Last updated on 2024-11-09 05:49:49 CET.
| Package | WARN | NOTE | OK |
|---|---|---|---|
| adamethods | 8 | 5 | |
| Anthropometry | 1 | 9 | 3 |
| BAwiR | 13 |
Current CRAN status: NOTE: 8, OK: 5
Version: 1.2.1
Check: LazyData
Result: NOTE
'LazyData' is specified without a 'data' directory
Flavors: r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Current CRAN status: WARN: 1, NOTE: 9, OK: 3
Version: 1.19
Check: Rd files
Result: NOTE
checkRd: (-1) Anthropometry-internalHipamAnthropom.Rd:16: Lost braces; missing escapes or markup?
16 | Several internal functions used by both $HIPAM_{MO}$ and $HIPAM_{IMO}$ algorithms
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checkRd: (-1) Anthropometry-internalHipamAnthropom.Rd:16: Lost braces; missing escapes or markup?
16 | Several internal functions used by both $HIPAM_{MO}$ and $HIPAM_{IMO}$ algorithms
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checkRd: (-1) Anthropometry-internalHipamAnthropom.Rd:19: Lost braces; missing escapes or markup?
19 | This file contains several functions called for both $HIPAM_{MO}$ and $HIPAM_{IMO}$ algorithms. Therefore, they are not used directly.
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checkRd: (-1) Anthropometry-internalHipamAnthropom.Rd:19: Lost braces; missing escapes or markup?
19 | This file contains several functions called for both $HIPAM_{MO}$ and $HIPAM_{IMO}$ algorithms. Therefore, they are not used directly.
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checkRd: (-1) Anthropometry-internalHipamAnthropom.Rd:21: Lost braces; missing escapes or markup?
21 | The $HIPAM_{MO}$ and $HIPAM_{IMO}$ algorithms are different in the way to generate and validate a clustering partition. However, the functions related to the further clustering steps are common to both of them. These functions are those collected in this file.
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checkRd: (-1) Anthropometry-internalHipamAnthropom.Rd:21: Lost braces; missing escapes or markup?
21 | The $HIPAM_{MO}$ and $HIPAM_{IMO}$ algorithms are different in the way to generate and validate a clustering partition. However, the functions related to the further clustering steps are common to both of them. These functions are those collected in this file.
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checkRd: (-1) Anthropometry-package.Rd:22: Lost braces; missing escapes or markup?
22 | Anthropometry-internalHipamAnthropom: Several internal functions used by both $HIPAM_{MO}$ and $HIPAM_{IMO}$ algorithms.\cr
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checkRd: (-1) Anthropometry-package.Rd:22: Lost braces; missing escapes or markup?
22 | Anthropometry-internalHipamAnthropom: Several internal functions used by both $HIPAM_{MO}$ and $HIPAM_{IMO}$ algorithms.\cr
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checkRd: (-1) Anthropometry-package.Rd:31: Lost braces; missing escapes or markup?
31 | checkBranchLocalIMO: Evaluation of the candidate clustering partition in $HIPAM_{IMO}$.\cr
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checkRd: (-1) Anthropometry-package.Rd:32: Lost braces; missing escapes or markup?
32 | checkBranchLocalMO: Evaluation of the candidate clustering partition in $HIPAM_{MO}$.\cr
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checkRd: (-1) Anthropometry-package.Rd:39: Lost braces; missing escapes or markup?
39 | getBestPamsamIMO: Generation of the candidate clustering partition in $HIPAM_{IMO}$. \cr
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checkRd: (-1) Anthropometry-package.Rd:40: Lost braces; missing escapes or markup?
40 | getBestPamsamMO: Generation of the candidate clustering partition in $HIPAM_{MO}$.\cr
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checkRd: (-1) checkBranchLocalIMO.Rd:4: Lost braces; missing escapes or markup?
4 | Evaluation of the candidate clustering partition in $HIPAM_{IMO}$
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checkRd: (-1) checkBranchLocalIMO.Rd:9: Lost braces; missing escapes or markup?
9 | In this version of HIPAM, called $HIPAM_{IMO}$, there are three different stopping criteria: First, if $|P| leq 2$, then P is a terminal node. If not, the second stopping refers to the INCA (Index Number Clusters Atypical) criterion (Irigoien et al. (2008)): if $INCA_k leq 0.2$ for all k, then P is a terminal node. Finally, the third stopping criteria uses the Mean Split Silhouette. See Vinue et al. (2014) for more details.
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checkRd: (-1) checkBranchLocalIMO.Rd:40: Lost braces; missing escapes or markup?
40 | Option 'IMO' for using $HIPAM_{IMO}$.
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checkRd: (-1) checkBranchLocalIMO.Rd:70: Lost braces; missing escapes or markup?
70 | This function belongs to the $HIPAM_{IMO}$ algorithm and it is not solely used. That is why there is no section of \emph{examples} in this help page. See \code{\link{hipamAnthropom}}.
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checkRd: (-1) checkBranchLocalMO.Rd:4: Lost braces; missing escapes or markup?
4 | Evaluation of the candidate clustering partition in $HIPAM_{MO}$
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checkRd: (-1) checkBranchLocalMO.Rd:9: Lost braces; missing escapes or markup?
9 | In this version of HIPAM, called $HIPAM_{MO}$, there are two different stopping criteria: First, if $|P| leq 2$, then P is a terminal node. If not, the second stopping criteria uses the Mean Split Silhouette. See Vinue et al. (2014) for more details.
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checkRd: (-1) checkBranchLocalMO.Rd:40: Lost braces; missing escapes or markup?
40 | Option 'MO' for using $HIPAM_{MO}$.
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checkRd: (-1) checkBranchLocalMO.Rd:66: Lost braces; missing escapes or markup?
66 | This function belongs to the $HIPAM_{MO}$ algorithm and it is not solely used. That is why there is no section of \emph{examples} in this help page. See \code{\link{hipamAnthropom}}.
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checkRd: (-1) getBestPamsamIMO.Rd:4: Lost braces; missing escapes or markup?
4 | Generation of the candidate clustering partition in $HIPAM_{IMO}$
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checkRd: (-1) getBestPamsamIMO.Rd:9: Lost braces; missing escapes or markup?
9 | In this version of HIPAM, called $HIPAM_{IMO}$, the number k of (child) clusters is obtained by using the INCA (Index Number Clusters Atypical) criterion (Irigoien et al. (2008)) in the following way: at each node P, if there is k such that $INCA_k > 0.2$, then the k prior to the first largest slope decrease is selected. However, this procedure does not apply either to the top node or to the generation of the new partitions from which the Mean Split Silhouette is calculated. In these cases, even when all $INCA_k < 0.2$, k = 3 is fixed as the number of groups to divide and proceed. See Vinue et al. (2014) for more details.
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checkRd: (-1) getBestPamsamIMO.Rd:27: Lost braces; missing escapes or markup?
27 | Option 'IMO' for using $HIPAM_{IMO}$.
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checkRd: (-1) getBestPamsamIMO.Rd:74: Lost braces; missing escapes or markup?
74 | This function belongs to the $HIPAM_{IMO}$ algorithm and it is not solely used. That is why there is no section of \emph{examples} in this help page. See \code{\link{hipamAnthropom}}.
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checkRd: (-1) getBestPamsamMO.Rd:4: Lost braces; missing escapes or markup?
4 | Generation of the candidate clustering partition in $HIPAM_{MO}$
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checkRd: (-1) getBestPamsamMO.Rd:9: Lost braces; missing escapes or markup?
9 | In this version of HIPAM, called $HIPAM_{MO}$, the number k of (child) clusters is obtained by maximizing the silhouette width (asw). See Vinue et al. (2014) for more details.
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checkRd: (-1) getBestPamsamMO.Rd:27: Lost braces; missing escapes or markup?
27 | Option 'MO' for using $HIPAM_{MO}$.
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checkRd: (-1) getBestPamsamMO.Rd:70: Lost braces; missing escapes or markup?
70 | This function belongs to the $HIPAM_{MO}$ algorithm and it is not solely used. That is why there is no section of \emph{examples} in this help page. See \code{\link{hipamAnthropom}}.
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checkRd: (-1) hipamAnthropom.Rd:9: Lost braces; missing escapes or markup?
9 | This function is a HIPAM algorithm adapted to deal with anthropometric data. To that end, a different dissimilarity function is incorporated. This function is that explained in McCulloch et al. (1998) and it is implemented in \code{\link{getDistMatrix}}. We call it $d_{MO}$. In addition, a different method to obtain a classification tree is also incorporated.
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checkRd: (-1) hipamAnthropom.Rd:11: Lost braces; missing escapes or markup?
11 | Two HIPAM algorithms are proposed. The first one, called $HIPAM_{MO}$, is a HIPAM that uses $d_{MO}$. The second one, $HIPAM_{IMO}$, is a HIPAM algorithm that uses $d_{MO}$ and the INCA (Index Number Clusters Atypical) statistic criterion (Irigoien et al. (2008)) to decide the number of child clusters and as a stopping rule.
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checkRd: (-1) hipamAnthropom.Rd:11: Lost braces; missing escapes or markup?
11 | Two HIPAM algorithms are proposed. The first one, called $HIPAM_{MO}$, is a HIPAM that uses $d_{MO}$. The second one, $HIPAM_{IMO}$, is a HIPAM algorithm that uses $d_{MO}$ and the INCA (Index Number Clusters Atypical) statistic criterion (Irigoien et al. (2008)) to decide the number of child clusters and as a stopping rule.
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checkRd: (-1) hipamAnthropom.Rd:11: Lost braces; missing escapes or markup?
11 | Two HIPAM algorithms are proposed. The first one, called $HIPAM_{MO}$, is a HIPAM that uses $d_{MO}$. The second one, $HIPAM_{IMO}$, is a HIPAM algorithm that uses $d_{MO}$ and the INCA (Index Number Clusters Atypical) statistic criterion (Irigoien et al. (2008)) to decide the number of child clusters and as a stopping rule.
| ^
checkRd: (-1) hipamAnthropom.Rd:11: Lost braces; missing escapes or markup?
11 | Two HIPAM algorithms are proposed. The first one, called $HIPAM_{MO}$, is a HIPAM that uses $d_{MO}$. The second one, $HIPAM_{IMO}$, is a HIPAM algorithm that uses $d_{MO}$ and the INCA (Index Number Clusters Atypical) statistic criterion (Irigoien et al. (2008)) to decide the number of child clusters and as a stopping rule.
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checkRd: (-1) hipamAnthropom.Rd:36: Lost braces; missing escapes or markup?
36 | Type of HIPAM algorithm to be used. The possible options are 'MO' (for $HIPAM_{MO}$) and 'IMO' (for $HIPAM_{IMO}$).
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checkRd: (-1) hipamAnthropom.Rd:36: Lost braces; missing escapes or markup?
36 | Type of HIPAM algorithm to be used. The possible options are 'MO' (for $HIPAM_{MO}$) and 'IMO' (for $HIPAM_{IMO}$).
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checkRd: (-1) hipamAnthropom.Rd:49: Lost braces; missing escapes or markup?
49 | The $HIPAM_{MO}$ algorithm uses the \code{\link{getBestPamsamMO}} and \code{\link{checkBranchLocalMO}} functions, while the $HIPAM_{IMO}$ algorithm uses the \code{\link{getBestPamsamIMO}} and \code{\link{checkBranchLocalIMO}} functions.
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checkRd: (-1) hipamAnthropom.Rd:49: Lost braces; missing escapes or markup?
49 | The $HIPAM_{MO}$ algorithm uses the \code{\link{getBestPamsamMO}} and \code{\link{checkBranchLocalMO}} functions, while the $HIPAM_{IMO}$ algorithm uses the \code{\link{getBestPamsamIMO}} and \code{\link{checkBranchLocalIMO}} functions.
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checkRd: (-1) hipamAnthropom.Rd:94: Lost braces; missing escapes or markup?
94 | All the functions related to the HIPAM algorithm were originally created by E. Wit et al., and they are available freely on \url{https://www.math.rug.nl/~ernst/book/smida.html}. In order to develop the $HIPAM_{MO}$ and $HIPAM_{IMO}$ algorithms, we have used and adapted them.
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checkRd: (-1) hipamAnthropom.Rd:94: Lost braces; missing escapes or markup?
94 | All the functions related to the HIPAM algorithm were originally created by E. Wit et al., and they are available freely on \url{https://www.math.rug.nl/~ernst/book/smida.html}. In order to develop the $HIPAM_{MO}$ and $HIPAM_{IMO}$ algorithms, we have used and adapted them.
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Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64
Version: 1.19
Check: Rd cross-references
Result: NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
HartiganShapes.Rd: procGPA
LloydShapes.Rd: procGPA
archetypesBoundary.Rd: stepArchetypes, archetypes
archetypoids.Rd: archetypes, stepArchetypes
shapes3dShapes.Rd: shapes3d
stepArchetypesRawData.Rd: stepArchetypes, archetypes
stepArchetypoids.Rd: stepArchetypes, archetypes
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64
Version: 1.19
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘Anthropometry.Rnw’ using knitr
Error: processing vignette 'Anthropometry.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'Anthropometry.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.442 \hlkwd{library}\hldef
{(}\hlsng{"Anthropometry"}\hldef{)}
?
! Emergency stop.
! Emergency stop.
l.442
End of file on the terminal!
! ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘Anthropometry.Rnw’
SUMMARY: processing the following file failed:
‘Anthropometry.Rnw’
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-macos-x86_64
Current CRAN status: OK: 13