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NEWS.md

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flycircuit 0.6.9

  • new functions fc_read_neurons() to read traced skeletons from the flycircuit website, fc_get_ids() to get a list of neuron identifiers, fc_page() to see the details page for a neuron (#44) (thanks to @alexanderbates)
  • Fix FCWBNP.surf by updating to nat.flybrains version (#43)
  • switch to natverse github organisation

flycircuit 0.6.8

  • Ensure that flycircuit package can be installed from github with development versions of all its dependencies (fixes to github remotes etc). This was as a result of difficulties installing on the VFB opencpu docker instance.
  • dev: fixes to travis build configuration (switch to non sudo trusty dist)

flycircuit 0.6.7

  • Update annotation database (1 August 2016, now 7021 NeuronType annotations)

flycircuit 0.6.6

  • Add fc_neuron_type
  • Add online docs with pkgdown
  • Insist on nat >= 1.8.8

flycircuit 0.6.5

  • update annotation database (1 April 2015, now 6565 NeuronType annotations)
  • add fc_glom function to find antennal lobe glomeruli for fc neurons
  • dev: update to roxygen2 v4.1.1

flycircuit 0.6.4

  • update annotation database

flycircuit 0.6.3

  • load_si_data works with bigmat pairs of the form x.desc+x.bin
  • load_si_data no longer attempts to check for object existence
  • doc: load_si_data improvements
  • dev: fix check errors

flycircuit 0.6.2

  • depend on nat

flycircuit 0.6.1

  • fix bug when creating data directories (based on rappdirs location) on a new system

flycircuit 0.6

  • Store persistent data in directory determined by rappdirs package
  • add load_si_data
  • add plot3d.APResult
  • Add apclusterfc
  • fc_download_data (always) returns path to file
  • ... and can use local file (with warning) if remote url unreadable
  • ... plus additional bug fixes
  • add as.data.frame.APResult for affinity propagation clustering results
  • fc_nblast normalises like sub_score_mat

flycircuit 0.5.3

  • add fc_sex utility function to find sex of animal for any valid flycircuit neuron identifier.
  • give hclustfc an unsquare argument

flycircuit 0.5.2

  • fix subtle bug in plot3dfc revealed only when this is used inside a function.
  • plot3dfc can now accept a character vector for the db argument.

flycircuit 0.5.1

  • fix hclustfc (was not attaching scoremat)
  • refactor fc_subscoremat (using nat.nblast::sub_score_mat)
  • dev: remove internal diagonal function and tests

flycircuit 0.5

  • deprecated pop3dfc in favour of nat::npop3d
  • refactored plot3dfc to use nat::plot3d.character. plot3dfc will be deprecated in favour of plot3d.character when that function can coped with multiple identifier styles.

flycircuit 0.4.1

  • extensive refactoring so that fc_nblast, hclustfc and friends are now thin wrappers on more generic functions in nat.nblast
  • plot3dfc can handle NA soma positions
  • update annotation table
  • docs: plot3dfc improvements
  • add fcgn_forfile

flycircuit 0.3.1

  • significant (20x in my tests) speedup for hclustfc using large ff objects containing raw scores.

flycircuit 0.3

  • ready for use by external code
  • add subset.hclust, plot3d.hclust
  • make sure that clustering based on pre-computed nblast scores all works properly and that ff cached versions of the data are available
  • only provide ff cached versions of raw scores for download and normalise on the fly
  • fix errors in package vignette