diff --git a/docs/404.html b/docs/404.html index 8c9b909..a15d06c 100644 --- a/docs/404.html +++ b/docs/404.html @@ -32,7 +32,7 @@ lax - 1.2.1 + 1.2.2 diff --git a/docs/articles/index.html b/docs/articles/index.html index 1ee7db8..034835c 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -17,7 +17,7 @@ lax - 1.2.1 + 1.2.2 diff --git a/docs/articles/lax-vignette.html b/docs/articles/lax-vignette.html index 4eb9b7b..602112a 100644 --- a/docs/articles/lax-vignette.html +++ b/docs/articles/lax-vignette.html @@ -33,7 +33,7 @@ lax - 1.2.1 + 1.2.2 @@ -82,7 +82,7 @@

An overview of lax

Paul Northrop

-

2023-09-09

+

2023-12-02

Source: vignettes/lax-vignette.Rmd @@ -263,8 +263,6 @@

texmex 

 library(texmex, quietly = TRUE)
-#> Warning: package 'texmex' was built under R version 4.2.3
-#> Warning: package 'mvtnorm' was built under R version 4.2.3
 # Note: phi = log(scale)
 evm_fit <- evm(temp, ow, gev, mu = ~ loc, phi = ~ loc, xi = ~loc)
 adj_evm_fit <- alogLik(evm_fit, cluster = ow$year)
@@ -285,7 +283,6 @@ 
evd
 parameter.

 
 library(evd, quietly = TRUE)
-#> Warning: package 'evd' was built under R version 4.2.3
 fgev_fit <- fgev(ow$temp, nsloc = ow[, "loc"])
 adj_fgev_fit <- alogLik(fgev_fit, cluster = ow$year)
 summary(adj_fgev_fit)
@@ -353,7 +350,6 @@ 
fExtremes
 library(fExtremes, quietly = TRUE)
-#> Warning: package 'fExtremes' was built under R version 4.2.3
 gevFit_fit <- gevFit(ow$temp)
 adj_gevFit_fit <- alogLik(gevFit_fit)
 summary(adj_gevFit_fit)
@@ -369,7 +365,6 @@ 
mev
 stationary GEV models.

 
 library(mev, quietly = TRUE)
-#> Warning: package 'mev' was built under R version 4.2.3
 gfit <- fit.gev(ow$temp)
 adj_gfit <- alogLik(gfit)
 summary(adj_gfit)
diff --git a/docs/authors.html b/docs/authors.html
index 7e91c4a..d3c74c7 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -17,7 +17,7 @@
       
       
         lax
-        1.2.1
+        1.2.2
       
     

 
diff --git a/docs/index.html b/docs/index.html
index f729a06..c7723cd 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -53,7 +53,7 @@
       
       
         lax
-        1.2.1
+        1.2.2
       
     

 
diff --git a/docs/news/index.html b/docs/news/index.html
index 0d28ea8..36feb36 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -17,7 +17,7 @@
       
       
         lax
-        1.2.1
+        1.2.2
@@ -57,6 +57,13 @@

Changelog

Source: NEWS.md +
+

lax 1.2.2

+
+

Bug fixes

+
  • Fixed issues with the incorrect use of in some Rd files.
    • +
+

lax 1.2.12023-09-02

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 96658d8..b9e5879 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,7 +1,7 @@ -pandoc: 2.17.1.1 +pandoc: 3.1.1 pkgdown: 2.0.7 pkgdown_sha: ~ articles: lax-vignette: lax-vignette.html -last_built: 2023-09-09T14:58Z +last_built: 2023-12-02T18:36Z diff --git a/docs/reference/POT.html b/docs/reference/POT.html index 50399f6..72ba616 100644 --- a/docs/reference/POT.html +++ b/docs/reference/POT.html @@ -20,7 +20,7 @@ lax - 1.2.1 + 1.2.2
diff --git a/docs/reference/alogLik.html b/docs/reference/alogLik.html index c4a608c..aa2d21e 100644 --- a/docs/reference/alogLik.html +++ b/docs/reference/alogLik.html @@ -30,7 +30,7 @@ lax - 1.2.1 + 1.2.2
@@ -175,8 +175,9 @@

Value

adjust_loglik.

-

The original fitted model object is available as an attribute named - code"original_fit", accessible using attr(name, "original_fit"), +

The original fitted model object is available as an attribute named

+

+

"original_fit", accessible using attr(name, "original_fit"), where name is the name of the object to which the object returned from alogLik is assigned.

@@ -236,22 +237,22 @@

Value

Details

Object x must have the following S3 - methods:

  • logLikVec: returns a vector of the contributions to the + methods:

    • logLikVec: returns a vector of the contributions to the independence loglikelihood from individual observations;

      • -

    • coef: returns a vector of model coefficients, see +

    • coef: returns a vector of model coefficients, see coef;

      • -

    • nobs: returns the number of (non-missing) observations +

    • nobs: returns the number of (non-missing) observations used in a model fit, see nobs;

      • -

    and may have the following S3 methods

    • vcov: returns the estimated variance-covariance matrix of +

    and may have the following S3 methods

    • vcov: returns the estimated variance-covariance matrix of the (main) parameters of a fitted model, see vcov;

      • -

    • estfun: returns an \(n\) by \(k\) matrix, in which each +

    • estfun: returns an \(n\) by \(k\) matrix, in which each column gives the derivative of the loglikelihood at each of \(n\) observation with respect to the \(k\) parameters of the model, see estfun.

    Loglikelihood adjustment is performed using the adjust_loglik function in the - chandwich package. + chandwich package. The relevant arguments to adjust_loglik, namely loglik, mle, H and V, are created based on the class of the object x.

    diff --git a/docs/reference/anova.lax.html b/docs/reference/anova.lax.html index ec244cd..49a6230 100644 --- a/docs/reference/anova.lax.html +++ b/docs/reference/anova.lax.html @@ -21,7 +21,7 @@ lax - 1.2.1 + 1.2.2
@@ -155,7 +155,6 @@

Examples

adj1 <- alogLik(M1) anova(adj1, adj0) } -#> Warning: package 'evd' was built under R version 4.2.3 #> Analysis of (Adjusted) Deviance Table #> #> Model.Df Df ALRTS Pr(>ALRTS) @@ -175,9 +174,7 @@

Examples

adj_tiny <- alogLik(tiny, cluster = ow$year) anova(adj_large, adj_medium, adj_small, adj_tiny) } -#> Warning: package 'texmex' was built under R version 4.2.3 #> Loading required package: mvtnorm -#> Warning: package 'mvtnorm' was built under R version 4.2.3 #> Loading required package: ggplot2 #> #> Attaching package: 'texmex' diff --git a/docs/reference/bernoulli.html b/docs/reference/bernoulli.html index 9a49847..394d1ce 100644 --- a/docs/reference/bernoulli.html +++ b/docs/reference/bernoulli.html @@ -18,7 +18,7 @@ lax - 1.2.1 + 1.2.2 diff --git a/docs/reference/eva.html b/docs/reference/eva.html index 349c5fe..eb0d0d4 100644 --- a/docs/reference/eva.html +++ b/docs/reference/eva.html @@ -19,7 +19,7 @@ lax - 1.2.1 + 1.2.2 @@ -218,7 +218,6 @@

Examples

adj_result2 <- alogLik(result2) summary(adj_result2) } -#> Warning: package 'eva' was built under R version 4.2.3 #> #> Attaching package: 'eva' #> The following objects are masked from 'package:texmex': diff --git a/docs/reference/evd.html b/docs/reference/evd.html index 421cc8c..dfef785 100644 --- a/docs/reference/evd.html +++ b/docs/reference/evd.html @@ -21,7 +21,7 @@ lax - 1.2.1 + 1.2.2 diff --git a/docs/reference/evir.html b/docs/reference/evir.html index 28ec1ce..b81aa91 100644 --- a/docs/reference/evir.html +++ b/docs/reference/evir.html @@ -22,7 +22,7 @@ lax - 1.2.1 + 1.2.2 diff --git a/docs/reference/extRemes.html b/docs/reference/extRemes.html index df2629d..8785425 100644 --- a/docs/reference/extRemes.html +++ b/docs/reference/extRemes.html @@ -21,7 +21,7 @@ lax - 1.2.1 + 1.2.2 @@ -235,9 +235,7 @@

Examples

adj_fit <- alogLik(fit) summary(adj_fit) } -#> Warning: package 'extRemes' was built under R version 4.2.3 #> Loading required package: Lmoments -#> Warning: package 'Lmoments' was built under R version 4.2.3 #> Loading required package: distillery #> #> Attaching package: 'extRemes' diff --git a/docs/reference/fExtremes.html b/docs/reference/fExtremes.html index f5079c1..ae0e52c 100644 --- a/docs/reference/fExtremes.html +++ b/docs/reference/fExtremes.html @@ -23,7 +23,7 @@ lax - 1.2.1 + 1.2.2 @@ -188,7 +188,6 @@

Examples

adj_fit <- alogLik(fit) summary(adj_fit) } -#> Warning: package 'fExtremes' was built under R version 4.2.3 #> #> Attaching package: 'fExtremes' #> The following objects are masked from 'package:evir': diff --git a/docs/reference/index.html b/docs/reference/index.html index 14ee77a..07eed13 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -17,7 +17,7 @@ lax - 1.2.1 + 1.2.2 diff --git a/docs/reference/ismev.html b/docs/reference/ismev.html index 6b28c02..3fb1b4d 100644 --- a/docs/reference/ismev.html +++ b/docs/reference/ismev.html @@ -22,7 +22,7 @@ lax - 1.2.1 + 1.2.2 @@ -357,10 +357,9 @@

Examples

summary(adj_rfit2) # } } -#> Warning: package 'ismev' was built under R version 4.2.3 #> Loading required package: mgcv #> Loading required package: nlme -#> This is mgcv 1.8-41. For overview type 'help("mgcv-package")'. +#> This is mgcv 1.8-42. For overview type 'help("mgcv-package")'. #> #> Attaching package: 'ismev' #> The following object is masked from 'package:texmex': diff --git a/docs/reference/ismev_refits.html b/docs/reference/ismev_refits.html index 5abb14a..65a7c62 100644 --- a/docs/reference/ismev_refits.html +++ b/docs/reference/ismev_refits.html @@ -28,7 +28,7 @@ lax - 1.2.1 + 1.2.2 diff --git a/docs/reference/lax-internal.html b/docs/reference/lax-internal.html index d445f32..1f699c7 100644 --- a/docs/reference/lax-internal.html +++ b/docs/reference/lax-internal.html @@ -17,7 +17,7 @@ lax - 1.2.1 + 1.2.2 diff --git a/docs/reference/lax-package.html b/docs/reference/lax-package.html index 4bce10f..e72afe1 100644 --- a/docs/reference/lax-package.html +++ b/docs/reference/lax-package.html @@ -33,7 +33,7 @@ lax - 1.2.1 + 1.2.2 diff --git a/docs/reference/logLik.logLikVec.html b/docs/reference/logLik.logLikVec.html index c22edb4..6b557ac 100644 --- a/docs/reference/logLik.logLikVec.html +++ b/docs/reference/logLik.logLikVec.html @@ -17,7 +17,7 @@ lax - 1.2.1 + 1.2.2 diff --git a/docs/reference/logLikVec.html b/docs/reference/logLikVec.html index 8a77ba0..5902555 100644 --- a/docs/reference/logLikVec.html +++ b/docs/reference/logLikVec.html @@ -18,7 +18,7 @@ lax - 1.2.1 + 1.2.2 diff --git a/docs/reference/mev.html b/docs/reference/mev.html index f2b4c84..85934dc 100644 --- a/docs/reference/mev.html +++ b/docs/reference/mev.html @@ -21,7 +21,7 @@ lax - 1.2.1 + 1.2.2 @@ -220,7 +220,6 @@

Examples

adj_fitr <- alogLik(fitr) summary(adj_fitr) } -#> Warning: package 'mev' was built under R version 4.2.3 #> #> Attaching package: 'mev' #> The following object is masked _by_ '.GlobalEnv': diff --git a/docs/reference/ow.html b/docs/reference/ow.html index fe6bc83..2c7d8cf 100644 --- a/docs/reference/ow.html +++ b/docs/reference/ow.html @@ -18,7 +18,7 @@ lax - 1.2.1 + 1.2.2 diff --git a/docs/reference/plot.retlev.html b/docs/reference/plot.retlev.html index c9950cc..623b339 100644 --- a/docs/reference/plot.retlev.html +++ b/docs/reference/plot.retlev.html @@ -17,7 +17,7 @@ lax - 1.2.1 + 1.2.2 diff --git a/docs/reference/pot_refit.html b/docs/reference/pot_refit.html index eb779de..122a51d 100644 --- a/docs/reference/pot_refit.html +++ b/docs/reference/pot_refit.html @@ -23,7 +23,7 @@ lax - 1.2.1 + 1.2.2 diff --git a/docs/reference/print.retlev.html b/docs/reference/print.retlev.html index 68d518f..bbe925c 100644 --- a/docs/reference/print.retlev.html +++ b/docs/reference/print.retlev.html @@ -17,7 +17,7 @@ lax - 1.2.1 + 1.2.2 diff --git a/docs/reference/print.summary.retlev.html b/docs/reference/print.summary.retlev.html index 830ef7b..0c98214 100644 --- a/docs/reference/print.summary.retlev.html +++ b/docs/reference/print.summary.retlev.html @@ -17,7 +17,7 @@ lax - 1.2.1 + 1.2.2 diff --git a/docs/reference/return_level.html b/docs/reference/return_level.html index 4de33c1..17f3bd2 100644 --- a/docs/reference/return_level.html +++ b/docs/reference/return_level.html @@ -23,7 +23,7 @@ lax - 1.2.1 + 1.2.2 diff --git a/docs/reference/summary.retlev.html b/docs/reference/summary.retlev.html index 7b61543..874ed1e 100644 --- a/docs/reference/summary.retlev.html +++ b/docs/reference/summary.retlev.html @@ -17,7 +17,7 @@ lax - 1.2.1 + 1.2.2 diff --git a/docs/reference/texmex.html b/docs/reference/texmex.html index 67086d2..5401dbb 100644 --- a/docs/reference/texmex.html +++ b/docs/reference/texmex.html @@ -20,7 +20,7 @@ lax - 1.2.1 + 1.2.2 diff --git a/man/alogLik.Rd b/man/alogLik.Rd index 0d55da3..544f192 100644 --- a/man/alogLik.Rd +++ b/man/alogLik.Rd @@ -71,7 +71,7 @@ An object inheriting from class \code{"chandwich"}. See \code{\link[chandwich]{adjust_loglik}}. The original fitted model object is available as an attribute named - code{"original_fit"}, accessible using \code{attr(name, "original_fit")}, + \code{"original_fit"}, accessible using \code{attr(name, "original_fit")}, where \code{name} is the name of the object to which the object returned from \code{alogLik} is assigned. @@ -129,22 +129,22 @@ objects are explained in \strong{Details}. Object \code{x} \emph{must} have the following S3 methods: \itemize{ - \item{\code{logLikVec: }}{returns a vector of the contributions to the - independence loglikelihood from individual observations;} - \item{\code{coef: }}{returns a vector of model coefficients, see - \code{\link[stats]{coef}};} - \item{\code{nobs: }}{returns the number of (non-missing) observations - used in a model fit, see \code{\link[stats]{nobs}}}; + \item \code{logLikVec}: returns a vector of the contributions to the + independence loglikelihood from individual observations; + \item \code{coef}: returns a vector of model coefficients, see + \code{\link[stats]{coef}}; + \item \code{nobs}: returns the number of (non-missing) observations + used in a model fit, see \code{\link[stats]{nobs}}; } and \emph{may} have the following S3 methods \itemize{ - \item{\code{vcov: }}{returns the estimated variance-covariance matrix of + \item \code{vcov}: returns the estimated variance-covariance matrix of the (main) parameters of a fitted model, see - \code{\link[stats]{vcov}};} - \item{\code{estfun: }}{returns an \eqn{n} by \eqn{k} matrix, in which each + \code{\link[stats]{vcov}}; + \item \code{estfun}: returns an \eqn{n} by \eqn{k} matrix, in which each column gives the derivative of the loglikelihood at each of \eqn{n} observation with respect to the \eqn{k} parameters of the model, see - \code{\link[sandwich]{estfun}}.} + \code{\link[sandwich]{estfun}}. } Loglikelihood adjustment is performed using the \code{\link[chandwich]{adjust_loglik}} function in the diff --git a/man/ow.Rd b/man/ow.Rd index 3cf6d65..7365da6 100644 --- a/man/ow.Rd +++ b/man/ow.Rd @@ -7,12 +7,12 @@ \format{ A dataframe with 80 rows and 4 columns. \itemize{ - \item{Column 1, \code{temp}: }{annual maximum temperatures in degrees - Fahrenheit.} - \item{Column 2, \code{year}: }{year in which the maximum was recorded.} - \item{Column 3, \code{name}: }{name of location, "oxford" or "worthing"} - \item{Column 4, \code{loc}: }{location: 1 for "oxford", -1 for - "worthing"} + \item Column 1, \code{temp}: annual maximum temperatures in degrees + Fahrenheit. + \item Column 2, \code{year}: year in which the maximum was recorded. + \item Column 3, \code{name}: name of location, "oxford" or "worthing" + \item Column 4, \code{loc}: location: 1 for "oxford", -1 for + "worthing" } } \source{ diff --git a/man/return_level.Rd b/man/return_level.Rd index 828c5d4..a6144dc 100644 --- a/man/return_level.Rd +++ b/man/return_level.Rd @@ -71,18 +71,18 @@ At present \code{return_level} only supports GEV models. \strong{Care must be taken in specifying the input value of \code{npy}.} \itemize{ - \item{\strong{GEV models}: }{it is common to have one observation per year, + \item \strong{GEV models}: it is common to have one observation per year, either because the data are annual maxima or because for each year only the maximum value over a particular season is extracted from the raw data. In this case, \code{npy = 1}, which is the default. If instead we extract the maximum values over the first and second halves of each - year then \code{npy = 2}.} - \item{\strong{Binomial-GP models}: }{\code{npy} provides information + year then \code{npy = 2}. + \item \strong{Binomial-GP models}: \code{npy} provides information about the (intended) frequency of sampling in time, that is, the number of observations that would be observed in a year if there are no missing values. If the number of observations may vary between years then \code{npy} should be set equal to the mean number of observations - per year.} + per year. } \strong{Supplying \code{npy} for binomial-GP models.} The value of \code{npy} (or an equivalent, perhaps differently named,