Module autostreamtree.report_refs

Functions

def fetch_references(params)

Build an output reference string for all methods a user chose in a run.

Parameters:

params : object An object containing all user input parameters.

Returns:

refs : str A string containing all relevant references to be cited.

Expand source code

def fetch_references(params):
    """
    Build an output reference string for all methods a user chose in a run.

    Parameters:
    -----------
    params : object
        An object containing all user input parameters.

    Returns:
    --------
    refs : str
        A string containing all relevant references to be cited.
    """
    refs = "\n\nIf you found this software useful for your research please \
cite the following (a full manuscript will come at a later date):"
    refs = refs + "\nChafin TK, Mussmann SM, Douglas MR, Douglas ME. 2023. \
autoStreamTree: Automated workflows for examining patterns of genetic \
    differentiation in stream networks. github.com/tkchafin/autoStreamTree"

    if params.run == "STREAMTREE" or params.run == "ALL":
        refs = refs + "\n\nPlease cite the StreamTree method as: \nKalinowski \
ST, MH Meeuwig, SR Narum, ML Taper (2008) Stream trees: a statistical method \
for mapping genetic differences between populations of freshwater organisms to\
the sections of streams that connect them. Canadian Journal of Fisheries and \
Aquatic Sciences (65:2752-2760)"
        if params.weight == "FM67":
            refs = refs + "\n\nFor the LS optimization, you chose the FM67 \
weighting. Please also cite: \nFitch WM, Margloiash E. 1967. \
Construction of phylogenetic trees. Science.155: 279-84"
        elif params.weight == "CSE67":
            refs = refs + "\n\nFor the LS optimization, you chose the CSE67 \
weighting. Please also cite: \nCavalli-Sforza LL, Edwards AWF. 1967. \
Phylogenetic analysis: model and estimation procedures. American Journal of \
Human Genetics. 19: 233-257"
        elif params.weight == "BEYER74":
            refs = refs + "\n\nFor the LS optimization, you chose the BEYER74 \
weighting. Please also cite: \nBeyer WM, Stein M, Smith T, Ulam S. 1974. A \
molecular sequence metric and evolutionary trees. Mathematical Biosciences. \
19: 9-25"
    if params.run != "STREAMDIST" and not params.genmat:
        if params.dist != "PDIST":
            refs = refs + "\n\nPlease cite the following for your genetic \
distance calculations:"
            if params.dist == "JC69":
                refs = refs + "\nJukes TH, Cantor CR. 1969. Evolution of \
protein molecules. New York: Academic Press."
            elif params.dist == "FST":
                refs = refs + "\nWeir BS, Cockerham CC. 1984. Estimating \
F-statistics for the analysis of population structure. Evolution. 38: \
1358-1370."
                refs = refs + "\nNei M. 1987. Molecular Evolutionary \
Genetics. Columbia University Press, New York"
            elif params.dist == "LINFST":
                refs = refs + "\nRousset F. 1997. Genetic differentiation and \
estimation of gene flow from F-statistics under isolation by distance. \
Genetics. 145: 1219-28."
                refs = refs + "\nWeir BS, Cockerham CC. 1984. Estimating \
F-statistics for the analysis of population structure. Evolution. 38: \
1358-1370."
            elif params.dist == "JOST":
                refs = refs + "\nJost L. 2008. Gst and its relatives do not \
measure differentiation. Molecular Ecology. 17: 4015-4026."
            elif params.dist == "NEI83":
                refs = refs + "\nNei M, Chesser RK. 1983. Estimation of \
fixation indices and gene diversities. Annals of Human Genetics 47(3): 253-259"
            elif params.dist == "CHORD":
                refs = refs + "\nCavalli-Sforza LL, Edwards AWF. 1967. \
Phylogenetic analysis: model and estimation procedures. American Journal of \
Human Genetics. 19: 233-257."

    if params.run == "IBD" or params.run == "ALL":
        refs = refs + "\n\nFor the Mantel test, please cite:\nMantel N. 1967. \
The detection of disease clustering and a generalized regression approach. \
Cancer Research 27(2): 209-220."

    if params.clusterpop:
        refs = refs + "\n\nFor the DBSCAN approach, please cite:"
        refs = refs + "\nEster M, Kriegel HP, Sander J, Xu X. 1996. A \
density-based algorithm for discovering  clusters in large spatial databases \
with noise. IN: Simoudis E, Han J, Fayyad UM. (eds.). Proceedings of the \
Second International Conference on Knowledge Discovery and Data Mining \
(KDD-96). AAAI Press. pp. 226–231."
        refs = refs + "\nPedregosa F, Varoquaux G, Gramfort A, Michel V, \
Thirion B, Grisel O, Blondel M, Prettenhofer P, Weiss R, Dubourg V, \
Vanderplas J. 2011. Scikit-learn: Machine learning in Python. The Journal of \
machine Learning research. 1(12):2825-30"

    if params.pop_agg == "ADJHARM" or params.loc_agg == "ADJHARM":
        refs = refs + "\n\nFor the adjusted harmonic mean, please cite:\
 \nRossmann LA. DFLOW User's Manual. U.S. Environmental Protection Agency."

    if params.run != "GENDIST":
        refs = refs + "\n\nFor the network methods, please cite: \nHagberg A, \
Swart P, S Chult D. 2008. Exploring network structure, dynamics, and function \
using NetworkX. Los Alamos National Lab.(LANL), Los Alamos, NM"

    refs = refs + "\n"

    return refs