These functions implement collocation-inference
    for continuous-time and discrete-time stochastic processes.
    They provide model-based smoothing, gradient-matching,
    generalized profiling and forwards prediction error methods.

Markov chain Monte Carlo based inference routines for collapsed latent position cluster models or social networks, which includes searches over the model space (number of clusters in the latent position cluster model). The label switching algorithm used is that of Nobile and Fearnside (2007) <doi:10.1007/s11222-006-9014-7> which relies on the algorithm of Carpaneto and Toth (1980) <doi:10.1145/355873.355883>.

Weekly notified dengue cases and climate variables in Colombo district Sri Lanka from 2008/ week-52 to 2014/ week-21.

Performs the colocalisation tests described in
    Giambartolomei et al (2013) <doi:10.1371/journal.pgen.1004383>,
    Wallace (2020) <doi:10.1371/journal.pgen.1008720>,
    Wallace (2021) <doi:10.1371/journal.pgen.1009440>.

Calculate the colocalization index, NSInC, in two different ways as described in the paper (Liu et al., 2019. Manuscript submitted for publication.) for multiple-species spatial data which contain the precise locations and membership of each spatial point. The two main functions are nsinc.d() and nsinc.z(). They provide the Pearson’s correlation coefficients of signal proportions in different memberships within a concerned proximity of every signal (or every base signal if single direction colocalization is considered) across all (base) signals using two different ways of normalization. The proximity sizes could be an individual value or a range of values, where the default ranges of values are different for the two functions.

Also abbreviates to "CCSeq". Finds clusters of colocalized sequences in .bed annotation files
    up to a specified cut-off distance. Two sequences are colocalized if they
    are within the cut-off distance of each other, and clusters are sets of
    sequences where each sequence is colocalized to at least one other sequence
    in the cluster. For a set of .bed annotation tables provided in a list 
    along with a cut-off distance, the program will output a file containing
    the locations of each cluster. Annotated .bed files are from 
    the 'pwmscan' application at <https://ccg.epfl.ch/pwmtools/pwmscan.php>. 
    Personal machines might crash or take excessively long depending 
    on the number of annotated sequences in each file and whether chromsearch() 
    or gensearch() is used.