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Translate spatialMixture functions to R #3

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64 of 68 tasks
wleoncio opened this issue Nov 9, 2020 · 0 comments
Open
64 of 68 tasks

Translate spatialMixture functions to R #3

wleoncio opened this issue Nov 9, 2020 · 0 comments
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@wleoncio
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enhancement New feature or request
Projects
Translate base BAPS to R
Milestone
Translated all ba...

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@wleoncio
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wleoncio commented Nov 9, 2020 •
edited

  • spatialMixture
  • clearGlobalVars
  • computeRows(rowsFromInd, inds, ninds)
  • addToSummary(logml, partitionSummary, worstIndex)
  • arvoSeuraavaTila(muutokset, logml)
  • rand_disc(CDF)
  • updateGlobalVariables(ind, i2, rowsFromInd, diffInCounts, ...
  • updateGlobalVariables2(i1, i2, rowsFromInd, diffInCounts, ...
  • updateGlobalVariables3(muuttuvat, rowsFromInd, diffInCounts, ...
  • returnInOrder(inds, pop, rowsFromInd, data, adjprior, priorTerm)
  • laskeMuutokset(ind, rowsFromInd, ...
  • laskeMuutokset2(i1, rowsFromInd, ...
  • laskeMuutokset3(T2, inds2, rowsFromInd, ...
  • laskeMuutokset5(inds, rowsFromInd, data, adjprior, ...
  • computeDiffInCounts(rows, max_noalle, nloci, data)
  • computePopulationLogml(pops, adjprior, priorTerm)
  • poistaTyhjatPopulaatiot(npops)
  • admixture_initialization(data_matrix,nclusters,Z)
  • cluster_own(Z,nclust)
  • clusternum(X, T, k, c)
  • handleData(raw_data)
  • newGetDistances(data, rowsFromInd)
  • getDistances(data_matrix,nclusters)
  • linkage(Y, method)
  • initPopNames(nameFile, indexFile)
  • computeCounts(cliques, separators, npops, PARTITION)
  • computeDiffInCliqCounts(cliques, inds)
  • computeLogml(adjprior,priorTerm, ...
  • initializeGammaln(ninds, rowsFromInd, maxSize)
  • laskeOsaDist(inds2, dist, ninds)
  • testaaGenePopData(tiedostonNimi)
  • lueGenePopData(tiedostonNimi)
  • lueNimi(line)
  • selvitaDigitFormat(line)
  • rivinSisaltamienMjonojenLkm(line)
  • testaaPop(rivi)
  • addAlleles(data, ind, line, divider)
  • writeMixtureInfo(logml, rowsFromInd, data, adjprior, ...
  • dispLine;
  • takeLine(description,width)
  • omaRound(num)
  • palautaYks(num,yks)
  • kldiv2str(div)
  • testaaOnkoKunnollinenBapsData(data)
  • testFastaData(inFile)
  • handleCoords(coordinates)
  • laskeKlikit(M, maxCliqSize,maxSepSize)
    • mysubset()
    • neighbors()
    • triangulate()
    • myintersect()
    • findCliques()
    • myunion()
    • cliques_to_jtree()
    • minimum_spanning_tree()
    • elim_order()
    • argmin()
    • ind2subv()
      • dec2bitv()
    • mysize()
    • myisvector()
    • setdiag()
  • mysetdiff(A,B)
  • checkLogml(priorTerm, adjprior, cliques, separators)
  • findEmptyPop(npops)
  • testaaKoordinaatit(ninds, coordinates)
  • laskeVarmuus(rowsFromInd, data, adjprior, priorTerm, ...
  • initialCounts(partition, data, npops, rows, noalle, adjprior)
@wleoncio wleoncio added the enhancement New feature or request label Nov 9, 2020
@wleoncio wleoncio added this to the Next major release milestone Nov 9, 2020
@wleoncio wleoncio self-assigned this Nov 9, 2020
@wleoncio wleoncio added this to To do in Translate base BAPS to R via automation Nov 9, 2020
@wleoncio wleoncio modified the milestones: CRAN release, Translated all basic functions Sep 3, 2021
wleoncio added a commit that referenced this issue Jul 28, 2022
@wleoncio
Translated computeCounts() (#3)
31ab81a
wleoncio added a commit that referenced this issue Jul 28, 2022
@wleoncio
Translated computeDiffInCliqCounts() (#3)
84e0eb6
wleoncio added a commit that referenced this issue Jul 28, 2022
@wleoncio
Translated mysetdiff() (#3)
86a5dda
wleoncio added a commit that referenced this issue Aug 25, 2022
@wleoncio
Translated laskeVarmuus (#3)
c05a500
wleoncio added a commit that referenced this issue Sep 15, 2022
@wleoncio
Translated laskemuutokset{1-5}() (#3)
46dc089
wleoncio added a commit that referenced this issue Sep 15, 2022
@wleoncio
Translated checkLogml() (#3)
53bae46
wleoncio added a commit that referenced this issue Nov 16, 2022
@wleoncio
Translated testaaKoordinaatit() (#3)
85c412f
wleoncio added a commit that referenced this issue Nov 16, 2022
@wleoncio
Added unit tests (#3)
a354202
wleoncio added a commit that referenced this issue Dec 22, 2022
@wleoncio
Removed translating TODOs
73438af 
Replaced with built-in TODO list in Issue #3's body
wleoncio added a commit that referenced this issue Dec 23, 2022
@wleoncio
Translated minimum_spanning_tree() (#3)
547bb73
wleoncio added a commit that referenced this issue Dec 23, 2022
@wleoncio
Translated ind2subv() (#3)
ce53f1f
wleoncio added a commit that referenced this issue Dec 23, 2022
@wleoncio
Translated dec2bitv() (#3)
98cde6b
wleoncio added a commit that referenced this issue Dec 23, 2022
@wleoncio
Making it clear which package log2() is coming from (#3)
3a479d1
wleoncio added a commit that referenced this issue Jan 23, 2023
@wleoncio
Translated testFastaData() (#3)
8ce9f3a
wleoncio added a commit that referenced this issue Jan 23, 2023
@wleoncio
Fixed synxtax of zeallot call (#3)
257046d
wleoncio added a commit that referenced this issue Feb 7, 2023
@wleoncio
fixup! Translated testFastaData() (#3)
3cfbe5b
wleoncio added a commit that referenced this issue Feb 7, 2023
@wleoncio
Added unit tests (#3)
5171a4f
wleoncio added a commit that referenced this issue Feb 10, 2023
@wleoncio
Added tests, fixed subfunctions (#3)
a8cae95
@wleoncio wleoncio moved this from To do to In progress in Translate base BAPS to R Feb 15, 2023
wleoncio added a commit that referenced this issue Feb 16, 2023
@wleoncio
Syntax fixes (#3)
8bddd70
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Labels
enhancement New feature or request
Projects
Translate base BAPS to R
  
In progress
Milestone
Translated all basic functions
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