sp_frame() function to create
sp_frame objects for use with plot() and
summary() for sampling frames and analysis data.
sp_frame objects have class sp_frame.sp_unframe() function to transform
sp_frame objects back into their original object type.grts() and irs() are
now called sp_design objects instead of
spdesign objects.
sp_design objects have class
sp_design.summary() now works with sp_frame objects
and sp_design objects.
sp_summary() yields equivalent summaries and is
currently maintained for backwards compatibility (i.e.,
sp_summary() has not changed).summary functions now also summarize sf
object geometries if the name of the geometry list-column is provided in
the summary formula.plot() now works with sp_frame objects and
sp_design objects.
sp_plot() yields equivalent plots and is currently
maintained for backwards compatibility (i.e., sp_plot() has
not changed).plot() now works with sp_CDF objects that
are output from the CDF element of
cont_analysis().
cdf_plot() yields equivalent plots and is currently
maintained for backwards compatibility (i.e., cdf_plot()
has not changed).summary() or sp_summary() so that they are
clearer and easier to read.sp_design objects. Now, a
summary of site counts by site type (Legacy,
Base, Over Near) crossed by
strata or unequal probability levels or both is provided.stratum_var, caty_var, and
aux_var elements to the design list in
sp_design objects.legacy_stratum_var, legacy_caty_var,
and legacy_aux_var elements to the design list in
sp_design objects when legacy sites are used."total" option to test in
change_analysis().Indicator column when using change_analysis()
with test = median.change_analysis sensititve to the
ordering of the levels of variables in var_cat if those
variables were factors.sp_summary() that incorrectly ordered
the siteuse variable.sp_summary() that failed to summarize
data frames that did not have an sf_column attribute.*_analysis() functions when
popsize is a list intended for use with
survey::calibrate().*analysis() functions that returned an
error while performing percentile estimation when there was no
variability in at least one variable in vars for at least
one level of one variable in subpops.grts() that caused an error for some
combinations of n_base and n_over.change_analysis() that returned an error
when at least one varible in vars_cat has only one unique
value.projcrs_check argument to grts()
and irs(), which checks whether projected coordinates are
required (projcrs_check = TRUE) or not
(projcrs_check = FALSE).n_near) in grts() or irs() are
now also generated for each observation in
legacy_sites.attrisk_analysis(),
diffrisk_analysis(), and relrisk_analysis()
that sometimes caused names in response_levels to not be
found.grts() and irs() that
returned an error when the name of the geometry column in
sframe and legacy_sites differed. Now when
this occurs, the geometry column in
legacy_sites is renamed to have the same name as the
geometry column in sframe.grts() and irs() that
prevented legacy_stratum_var, legacy_caty_var
and legacy_aux_var from performing properly.grts() and irs() that
returned an error when at least one stratum in legacy_sites
had zero observations.grts() and irs() that
prevented warnprnt() from performing properly.grts() and irs()
that indicated when m or z values in sframe or
legacy_sites were dropped. Now, the dropping of m or z
values is explained in the documentation.grts() and irs() that
indicated when row names were set if legacy_sites was a
tibble. Now, legacy_sites is coerced to a base R data frame
(i.e., not a tibble) before setting row names.grts() and irs() when
legacy_stratum_var (and legacy_caty_var and
legacy_aux_var) are NULL but the name of
stratum_var in sframe is not contained in
legacy_sites.grts() and irs() that
checks whether sframe and legacy_sites have
the same crs.pt_density in
grts() and irs() to indicate that
pt_density must be a positive integer.sp_summary() that returned an error when
formula = ~ . and the geometry column was not named
"geometry". Now, sp_summary() works with
formula = ~ . regardless of the name of the geometry
column.grts() and irs() that
affected minimum distance performance when legacy sites were used.grts() and irs() to
specify reverse hierarchically ordered replacement sites with unequal
selection probabilities by requiring n_over be an integer
and removing caty_n_over.grts() and irs()
called sep, which acts as a separator between the character
string created by DesignID and SiteBegin in
the sites output.pt_density argument in grts() and
irs() now reflects the site multiplier (instead of the
per-unit density of sframe) that generates the
approximation to sframe when sampling from
LINESTRING, MULTILINESTRING,
POLYGON, or MULTIPOLYGON sf objects.grts() and irs() that
prevented use when the geometry column of sframe was not
named "geometry".grts() and irs() that
sometimes caused unequal selection probabilities to be misrepresented
when reverse hierarchically ordered replacement sites were desired.grts() and irs() that
sometimes prevented the dropping of an sf object’s z or m
dimension.grts() and irs() that
sometimes incorrectly copied stratum values as
caty values in the sites output.grts() and irs() that
prevented sampling from LINESTRING,
MULTILINESTRING, POLYGON, or
MULTIPOLYGON sf objects when pt_density was
excessively large.Total option to the statistics
argument in cont_analysis().localmean_weight(), localmean_var(),
and localmean_cov() functions to compute the local
neighborhood variance estimator outside of the *_analysis()
functions.fix_bbox argument in sp_plot().grts() and irs()
that stops the function when geographic coordinates are used.grts() and irs()
that stops the function when too many expected samples are specified for
at least one level of an unequal probability variable.caty_n_over argument to grts() and
irs() that makes it easier to specify reverse
hierarchically ordered replacement sites for unequal probability
sampling designs.n_over and
n_near arguments in grts() and
irs() (list arguments were already supported).siteID in
attrisk_analysis(), cat_analysis(),
cont_analysis(), diffrisk_analysis(), and
relrisk_analysis() that assumes each row in
dframe represents a unique site.irs() that made the algorithm sensitive
to the ordering of sframe.cont_analysis() that incorrectly copied estimate
values.grts() and irs() that
prevented sampling from sframe when the geometry type was
LINESTRING, MULTILINESTRING,
POLYGON, or MULTIPOLYGON and the number of
desired samples exceeded the number of rows.Syntax for the grts() (Generalized Random
Tessellation Stratified) and irs() (Independent Random
Sampling) functions has been significantly simplified. These functions
now require the sampling frame is an sf object.
The grts() and irs() functions now
accommodate legacy (or historical) sites, a minimum distance between
sites, and two approaches for selecting replacement sites (reverse
hierarchical ordering and nearest neighbor).
Syntax for the analysis functions (*_analysis()) has
been significantly simplified.
Risk difference analysis is now available using the
diffrisk_analysis() function.
Trend analysis is now available using the
trend_analysis() function.
The sp_summary() function is now available to
summarize sampling frames, design sites, and analysis data.
The sp_plot() function is now available to visualize
sampling frames, design sites, and analysis data.
Fixed code so that sp design objects inherit CRS of input files and shapefiles written out also have inherited projection from input file. (#2)
Variable sframe$len was used in grts function and never defined. Now uses length_mdm that is calculated earlier. (#6)
sf and changes to crs described herelocalmean.weight function to correct when class
for matrix objects was causing an indicator variable to have length two
rather than length one, which caused an error in a while statement.Functions that create survey designs were modified to replace use
of shapefiles to provide the survey frame with use of simple features
sf objects to provide the survey frame. To accommodate this
change, argument src.frame for functions grts and
irs now will accept the choice sf.object to
indicate that an sf object will be used as the source of
the survey frame. In addition, a new argument named
sf.object was added to functions grts and
irs to allow input of an sf object as the
survey frame. Also, note that arguments id, maxtry, and prjfilename for
functions grts and irs have been depricated
since they are no longer needed. Finally, the three rda files in the
data directory that contain survey frame objects (NE_lakes,
Luck_Ash_streams, and UT_ecoregions) were
revised to contain sf objects rather than objects belonging
to classes that are defined in the sp package.
The package no longer contains any functions written in C. The C
functions were either no longer required due to the transition to use of
sf objects to contain the survey frame or were replaced
with functions written in R. The new R functions are:
cellWeight, constructAddr,
insideAreaGridCell, insideLinearGridCell,
make_grid, numLevels,
pickFiniteSamplePoints, pickGridCells,
pickSamplePoints, ranho, and
selectFeatureID.
numLevels that determines
the number of hierarchical levels for a generalized random-tessellation
stratified (GRTS) survey design now includes code to ensure that the
maximum number of levels (which is currently 11) is not bypassed when
creating a survey design.input.check to check for missing
values among the x-coordinates and y-coordinates for location.Necessary changes were enacted so that the package can be built within RStudio, e.g., roxygen comments were added to R source files.
Created functions that create panel designs and that compute and
plot power for panel designs given a linear trend. Function
revisit_dsgn creates a panel revisit design. Function
revisit_bibd creates a balanced incomplete block panel
revisit design. Function revisit_rand creates a revisit
design with random assignment to panels and time periods. Function
panel_summary summarizes characteristics of a revisit panel
design. Function power.dsgn calculates power for multiple
panel designs. Function cov.panel.dsgn creates the
covariance matrix for a panel design. Function
plot.powerpaneldesign plots power curves for panel
designs.
readDbfFile to avoid PROTECT
errors.Modified C functions insideAreaGridCell,
insideLinearGridCell, linSample,
linSampleIRS, numLevels,
pickAreaSamplePoints, pickLinearSamplePoints,
and pointInPolygonFile to avoid PROTECT errors.
Modified function change.analysis to assign the
support_2 variable from the design_2 data frame rather than from the
design_1 data frame.
Modified function change.analysis to use a revised
procedure for ensuring that each repeated visit site is present in both
surveys for subpopulation estimation.
Modified C functions writeShapeFilePoint and
writeShapeFilePolygon to correct memory access
errors.
Modified C function readDbfFile to ensure that
missing values (NA) are handled correctly.
grts, grtsarea,
grtslin, grtspts, irs,
irsarea, irslin, read.dbf, and
read.shape to prevent the functions from being executed on
big-endian processors.order.h and replaced C
functions readBigEndian and readLittleEndian
with the version of those functions from spsurvey version
3.1.Created a vignette for change estimation.
Modified functions change.analysis and
change.est to include estimation for difference in median
values for change estimation using continuous variables.
Created a function named examine that examines
variables in a data frame by printing either a table or the results of a
call to the describe function in the Hmisc
package.
Modified function sp2shape to accommodate objects of
class SpatialDesign created by either the grts
or irs functions.
Added a C header file named order.h that determines
whether the CPU employs big-endian or little-endian byte order. Also,
modified C functions readBigEndian and
readLittleEndian to use constants created by the header
file to ensure that computer words are read in the correct byte
order.
Modified function input.check to ensure that use of
numeric variables for arguments stratum and
cluster are handled correctly when finite or continuous
population correction factors are utilized.
Modified function cdf.test to ensure upper bounds
that define classes for the CDFs are unique. Also, modified functions
cont.cdftest and cdf.test to reduce the
minimum number of upper bounds that define classes for the CDFs from
three to two.
Modified functions sp2shape and
read.dbf to ensure that missing values are handled without
error for character vectors.
Modified functions grts and irs to
ensure that a dataframe object is assigned to argument
att.frame when argument src.frame is assigned
value att.frame.
Modified function change.analysis to ensure that
each repeated visit site is present in both surveys for subpopulation
estimation.
Modified function read.sas to use “C:/Program
Files/SASHome/SASFoundation/9.4/sas.exe” as the default value for
argument sascmd.
malloc are of type unsigned integer.Created a class named SpatialDesign that contains
class SpatialPointsDataFrame, which is defined in package
sp. The class is used for the output objects created by
functions grts and irs. Objects of class
SpatialDesign include the survey design list as a slot
rather than as an attribute, which was used previously.
Created S3 and S4 methods for generic functions plot
and summary for objects of class
SpatialDesign.
Modified C functions to change the type declaration for variable
shpFileName from const char * to
char * restrict.
Modified C functions writeDbfFile,
writeShapeFilePoint, and writeShapeFilePolygon
to change the return type from void to SEXP NULL, i.e.,
R_NilValue.
Modified function input.check to remove missing
values from final adjusted weights prior to checking that all values are
positive.
Modified functions grtspts, grtslin,
and grtsarea to ensure that argument nlev
(number of hierarchical levels) for C function
constructAddr was stored as type integer.
cex.main argument to the
cont.cdfplot and cdf.plot functions.warnprnt to use correct variable
names in the output data frame so that partial matching warnings for the
names are not generated.Modified function change.analysis to allow analysis
of surveys with no repeat visit sites.
Modified function change.est to ensure that levels
for a categorical response variable are listed in the desired order
rather than sorted order.
Modified function localmean.weight to allow recovery
from an error in the singular value decomposition function
La.svd that is called by the generalized inverse function
ginv in the MASS package. Also, created a
support function named localmean.weight2.
grtspts and C function
numLevels to calculate the sampling grid random shift
values only once rather than each time the number of hierarchical levels
is incremented.Modified functions attrisk.analysis,
cat.analysis, change.analysis,
cont.analysis, and relrisk.analysis to replace
NA values with FALSE in the indicator variables for
subpopulations.
Modified function spbalance to include all grid
cells with nonzero extent for the frame when calculating the Pielou
evenness measure for a rectangular grid.
Modified function localmean.weight to ensure that
the initial set of weights are inversely proportional to
distance.
Modified functions cont.cdftest and
cdf.test to ensure that the number of classes into which
the CDFs will be divided (binned) is at least three.
Modified function dframe.check to ensure proper
handling of repeated site ID values in the sites data frame.
Created a vignette that presents deconvolution of a cumulative distribution function (CDF) generated by a GRTS survey design.
Created a function named spbalance that calculates
spatial balance metrics for a survey design.
Created functions named sbcframe and
sbcsamp that calculate spatial balance grid cell extent and
proportions for a sample frame and for a survey design,
respectively.
Modified function change.est to include calculation
of resource size change estimates for categorical variables.
Created a function named changevar.size to calculate
covariance or correlation estimates of the estimated change in class
resource size estimates between two probability surveys.
Modified function change.est to correct errors in
the output values for categorical variables from survey designs that
lack repeat visit sites.
Modified the following functions to assign consecutive numbers to
the row names for the output data frame(s):
attrisk.analysis, cat.analysis,
change.analysis, cont.analysis,
cont.cdftest, and relrisk.analysis.
Created a function named change.analysis that
conducts change analysis for a collection of response variables
(categorical and continuous) generated by two probability
surveys.
Created functions named change.est,
changevar.prop, and changevar.mean to
calculate estimates of change and its associated variance.
Created a vignette that presents cumulative distribution function (CDF) analysis of a GRTS survey design.
Added a function named ash1.wgt that computes the
average shifted histogram (ASH) for weighted data.
Modified function grtspts to correct an error that
occurs when argument src.frame equals
att.frame and the number of hierarchical levels equals
eleven.
Modified C functions printAddrList,
printColCharList, code{printDbf to replace
calls to the printf function with calls to the
Rprintf function.
Modified C function pickAreaSamplePoints to correct
an error that occurs when selecting sample points for PolygonZ and
PolygonM type shapefiles.
Created an .onAttach function that prints a message
when the spsurvey package is attached. Removed the
.onLoad function, which prior versions used to to print a
startup message.
In order to reduce package size, removed demonstration (demo) R scripts and the associated data directory.
Created vignettes that present analyses of GRTS survey designs for finite, linear, and areal resources.
Created a function named attrisk.analysis that
conducts attributable risk analysis for a collection of response
variables generated by a probability survey.
Created functions named attrisk.est and
attrisk.var to calculate estimates of attributable risk and
its associated variance.
Modified function relrisk.est to change the way the
relative risk estimate is calculated for a stratified sample.
Modified functions cat.analysis,
cont.analysis, cont.cdftest,
relrisk.analysis, category.est,
cdf.est, cdf.decon, total.est,
cdf.test, relrisk.est,
catvar.prop, catvar.size,
cdfvar.prop, cdfvar.total,
cdfvar.size.prop, cdfvar.size.total,
dcdfvar.prop, dcdfvar.total,
dcdfvar.size.prop, dcdfvar.size.total,
total.var, cdfvar.test, and
relrisk.var to allow variance estimates to be calculated
when a two stage sample has stage one sampling units that contain a
single stage two sampling unit. Variance for those stage one sampling
units is calculated using the mean of the variance estimates for stage
one sampling units that contain two or more stage two sampling
units.
Modified function grtslin to improve efficiency of
sample point selection. Created a C function named
insideLinearGridCell that, for each grid cell selected to
receive a sample point, returns the ID value for shapefile records
contained in the cell and the clipped length of the polyline segments
within the cell for each record. Created a C function named
pickLinearSamplePoints that selects sample points.
Modified function grtsarea to improve efficiency of
sample point selection. Created a C function named
insideAreaGridCell that, for each grid cell selected to
receive a sample point, returns the ID value for shapefile records
contained in the cell and the clipped area of the polygon within the
cell for each record. Created a C function named
pickAreaSamplePoints that selects sample points.
Modified function input.check to include
determination of whether a valid value was provided for argument
vartype.
Modified functions grts and irs so that
correct survey design weights are created for linear and areal designs
when the type of random selection is “continuous”.
Modified functions grtspts, grtslin,
and grtsarea to execute without error for a stratum sample
size of one.
Modified function dframe.check to terminate
execution when missing values are encountered in the logical variable of
the sites data frame.
Created vignettes that present examples of GRTS survey designs for finite, linear, and areal resources.
Created a function named geodalbers that projects
latitude and longitude (spheroid) models of the globe to Albers
projection in the plane.
Modified function dsgnsum to produce summary tables
for the actual set of design variables that are present rather than a
standard set of design variables.
Modified function dframe.check to terminate
execution when missing site ID values or repeated site ID values are
encountered in the sites, design,
subpop, data.cat, data.cont, or
data.rr data frames. Note that dframe.check is
called by functions cat.analysis,
cont.analysis, cont.cdftest, and
relrisk.analysis.
Modified function cont.cdftest to correct an error
caused by improper handling of an empty subpopulation.
Modified function relrisk.analysis to correct an
error resulting from inclusion of more than one response variable in the
response.var argument.
Eliminated use of argument unitsize (known sum of
size-weights) by package functions. Restricted argument
popsize to provide only the known size of the resource for
use in ratio adjustment of estimators. Created a new argument named
pcfsize to provide resource size for calculation of finite
and continuous population correction factors for single-stage
samples.
Modified functions cat.analysis,
cont.analysis, cont.cdftest, and
relrisk.analysis to add logical variables to their argument
lists that specify use of finite or continuous population correction
factors or use of size-weights in analysis routines.
Modified functions category.est,
cdf.decon, cdf.est, cdf.test,
relrisk.est and total.est to add logical
variables to their argument lists that specify use of finite or
continuous population correction factors or use of
size-weights.
Modified function irs to eliminate checking for
existence of x-coordinates and y-coordinates when the type of frame is
“finite” and the frame is included in the att.frame data
frame.
Modified C functions parseFields and
readDbfFile to ensure that blank values in the shapefile
attributes (dbf) file are converted to R missing values (NA).
Modified C function writeDbfFile to output blank
values for R missing values (NA) when creating the shapefile attributes
(dbf) file.
Modified functions grts, irs, and
sp2shape to ensure that an output shapefile attributes
(dbf) file containing character variables with missing values can be
read without error.
Created a function named cont.cdftest that tests for
differences between cumulative distribution functions (CDFs) for pairs
of subpopulations within a population Type for a collection
of response variables generated by a probability survey. Also, modified
function cdf.test so that it is consistent with functions
that are called by high-level functions cat.analysis and
cont.analysis.
Modified function grtspts so that, when source of
the frame equals “att.frame”, the current number of grid levels for
hierarchical randomization and the final number of grid levels is
printed to the console while the function is executing.
Created a function named relrisk.analysis that
conducts relative risk analysis for a collection of response variables
generated by a probability survey. Also, renamed function
relrisk to relrisk.est and modified the
function so that it is consistent with functions that are called by
high-level functions cat.analysis and
cont.analysis.
Modified function grtspts and C function
numLevels to terminate the algorithm for determining the
number of grid levels for hierarchical randomization when the maximum
value of total inclusion probability for the grid cells stops changing
as the number of levels increases.
Created functions named cdf.plot and
cont.cdfplot that create cumulative distribution function
(CDF) plots using the data frame named “CDF” contained in the output
object created by function cont.analysis. Function
cdf.plot creates a single CDF plot, and function
cont.cdfplot creates a set of CDF plots.
Created a function named read.sas that can read SAS
datasets or a SAS XPORT (transport) file.
Modified C functions intersect,
linSampleIRS, lintFcn, and
linSample to eliminate warning messages that were generated
during package creation.
Modified function grts so that argument
do.sample provides a value for each stratum.
Modified C functions getRecordShapeSizes,
readDbfFile, parsePoints,
parsePointsZ, parsePointsM,
parsePolygon, parsePolygonZ, and
parsePolygonM to generate error messages and terminate
execution when a shapefile containing a Null record is
encountered.
Modified functions irslin and irsarea
in addition to C function getRecordIDs to ensure that
sample points are selected in random order for linear and areal IRS
designs.
Modified function grts to ensure that, when the type
of random selection is “unequal”, an oversample is apportioned correctly
whenever the category sample sizes are proportional to the oversample
size.
For C functions that read shapefiles from the current directory,
replaced calls to _findfirst and _findnext
with code using calls to readdir. These changes were
implemented to facilitate portability of the package.
Created a C function named matchFiles that
determines whether file names in the current directory have a desired
file extension. This change was implemented to facilitate portability of
the package.
Modified functions grts and irs to
accommodate use of a factor for the ID variable in the attributes data
frame.
Modified functions grts and irs to
ensure that sample weights are correctly adjusted when an oversample is
present and the type of random selection is “Continuous”.
getRecordShapeSizes and
lintFcn to accommodate Polyline shapefiles that have
multiple parts.Modified functions dsgnsum and sp2shape
to accommodate the change in representation from
AttributeList to data.frame for the data slot
of sp package objects belonging to class
SpatialPointsDataFrame.
Modified functions grts and irs to
print a warning message when the type of frame equals “finite” and a
stratum name in the design list matches only a single value in the
stratum column of the attributes data frame. For this case, function
grtspts or irspts is not called since the
sample will be composed of a single point.
Modified functions grts, grtspts,
grtslin, and grtsarea to change the maximum
value allowed for arguments startlev (the initial number of hierarchical
levels to use for the GRTS grid) and maxlev (the maximum number of
hierarchical levels to use for the GRTS grid) from 12 to 11.
Added an example polylines dataset to the data directory.
Modified functions grts and irs to
allow use of an sp package object as the source of the frame. An
argument named sp.object was added to the argument list for
grts and irs.
Modified functions grts, grtspts,
grtslin, grtsarea, irs,
irspts, irslin, and irsarea to
remove use of argument xy.frame as an option for source of
the frame. Then modified functions grts,
grtspts, irs, and irspts to allow
incorporation of frame coordinates into the attributes data frame when
the type of frame equals “finite”. Also, removed argument
elmsize from functions grts and
irs since the argument no longer was required.
Modified functions grts and irs to
print a warning message when the type of frame equals “finite” and a
stratum name in the design list matches only a single value in the
stratum column of the attributes data frame. For this case, function
grtspts or irspts is not called since the
sample will be composed of a single point.
Modified functions grts and irs to
ensure that the ID values for elements of the frame provided in
att.frame are unique.
Modified functions grts and irs to
ensure that valid values are provided for the panel and
caty.n arguments in the design list.
Added an example polygons dataset to the data directory.
Incorporated the CHANGES, README, and UserGuide files into the help page.
sp2shape and a C function
named writeShapeFilePolygon that convert objects created by
package sp to ESRI shapefiles. Also, renamed the C function
writeShapeFile to writeShapeFilePoint.irsarea and created a C function
named getRecordIDs to ensure that an IRS sample is selected
when argument type.frame is set to “area” in function
irs.Modified functions grts and irs to
ensure that the levels of mdcaty (the variable in the
attributes data frame that specifies the unequal probability category
for each element in the frame) are equivalent to the names in
caty.n (the vector of sample sizes for each category in
mdcaty, which is required for each element of the design
list for which the selection type is “Unequal”).
Modified functions grts and irs to
ensure that the columns of xy.frame are named “x” and “y”
when xy.frame is provided and type.frame
equals “finite”.
Modified functions grts and irs so that
the sample weights are correctly adjusted when an oversample is
requested and the realized sample size is less than the desired sample
size.