing tests of parallel computing since these fail on some
- systems and since parallel computing is only under development
+ systems and since parallel computing is only under development
version 0.7-10 2019/07/01
update(): corrections that allow updating different aspects of n, theta
and xi in combination
@@ -10,7 +15,7 @@
refine(): Change argument name 'n.iter' to 'factor' (to show that there
is a difference to n.iter in calc).
refine(): Do not change slot 'iter' of the power-object.
- Handling of forceDivisor, a best guess for the divisor is added based
+ Handling of forceDivisor, a best guess for the divisor is added based
on the chosen n-values.
Refining many test.
Adding some test for the current implementation of parallel computing.
Modified: pkg/sse/DESCRIPTION
===================================================================
--- pkg/sse/DESCRIPTION 2019-08-16 20:37:45 UTC (rev 32)
+++ pkg/sse/DESCRIPTION 2019-08-19 13:45:57 UTC (rev 33)
@@ -4,6 +4,8 @@
Version: 0.7-12
Author: Thomas Fabbro [aut, cre]
Maintainer: Thomas Fabbro <thomas.fabbro at unibas.ch>
+URL: http://r-forge.r-project.org/projects/power/
+BugReports: http://r-forge.r-project.org/projects/power/
Description: Provides functions to evaluate user-defined power functions for a parameter range, and draws a sensitivity plot. It also provides a resampling procedure for semi-parametric sample size estimation and methods for adding information to a Sweave report.
License: GPL-3
LazyLoad: yes
Modified: pkg/sse/R/power.R
===================================================================
--- pkg/sse/R/power.R 2019-08-16 20:37:45 UTC (rev 32)
+++ pkg/sse/R/power.R 2019-08-19 13:45:57 UTC (rev 33)
@@ -661,7 +661,8 @@
new.calc <- TRUE
any.change <- TRUE
} else if (!new.calc
- & any(!(round(slot(newObj, s), 10) %in% round(slot(object, s), 10)))) {
+ & any(!(round(slot(newObj, s), 10)
+ %in% round(slot(object, s), 10)))) {
message(strwrap(
"It contains some available elements ->
Ony the new elements will be calculated.",
@@ -669,8 +670,10 @@
## --- increase theta
increase.theta <- TRUE
} else if (!new.calc
- & all(round(slot(newObj, s), 10) %in% round(slot(object, s), 10))
- & length(slot(newObj, s) < length(slot(object, s)))) {
+ & all(round(slot(newObj, s), 10)
+ %in% round(slot(object, s), 10))
+ & length(slot(newObj, s)
+ < length(slot(object, s)))) {
message(strwrap(
"It contains only available elements ->
No new elements will be calculated.",
@@ -713,17 +716,19 @@
prefix = " ", initial = ""))
increase.xi <- TRUE
} else if (!new.calc
- & all(round(slot(newObj, s), 10) %in% round(slot(object, s), 10))
- & length(slot(newObj, s) < length(slot(object, s)))) {
+ & all(round(slot(newObj, s), 10)
+ %in% round(slot(object, s), 10))
+ & length(slot(newObj, s)
+ < length(slot(object, s)))) {
message(strwrap(
"It contains only available elements ->
No new elements will be evaluated.",
prefix = " ", initial = ""))
## --- shrink xi
- takeElements <-
- round(slot(newObj, s), 10) %in% round(slot(object, s), 10)
- giveElements <-
- round(slot(object, s), 10) %in% round(slot(newObj, s), 10)
+ takeElements <- (round(slot(newObj, s), 10)
+ %in% round(slot(object, s), 10))
+ giveElements <- (round(slot(object, s), 10)
+ %in% round(slot(newObj, s), 10))
takeObj at core <- array(NA,
dim = c(length(takeObj at n),
length(takeObj at theta),
@@ -1122,7 +1127,8 @@
## ## if (powFun.info at return.power){
## ## size.array <- array(NA, dim = c(dim(object), n.size))
## ## } else {
- ## ## size.array <- array(NA, dim = c(dim(object), n.size, n.iter))
+ ## ## size.array <- array(NA,
+ ## dim = c(dim(object), n.size, n.iter))
## ## }
## } else {
x at return.list <- FALSE
@@ -1838,20 +1844,19 @@
} else {
## for method "default" or "lm" we set the lm.range to 0.2 or if provided
## test it.
- if (is.na(lm.range)) {
- lm.range <- 0.2
- } else {
- if (length(lm.range) > 1){
+ if (length(lm.range) > 1) {
warning(strwrap(
"The argument 'lm.range' should have a length of one.
Only the first element is used",
prefix = " ", initial = ""))
lm.range <- lm.range[1]
- }
- if (lm.range < 0 | lm.range > 1){
- stop("The argument 'lm.range' should be in the range [0; 1]")
- }
}
+ if (is.na(lm.range)) {
+ lm.range <- 0.2
+ }
+ if (lm.range < 0 | lm.range > 1){
+ stop("The argument 'lm.range' should be in the range [0; 1]")
+ }
}
## --- forceDivisor
## handle forceDivisor and generate divisor
@@ -1925,6 +1930,10 @@
# ---
## handling the smooth-argument
+ if (length(smooth) > 1) {
+ warning("Only the first element of <smooth> is used.")
+ smooth <- smooth[1]
+ }
if (is.logical(smooth) & smooth) {
span <- 0.75
dat[!is.na(dat$power) & dat$power > 0 & dat$power < 1, "power"] <- fitted(
@@ -1933,10 +1942,6 @@
span = span))
}
if (is.numeric(smooth)) {
- if (length(smooth) > 1) {
- warning("Only the first element of <smooth> is used.")
- smooth <- smooth[1]
- }
if (smooth <= 0) {
stop(strwrap(
"The argument 'smooth' has to be > 0,
Modified: pkg/sse/inst/slowTests/testthat/test-advanced.R
===================================================================
--- pkg/sse/inst/slowTests/testthat/test-advanced.R 2019-08-16 20:37:45 UTC (rev 32)
+++ pkg/sse/inst/slowTests/testthat/test-advanced.R 2019-08-19 13:45:57 UTC (rev 33)
@@ -110,7 +110,8 @@
test_that("List as return", {
powFun.list <- function(psi){
a <- sample(pp(psi, "F.hat"), size = n(psi) / 2, replace = TRUE)
- b <- sample(pp(psi, "F.hat"), size = n(psi) / 2, replace = TRUE) + theta(psi)
+ b <- sample(pp(psi, "F.hat"),
+ size = n(psi) / 2, replace = TRUE) + theta(psi)
w <- wilcox.test(a, b)$p.value < 0.05
t <- t.test(a, b)$p.value < 0.05
length(c(a,b) %% 2)
Modified: pkg/sse/tests/testthat/test-standard.R
===================================================================
--- pkg/sse/tests/testthat/test-standard.R 2019-08-16 20:37:45 UTC (rev 32)
+++ pkg/sse/tests/testthat/test-standard.R 2019-08-19 13:45:57 UTC (rev 33)
@@ -125,9 +125,17 @@
inspect(powEx(calc.resample, theta = 1, power = 0.9, method = "step"))
inspect(powEx(calc.resample2, theta = 1, power = 0.9, method = "step"))
-inspect(powEx(calc.resample2, theta = 1, power = 0.9, method = "step", forceDivisor = 2))
+inspect(powEx(calc.resample2,
+ theta = 1,
+ power = 0.9,
+ method = "step",
+ forceDivisor = 2))
inspect(
- powEx(calc.resample2, theta = 1, power = 0.9, method = "step", forceDivisor = TRUE)
+ powEx(calc.resample2,
+ theta = 1,
+ power = 0.9,
+ method = "step",
+ forceDivisor = TRUE)
)
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