Merge pull request #88 from stocnet/develop

Update url addresses to new orga and solve some issues

.github/OpenMP_mac.md

@@ -33,3 +33,55 @@ SHLIB_LIBADD = -L/usr/local/lib
 ```
 
 6. Installing goldfish from source should work now. Otherwise get in contact with the developer team.
+
+### Update for M1, M2, ... machines 
+
+If you are using an M1, M2, ... machine, you could follow the previous instructions to install a `gcc` compiler and setting up the compilers for `R`.
+Thanks to @eugeniagilpa, here there is an alternative version of the `Makevars` file that should work for M1, M2, ... machines:
+
+```
+XCBASE:=$(shell xcrun --show-sdk-path)
+GCCBASE:=$(shell brew --prefix gcc)
+GETTEXT:=$(shell brew --prefix gettext)
+
+CC=$(GCCBASE)/bin/gcc-13
+CXX=$(GCCBASE)/bin/g++-13
+CXX11=$(GCCBASE)/bin/g++-13
+CXX14=$(GCCBASE)/bin/g++-13
+CXX17=$(GCCBASE)/bin/g++-13 
+CXX20=$(GCCBASE)/bin/g++-13
+CXX23=$(GCCBASE)/bin/g++-13
+SHLIB_CXXLD=$(GCCBASE)/bin/g++-13
+FC=$(GCCBASE)/bin/gfortran
+F77=$(GCCBASE)/bin/gfortran
+FLIBS=-L/$(GCCBASE)/lib/gcc/13/ -lm -lgfortran
+
+CPPFLAGS=-isystem "$(GCCBASE)/include" -isysroot "$(XCBASE)"
+LDFLAGS=-L"$(GCCBASE)/lib" -L"$(GETTEXT)/lib" --sysroot="$(XCBASE)"
+
+MAKE=make -j8
+
+SHLIB_OPENMP_CFLAGS=-fopenmp
+SHLIB_OPENMP_CXXFLAGS=-fopenmp
+SHLIB_OPENMP_FCFLAGS=-fopenmp 
+SHLIB_OPENMP_FFLAGS=-fopenmp 
+
+SHLIB_CXXLDFLAGS = -dynamiclib -Wl,-ld_classic,-headerpad_max_install_names -undefined dynamic_lookup $(CXXFLAGS) $(CXXPICFLAGS) $(LTO_LD)
+SHLIB_CXX11LDFLAGS = -dynamiclib -Wl,-ld_classic,-headerpad_max_install_names -undefined dynamic_lookup $(CXX11FLAGS) $(CXX11PICFLAGS) $(LTO_LD)
+SHLIB_CXX14LDFLAGS = -dynamiclib -Wl,-ld_classic,-headerpad_max_install_names -undefined dynamic_lookup $(CXX14FLAGS) $(CXX14PICFLAGS) $(LTO_LD)
+SHLIB_CXX17LDFLAGS = -dynamiclib -Wl,-ld_classic,-headerpad_max_install_names -undefined dynamic_lookup $(CXX17FLAGS) $(CXX17PICFLAGS) $(LTO_LD)
+SHLIB_CXX20LDFLAGS = -dynamiclib -Wl,-ld_classic,-headerpad_max_install_names -undefined dynamic_lookup $(CXX20FLAGS) $(CXX20PICFLAGS) $(LTO_LD)
+SHLIB_CXX23LDFLAGS = -dynamiclib -Wl,-ld_classic,-headerpad_max_install_names -undefined dynamic_lookup $(CXX23FLAGS) $(CXX23PICFLAGS) $(LTO_LD)
+
+SHLIB_FCLDFLAGS = -dynamiclib -Wl,-ld_classic,-headerpad_max_install_names -undefined dynamic_lookup $(FCFLAGS) $(FPICFLAGS)
+SHLIB_LDFLAGS = -dynamiclib -Wl,-ld_classic,-headerpad_max_install_names -undefined dynamic_lookup $(CFLAGS) $(CPICFLAGS) $(LTO_LD)
+SHLIB_LDFLAGS_R = -dynamiclib -Wl,-ld_classic,-headerpad_max_install_names -undefined dynamic_lookup $(CFLAGS) $(CPICFLAGS) $(LTO_LD)
+```
+
+In step 5 the path to the library should be:
+
+```
+SHLIB_LIBADD = -L/opt/homebrew/opt/gfortran/lib
+```
+
+Please share feedback on which of these work (shortcuts or unnecessary parts) and we will update the installation guide accordingly.

DESCRIPTION

@@ -2,8 +2,8 @@ Encoding: UTF-8
 Package: goldfish
 Type: Package
 Title: Statistical Network Models for Dynamic Network Data
-Version: 1.6.5
-Date: 2023-06-20
+Version: 1.6.6
+Date: 2024-03-13
 Authors@R: c(person("James", "Hollway", role = c("cre", "aut", "dtc"), 
                     email = "[email protected]",
                     comment = c("IHEID", ORCID = "0000-0002-8361-9647")),
@@ -28,8 +28,8 @@ Description: Tools for fitting statistical network models to dynamic network dat
    Stadtfeld, Hollway, and Block (2017b) <doi:10.1177/0081175017733457>,
    Stadtfeld and Block (2017) <doi:10.15195/v4.a14>,
    Hoffman et al. (2020) <doi:10.1017/nws.2020.3>.
-URL: https://snlab-ch.github.io/goldfish/
-BugReports: https://github.com/snlab-ch/goldfish/issues
+URL: https://stocnet.github.io/goldfish/ 
+BugReports: https://github.com/snlab-ch/goldfish/issues/ 
 Depends: R (>= 3.5.0)
 Imports:
     Rcpp (>= 1.0.1),
@@ -54,6 +54,7 @@ Suggests:
     igraph,
     ggraph,
     migraph,
+    manynet,
     broom,
     lmtest
 VignetteBuilder: knitr 

NAMESPACE

@@ -18,6 +18,7 @@ S3method(print,summary.result.goldfish)
 S3method(summary,result.goldfish)
 S3method(tidy,result.goldfish)
 S3method(vcov,result.goldfish)
+export(GatherPreprocessing)
 export(defineDependentEvents)
 export(defineGlobalAttribute)
 export(defineGroups_interaction)

NEWS.md

@@ -1,7 +1,17 @@
+# goldfish 1.6.6
+
+* Debugging and extend documentation for `GatherPreprocessing()`.
+* Fix note from CRAN checks.
+* Debug issue when using a preprocess init object in `estimate()`.
+* Debug issue with opportunity list in `estimate()` for `DyNAM` models.
+* Fix error in printing output from `estimate()` when using
+  a parameter is fixed to a value.  
+
 # goldfish 1.6.5
 
 * Solves `startTime` and `endTime` bug on `DyNAM` and `REM` models
   preprocessing.
+* Export `GatherPreprocessing()`. Experimental functionality.
 * Clean unnecessary functions imports.
 * Solves `aes_string()` deprecation.
 * Solves issue on `C++` engine on DyNAM-rate.

R/data_Fisheries_Treaties_6070.R

@@ -4,8 +4,8 @@
 #' including only bilateral agreements, fewer variables,
 #' and ranging only between 1960 and 1970 inclusive.
 #' This data set is only meant for testing, and not for inference.
-#' It provides an example of an undirected, weighted (by integer/increment) network,
-#' with composition change and both monadic and dyadic covariates.
+#' It provides an example of an undirected, weighted (by integer/increment)
+#' network, with composition change and both monadic and dyadic covariates.
 #' Monadic variables include the dates states gain or lose sovereign status,
 #' their polity score, and their GDP.
 #' Dyadic variables include bilateral fisheries agreements between states,
@@ -24,38 +24,42 @@
 #' See below for variables and formats.
 #'
 #' \tabular{lll}{
-#'    \strong{Object}      \tab  \strong{Description}                      \tab    \strong{Format}       \cr
-#'    states$label         \tab   Node identifier labels                   \tab     character            \cr
-#'    states$present       \tab   Node present in dataset                  \tab     boolean              \cr
-#'    states$regime        \tab   Placeholder for regime variable          \tab     numeric (NA)         \cr
-#'    states$gdp           \tab   Placeholder for GDP variable             \tab     numeric (NA)         \cr
-#'    sovchanges$time     \tab   Date of state sovereignty update         \tab     POSIXct              \cr
-#'    sovchanges$node     \tab   Node for state sovereignty update        \tab     integer              \cr
-#'    sovchanges$replace  \tab   State sovereignty update                 \tab     boolean              \cr
-#'    regchanges$time          \tab   Date of regime update                    \tab     POSIXct              \cr
-#'    regchanges$node          \tab   Node for regime update                   \tab     integer              \cr
-#'    regchanges$replace       \tab   Regime update                            \tab     integer (-10--10)    \cr
-#'    gdpchanges$time             \tab   Date of GDP update                       \tab     POSIXct              \cr
-#'    gdpchanges$node             \tab   Node for GDP update                      \tab     integer              \cr
-#'    gdpchanges$replace          \tab   GDP update                               \tab     numeric              \cr
-#'    bilatchanges$time    \tab   Date of bilateral change                 \tab     POSIXct              \cr
-#'    bilatchanges$sender  \tab   First bilateral change node              \tab     integer              \cr
-#'    bilatchanges$receiver \tab   Second bilateral change node            \tab     integer              \cr
-#'    bilatchanges$increment \tab   Create or dissolve action              \tab     numeric (-1 or 1)    \cr
-#'    contigchanges$time      \tab   Date of contiguity change                \tab     POSIXct              \cr
-#'    contigchanges$sender    \tab   First contiguity change node             \tab     integer              \cr
-#'    contigchanges$receiver  \tab   Second contiguity change node            \tab     integer              \cr
-#'    contigchanges$replace   \tab   New contiguity value                     \tab     numeric              \cr
+#'    \strong{Object} \tab \strong{Description} \tab \strong{Format} \cr
+#'    states$label \tab Node identifier labels \tab character \cr
+#'    states$present \tab Node present in dataset \tab boolean \cr
+#'    states$regime \tab Placeholder for regime variable \tab numeric (NA) \cr
+#'    states$gdp \tab Placeholder for GDP variable \tab numeric (NA) \cr
+#'    sovchanges$time \tab Date of state sovereignty update \tab POSIXct \cr
+#'    sovchanges$node \tab Node for state sovereignty update \tab integer \cr
+#'    sovchanges$replace \tab State sovereignty update \tab boolean \cr
+#'    regchanges$time \tab Date of regime update \tab POSIXct \cr
+#'    regchanges$node \tab Node for regime update \tab integer \cr
+#'    regchanges$replace \tab Regime update \tab integer (-10--10) \cr
+#'    gdpchanges$time \tab Date of GDP update \tab POSIXct \cr
+#'    gdpchanges$node \tab Node for GDP update \tab integer \cr
+#'    gdpchanges$replace \tab GDP update \tab numeric \cr
+#'    bilatchanges$time \tab Date of bilateral change \tab POSIXct \cr
+#'    bilatchanges$sender \tab First bilateral change node \tab integer \cr
+#'    bilatchanges$receiver \tab Second bilateral change node \tab integer \cr
+#'    bilatchanges$increment\tab Create or dissolve tie\tab numeric (-1 or 1)\cr
+#'    contigchanges$time \tab Date of contiguity change \tab POSIXct \cr
+#'    contigchanges$sender \tab First contiguity change node \tab integer \cr
+#'    contigchanges$receiver \tab Second contiguity change node \tab integer \cr
+#'    contigchanges$replace \tab New contiguity value \tab numeric \cr
 #'  }
 #'
 #' @references
-#' Hollway, James, and Johan Koskinen. 2016. Multilevel Embeddedness: The Case of the Global Fisheries
-#' Governance Complex. \emph{Social Networks}, 44: 281-94. doi:10.1016/j.socnet.2015.03.001.
+#' Hollway, James, and Johan Koskinen. 2016.
+#' Multilevel Embeddedness: The Case of the Global Fisheries Governance Complex.
+#' \emph{Social Networks}, 44: 281-94. \doi{10.1016/j.socnet.2015.03.001}.
 #'
-#' Hollway, James, and Johan H Koskinen. 2016. Multilevel Bilateralism and Multilateralism: States' Bilateral and
+#' Hollway, James, and Johan H Koskinen. 2016.
+#' Multilevel Bilateralism and Multilateralism: States' Bilateral and
 #' Multilateral Fisheries Treaties and Their Secretariats.
-#' In \emph{Multilevel Network Analysis for the Social Sciences}, edited by Emmanuel Lazega and Tom A B Snijders,
-#' 315-32. Cham: Springer International Publishing. doi:10.1007/978-3-319-24520-1_13.
+#' In \emph{Multilevel Network Analysis for the Social Sciences},
+#' edited by Emmanuel Lazega and Tom A B Snijders,
+#' 315-32. Cham: Springer International Publishing.
+#' \doi{10.1007/978-3-319-24520-1_13}.
 #'
 #' @keywords datasets dynamic political network states fisheries
 NULL

R/data_RFID_Validity_Study.R

@@ -14,31 +14,39 @@
 #' @docType data
 #' @usage data(RFID_Validity_Study)
 #' @format 3 dataframes: \cr
-#' - participants (11 rows, 7 columns): attributes of the experiment's participants\cr
-#' - rfid (1011 rows, 4 columns): dyadic interactions detected by the RFID badges (after data processing)\cr
-#' - video (219 rows, 4 columns): dyadic interactions detected by the video rating\cr
+#' - participants (11 rows, 7 columns):
+#'  attributes of the experiment's participants\cr
+#' - rfid (1011 rows, 4 columns): dyadic interactions detected
+#'  by the RFID badges (after data processing)\cr
+#' - video (219 rows, 4 columns): dyadic interactions detected
+#'  by the video rating\cr
 #' and one network:\cr
 #' - known.before (11 rows, 11 columns): network of previous acquaintances\cr
 #' See below for variables and formats.\cr
 #'
-#'\tabular{lll}{
+#' \tabular{lll}{
 #'   \strong{Object} \tab \strong{Description} \tab \strong{Format} \cr
-#'   participants$actor   \tab  Identifier of the actor                      \tab  integer        \cr
-#'   participants$label   \tab  (Anonymized) name                            \tab  Factor         \cr
-#'   participants$present \tab  Presence of the actor (all actors are present) \tab  logical      \cr
-#'   participants$age     \tab  Actor's age                                  \tab  integer        \cr
-#'   participants$gender  \tab  Actor's gender (0: male, 1: female)          \tab  integer        \cr
-#'   participants$group   \tab  Actor's group affiliation (groups have distinct ids) \tab  integer \cr
-#'   participants$level   \tab  Actor's seniority (1: MSc student, 2: PhD student, 3: PostDoc, 4: Prof)
-#'                                                                           \tab  integer        \cr
-#'   rfid$NodeA      \tab  Identifier for the first actor                    \tab  chr            \cr
-#'   rfid$NodeB      \tab  Identifier for the second actor                   \tab  chr            \cr
-#'   rfid$Start      \tab  Time of the beginning of the dyadic interaction   \tab  integer        \cr
-#'   rfid$End        \tab  Time of the end of the dyadic interaction         \tab  integer        \cr
-#'   video$NodeA     \tab  Identifier for the first actor                    \tab  chr            \cr
-#'   video$NodeB     \tab  Identifier for the second actor                   \tab  chr            \cr
-#'   video$Start     \tab  Time of the beginning of the dyadic interaction   \tab  integer        \cr
-#'   video$End       \tab  Time of the end of the dyadic interaction         \tab  integer        \cr
+#'   participants$actor \tab Identifier of the actor \tab  integer \cr
+#'   participants$label \tab (Anonymized) name \tab  Factor \cr
+#'   participants$present \tab Presence of the actor (all actors are present)
+#'     \tab logical \cr
+#'   participants$age \tab Actor's age \tab integer \cr
+#'   participants$gender \tab Actor's gender (0: male, 1: female)
+#'     \tab integer \cr
+#'   participants$group
+#'   \tab Actor's group affiliation (groups have distinct ids) \tab integer \cr
+#'   participants$level \tab Actor's seniority
+#'   (1: MSc student, 2: PhD student, 3: PostDoc, 4: Prof) \tab integer \cr
+#'   rfid$NodeA \tab Identifier for the first actor \tab  chr \cr
+#'   rfid$NodeB \tab Identifier for the second actor \tab  chr \cr
+#'   rfid$Start \tab Time of the beginning of the dyadic interaction
+#'     \tab integer \cr
+#'   rfid$End \tab Time of the end of the dyadic interaction \tab integer \cr
+#'   video$NodeA \tab Identifier for the first actor \tab chr \cr
+#'   video$NodeB \tab Identifier for the second actor \tab chr \cr
+#'   video$Start \tab Time of the beginning of the dyadic interaction
+#'   \tab integer \cr
+#'   video$End \tab Time of the end of the dyadic interaction \tab integer \cr
 #'  }
 #'
 #' @source \url{https://osf.io/rrhxe/}

R/data_Social_Evolution.R

@@ -10,29 +10,35 @@
 #' @name Social_Evolution
 #' @docType data
 #' @usage data(Social_Evolution)
-#' @format 3 dataframes: actors (84 rows, 4 columns), calls (439 rows, 4 columns), friendship (766 rows, 4 columns).
+#' @format 3 dataframes: actors (84 rows, 4 columns),
+#'  calls (439 rows, 4 columns), friendship (766 rows, 4 columns).
 #' See below for variables and formats.
 #'
 #' \tabular{lll}{
-#'    \strong{Object}      \tab  \strong{Description}                      \tab    \strong{Format}       \cr
-#'    actors$label         \tab   Actor identifier labels                  \tab     character            \cr
-#'    actors$present       \tab   Actor present in dataset                 \tab     boolean              \cr
-#'    actors$floor         \tab   Floor of residence actor lives on        \tab     numeric (1-9)        \cr
-#'    actors$gradeType     \tab   Degree level                             \tab     numeric (1-5)        \cr
-#'    calls$time           \tab   Time and date of call                    \tab     numeric from POSIXct \cr
-#'    calls$sender         \tab   Initiator of phone call                  \tab     character            \cr
-#'    calls$receiver       \tab   Recipient of phone call                  \tab     character            \cr
-#'    calls$increment      \tab   Indicates call number increment (all 1s) \tab     numeric (1)          \cr
-#'    friendship$time      \tab   Time and date of friend nomination       \tab     numeric from POSIXct \cr
-#'    friendship$sender    \tab   Nominator of friendship                  \tab     character            \cr
-#'    friendship$receiver  \tab   Nominee of friendship                    \tab     character            \cr
-#'    friendship$replace   \tab   Indicates friendship value at $time      \tab     numeric              \cr
+#'    \strong{Object} \tab \strong{Description} \tab\strong{Format} \cr
+#'    actors$label \tab  Actor identifier labels \tab character \cr
+#'    actors$present \tab  Actor present in dataset \tab boolean \cr
+#'    actors$floor \tab  Floor of residence actor lives on
+#'      \tab numeric (1-9) \cr
+#'    actors$gradeType \tab  Degree level \tab numeric (1-5) \cr
+#'    calls$time \tab  Time and date of call \tab numeric from POSIXct \cr
+#'    calls$sender \tab  Initiator of phone call \tab character \cr
+#'    calls$receiver \tab  Recipient of phone call \tab character \cr
+#'    calls$increment \tab  Indicates call number increment (all 1s)
+#'      \tab numeric (1) \cr
+#'    friendship$time \tab  Time and date of friend nomination
+#'      \tab numeric from POSIXct \cr
+#'    friendship$sender \tab  Nominator of friendship \tab character \cr
+#'    friendship$receiver \tab  Nominee of friendship \tab character \cr
+#'    friendship$replace \tab  Indicates friendship value at $time
+#'      \tab numeric \cr
 #'  }
 #'
 #' @source \url{http://realitycommons.media.mit.edu/socialevolution.html}
 #' @references
-#' A. Madan, M. Cebrian, S. Moturu, K. Farrahi, A. Pentland (2012). Sensing the 'Health State' of a Community.
-#' \emph{Pervasive Computing. 11}, 4, pp. 36-45.
+#' A. Madan, M. Cebrian, S. Moturu, K. Farrahi, A. Pentland (2012).
+#' Sensing the 'Health State' of a Community.
+#' \emph{Pervasive Computing. 11}, 4, pp. 36-45. \doi{10.1109/MPRV.2011.79}.
 #'
 #' @keywords datasets social evolution network
 NULL