What is new in the intrval R package?

January 26, 2017 Code R functions special intrval

An update (v 0.1-1) of the intrval package was recently published on CRAN. The package simplifies interval related logical operations (read more about the motivation in this post). So what is new in this version? Some of the inconsistencies in the 1st CRAN release have been cleaned up, and I have been pushed hard (see GitHub issue to implement all the 16 interval-to-interval operators. These operators define the open/closed nature of the lower/upper limits of the intervals on the left and right hand side of the o in the middle as in c(a1, b1) %[]o[]% c(a2, b2).

Interval 1: Interval 2: [] [) (] ()
[] %[]o[]% %[]o[)% %[]o(]% %[]o()%
[) %[)o[]% %[)o[)% %[)o(]% %[)o()%
(] %(]o[]% %(]o[)% %(]o(]% %(]o()%
() %()o[]% %()o[)% %()o(]% %()o()%

The overlap of two closed intervals, [a1, b1] and [a2, b2], is evaluated by the %[]o[]% (%[o]% is an alias) operator (a1 <= b1, a2 <= b2). Endpoints can be defined as a vector with two values (c(a1, b1)) or can be stored in matrix-like objects or a lists in which case comparisons are made element-wise.

If lengths do not match, shorter objects are recycled. These value-to-interval operators work for numeric (integer, real) and ordered vectors, and object types which are measured at least on ordinal scale (e.g. dates). Note that interval endpoints are sorted internally thus ensuring the conditions a1 <= b1 and a2 <= b2 is not necessary.

c(2, 3) %[]o[]% c(0, 1)
list(0:4, 1:5) %[]o[]% c(2, 3)
cbind(0:4, 1:5) %[]o[]% c(2, 3)
data.frame(a=0:4, b=1:5) %[]o[]% c(2, 3)

If lengths do not match, shorter objects are recycled. These value-to-interval operators work for numeric (integer, real) and ordered vectors, and object types which are measured at least on ordinal scale (e.g. dates).

%)o(% is used for the negation of two closed interval overlap (%[o]%), directional evaluation is done via the operators %[<o]% and %[o>]%. The overlap of two open intervals is evaluated by the %(o)% (alias for %()o()%). %]o[% is used for the negation of two open interval overlap, directional evaluation is done via the operators %(<o)% and %(o>)%. Overlap operators with mixed endpoint do not have negation and directional counterparts.

Equal Not equal Less than Greater than
%[o]% %)o(% %[<o]% %[o>]%
%(o)% %]o[% %(<o)% %(o>)%

Thanks for all the feedback so far and please keep’em coming: leave a comment below or use the issue tracker to provide feedback or report a problem.

Statistical computing meets biodiversity conservation and natural resource management

Phylogeny and species traits predict bird detectability

It all started with this paper in Methods in Ecol. Evol. where we looked at detectability of many species. So we wanted to use life history traits to validate our results. But we had to cut the manuscript, and there was this leftover with some neat patterns, but without much focus. It took a few years, and the most positive peer-review experience ever, and the paper is now early view in Ecography. This post is a quick summary of the goodies stuffed inside the lhreg R package that makes the whole analysis reproducible, and provides some functions for similar PGLMM models.

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