2018 non-functionality #34
Comments
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yes, there are no strata areas in songbird project, so abundance cannot be computed, but many other things break when trying to duplicate analysis in which size-biased regression by stratum is requested: no object is created quite an exotic P_a is computed from the fitted detection function: |
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Still working with songbird project, but trying second analysis with cluster size as detection function covariate: But |
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Contrary to my confidence this afternoon, I can't reproduce step one here where the |
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still the same result: |
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Odd. I wonder if this is a Windows issue? I'll try to source some way of
testing that. In the meantime can you upload the project here so I can
double check?
…On 10/03/2018 10:52, erex wrote:
still the same result:
| > library(readdst) > tmp <-
convert_project("C:\\Users\\erexstad\\Desktop\\readdst-test-projects\\songbird")
Loading required package: RODBC > one <- run_analysis(tmp[[1]]) > fred
<- test_stats(tmp[[1]], statuses=2) Error in create.varstructure(model,
region.table, sample.table, obs.table) : Invalid or missing Area values
for regions In addition: Warning messages: 1: In predict.lm(size_lm,
pred_data) : prediction from a rank-deficient fit may be misleading 2:
In predict.lm(size_lm, pred_data) : prediction from a rank-deficient fit
may be misleading 3: In predict.lm(size_lm, pred_data) : prediction from
a rank-deficient fit may be misleading 4: In predict.lm(size_lm,
pred_data) : prediction from a rank-deficient fit may be misleading 5:
In predict.lm(size_lm, pred_data) : prediction from a rank-deficient fit
may be misleading 6: In predict.lm(size_lm, pred_data) : prediction from
a rank-deficient fit may be misleading 7: In predict.lm(size_lm,
pred_data) : prediction from a rank-deficient fit may be misleading 8:
In create.varstructure(model, region.table, sample.table, obs.table) :
Some samples not included in the analysis > sessionInfo() R version
3.4.3 (2017-11-30) Platform: i386-w64-mingw32/i386 (32-bit) Running
under: Windows >= 8 x64 (build 9200) Matrix products: default locale:
[1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United
Kingdom.1252 [3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252 attached base packages: [1]
stats graphics grDevices utils datasets methods base other attached
packages: [1] RODBC_1.3-15 readdst_0.0.4 loaded via a namespace (and not
attached): [1] RColorBrewer_1.1-2 checkmate_1.8.5 cluster_2.0.6
rstudioapi_0.7 [5] magrittr_1.5 acepack_1.4.1 gtable_0.2.0 minqa_1.2.4
[9] data.table_1.10.4-3 base64enc_0.1-3 pillar_1.2.1 htmltools_0.3.6
[13] stringr_1.3.0 truncnorm_1.0-8 splines_3.4.3 Formula_1.2-2 [17]
lattice_0.20-35 survival_2.41-3 Rvmmin_2017-7.18 setRNG_2013.9-1 [21]
htmlwidgets_1.0 testthat_2.0.0 plyr_1.8.4 knitr_1.20 [25] gridExtra_2.3
Matrix_1.2-12 R6_2.2.2 optimx_2013.8.7 [29] numDeriv_2016.8-1
digest_0.6.15 colorspace_1.3-2 Rsolnp_1.16 [33] stringi_1.1.6
yaml_2.1.18 lazyeval_0.2.1 Hmisc_4.1-1 [37] dfoptim_2017.12-1
tibble_1.4.2 mgcv_1.8-23 compiler_3.4.3 [41] Rcgmin_2013-2.21
rpart_4.1-11 backports_1.1.2 htmlTable_1.11.2 [45] munsell_0.4.3
Rcpp_0.12.15 optextras_2016-8.8 BB_2014.10-1 [49] svUnit_0.7-12
parallel_3.4.3 ggplot2_2.2.1 ucminf_1.1-4 [53] mrds_2.1.18
latticeExtra_0.6-28 tools_3.4.3 foreign_0.8-69 [57] nnet_7.3-12
scales_0.5.0 quadprog_1.5-5 rlang_0.2.0 [61] nlme_3.1-131.1 grid_3.4.3 |
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as requested |
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hmm, okay, can you ensure you have the latest I am now getting the warnings that you get, now that I am using this data set: but not the error. When we looked at this in your office I don't recall seeing the |
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Okay, one possible issue here: wonder why this doesn't cause an error for me but does for you... In this case (where areas are 0) I guess we should not return comparisons of Nhat? What does Distance do in this situation? FYI, the output of running the above for me: |
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Guess I'll grab a 2.2.0 version of mrds and see what happens. Appears to have gotten the version bump in October of last year when you were dealing with the K-S test revamp; with estimated values of the distribution parameters Without stratum areas provided, Distance 7 simply omits any attempt to produce abundance estimates and only reports density estimates: |
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results using mrds 2.2.0 btw: the 'as.numeric()' statement did exist in earlier versions of readdst |
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Okay, well that's annoying that didn't fix things. On the other hand, I do think your version of |
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26b0688 gets around this error, but do need to implement a density estimator (for groups and individuals and their respective s.e.s) when |
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Indeed the most recent commit does sneak around the error trying to produce the abundance estimate in The D7-GUI fits a single adjustment term, whereas mrds fits 4 adjustment terms, (having a reasonably similar log-likelihood) with the end result being absurd estimate of detection probability: |
20Mar effortsHouse wren sample project: point transects, multiple visits, with observer as potential covariate
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Revert to Stratify solutions projectThis was used for readdst testing two years ago when it was being created resulted in somehow |
Visit Tiago's amakihi projectfirst oddity is that Eventually however, |
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stratify solution project and amakihi Distance projects (in zip format) found at and https://my.pcloud.com/publink/show?code=XZc1Y87ZWVLWUCcvDX8Ue7R1h7mqbQxGhCLy respectively |
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Stratify project error should be fixed in b2081c5. |
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Fast work on stratify solution problem. Running the first analysis (full geographic stratification) generates this comparison agains the Distance7 result If the likelihood is spot-on, I assume this means the detection function and hence P_a ought to be spot on. However, as there are stratum-specific P_a, they aren't presented in the summary table. I'll refresh my memory on how density estimate is being produced for this analysis |
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As to the second amakihi error... it looks like there are some issues with how this analysis is put together. Is it the case that the detection function is being estimated per stratum? |
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This, I believe, is what the first amakihi analysis (number 139, labelled "HN by strat f0 pooled w82.5") is trying to do |
Error arises when doing conversion of (allegedly) simple project (songbird, filtering for song sparrow, w=68)
Tracked error to function
unit_tab()The beast created by
read.delim()trick is messy. Solution appears to be this:I'll made that change and commit
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