soiltestcorr 2.2.0
Updates of the new version:
- Bootstrapping:
- New bootstrapping functions for all models to better approximate
distributions of CSTVs and parameters or derived quantities of interest.
Functions include: (i)
boot_cn_1965()
, (ii)
boot_cn_1971()
, (iii) boot_mod_alcc()
, (iv)
boot_linear_plateau()
, (v)
boot_quadratic_plateau()
, and (vi)
boot_mitscherlich()
.
- P-value for non-linear models:
- Including
p-value
estimation for non-linear models
using an F-test approach comparing the non-linear model vs. a null-model
(intercept-only).
cate_nelson_1965()
and
cate_nelson_1971()
:
- tidy = TRUE as default
- Including AIC, BIC, and RMSE of anova.model results
- Add flexibility to STV scales
boot...()
output including quadrants count
mitscherlich()
updates:
- Adding RMSE, and BIC outputs
- default type = 1
- target default now 95 and should not be NULL (prevent CSTV =
Inf)
- tidy = TRUE default (output is tibble)
- alternative names for type: “free” to “no restriction”, “100” to
“asymptote 100”, and “fixed” to “asymptote 100 from 0”.
- Do not round in results table (rounding throws off bootstrap
distributions), round only in display equations and plot
- add stop if target = NULL
- add warning if target > asymptote
- make results into tidy tibble
- use return() explicitly to return bootstrap data frame
- in keeping with ggplot2 updates, line
sizes
are now
line linewidth
- add scale_x_continuous to attempt auto rescaling
- corrected description of b parameter (as -x_intercept)
- add y_intercept to output table (for comparing to y_intercept of LP
and QP)
- corrected XY order of STV and RY in boot_mitscherlich
- added set.seed to bootstrapping section of vignette
- added na.rm = TRUE on quantile calc
linear_plateau()
and quadratic_plateau()
updates:
- Adding RMSE, and BIC outputs
- default to tidy = TRUE
- join point is now referred to as jp throughout the internal code -
equation now shows JP value instead of text “CSTV”
- simplified code repetition for readibility concerning the
coef(lp_model)[[3]] by saving join point to
jp
variable
instead
- return tibble instead of dataframe (dplyr has tibble and as_tibble
so no new dependencies)
- if target = NULL, defaults to join point (promote the use of join
point)
- section CSTV for plateau or for target mistakenly checked if target
is greater than CSTV, but it should be greater than plateau. Now it
reports that targets greater than plateau will result in CSTV at join
point.
- STVt should be reported right after target in the table
- Use lowerCL and upperCL instead of LL_cstv and UL_cstv
- replace “Wald Conf. Interval” with “Wald, 95%”
- Always calculate and report Wald CI for CSTV (join point parameter)
now that we have a STVt to find a soil value at the target. The STVt
doesn’t represent CSTV
- removed code for creating “predicted” data.frame as the qp_line is
being used instead
- cleaned up plotting code (line wraps, vlines with c(lower, upper)
instead of two vlines)
- move LP line up so it is underneath vlines
- change size to linewidth arg in the line geoms
- removed extra irrelevant columns in bootstrap output like Wald CI
and equation for neater tibble
- simplified vignette: changing group_map to group_modify to preserve
tibble over lists
mod_alcc()
update including:
- including Root Mean Square Error (RMSE_alcc) of the ALCC curve with
respect to observed RY values as a potential indicator of model’s
quality.
- including the estimation of Akaike Information Criteria (AIC_sma),
and Bayesian Information Criteria (BIC_sma) for the “underlying”
bivariate SMA models.
- using “tibble” instead of “dataframe”.
- implementing tidy=TRUE as default.
- using linewidth instead of “size” for geom_line().
- reordering variables of the output (e.g. goodness of fit indicators
first)
- Add AIC for ALCC model to predict RY in terms of the original units
following and approximation of the logLik of the ALCC curve
(Dr. Fernando Miguez contribution).
- add scale_x_continuous to attempt auto rescaling on ggplot
objects
- New dependencies:
nlraa
is now included as a dependency to facilitate
self-start of non-linear models.
smatr
is a new dependency (to get AIC and BIC of SMA
models).
- Documentation:
- Updated documentation and vignettes including bootstrapping
functions for each of the models.
- New Bootstrapping vignette.
- Add a
CITATION
file into “inst/” folder following
bibentry
format.
- Code of Conduct and Contribution:
- Including code of conduct and contribution guidelines.
- Plots:
- Add more flexibility to STV scales for default plots.
soiltestcorr 2.1.2
General maintenance update. - Documentation updating authors’
contributions, and mention main research projects supporting the
development of the package (FRST and SIIL). - Fixing minor bugs on the
CSTV estimation (and plot) when using the “target” argument within
linear_plateau() and quadratic_plateau() functions. When “target” is
activated for these functions, output is STVt (stv-target) instead of
CSTV (which corresponds to the plateau level) - Minor typos on the
vignettes.
Previous versions
soiltestcorr 2.1.1
- First CRAN release, accepted on May 11th, 2022.
soiltestcorr 2.1.1
Maintenance update fixing minor details in documentation after
feedback from CRAN submission of v2.1.0. Changes include: i) adding
references in DESCRIPTION, functions, and vignettes; and ii) removing
brackets from examples (replacing ‘dontrun’ by ‘donttest’).
soiltestcorr 2.1.0
Maintenance update fixing minor typos on vignettes (linear_plateau(),
quadratic_plateau(), mitscherlich()), fixed bugs on examples within
functions cate_nelson_1965(), cate_nelson_1971(), quadratic_plateau(),
and mitscherlich().
Soiltestcorr v2.0.2 is maintenance update fixing minor bugs related
to checks before CRAN submission (e.g. spelling check, links, data
source URLs, DOIs, etc.)
Previous versions
Major: soiltestcorr v2.0.1 fixes the versioning of the package (this
version was previously named as v1.0.7); it introduces the Mitscherlich
response model, and it introduces the the “target” argument into
linear_plateau() and quadratic_plateau() functions, allowing to estimate
critical soil test values for relative yields different than the plateau
level.
Minor: added ‘Date’ field on DESCRIPTION file, removed unused
Imports-packages from Description file, fixed DOI source of
‘data_test.Rd’ and ‘freitas.Rd’.
Patch: fixes some minor typos in the comments within the functions.
Apr, 28, 2022. The soiltestcorr v1.0.6 uses consistent arguments
across all functions using lowercase (e.g. stv, ry) and includes warning
and stop messages to improve users experience.
Apr, 18, 2022. The soiltestcorr v1.0.5 includes the option for
fitting self-starting quadratic-plateau models with the
quadratic_plateau() function.
Apr, 14, 2022. The soiltestcorr v1.0.4 updated its name
(previously soiltestR) in order to follow good coding practices using
all lowercase letters. For the same reason, the old modALCC() function
was renamed as mod_alcc().
The soiltestcorr v1.0.3 includes the option for fitting
linear-plateau models, includes the ‘plot’ arg (Boolean) in all
functions, and the ‘tidy’ arg for choosing outputs as type list (tidy =
FALSE) or data.frame (tidy = TRUE).
The soiltestcorr v1.0.2 includes the option for running the
quadrants approach described by Cate & Nelson (1971).
The soiltestcorr v1.0.1 includes the option for running the
quadrants approach described by Cate & Nelson (1965).
The soiltestcorr v1.0.0 includes the option for running the
modified arcsine-log calibration curve described Correndo et
al. (2017).