Automated build.

jeksterslab · Dec 31, 2024 · f250539 · f250539
1 parent fe74f41
commit f250539
Show file tree

Hide file tree

Showing 38 changed files with 5,620 additions and 45 deletions.
diff --git a/.setup/build/cTMed.pdf b/.setup/build/cTMed.pdf
diff --git a/.setup/build/cTMed_1.0.4.tar.gz b/.setup/build/cTMed_1.0.4.tar.gz
diff --git a/.setup/latex/bib/quarto.bib b/.setup/latex/bib/quarto.bib
diff --git a/.setup/latex/pdf/.gitignore b/.setup/latex/pdf/.gitignore
@@ -0,0 +1,5 @@
+*
+*/
+!*.pdf
+!.gitignore
+!bib.bib
diff --git a/.setup/latex/pdf/bib.bib b/.setup/latex/pdf/bib.bib
diff --git a/.setup/latex/pdf/cTMed-001-description.pdf b/.setup/latex/pdf/cTMed-001-description.pdf
diff --git a/.setup/latex/pdf/cTMed-999-session.pdf b/.setup/latex/pdf/cTMed-999-session.pdf
diff --git a/.setup/latex/pdf/cTMed-zzz-references.pdf b/.setup/latex/pdf/cTMed-zzz-references.pdf
diff --git a/.setup/latex/pdf/cTMed-zzz-tests-benchmark.pdf b/.setup/latex/pdf/cTMed-zzz-tests-benchmark.pdf
diff --git a/.setup/latex/pdf/cTMed-zzz-tests-external.pdf b/.setup/latex/pdf/cTMed-zzz-tests-external.pdf
diff --git a/.setup/latex/pdf/cTMed-zzz-tests-internal.pdf b/.setup/latex/pdf/cTMed-zzz-tests-internal.pdf
diff --git a/.setup/latex/pdf/cTMed-zzz-tests-staging.pdf b/.setup/latex/pdf/cTMed-zzz-tests-staging.pdf
diff --git a/R/cTMed-med-std.R b/R/cTMed-med-std.R
@@ -30,7 +30,7 @@
 #'     \item{args}{Function arguments.}
 #'     \item{fun}{Function used ("MedStd").}
 #'     \item{output}{A standardized matrix of
-#'       total, direct, and indirect effects.}
+#'         total, direct, and indirect effects.}
 #'   }
 #'
 #' @examples

diff --git a/README.md b/README.md
@@ -1,7 +1,7 @@
 cTMed
 ================
 Ivan Jacob Agaloos Pesigan
-2024-12-30
+2024-12-31
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 

diff --git a/vignettes/fig-vignettes-med-boot-boot-1.png b/vignettes/fig-vignettes-med-boot-boot-1.png
diff --git a/vignettes/fig-vignettes-med-boot-boot-2.png b/vignettes/fig-vignettes-med-boot-boot-2.png
diff --git a/vignettes/fig-vignettes-med-boot-boot-3.png b/vignettes/fig-vignettes-med-boot-boot-3.png
diff --git a/vignettes/fig-vignettes-med-boot-boot-4.png b/vignettes/fig-vignettes-med-boot-boot-4.png
diff --git a/vignettes/fig-vignettes-med-boot-boot-5.png b/vignettes/fig-vignettes-med-boot-boot-5.png
diff --git a/vignettes/fig-vignettes-med-boot-boot-6.png b/vignettes/fig-vignettes-med-boot-boot-6.png
diff --git a/vignettes/fig-vignettes-med-boot-boot-std-1.png b/vignettes/fig-vignettes-med-boot-boot-std-1.png
diff --git a/vignettes/fig-vignettes-med-boot-boot-std-2.png b/vignettes/fig-vignettes-med-boot-boot-std-2.png
diff --git a/vignettes/fig-vignettes-med-boot-boot-std-3.png b/vignettes/fig-vignettes-med-boot-boot-std-3.png
diff --git a/vignettes/fig-vignettes-med-boot-boot-std-4.png b/vignettes/fig-vignettes-med-boot-boot-std-4.png
diff --git a/vignettes/fig-vignettes-med-boot-boot-std-5.png b/vignettes/fig-vignettes-med-boot-boot-std-5.png
diff --git a/vignettes/fig-vignettes-med-boot-boot-std-6.png b/vignettes/fig-vignettes-med-boot-boot-std-6.png
diff --git a/vignettes/fig-vignettes-med-mc-1.png b/vignettes/fig-vignettes-med-mc-1.png
diff --git a/vignettes/fig-vignettes-med-mc-2.png b/vignettes/fig-vignettes-med-mc-2.png
diff --git a/vignettes/fig-vignettes-med-mc-3.png b/vignettes/fig-vignettes-med-mc-3.png
diff --git a/vignettes/fig-vignettes-med-std-mc-1.png b/vignettes/fig-vignettes-med-std-mc-1.png
diff --git a/vignettes/fig-vignettes-med-std-mc-2.png b/vignettes/fig-vignettes-med-std-mc-2.png
diff --git a/vignettes/fig-vignettes-med-std-mc-3.png b/vignettes/fig-vignettes-med-std-mc-3.png
diff --git a/vignettes/fit-ct-var-dynr.Rmd b/vignettes/fit-ct-var-dynr.Rmd
@@ -1,7 +1,7 @@
 ---
 title: "Fit the Continuous-Time Vector Autoregressive Model Using the dynr Package"
 author: Ivan Jacob Agaloos Pesigan
-date: "2024-12-30"
+date: "2024-12-31"
 bibliography: "vignettes.bib"
 csl: https://raw.githubusercontent.com/citation-style-language/styles/master/apa.csl
 nocite: |
@@ -297,8 +297,8 @@ fit <- dynr.cook(
 #> 
 #> Doing end processing
 #> Successful trial
-#> Total Time: 6.004809 
-#> Backend Time: 5.992732
+#> Total Time: 6.098897 
+#> Backend Time: 6.086231
 summary(fit)
 #> Coefficients:
 #>             Estimate Std. Error t value  ci.lower  ci.upper Pr(>|t|)    

diff --git a/vignettes/fit-ct-var-mx.Rmd b/vignettes/fit-ct-var-mx.Rmd
@@ -1,7 +1,7 @@
 ---
 title: "Fit the Continuous-Time Vector Autoregressive Model Using the OpenMx Package"
 author: Ivan Jacob Agaloos Pesigan
-date: "2024-12-30"
+date: "2024-12-31"
 bibliography: "vignettes.bib"
 csl: https://raw.githubusercontent.com/citation-style-language/styles/master/apa.csl
 nocite: |
@@ -531,8 +531,8 @@ summary(fit)
 #> RMSEA:  0  [95% CI (NA, NA)]
 #> Prob(RMSEA <= 0.05): NA
 #> To get additional fit indices, see help(mxRefModels)
-#> timestamp: 2024-12-30 06:35:30 
-#> Wall clock time: 202.4342 secs 
+#> timestamp: 2024-12-31 00:27:10 
+#> Wall clock time: 209.4249 secs 
 #> optimizer:  SLSQP 
 #> OpenMx version number: 2.21.13 
 #> Need help?  See help(mxSummary)

diff --git a/vignettes/med-boot.Rmd b/vignettes/med-boot.Rmd
@@ -1,7 +1,7 @@
 ---
 title: "Total, Direct, and Indirect Effects in Continuous-Time Mediation Model (Bootstrap)"
 author: Ivan Jacob Agaloos Pesigan
-date: "2024-12-30"
+date: "2024-12-31"
 bibliography: "vignettes.bib"
 csl: https://raw.githubusercontent.com/citation-style-language/styles/master/apa.csl
 nocite: |
@@ -222,21 +222,18 @@ boot <- PBSSMOUFixed(
   ncores = parallel::detectCores(),
   seed = 42
 )
-#> Error in PBSSMOUFixed(R = R, path = path, prefix = prefix, n = n, time = time, : unused arguments (path = path, prefix = prefix)
 ```
 
 The `extract` function from the `simStateSpace` package is used to extract the bootstrap phi matrices as well as the sigma matrices.
 
 
 ``` r
 phi <- extract(object = boot, what = "phi")
-#> Error in extract(object = boot, what = "phi"): could not find function "extract"
 ```
 
 
 ``` r
 sigma <- extract(object = boot, what = "sigma")
-#> Error in extract(object = boot, what = "sigma"): could not find function "extract"
 ```
 
 In this example, we aim to calculate the total, direct, and indirect effects of `x` on `y`, mediated through `m`, over time intervals ranging from 0 to 10.
@@ -304,15 +301,17 @@ boot <- BootMed(
   med = "m",
   ncores = parallel::detectCores() # use multiple cores
 )
-#> Warning in parallel::mclapply(X = phi, FUN = .Med, delta_t = i, from = from, :
-#> all scheduled cores encountered errors in user code
-#> Error in dimnames(x) <- dn: length of 'dimnames' [2] not equal to array extent
 plot(boot)
-#> Error: object 'boot' not found
+```
+
+<img src="fig-vignettes-med-boot-boot-1.png" width="3300" /><img src="fig-vignettes-med-boot-boot-2.png" width="3300" /><img src="fig-vignettes-med-boot-boot-3.png" width="3300" />
+
+``` r
 plot(boot, type = "bc")
-#> Error: object 'boot' not found
 ```
 
+<img src="fig-vignettes-med-boot-boot-4.png" width="3300" /><img src="fig-vignettes-med-boot-boot-5.png" width="3300" /><img src="fig-vignettes-med-boot-boot-6.png" width="3300" />
+
 The following generates bootstrap confidence intervals for the standardized effects.
 
 
@@ -328,15 +327,17 @@ boot <- BootMedStd(
   med = "m",
   ncores = parallel::detectCores() # use multiple cores
 )
-#> Warning in parallel::mclapply(X = phis, FUN = function(x, delta_t, from, : all
-#> scheduled cores encountered errors in user code
-#> Error in dimnames(x) <- dn: length of 'dimnames' [2] not equal to array extent
 plot(boot)
-#> Error: object 'boot' not found
+```
+
+<img src="fig-vignettes-med-boot-boot-std-1.png" width="3300" /><img src="fig-vignettes-med-boot-boot-std-2.png" width="3300" /><img src="fig-vignettes-med-boot-boot-std-3.png" width="3300" />
+
+``` r
 plot(boot, type = "bc")
-#> Error: object 'boot' not found
 ```
 
+<img src="fig-vignettes-med-boot-boot-std-4.png" width="3300" /><img src="fig-vignettes-med-boot-boot-std-5.png" width="3300" /><img src="fig-vignettes-med-boot-boot-std-6.png" width="3300" />
+
 ## References
 
 
diff --git a/vignettes/med-std.Rmd b/vignettes/med-std.Rmd
@@ -1,7 +1,7 @@
 ---
 title: "Standardized Total, Direct, and Indirect Effects in Continuous-Time Mediation Model"
 author: Ivan Jacob Agaloos Pesigan
-date: "2024-12-30"
+date: "2024-12-31"
 bibliography: "vignettes.bib"
 csl: https://raw.githubusercontent.com/citation-style-language/styles/master/apa.csl
 nocite: |

diff --git a/vignettes/med.Rmd b/vignettes/med.Rmd
@@ -1,7 +1,7 @@
 ---
 title: "Total, Direct, and Indirect Effects in Continuous-Time Mediation Model"
 author: Ivan Jacob Agaloos Pesigan
-date: "2024-12-30"
+date: "2024-12-31"
 bibliography: "vignettes.bib"
 csl: https://raw.githubusercontent.com/citation-style-language/styles/master/apa.csl
 nocite: |

diff --git a/vignettes/session.Rmd b/vignettes/session.Rmd
@@ -43,8 +43,8 @@ sessionInfo()
 #> [1] stats     graphics  grDevices utils     datasets  methods   base     
 #> 
 #> other attached packages:
-#> [1] cTMed_1.0.4              OpenMx_2.21.13           dynr_0.1.16-109         
-#> [4] ggplot2_3.5.1            simStateSpace_1.2.3.9000
+#> [1] cTMed_1.0.4         OpenMx_2.21.13      dynr_0.1.16-109    
+#> [4] ggplot2_3.5.1       simStateSpace_1.2.4
 #> 
 #> loaded via a namespace (and not attached):
 #>  [1] gtable_0.3.6        shape_1.4.6.1       xfun_0.49          
@@ -84,7 +84,6 @@ sessionInfo()
 installed.packages()[, c("Package", "Version")]
 #>                   Package             Version      
 #> cTMed             "cTMed"             "1.0.4"      
-#> rProject          "rProject"          "0.0.14"     
 #> abind             "abind"             "1.4-8"      
 #> arm               "arm"               "1.14-4"     
 #> arrow             "arrow"             "17.0.0.1"   
@@ -96,7 +95,7 @@ installed.packages()[, c("Package", "Version")]
 #> base64enc         "base64enc"         "0.1-3"      
 #> betaDelta         "betaDelta"         "1.0.5.9000" 
 #> betaMC            "betaMC"            "1.3.2.9000" 
-#> betaNB            "betaNB"            "1.0.4.9000" 
+#> betaNB            "betaNB"            "1.0.5"      
 #> betaSandwich      "betaSandwich"      "1.0.7.9000" 
 #> BH                "BH"                "1.87.0-1"   
 #> bibtex            "bibtex"            "0.5.1"      
@@ -134,7 +133,7 @@ installed.packages()[, c("Package", "Version")]
 #> crayon            "crayon"            "1.5.3"      
 #> credentials       "credentials"       "2.0.2"      
 #> crosstalk         "crosstalk"         "1.2.1"      
-#> cTMed             "cTMed"             "1.0.3"      
+#> cTMed             "cTMed"             "1.0.4"      
 #> ctsem             "ctsem"             "3.10.1"     
 #> curl              "curl"              "6.0.1"      
 #> cyclocomp         "cyclocomp"         "1.1.1"      
@@ -319,7 +318,7 @@ installed.packages()[, c("Package", "Version")]
 #> promises          "promises"          "1.3.2"      
 #> proto             "proto"             "1.0.0"      
 #> ps                "ps"                "1.8.1"      
-#> psych             "psych"             "2.4.6.26"   
+#> psych             "psych"             "2.4.12"     
 #> purrr             "purrr"             "1.0.2"      
 #> qgraph            "qgraph"            "1.9.8"      
 #> qpdf              "qpdf"              "1.3.4"      
@@ -384,7 +383,7 @@ installed.packages()[, c("Package", "Version")]
 #> sfd               "sfd"               "0.1.0"      
 #> shape             "shape"             "1.4.6.1"    
 #> shiny             "shiny"             "1.10.0"     
-#> simStateSpace     "simStateSpace"     "1.2.3.9000" 
+#> simStateSpace     "simStateSpace"     "1.2.4"      
 #> slider            "slider"            "0.3.2"      
 #> snow              "snow"              "0.4-4"      
 #> snowfall          "snowfall"          "1.84-6.3"   
@@ -490,7 +489,7 @@ installed.packages()[, c("Package", "Version")]
 #> Stepping:                             1
 #> CPU max MHz:                          2900.0000
 #> CPU min MHz:                          1200.0000
-#> BogoMIPS:                             4389.99
+#> BogoMIPS:                             4390.20
 #> Flags:                                fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc cpuid aperfmperf pni pclmulqdq dtes64 monitor ds_cpl smx est tm2 ssse3 sdbg fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch cpuid_fault epb cat_l3 cdp_l3 invpcid_single pti ssbd ibrs ibpb stibp fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm rdt_a rdseed adx smap intel_pt xsaveopt cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts md_clear flush_l1d
 #> L1d cache:                            768 KiB (24 instances)
 #> L1i cache:                            768 KiB (24 instances)
@@ -520,7 +519,7 @@ installed.packages()[, c("Package", "Version")]
 
 ```
 #>                total        used        free      shared  buff/cache   available
-#> Mem:           125Gi       4.4Gi        21Gi       5.3Gi       100Gi       115Gi
+#> Mem:           125Gi       4.4Gi        30Gi       5.5Gi        90Gi       114Gi
 #> Swap:             0B          0B          0B
-#> Total:         125Gi       4.4Gi        21Gi
+#> Total:         125Gi       4.4Gi        30Gi
 ```