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[R-package on CRAN] Analyze fgeo data.

Home Page: https://forestgeo.github.io/fgeo.analyze/

License: GNU General Public License v3.0

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r r-package forestgeo fgeo abundance demography

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fgeo.analyze's Issues

Website is now build on Travis CI and pushed served on the gh-pages branch.</p>

fgeo.analyze/docs/news/index.html

Lines 134 to 139 in 14e7c83

<p>TODO Website is now build on Travis CI and pushed served on the gh-pages branch.</p>
</div>
<div id="fgeo-analyze-1-1-3-github-and-drat" class="section level1">
<h1 class="page-header">
<a href="#fgeo-analyze-1-1-3-github-and-drat" class="anchor"></a>fgeo.analyze 1.1.3 (<a href="https://github.com/forestgeo/fgeo.analyze/releases">GitHub</a> and <a href="https://forestgeo.github.io/drat/">drat</a>)</h1>
<ul>

This issue was generated by todo based on a TODO comment in 14e7c83 when #77 was merged. cc @maurolepore.

Website is now build on Travis CI and pushed served on the gh-pages branch.</p>

fgeo.analyze/docs/news/index.html

Lines 134 to 139 in 5e6af2d

<p>TODO Website is now build on Travis CI and pushed served on the gh-pages branch.</p>
</div>
<div id="fgeo-analyze-1-1-3-github-and-drat" class="section level1">
<h1 class="page-header">
<a href="#fgeo-analyze-1-1-3-github-and-drat" class="anchor"></a>fgeo.analyze 1.1.3 (<a href="https://github.com/forestgeo/fgeo.analyze/releases">GitHub</a> and <a href="https://forestgeo.github.io/drat/">drat</a>)</h1>
<ul>

This issue was generated by todo based on a TODO comment in 5e6af2d. It's been assigned to @maurolepore because they committed the code.

Website is now build on Travis CI and pushed served on the gh-pages branch.

fgeo.analyze/NEWS.md

Lines 11 to 16 in 5e6af2d

TODO Website is now build on Travis CI and pushed served on the gh-pages branch.
# fgeo.analyze 1.1.3 ([GitHub](https://github.com/forestgeo/fgeo.analyze/releases) and [drat](https://forestgeo.github.io/drat/))
* Meet CRAN standards.
* `dplyr::n()` is now imported to avoid [`error could not find function "n"`](https://dplyr.tidyverse.org/news/index.html#breaking-changes).

This issue was generated by todo based on a TODO comment in 5e6af2d. It's been assigned to @maurolepore because they committed the code.

Release fgeo.analyze 1.1.12

Prepare for release:

  • Check current CRAN check results
  • devtools::check(remote = TRUE, manual = TRUE)
  • devtools::check_win_devel()
  • rhub::check_for_cran()
  • revdepcheck::revdep_check(num_workers = 4)
  • Update cran-comments.md
  • Polish NEWS
  • Review pkgdown reference index for, e.g., missing topics

Submit to CRAN:

  • usethis::use_version('patch')
  • devtools::submit_cran()
  • Approve email

Wait for CRAN...

  • Accepted 🎉
  • usethis::use_github_release()
  • usethis::use_dev_version()

tt_test() errs with relatively high number of habitats 

library(tidyverse)
#> Warning: package 'purrr' was built under R version 3.5.3
library(fgeo)
#> -- Attaching packages -------------------------------------------- fgeo 1.1.2.9000 --
#> v fgeo.analyze 1.1.4          v fgeo.tool    1.2.2     
#> v fgeo.plot    1.1.3.9000     v fgeo.x       1.1.2
#> -- Conflicts ---------------------------------------------------- fgeo_conflicts() --
#> x fgeo.tool::filter() masks dplyr::filter(), stats::filter()
#> x dplyr::intersect()  masks base::intersect()
#> x dplyr::lag()        masks stats::lag()
#> x dplyr::setdiff()    masks base::setdiff()
#> x dplyr::setequal()   masks base::setequal()
#> x dplyr::union()      masks base::union()
set.seed(1)

# Small dataset from Luquillo
cns_luq <- fgeo.x::tree6_3species
hab_luq <- fgeo.x::habitat
sp_top3_luq <- unique(fgeo.x::tree6_3species$sp)
pdim_luq <- c(320, 500)
gsize_luq <- 20

# Passes
hab <- fgeo_habitat(fgeo.x::elevation, 20, 8)
as_tibble(tt_test(cns_luq, hab))
#> Using `plotdim = c(320, 500)`. To change this value see `?tt_test()`.
#> Using `gridsize = 20`. To change this value see `?tt_test()`.
#> # A tibble: 24 x 8
#>    habitat sp     N.Hab Gr.Hab Ls.Hab Eq.Hab Rep.Agg.Neut Obs.Quantile
#>  * <chr>   <chr>  <dbl>  <dbl>  <dbl>  <dbl>        <dbl>        <dbl>
#>  1 1       CASARB    11    587   1012      1            0        0.367
#>  2 2       CASARB    16   1433    163      4            0        0.896
#>  3 3       CASARB     2   1200    368     32            0        0.75 
#>  4 4       CASARB    14    886    710      4            0        0.554
#>  5 5       CASARB     6    223   1365     12            0        0.139
#>  6 6       CASARB     6    418   1177      5            0        0.261
#>  7 7       CASARB     5    932    658     10            0        0.582
#>  8 8       CASARB     6   1423    171      6            0        0.889
#>  9 1       PREMON    49   1223    374      3            0        0.764
#> 10 2       PREMON    37    627    968      5            0        0.392
#> # ... with 14 more rows
autoplot(hab)

# Errs
hab <- fgeo_habitat(fgeo.x::elevation, 20, 16)
as_tibble(tt_test(cns_luq, hab))
#> Using `plotdim = c(320, 500)`. To change this value see `?tt_test()`.
#> Using `gridsize = 20`. To change this value see `?tt_test()`.
#> Error in if (spprophab[i] > Torspprophab[i]) {: missing value where TRUE/FALSE needed

autoplot(hab)

Created on 2019-03-22 by the reprex package (v0.2.1)

Release 1.1.4

Prepare for release:

  • Create pre-release branch.
  • devtools::check_win_devel()
  • rhub::check_on_macos()
  • revdepcheck::revdep_check(num_workers = 4)
  • Style NEWS (may use version.9000 temporarily)
  • Merge.

Perform release:

  • Have you updated packages with (update.packages())?
  • Create release branch
  • Bump version (in DESCRIPTION and NEWS)

(Walk through devtools::release() but don't submit)

  • Have you run R CMD check locally?
  • Have you checked for spelling errors (with spell_check())?
  • Were devtool's checks successful?
  • devtools::check_win_devel().
  • rhub::check_for_cran().
  • Have you updated NEWS.md file?
  • Have you updated DESCRIPTION (version number, use_tidy_version(), use_tidy_description())?
  • Have you updated cran-comments.md?
  • Merge

Publish release:

  • Check website built OK (e.g. version, News)
  • Release on GitHub
  • Release on drat (should automate with the drat.build package)
  • Build source and win binary locally and add to drat
  • With source build mac binary on https://builder.r-hub.io/ and add to drat
  • Update README.Rmd
  • Bump dev version

Announce

  • Write blog post
  • Add link to blog post in pkgdown news menu
  • Tweet

Templatate at forestgeo/learn#182 (adapted from https://github.com/r-lib/usethis/issues/338).

tt_test returns Error when I use a file with a single species (with relatively low sample size)

@maurolepore
When I use a dataset with a single species, I get an error message related to the issue https://github.com/forestgeo/fgeo.analyze/issues/40. The Error can be reproduced using the example data in the tt_test function:

# Using the same example of tt_test
library(fgeo.tool, warn.conflicts = FALSE)
assert_is_installed("fgeo.x")
tree <- fgeo.x::tree6_3species
elevation <- fgeo.x::elevation

# Pick alive trees, of 10 mm or more
census <- filter(tree, status == "A", dbh >= 10)

# Selecting CASARB species
w <- which(census$sp == "CASARB")
census.CASARB <- census[w,]

# An error occur with any of the following codes when you use a file with a single species
fgeo.analyze::tt_test(census.CASARB, fgeo.x::habitat)
#> Using `plotdim = c(320, 500)`. To change this value see `?tt_test()`.Using
#> `gridsize = 20`. To change this value see `?tt_test()`.
#> Error:   Every quadrat in the dataset must have at lease one tree.
#>   For more information see https://github.com/forestgeo/fgeo.analyze/issues/40.
fgeo.analyze::tt_test(census.CASARB, fgeo.x::habitat, sp = "CASARB")
#> Using `plotdim = c(320, 500)`. To change this value see `?tt_test()`.Using
#> `gridsize = 20`. To change this value see `?tt_test()`.
#> Error:   Every quadrat in the dataset must have at lease one tree.
#>   For more information see https://github.com/forestgeo/fgeo.analyze/issues/40.

# I think it doesn't have to do with the low sample size issue and the error is being incorrectly reported because no error is returned when the species is included along with other species
fgeo.analyze::tt_test(census, fgeo.x::habitat, sp = "CASARB")
#> Using `plotdim = c(320, 500)`. To change this value see `?tt_test()`.Using
#> `gridsize = 20`. To change this value see `?tt_test()`.
#> [[1]]
#>        N.Hab.1 Gr.Hab.1 Ls.Hab.1 Eq.Hab.1 Rep.Agg.Neut.1 Obs.Quantile.1
#> CASARB      29     1242      356        2              0        0.77625
#>        N.Hab.2 Gr.Hab.2 Ls.Hab.2 Eq.Hab.2 Rep.Agg.Neut.2 Obs.Quantile.2
#> CASARB      20      390     1206        4              0        0.24375
#>        N.Hab.3 Gr.Hab.3 Ls.Hab.3 Eq.Hab.3 Rep.Agg.Neut.3 Obs.Quantile.3
#> CASARB      12      778      817        5              0        0.48625
#>        N.Hab.4 Gr.Hab.4 Ls.Hab.4 Eq.Hab.4 Rep.Agg.Neut.4 Obs.Quantile.4
#> CASARB       5      932      658       10              0         0.5825

Helper to pick sufficiently abundant species

Sabrina Russo said:

... I guess there’s a wrapper function in which the user can pick what minimum tree abundance they wish to use and that then subsets the data so that only the species meeting the minimum abundance criterion are run for the TT? If not, then there should be one.

Update tables of mortality and growth

Tue, Dec 4, 2018 at 1:45 PM Lao, Suzanne [email protected]

As was done with the species abundance tables, we need to update the BCI growth and mortality tables on the forestgeo website also. ... The numbers should be very similar to the ones on the website, and you would have 2 more census intervals: https://forestgeo.si.edu/sites/south-america/barro-colorado-island/bci-species-growth-and-mortality

Paper that explains how the tables were calculated and code:

Some items yet unclear to me:

  • Should I use the data I used for the tables of abundance and basal area?

  • How are the time-intervals defined? For example, From the website it is not obvious how to resolve this: The interval 1995-2000 includes six years (1995, 1996, 1997, 1998, 1999, 2000), and 2000 overlaps with the interval 2000-2005.

Background:

On Tue, Dec 4, 2018 at 5:05 PM Lao, Suzanne [email protected] wrote:

talk to Stuart and ask him whether we should leave the site as is, or whether we should recalculate the relative growth rates and add 2005-2010 and 2010-2015

What the columns mean and how the rates were calculated:

growth:

rate: observed relative growth rate (mean of log-transformed relative growth rates of individual trees, subsequently back-transformed); fitted: estimated growth rate from Gibbs sampler; lower and upper: 95 pct. confidence limits of the fitted rate, based on the Gibbs sampler (see Methods in Supporting Online Material). All rates are percentages, that is, 100 times the relative growth. _10 indicates data for the 10-99-mm dbh category, and _100 for stems dbh 100 and above.

mortality:

rate: observed mortality rate constant (based only on N, S, time); fitted: estimated mortality rate constant from Gibbs sampler; lower and upper: 95 pct. confidence limits of the fitted rate, based on the Gibbs sampler (see Methods in Supporting Online Material). All rates are percentages, that is, 100 times the rate constant. _10 indicates data for the 10-99-mm dbh category, _100 for stems dbh 100 and above.

Release 1.1.13

Prepare for release:

  • Check that description is informative
  • Check licensing of included files
  • usethis::use_cran_comments()
  • devtools::check(remote = TRUE, manual = TRUE)
  • devtools::check_win_devel()
  • rhub::check_for_cran()
  • revdep_check(num_workers = 4)
  • Update cran-comments.md

Submit to CRAN:

  • usethis::use_version('patch')
  • devtools::submit_cran()
  • Approve email

Wait for CRAN...

  • Accepted 🎉
  • usethis::use_github_release()
  • usethis::use_dev_version()

Fix docs abundance

From forestgeo/forum#19 (comment):

"count woods" sounds weird. Maybe say "count individuals"?

I think vft2[2,3] should be 1.2, isn't it ?

would be good to show how to count abundance of stems and not only individual trees (e.i. a multi-stem tree with 2 stems counts for 2)

Release fgeo.analyze-1.1.11

Prepare for release:

  • Create pre-release branch.
  • Change maintainer's email
  • Use full URLs.
  • devtools::check_win_devel()

Copy job results to results object in the global environment:

  • revdepcheck::revdep_check(num_workers = 4)
  • ck_remote <- devtools::check(remote = TRUE)
  • ck_cran <- rhub::check_for_cran()
  • ck_macos <- rhub::check_on_macos()
  • ck_fedora_cd <- rhub::check(platform = "fedora-clang-devel")
  • ck_fedora_gd <- rhub::check(platform = "fedora-gcc-devel")
  • ck_solaris <- rhub::check_on_solaris()

Also:

  • Update NEWS.md (tidyverse style ); May temporarily use version.9000
  • Merge.

Perform release:

  • Have you updated packages with (update.packages())?
  • Create release branch
  • usethis::use_version()
  • Walk through devtools::release()
  • Submit to CRAN
  • Approve submission by replying to email from CRAN
  • Confirm change of mainteriner's email address by replying-to-all to email from CRAN

Wait for CRAN...

  • Accepted
  • Tag release
  • Merge release branch back to master branch
  • usethis::use_github_release()
  • usethis::use_dev_version()

Templatate at forestgeo/learn#182 (adapted from

Website is now build on Travis CI and pushed served on the gh-pages branch.

fgeo.analyze/NEWS.md

Lines 11 to 16 in 14e7c83

TODO Website is now build on Travis CI and pushed served on the gh-pages branch.
# fgeo.analyze 1.1.3 ([GitHub](https://github.com/forestgeo/fgeo.analyze/releases) and [drat](https://forestgeo.github.io/drat/))
* Meet CRAN standards.
* `dplyr::n()` is now imported to avoid [`error could not find function "n"`](https://dplyr.tidyverse.org/news/index.html#breaking-changes).

This issue was generated by todo based on a TODO comment in 14e7c83 when #77 was merged. cc @maurolepore.

Mortality rate with different interval lengths for the different observations

Contributed by Gabriel Arellano (via @)

# Mortality rate calculation using different interval lengths 
# for the different observations. Based on Kubo et al. 2000.
mortality_rate_Kubo <- function(data)
{
  # Approach taken by Kubo et al., using different
  # intervals for each observation, and the same
  # mortality rate for all the individuals:
  # Journal of Tropical Ecology (2000) 16:753-756.
  # The mortality rate is the value that makes
  # Equation 3 of Kubo et al. 2000 equal to 0.
  Eq3 <- function(mortality.rate, data)
  {
    alive <- which(data$status == "A")
    dead <- which(data$status == "D")
    Ti <- data[alive, "t"]
    Tj <- data[dead, "t"]
    x = -sum(Ti) + sum((Tj * exp(-mortality.rate * Tj))/(1 - exp(-mortality.rate * Tj)))
    abs(x)
  }
  
  # It is a single-parameter optimization problem.
  # The upper limit of the instantaneous mortality rate is +Inf in theory,
  # but at low mortality rates it should be almost equal to the truly annual
  # mortality rate, which is constrained within [0, 1]. In our system the
  # mortality rates are typically low, so often an upper limit of 1 is reasonable.
  # In some cases (certain species, seedling data with very short intervals, ...)
  # this upper limit should be increased to allow mortality rates > 1.
  
  # Definition of the upper limit, as 10 times the "typical" mortality rate:
  N = sum(data$status %in% c("A", "D"))
  S = sum(data$status == "A")
  mean.t = mean(data$t[data$status %in% c("A", "D")])
  U = 10 * ((log(N) - log(S))/mean.t)
  
  # (Very loosely) constrained optimization:
  mortality.rate <- optimize(f = Eq3, lower = 0, upper = U, data = data)$minimum
  return(mortality.rate)
}


if(FALSE) # example -- if FALSE it will not run by doing source
{
  # Comparison between methods:
  N = 1000
  data <- data.frame(id = 1:N, 
                     status = sample(c("A", "D"), size = N, prob = c(0.6, 0.4), replace = TRUE), 
                     t = runif(N, min = 1, max = 8))
  
  # Typical calculation of the mortality rate,
  # assuming the average time for all the observations:
  N = sum(data$status %in% c("A", "D"))
  S = sum(data$status == "A")
  mean.t = mean(data$t[data$status %in% c("A", "D")])
  (log(N) - log(S))/mean.t
  
  # Alternative calculation
  # (should be very similar).
  mortality_rate_Kubo(data)
  
  # Using extremely high mortality rates (>1)
  data2 <- data
  data2$t <- data2$t / 100
  
  N = sum(data2$status %in% c("A", "D"))
  S = sum(data2$status == "A")
  mean.t = mean(data2$t[data2$status %in% c("A", "D")])
  (log(N) - log(S))/mean.t
  
  mortality_rate_Kubo(data2)
}

tt_test example gives an error

The example in the help file of tt_test gives an error.

(NOTE: I don't think I'll use that function, but I just wanted to give a heads up about it here)

library(fgeo.tool)
assert_is_installed("fgeo.x")

# Example data
tree <- fgeo.x::tree6_3species
Error: 'tree6_3species' is not an exported object from 'namespace:fgeo.x'
elevation <- fgeo.x::elevation
> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] fgeo.tool_1.2.2           fgeo.analyze_1.1.4        fgeo.abundance_0.0.0.9006 fgeo_0.0.0.9002          
 [5] rlang_0.3.1               fgeo.base_0.0.0.9001      stringr_1.3.1             MuMIn_1.42.1             
 [9] lme4_1.1-21               Matrix_1.2-15             sm_2.2-5.6                jpeg_0.1-8               
[13] raster_2.8-4              sp_1.3-1                  SDMTools_1.1-221         

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.0                 pillar_1.3.1               compiler_3.5.1             nloptr_1.2.1              
 [5] fgeo.ctfs_0.0.0.9003       R.methodsS3_1.7.1          R.utils_2.7.0              tools_3.5.1               
 [9] drat_0.1.5                 boot_1.3-20                tibble_2.0.1               nlme_3.1-137              
[13] lattice_0.20-35            pkgconfig_2.0.2            fgeo.demography_0.0.0.9103 cli_1.0.1                 
[17] rstudioapi_0.10            yaml_2.2.0                 rgdal_1.3-6                parallel_3.5.1            
[21] dplyr_0.8.0.1              stats4_3.5.1               grid_3.5.1                 tidyselect_0.2.5          
[25] glue_1.3.0                 R6_2.3.0                   tcltk_3.5.1                minqa_1.2.4               
[29] purrr_0.3.2                magrittr_1.5               codetools_0.2-15           MASS_7.3-51.1             
[33] splines_3.5.1              assertthat_0.2.0           fgeo.x_1.1.2               stringi_1.2.4             
[37] crayon_1.3.4               R.oo_1.22.0

Acknowledgement

  • ThomasSmithIRE fixed typos.
  • ToniaSeenauth helped me notice inconsistent use of title case.

Every quadrat in the dataset must have at lease one tree

@srusso2 and @DanielZuleta,

Small tree tables used to err because

  Torspstcnthab / Tortotstcnthab = NaN

(edited, thanks @srusso2 for noticing the mistake via #40 (comment))

Now they no longer err because I'm now converting NaN to 0 with a warning. Is this OK?

(I know that users "should only try to determine the habitat association for sufficiently abundant species" but we lack a formal definition of sufficiently abundant that I can use to programatically reject bad inputs.)

The warning is the one right below, and the code that implements this warning is here and here (see details in the example below):

#> Warning:   Using zero (`0`) where the relative stem density of focal species
#>   per habitat of the focal torus-based map can't be calculated
#>   because `Tortotstcnthab` and `Torspstcnthab` are zero:
#>   * `Tortotstcnthab` determines total number of stems per habitat of the
#>     focal torus-based map.
#>   * `Torspstcnthab` determines tot. no. stems for focal sp. per habitat of
#>     the focal torus-based map.

With large tree table throws everything is OK

suppressPackageStartupMessages(library(dplyr))
suppressPackageStartupMessages(library(fgeo))

tree <- fgeo.x::tree6_3species
autoplot(sp(tree))

tt_test(tree, fgeo.x::habitat)
#> Using `plotdim = c(320, 500)`. To change this value see `?tt_test()`.
#> Using `gridsize = 20`. To change this value see `?tt_test()`.
#> [[1]]
#>        N.Hab.1 Gr.Hab.1 Ls.Hab.1 Eq.Hab.1 Rep.Agg.Neut.1 Obs.Quantile.1
#> CASARB      29     1242      356        2              0        0.77625
#>        N.Hab.2 Gr.Hab.2 Ls.Hab.2 Eq.Hab.2 Rep.Agg.Neut.2 Obs.Quantile.2
#> CASARB      20      390     1206        4              0        0.24375
#>        N.Hab.3 Gr.Hab.3 Ls.Hab.3 Eq.Hab.3 Rep.Agg.Neut.3 Obs.Quantile.3
#> CASARB      12      778      817        5              0        0.48625
#>        N.Hab.4 Gr.Hab.4 Ls.Hab.4 Eq.Hab.4 Rep.Agg.Neut.4 Obs.Quantile.4
#> CASARB       5      932      658       10              0         0.5825
#> attr(,"fixed_nan")
#> [1] FALSE
#> 
#> [[2]]
#>        N.Hab.1 Gr.Hab.1 Ls.Hab.1 Eq.Hab.1 Rep.Agg.Neut.1 Obs.Quantile.1
#> PREMON      91     1093      504        3              0       0.683125
#>        N.Hab.2 Gr.Hab.2 Ls.Hab.2 Eq.Hab.2 Rep.Agg.Neut.2 Obs.Quantile.2
#> PREMON      89     1254      344        2              0        0.78375
#>        N.Hab.3 Gr.Hab.3 Ls.Hab.3 Eq.Hab.3 Rep.Agg.Neut.3 Obs.Quantile.3
#> PREMON      40      305     1292        3              0       0.190625
#>        N.Hab.4 Gr.Hab.4 Ls.Hab.4 Eq.Hab.4 Rep.Agg.Neut.4 Obs.Quantile.4
#> PREMON      14      270     1322        8              0        0.16875
#> attr(,"fixed_nan")
#> [1] FALSE
#> 
#> [[3]]
#>        N.Hab.1 Gr.Hab.1 Ls.Hab.1 Eq.Hab.1 Rep.Agg.Neut.1 Obs.Quantile.1
#> SLOBER      18      273     1324        3              0       0.170625
#>        N.Hab.2 Gr.Hab.2 Ls.Hab.2 Eq.Hab.2 Rep.Agg.Neut.2 Obs.Quantile.2
#> SLOBER      24      810      788        2              0        0.50625
#>        N.Hab.3 Gr.Hab.3 Ls.Hab.3 Eq.Hab.3 Rep.Agg.Neut.3 Obs.Quantile.3
#> SLOBER      17     1155      440        5              0       0.721875
#>        N.Hab.4 Gr.Hab.4 Ls.Hab.4 Eq.Hab.4 Rep.Agg.Neut.4 Obs.Quantile.4
#> SLOBER       7     1292      303        5              0         0.8075
#> attr(,"fixed_nan")
#> [1] FALSE

With small tree table (throws warning)

# Used to err because `Tortotstcnthab / Torspstcnthab = NaN` 
smaller_tree <- sample_n(tree, 50)
autoplot(sp(smaller_tree))

# Now no longer errs because I'm now converting `NaN` to `0` with a warning. 
# Is this OK?
tt_test(smaller_tree, fgeo.x::habitat)
#> Using `plotdim = c(320, 500)`. To change this value see `?tt_test()`.
#> Using `gridsize = 20`. To change this value see `?tt_test()`.
#> Warning:   Using zero (`0`) where the relative stem density of focal species
#>   per habitat of the focal torus-based map can't be calculated
#>   because `Tortotstcnthab` and `Torspstcnthab` are zero:
#>   * `Tortotstcnthab` determines total number of stems per habitat of the
#>     focal torus-based map.
#>   * `Torspstcnthab` determines tot. no. stems for focal sp. per habitat of
#>     the focal torus-based map.
#> [[1]]
#>        N.Hab.1 Gr.Hab.1 Ls.Hab.1 Eq.Hab.1 Rep.Agg.Neut.1 Obs.Quantile.1
#> SLOBER       4     1021      544       35              0       0.638125
#>        N.Hab.2 Gr.Hab.2 Ls.Hab.2 Eq.Hab.2 Rep.Agg.Neut.2 Obs.Quantile.2
#> SLOBER       4     1120      408       72              0            0.7
#>        N.Hab.3 Gr.Hab.3 Ls.Hab.3 Eq.Hab.3 Rep.Agg.Neut.3 Obs.Quantile.3
#> SLOBER       0        0     1054      546             -1              0
#>        N.Hab.4 Gr.Hab.4 Ls.Hab.4 Eq.Hab.4 Rep.Agg.Neut.4 Obs.Quantile.4
#> SLOBER       0        0      676      924             -1              0
#> attr(,"fixed_nan")
#> [1] TRUE
#> 
#> [[2]]
#>        N.Hab.1 Gr.Hab.1 Ls.Hab.1 Eq.Hab.1 Rep.Agg.Neut.1 Obs.Quantile.1
#> PREMON       9      388     1179       33              0         0.2425
#>        N.Hab.2 Gr.Hab.2 Ls.Hab.2 Eq.Hab.2 Rep.Agg.Neut.2 Obs.Quantile.2
#> PREMON      10      487     1072       41              0       0.304375
#>        N.Hab.3 Gr.Hab.3 Ls.Hab.3 Eq.Hab.3 Rep.Agg.Neut.3 Obs.Quantile.3
#> PREMON       6     1318      236       46              0        0.82375
#>        N.Hab.4 Gr.Hab.4 Ls.Hab.4 Eq.Hab.4 Rep.Agg.Neut.4 Obs.Quantile.4
#> PREMON       4     1117        0      483              0       0.698125
#> attr(,"fixed_nan")
#> [1] TRUE
#> 
#> [[3]]
#>        N.Hab.1 Gr.Hab.1 Ls.Hab.1 Eq.Hab.1 Rep.Agg.Neut.1 Obs.Quantile.1
#> CASARB       3     1154      394       52              0        0.72125
#>        N.Hab.2 Gr.Hab.2 Ls.Hab.2 Eq.Hab.2 Rep.Agg.Neut.2 Obs.Quantile.2
#> CASARB       2      654      878       68              0        0.40875
#>        N.Hab.3 Gr.Hab.3 Ls.Hab.3 Eq.Hab.3 Rep.Agg.Neut.3 Obs.Quantile.3
#> CASARB       1      861      664       75              0       0.538125
#>        N.Hab.4 Gr.Hab.4 Ls.Hab.4 Eq.Hab.4 Rep.Agg.Neut.4 Obs.Quantile.4
#> CASARB       0        0      683      917             -1              0
#> attr(,"fixed_nan")
#> [1] TRUE

Created on 2018-12-31 by the reprex package (v0.2.1)

Release fgeo.analyze 1.1.14

Prepare for release:

Submit to CRAN:

  • usethis::use_version('patch')
  • devtools::submit_cran()
  • Approve email

Wait for CRAN...

  • Accepted 🎉
  • usethis::use_github_release()
  • usethis::use_dev_version()

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