distLfit: fitting of lap excluded temporarily to avoid cdflap bug in …

…lmomco 2.2.2

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: extremeStat
 Type: Package
 Title: Extreme Value Statistics and Quantile Estimation
-Version: 0.5.12
-Date: 2016-03-29
+Version: 0.5.13
+Date: 2016-03-30
 Imports:
     lmomco (>= 2.1.3),
     berryFunctions (>= 1.9.21),

R/distLfit.R

@@ -133,7 +133,8 @@ if( ! is.null(selection) )
 else
 # remove some to save time and errors, see ?dist.list # gld, gov and tri added
 if(speed) dn <- dn[ ! dn %in%
-   c("aep4","cau","emu","gep","gld","gov","kmu","kur","lmrq","sla","st3","texp","tri")]
+   c("aep4","cau","emu","gep","gld","gov","kmu","kur","lmrq","sla","st3","texp","tri", "lap")]
+### lap (Laplace) is taken out only temporarily until bug in cdflap in lmomco 2.2.2 (2016-03-20) is fixed
 #
 # Check remaining sample size
 if(length(dat) < 5) {if(!ssquiet)on.exit(message("Note in distLfit: sample size (",

inst/doc/extremeStat.Rmd

@@ -150,7 +150,7 @@ d <- distLquantile(rain, truncate=0.9, plot=TRUE, probs=0.999, quiet=TRUE, break
 
 ## Truncation effect
 
-To examine the effect of the truncation percentage, we can compute the quantiles for different cutoff percentages. This is quite time consuming, so the code is not performed upon vignette creation. The result is loaded instead. 
+To examine the effect of the truncation percentage, we can compute the quantiles for different cutoff percentages. This is quite time consuming, so the code is not performed upon vignette creation. The [result](https://github.com/brry/extremeStat/raw/master/vignettes/qq.Rdata) is loaded instead. 
 
 ```{r teff, eval=FALSE}
 tt <- seq(0,0.95, len=50) 
@@ -208,6 +208,7 @@ sq <- pbapply::pbreplicate(n=100, rainsamplequantile())
 save(ss,sq, file="vignettes/sq.Rdata")   
 ```
 
+Load the [resulting R objects](https://github.com/brry/extremeStat/raw/master/vignettes/sq.Rdata):
 
 ```{r ssdepplot, echo=-(1:3), fig.height=3.5, fig.width=5.5}
 path <- "S:/Dropbox/Public/extremeStat/vignettes"

tests/testthat/test-quantile.R

@@ -5,7 +5,7 @@ data(annMax, package="extremeStat") # Annual Discharge Maxima (streamflow)
 
 test_that("distLquantile generally runs fine",{
 distLquantile(annMax)
-expect_equal(nrow(distLquantile(annMax, addinfo=TRUE)), 37)
+expect_equal(nrow(distLquantile(annMax, addinfo=TRUE)), 37-1)
 expect_silent(distLquantile(annMax, truncate=0.6, gpd=FALSE, quiet=TRUE))
 expect_message(distLquantile(annMax, plot=FALSE, selection="wak", empirical=FALSE), 
   "Note in distLgof: Only wak was fitted, thus GOF can't be compared.")
@@ -41,9 +41,9 @@ test_that("distLquantile can deal with a given dlf",{
 })
 
 test_that("distLquantile can handle emp, truncate",{
-expect_equal(nrow(distLquantile(annMax, emp=FALSE)), 17) # only distributions in lmomco
+expect_equal(nrow(distLquantile(annMax, emp=FALSE)), 17-1) # only distributions in lmomco
 expect_message(aq <- distLquantile(annMax, truncate=0.8, probs=0.95)) # POT
-expect_equal(mean(aq, na.rm=TRUE), 102.055973)
+expect_equal(round(mean(aq, na.rm=TRUE),2), 102.13) # 102.055973 with lap
 expect_equal(sum(is.na(distLquantile(annMax, selection="gpa", weight=FALSE))), 3)
 })
 

vignettes/extremeStat.Rmd

@@ -150,7 +150,7 @@ d <- distLquantile(rain, truncate=0.9, plot=TRUE, probs=0.999, quiet=TRUE, break
 
 ## Truncation effect
 
-To examine the effect of the truncation percentage, we can compute the quantiles for different cutoff percentages. This is quite time consuming, so the code is not performed upon vignette creation. The result is loaded instead. 
+To examine the effect of the truncation percentage, we can compute the quantiles for different cutoff percentages. This is quite time consuming, so the code is not performed upon vignette creation. The [result](https://github.com/brry/extremeStat/raw/master/vignettes/qq.Rdata) is loaded instead. 
 
 ```{r teff, eval=FALSE}
 tt <- seq(0,0.95, len=50) 
@@ -208,6 +208,7 @@ sq <- pbapply::pbreplicate(n=100, rainsamplequantile())
 save(ss,sq, file="vignettes/sq.Rdata")   
 ```
 
+Load the [resulting R objects](https://github.com/brry/extremeStat/raw/master/vignettes/sq.Rdata):
 
 ```{r ssdepplot, echo=-(1:3), fig.height=3.5, fig.width=5.5}
 path <- "S:/Dropbox/Public/extremeStat/vignettes"