fitzLab-AL/gdm issues and pull requests

#51 - Update test_gdm.R to resolved CRAN issues

Pull Request - State: open - Opened by rvalavi 1 day ago

#50 - tutorial missing colorRamps package call or package dependency

Issue - State: open - Opened by francisvolh 20 days ago

#49 - CRAN check still fails on tinytest.R

Issue - State: open - Opened by fitzLab-AL 23 days ago - 4 comments

#48 - Update test_gdm.R to avoid permission issue

Pull Request - State: closed - Opened by rvalavi 29 days ago

#48 - Update test_gdm.R to avoid permission issue

Pull Request - State: closed - Opened by rvalavi 29 days ago

#47 - gdm.transform fail if `geo = TRUE` and i-splines for geographic distance are all zero

Issue - State: open - Opened by dinilu about 1 month ago

#46 - Error in predict function

Issue - State: closed - Opened by dinilu about 1 month ago - 6 comments

#45 - How are ecological and geographical distances computed?

Issue - State: open - Opened by LafontRapnouilTristan about 2 months ago - 3 comments

#44 - Error related to unit tests

Issue - State: closed - Opened by fitzLab-AL 2 months ago - 1 comment

#43 - negative deviance explained value with cross validation

Issue - State: closed - Opened by Basquill 3 months ago - 7 comments

#42 - Improving terra functions and fixing a bug

Pull Request - State: closed - Opened by rvalavi 3 months ago - 1 comment

#41 - Issue with long vectors

Issue - State: open - Opened by talkinser 5 months ago - 3 comments

#40 - Gdm weight by richness

Pull Request - State: closed - Opened by xinxxxin 7 months ago

#39 - Update gdm.formatsitepair.R

Pull Request - State: closed - Opened by xinxxxin 7 months ago

#38 - Reproducing Plot 4a in Mokany et al (2022)

Issue - State: closed - Opened by Basquill 8 months ago - 5 comments

#37 - cleaning terra functions

Pull Request - State: closed - Opened by rvalavi 8 months ago - 1 comment

#36 - Using terra() data objects with gdm ver v1.6.0 [e.g., for visualizing Multi-dimensional Biological patterns]

Issue - State: closed - Opened by Basquill 8 months ago - 8 comments

#35 - migration to terra completed!

Pull Request - State: closed - Opened by rvalavi 9 months ago

#34 - Variable importance assessment (knots error)

Issue - State: open - Opened by marcelglueck 12 months ago - 2 comments

#33 - Increasing the number of splines and knots reduces propability of model fitting

Issue - State: closed - Opened by marcelglueck 12 months ago - 3 comments

#32 - Error running formatsitepair function

Issue - State: closed - Opened by catarras about 1 year ago - 2 comments

#31 - dimname error when predictor gets dropped in gdm.varImp

Issue - State: closed - Opened by n8layman about 2 years ago - 1 comment

#30 - Can you share a vignette of phylogenetic generalised dissimilarity model with gdm package?

Issue - State: closed - Opened by Otoliths about 2 years ago - 1 comment

#29 - gdm.varimp error

Issue - State: closed - Opened by jamesryan1896 over 2 years ago - 4 comments

#28 - predict error

Issue - State: closed - Opened by willright28 over 2 years ago - 3 comments

#27 - Custom weights - error incorrect number of dimensions

Issue - State: closed - Opened by 03rcooke over 2 years ago - 3 comments

#26 - Possible bug in gdm.varImp

Issue - State: closed - Opened by grcolli over 2 years ago - 6 comments

#25 - How can I obtain the unique identifiers of the sites that are being compared by the Bray-Curtis index using formatsitepair()

Issue - State: closed - Opened by fsdias over 2 years ago

#24 - gdm.varImp() returns NA when using only one covariate

Issue - State: closed - Opened by fsdias over 2 years ago - 1 comment

#23 - Error when running gdm.varImp()

Issue - State: closed - Opened by fsdias over 2 years ago - 4 comments

#22 - gdm.VarImp failes if the sum of I-spline coefficients for the "Geographic" predictor == 0

Issue - State: closed - Opened by JulFrey over 2 years ago - 2 comments

#21 - gdm.varImp sensitive to predictor names

Issue - State: closed - Opened by JulFrey over 2 years ago - 1 comment

#20 - formatsiterepair undefined columns

Issue - State: closed - Opened by njm-data over 2 years ago - 1 comment

#19 - Installation error on Ubuntu 20.04 with R 4.1.3

Issue - State: closed - Opened by fsdias over 2 years ago - 6 comments

#18 - subsample argument in formatsitepair does not actually subsample sites

Issue - State: closed - Opened by fitzLab-AL almost 3 years ago

#17 - Consider forcing user to specify spline number

Issue - State: closed - Opened by sponslerdb about 3 years ago - 1 comment

#16 - plotUncertainty(): more documentation, custom plotting method

Issue - State: closed - Opened by sponslerdb about 3 years ago - 1 comment

#15 - Non-default spline number breaks gdm.varImp()

Issue - State: closed - Opened by sponslerdb about 3 years ago - 2 comments

#14 - Specifying non-equal spline numbers across variables breaks plot() and isplineExtract()

Issue - State: closed - Opened by sponslerdb about 3 years ago - 2 comments

#13 - Non-default splines argument breaks isplineExtract()

Issue - State: closed - Opened by sponslerdb about 3 years ago - 1 comment

#12 - Problem with gdm.varImp function

Issue - State: closed - Opened by burbrink over 3 years ago - 1 comment

#11 - Discussion: GDM assumption on increasing dissimilarity

Issue - State: closed - Opened by Leitemfa about 5 years ago

#10 - GDM without Coordinates

Issue - State: closed - Opened by Leitemfa over 5 years ago - 4 comments

#9 - par(ask=TRUE) will improve plot.gdm

Issue - State: closed - Opened by jamiemkass over 5 years ago - 1 comment

#8 - error in formatsiterepair function 'aggregation function missing: defaulting to length'

Issue - State: closed - Opened by anwar79melb over 5 years ago - 6 comments

#7 - Geographic distance calculated using Pythagorean theorem

Issue - State: open - Opened by claraqin over 6 years ago - 4 comments

#6 - gdm.transform function error

Issue - State: closed - Opened by kostask84 over 6 years ago - 1 comment

#5 - GDM not supported anymore by CRAN

Issue - State: closed - Opened by jivelasquezt almost 7 years ago - 1 comment

#4 - predData is necessary in formatsitepair, even though the help file states it is not

Issue - State: closed - Opened by leorjorge over 7 years ago - 1 comment

#3 - There appears to be a typo in the chunk of code that determines species count for each site and then filters sites with few species. There should be a comma inside the braket after "bioData so the apply function does not return "dim(x) must have a positive length." I think this is how the line in question should read: sppTotals <- cbind(as.data.frame(zst[,"siteCol"]), apply(sppDat, 1, function(m){sum(as.numeric(m))})) . The formatsitepair function does not work for me and I think this is why.

Issue - State: closed - Opened by richardastantonjr almost 8 years ago

#2 - Issues with gdm.varImp()

Issue - State: closed - Opened by jsocolar over 8 years ago - 1 comment

#1 - Reformat code for better readability

Pull Request - State: closed - Opened by howl-anderson about 9 years ago

GitHub / fitzLab-AL/gdm issues and pull requests