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Aqpdf #142

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merged 58 commits into from
Jun 19, 2020
Merged

Aqpdf #142

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c17e801
implement data.table and tibble support for data.frame slots of SoilP…
brownag May 30, 2020
3489e82
initial thinkin on implementation of group_by #118
brownag Jun 1, 2020
26af7e8
add intro
brownag Jun 1, 2020
6e5f0c7
untrack html and move
brownag Jun 1, 2020
d1117cc
basic testing panel for data.table/tbl_df/data.frame #94
brownag Jun 2, 2020
5987bdb
add expect_warning for new sp warnings
brownag Jun 2, 2020
60aac51
fix show method
brownag Jun 2, 2020
8f556f5
sp warnings are not generated by the R 3.6.3 windows binaries current…
brownag Jun 2, 2020
a383246
update comments on data.table to reflect the fact that it WORKS :)
brownag Jun 2, 2020
d77a286
revising some faulty logic for data with arbitrary sorting of numeric…
brownag Jun 2, 2020
546704e
aqp organizing
brownag Jun 3, 2020
43c594b
use .spc_in_sync as trial integrity method
brownag Jun 3, 2020
7c2e34c
incomplete work on SoilProfileCollection structure
brownag Jun 3, 2020
aeb82e1
SPC integrity -- further refinement; change metadata slot
brownag Jun 4, 2020
032a160
rebuild SPCs for list metadata
brownag Jun 4, 2020
b607a32
update tests
brownag Jun 4, 2020
64b4e3e
cleanup & fix show method -- I messed some stuff up -- and adjusting …
brownag Jun 4, 2020
e20a403
switch to horizon depth midpoint [provisionally] for get.increase.dep…
brownag Jun 4, 2020
506c83a
implement j-index wrapper function to facilitate use of multiple colu…
brownag Jun 4, 2020
6878425
fix min(SPC)/max(SPC) and add tests
brownag Jun 4, 2020
f3f0448
update rebuildSPC, show method, .as.data.frame.aqp
brownag Jun 4, 2020
b91d405
update test script
brownag Jun 4, 2020
84d3855
stringsAsFactors = FALSE & relax internal validity checks (need to pr…
brownag Jun 8, 2020
7b431ef
turn the [[<- method back on
brownag Jun 9, 2020
fb21599
fix typo
brownag Jun 11, 2020
f504146
add reorderHorizons method
brownag Jun 13, 2020
d3993d1
hm. no more spatial warnings?
brownag Jun 13, 2020
f081123
use ids argument for tests
brownag Jun 14, 2020
76e0276
exploring dependency graphs
brownag Jun 14, 2020
291438e
make unique a proper S4 method
brownag Jun 14, 2020
716843b
new classification of aqp functions using regex -- sorting stuff out …
brownag Jun 14, 2020
b5c1271
I am not sure that this is useful, or how it plays in/will work with …
brownag Jun 14, 2020
9e2d9fc
add basic tests of integrity and reorderHorizons
brownag Jun 14, 2020
d31b22c
roxygen for coercion-methods, integrity-methods, iterator-methods, SP…
brownag Jun 14, 2020
57c030f
Merge branch 'aqpdf' of http://github.com/ncss-tech/aqp into aqpdf
brownag Jun 15, 2020
2b9c7ce
usage of "^get" in function names of various packages
brownag Jun 15, 2020
94560ea
rename bracket to operators
brownag Jun 16, 2020
5349854
Merge branch 'master' into aqpdf
brownag Jun 17, 2020
d8dd634
update Rda files
brownag Jun 17, 2020
61174fd
this should be an error -- just like estimateSoilDepth
brownag Jun 17, 2020
b5ac4ca
remove .pdf file leftover from testing automatically
brownag Jun 17, 2020
a86339b
Merge branch 'aqpdf' of http://github.com/ncss-tech/aqp into aqpdf
brownag Jun 17, 2020
e8deeec
I still don't have the s4 methods figured out.
brownag Jun 17, 2020
5889db3
delete Rplots
brownag Jun 17, 2020
26a20b3
Revert "I am not sure that this is useful, or how it plays in/will wo…
brownag Jun 17, 2020
b696c15
incomplete work getting s4 docs sorted out
brownag Jun 17, 2020
35b2724
almost everything needed to pass R CMD check #139
brownag Jun 19, 2020
d03a546
rebuild RDA
brownag Jun 19, 2020
2ba36e5
deprecate various manpages -- store in misc for now -- still probably…
brownag Jun 19, 2020
3086ea8
update docs
brownag Jun 19, 2020
33ca321
Merge branch 'master' into aqpdf
brownag Jun 19, 2020
c9fb92d
couple more updates to docs
brownag Jun 19, 2020
65bac8f
numeric IDs are not character sorted now, so different number of hori…
brownag Jun 19, 2020
7070696
issue with profile_compare example; please see comment
brownag Jun 19, 2020
27308bb
Merge branch 'master' into aqpdf
brownag Jun 19, 2020
43b6f12
Merge branch 'master' into aqpdf
brownag Jun 19, 2020
ce41cab
fix obtuse logic as requested by @dylanbeaudette
brownag Jun 19, 2020
7c3fe66
reslove conflict in pc methods #140
brownag Jun 19, 2020
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4 changes: 2 additions & 2 deletions DESCRIPTION
Original file line number Diff line number Diff line change
@@ -1,12 +1,12 @@
Package: aqp
Version: 1.20
Version: 1.21
Date: 2020-06-18
Title: Algorithms for Quantitative Pedology
Authors@R: c(person(given="Dylan", family="Beaudette", role = c("aut", "cre"), email = "dylan.beaudette@usda.gov"), person(given="Pierre", family="Roudier", email="roudierp@landcareresearch.co.nz", role = c("aut", "ctb")), person(given="Andrew", family="Brown", email="andrew.g.brown@usda.gov", role = c("aut", "ctb")))
Author: Dylan Beaudette [aut, cre], Pierre Roudier [aut, ctb], Andrew Brown [aut, ctb]
Maintainer: Dylan Beaudette <dylan.beaudette@usda.gov>
Depends: R (>= 3.5.0)
Imports: grDevices, graphics, stats, utils, methods, plyr, reshape, grid, lattice, cluster, sp, stringr, scales, plotrix, RColorBrewer, MASS, digest, rlang
Imports: grDevices, graphics, stats, utils, methods, plyr, reshape, grid, lattice, cluster, sp, stringr, scales, plotrix, RColorBrewer, MASS, digest, rlang, data.table, tibble
Suggests: colorspace, maptools, foreign, ape, soilDB, latticeExtra, maps, compositions, sharpshootR, markovchain, xtable,
testthat, Gmedian, farver, Hmisc
Description: The Algorithms for Quantitative Pedology (AQP) project was started in 2009 to organize a loosely-related set of concepts and source code on the topic of soil profile visualization, aggregation, and classification into this package (aqp). Over the past 8 years, the project has grown into a suite of related R packages that enhance and simplify the quantitative analysis of soil profile data. Central to the AQP project is a new vocabulary of specialized functions and data structures that can accommodate the inherent complexity of soil profile information; freeing the scientist to focus on ideas rather than boilerplate data processing tasks <doi:10.1016/j.cageo.2012.10.020>. These functions and data structures have been extensively tested and documented, applied to projects involving hundreds of thousands of soil profiles, and deeply integrated into widely used tools such as SoilWeb <https://casoilresource.lawr.ucdavis.edu/soilweb-apps/>. Components of the AQP project (aqp, soilDB, sharpshootR, soilReports packages) serve an important role in routine data analysis within the USDA-NRCS Soil Science Division. The AQP suite of R packages offer a convenient platform for bridging the gap between pedometric theory and practice.
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5 changes: 5 additions & 0 deletions NAMESPACE
Original file line number Diff line number Diff line change
Expand Up @@ -126,6 +126,11 @@ importFrom(rlang,
enquos,
enquo)

importFrom(data.table,
as.data.table)

importFrom(tibble,
as_tibble)

exportClasses(SoilProfileCollection)

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