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pval_correct()
functionplot_cols
correctly renamed cols
in lrr_plot()
functionraster
in Imports with terra
because of imminent package retirementif()
conditions comparing class()
to string with inherits()
in functionstools
is no longer Importsutils
is now Suggests because “zzz.R” calls the
packageDescription()
functionncdfFlow
, flowWorkspaceData
are no longer
Suggests (for generating random data set randCyto
) because
“Package suggested but not available for checking” in the some CRAN
environmentsspatstat.core
and
spatstat.linnet
packages based on feedback from the
Spatstat Team (Adrian Baddeley and Ege Rubak). All random generators in
spatstat.core
were moved to a new package
spatstat.random
spatstat.geom
, spatstat.core
,
spatstat.linnet
, and spatstat (>=2.0-0)
are
no longer Dependsspatstat.geom
is now Importsdplyr
, ncdfFlow
,
flowWorkspaceData
, and usethis
now Suggests
(for generating random data set randCyto
)rlang
is in Depends.gating()
now includes a diagnostic message
saved as a character string for reference in a slot called
note
rlang::last_error()$out$note
after the unsuccessful run of
gating()
@importFrom fields image.plot
in
‘package.R’spatstat
package to new subsetted packages
based on feedback from the Spatstat Team (Adrian Baddeley and Ege
Rubak). Now spatstat.geom
, spatstat.core
,
spatstat.linnet
, and spatstat (>= 2.0-0)
are in Dependsvars
in dat
within the
gating()
functionspatstat
package to new subsetted packages
based on feedback from the Spatstat Team (Adrian Baddeley and Ege
Rubak). spatstat.geom
package replaces
spatstat
package in Importsbandw
to be added to gating()
,
lotrrs()
, and rrs()
functions to allow users
to specify bandwidth for the kernel density estimationpval_correct()
function from the correlog()
function in the pgrimess
package to the
modified.ttest()
function in the SpatialPack
packagelifecycle
package to document deprecated
arguments doplot
and verbose
in
lotrrs()
, rrs()
, and gating()
functionsgating()
function, creates a categorized
im
based on critical p-value, assigns that value to every
point in a ppp
object, and subsets points by categorymaptools
and sp
packages from
Importssave_gate
, name_gate
, and
path_gate
in lotrrs()
, rrs()
, and
gating()
to save plots as PNG files as outputdoplot
argument as plot_gate
for
consistency with new plotting argumentsverbose
argument in gating()
,
rrs()
, and lotrrs()
try()
error catches in rrs()
and
lotrrs()
for c1n
and c2n
argumentsright
argument in cut()
in
pval_plot()
to “TRUE” (the default for cut)make.names()
check for vars
and
colnames(dat)
in gating()
lotrrs()
, rrs()
,
and gating()
about the levels of condition(s)lotrrs()
that was mislabeling numerator
and denominator levels of second conditionc1n
and c2n
in
lotrrs()
, rrs()
, and gating()
to
specify the numerator levelncdFlow
, flowWorkspaceData
, and
knitr
packages from SuggestsrandCyto
and all
documentationrandCyto
dataThese binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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