v1.15.0 Docs.

SugiharaLab · Oct 23, 2023 · ea00e99 · ea00e99
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: rEDM
 Type:    Package
 Title:   Empirical Dynamic Modeling ('EDM')
 Version: 1.15.0
-Date:    2023-10-19
+Date:    2023-10-21
 Authors@R: c( person("Joseph", "Park", role = c("aut", "cre"),
                      email = "[email protected]",
                      comment = c(ORCID = "0000-0001-5411-1409")),

diff --git a/NEWS.md b/NEWS.md
@@ -1,16 +1,24 @@
 #### rEDM NEWS
 
-2023-07-03 version 1.14.2 <[email protected]>
+2023-10-21 version 1.15.0 <[email protected]>
 
 ---
 
 ##### NOTES:
-- It is recommended to use functions: `Simplex`, `SMap`, `CCM`, `Embed`, `Multiview`, `EmbedDimension`, `PredictInterval`, `PredictNonlinear`, `ComputeError` instead of the legacy version 0.7 signatures. See Version 1.3 notes.
+- It is required as of version 1.15 to use functions: `Simplex`, `SMap`, `CCM`, `Embed`, `Multiview`, `EmbedDimension`, `PredictInterval`, `PredictNonlinear`, `ComputeError` instead of the legacy version 0.7 signatures. See Version 1.3 notes.
 - Rcpp imposes a 20 parameter limit on functions. The rEDM wrapper of [cppEDM](https://github.com/SugiharaLab/cppEDM#empirical-dynamic-modeling-edm) therefore does not invoke the full cppEDM API. Users requiring the full API are referred to the [pyEDM](https://pypi.org/project/pyEDM/) wrapper.
 - `SMap` linear system solver regularization: The R [glmnet](https://CRAN.R-project.org/package=glmnet) package does not seperate the model from the data. This prevents integration in rEDM. Users requiring `SMap` regularization are referred to the [pyEDM](https://pypi.org/project/pyEDM/) wrapper.
 
 ---
 
+##### Version 1.15
+- `SMap()` `ignoreNan` parameter added. If `ignoreNan` is `TRUE` (default) the library is redefined to ignore embedding vectors with nan. If `ignoreNan` is `FALSE` no change is made, the user can manually specify library segments in `lib`.
+- `SMap()` return list includes data.frame of SVD singular values.
+- `noTime` parameter added, default `FALSE`. If `noTime` is `TRUE` the first column of the data is not required to be a time vector. A row index vector will be inserted and passed to cppEDM. 
+- `const_pred` parameter removed due to Rcpp 20 parameter limit.
+- `CCM()` `replacement` parameter removed.
+- Legacy overload functions removed.
+
 ##### Version 1.14
 - cppEDM core added `generateLibrary` parameter to `Simplex()` and `SMap()`.  If `TRUE` the state-space library has newly generated points added. Not available due to Rcpp 20 parameter limit. 
 - Version 1.14.2 Remove CCM multivariable warning, positive tau warning. Add Embedding application. 

diff --git a/man/CCM.Rd b/man/CCM.Rd
@@ -13,10 +13,10 @@ CCM(pathIn = "./", dataFile = "", dataFrame = NULL,
 \item{pathIn}{path to \code{dataFile}.}
 
 \item{dataFile}{.csv format data file name. The first column must be a time
-index or time values. The first row must be column names.}
+index or time values unless noTime is TRUE. The first row must be column names.}
 
 \item{dataFrame}{input data.frame. The first column must be a time
-index or time values. The columns must be named.}
+index or time values unless noTime is TRUE. The columns must be named.}
 
 \item{E}{embedding dimension.}
 
@@ -37,7 +37,8 @@ input data used to create the library.}
 
 \item{libSizes}{string of 3 whitespace separated integer values
   specifying the intial library size, the final library size,
-  and the library size increment.}
+  and the library size increment. Can also be a list of strictly
+  increasing library sizes.}
 
 \item{sample}{integer specifying the number of random samples to draw at
 each library size evaluation.}

diff --git a/man/EmbedDimension.Rd b/man/EmbedDimension.Rd
@@ -12,17 +12,19 @@ EmbedDimension(pathIn = "./", dataFile = "", dataFrame = NULL, pathOut = "",
 \item{pathIn}{path to \code{dataFile}.}
 
 \item{dataFile}{.csv format data file name. The first column must be a time
-index or time values. The first row must be column names.}
+index or time values unless noTime is TRUE. The first row must be column names.}
 
 \item{dataFrame}{input data.frame. The first column must be a time
-index or time values. The columns must be named.}
+index or time values unless noTime is TRUE. The columns must be named.}
 
 \item{pathOut}{path for \code{predictFile} containing output predictions.}
 
 \item{predictFile}{output file name.}
 
-\item{lib}{string with start and stop indices of input data rows used to
-create the library of observations. A single contiguous range is supported.}
+\item{lib}{string or vector with start and stop indices of input data
+rows used to create the library from observations. Mulitple row index
+pairs can be specified with each pair defining the first and last
+rows of time series observation segments used to create the library.}
 
 \item{pred}{string with start and stop indices of input data rows used for
 predictions. A single contiguous range is supported.}

diff --git a/man/Multiview.Rd b/man/Multiview.Rd
@@ -12,10 +12,10 @@ Multiview(pathIn = "./", dataFile = "", dataFrame = NULL,
 \item{pathIn}{path to \code{dataFile}.}
 
 \item{dataFile}{.csv format data file name. The first column must be a time
-index or time values. The first row must be column names.}
+index or time values. The first row must be column names unless noTime is TRUE.}
 
 \item{dataFrame}{input data.frame. The first column must be a time
-index or time values. The columns must be named.}
+index or time values unless noTime is TRUE. The columns must be named.}
 
 \item{lib}{a 2-column matrix, data.frame, 2-element vector or string of 
   row indice pairs, where each pair specifies the first and last *rows* of

diff --git a/man/PredictInterval.Rd b/man/PredictInterval.Rd
@@ -12,17 +12,19 @@ PredictInterval(pathIn = "./", dataFile = "", dataFrame = NULL, pathOut = "./",
 \item{pathIn}{path to \code{dataFile}.}
 
 \item{dataFile}{.csv format data file name. The first column must be a time
-index or time values. The first row must be column names.}
+index or time values unless noTime is TRUE. The first row must be column names.}
 
 \item{dataFrame}{input data.frame. The first column must be a time
-index or time values. The columns must be named.}
+index or time values unless noTime is TRUE. The columns must be named.}
 
 \item{pathOut}{path for \code{predictFile} containing output predictions.}
 
 \item{predictFile}{output file name.}
 
-\item{lib}{string with start and stop indices of input data rows used to
-create the library of observations. A single contiguous range is supported.}
+\item{lib}{string or vector with start and stop indices of input data
+  rows used to create the library from observations. Mulitple row index
+  pairs can be specified with each pair defining the first and last
+  rows of time series observation segments used to create the library.}
 
 \item{pred}{string with start and stop indices of input data rows used for
 predictions. A single contiguous range is supported.}

diff --git a/man/PredictNonlinear.Rd b/man/PredictNonlinear.Rd
@@ -12,17 +12,19 @@ PredictNonlinear(pathIn = "./", dataFile = "", dataFrame = NULL,
 \item{pathIn}{path to \code{dataFile}.}
 
 \item{dataFile}{.csv format data file name. The first column must be a time
-index or time values. The first row must be column names.}
+index or time values unless noTime is TRUE. The first row must be column names.}
 
 \item{dataFrame}{input data.frame. The first column must be a time
-index or time values. The columns must be named.}
+index or time values unless noTime is TRUE. The columns must be named.}
 
 \item{pathOut}{path for \code{predictFile} containing output predictions.}
 
 \item{predictFile}{output file name.}
 
-\item{lib}{string with start and stop indices of input data rows used to
-create the library of observations. A single contiguous range is supported.}
+\item{lib}{string or vector with start and stop indices of input data
+rows used to create the library from observations. Mulitple row index
+pairs can be specified with each pair defining the first and last
+rows of time series observation segments used to create the library.}
 
 \item{pred}{string with start and stop indices of input data rows used for
 predictions. A single contiguous range is supported.}

diff --git a/man/SMap.Rd b/man/SMap.Rd
@@ -14,13 +14,15 @@ SMap(pathIn = "./", dataFile = "", dataFrame = NULL,
 \item{pathIn}{path to \code{dataFile}.}
 
 \item{dataFile}{.csv format data file name. The first column must be a time
-index or time values. The first row must be column names.}
+index or time values unless noTime is TRUE. The first row must be column names.}
 
 \item{dataFrame}{input data.frame. The first column must be a time
-index or time values. The columns must be named.}
+index or time values unless noTime is TRUE. The columns must be named.}
 
-\item{lib}{string with start and stop indices of input data rows used to
-create the library of observations. A single contiguous range is supported.}
+\item{lib}{string or vector with start and stop indices of input data
+rows used to create the library from observations. Mulitple row index
+pairs can be specified with each pair defining the first and last
+rows of time series observation segments used to create the library.}
 
 \item{pred}{string with start and stop indices of input data rows used for
 predictions. A single contiguous range is supported.}

diff --git a/man/Simplex.Rd b/man/Simplex.Rd
@@ -12,17 +12,19 @@ Simplex(pathIn = "./", dataFile = "", dataFrame = NULL, pathOut = "./",
 \item{pathIn}{path to \code{dataFile}.}
 
 \item{dataFile}{.csv format data file name. The first column must be a time
-index or time values. The first row must be column names.}
+index or time values unless noTime is TRUE. The first row must be column names.}
 
 \item{dataFrame}{input data.frame. The first column must be a time
-index or time values. The columns must be named.}
+index or time values unless noTime is TRUE. The columns must be named.}
 
 \item{pathOut}{path for \code{predictFile} containing output predictions.}
 
 \item{predictFile}{output file name.}
 
-\item{lib}{string with start and stop indices of input data rows used to
-create the library of observations. A single contiguous range is supported.}
+\item{lib}{string or vector with start and stop indices of input data
+rows used to create the library from observations. Mulitple row index
+pairs can be specified with each pair defining the first and last
+rows of time series observation segments used to create the library.}
 
 \item{pred}{string with start and stop indices of input data rows used for
 predictions. A single contiguous range is supported.}

diff --git a/src/Makevars.win b/src/Makevars.win
@@ -14,4 +14,4 @@ $(SHLIB): cppEDM/src/libEDM.a
 
 cppEDM/src/libEDM.a:
 	@(cd cppEDM/src && $(MAKE) -f makefile.mingw \
-          CC="$(CC)" CFLAGS="-DCCM_THREADED -DMULTIVIEW_VALUES_OVERLOAD -I../ $(CPICFLAGS)" AR="$(AR)" RANLIB="$(RANLIB)")
+          CC="$(CC)" CFLAGS="-DCCM_THREADED -DUSING_R -I../ $(CPICFLAGS)" AR="$(AR)" RANLIB="$(RANLIB)")