Automated build.

.setup/latex/pdf/.gitignore

@@ -0,0 +1,5 @@
+*
+*/
+!*.pdf
+!.gitignore
+!bib.bib

CITATION.cff

@@ -8,7 +8,7 @@ message: 'To cite package "cTMed" in publications use:'
 type: software
 license: GPL-3.0-or-later
 title: 'cTMed: Continuous Time Mediation'
-version: 1.0.0
+version: 0.9.1
 abstract: Calculates standard errors and confidence intervals for effects in continuous
   time mediation models.
 authors:
@@ -25,7 +25,7 @@ preferred-citation:
     email: r.jeksterslab@gmail.com
     orcid: https://orcid.org/0000-0003-4818-8420
   year: '2024'
-  notes: R package version 1.0.0
+  notes: R package version 0.9.1
 repository-code: https://github.com/jeksterslab/cTMed
 url: https://jeksterslab.github.io/cTMed/
 contact:

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: cTMed
 Title: Continuous Time Mediation
-Version: 1.0.0
+Version: 0.9.1
 Authors@R: 
     person(given = "Ivan Jacob Agaloos",
            family = "Pesigan",

NEWS.md

@@ -1,3 +1 @@
-# cTMed 1.0.0
-
-* Initial release.
+# cTMed 0.9.1 (simulation version)

vignettes/session.Rmd

@@ -43,7 +43,7 @@ sessionInfo()
 #> [1] stats     graphics  grDevices utils     datasets  methods   base     
 #> 
 #> other attached packages:
-#> [1] cTMed_1.0.0
+#> [1] cTMed_0.9.1
 #> 
 #> loaded via a namespace (and not attached):
 #> [1] compiler_4.4.1  tools_4.4.1     Rcpp_1.0.13     rProject_0.0.14
@@ -56,7 +56,7 @@ sessionInfo()
 ``` r
 installed.packages()[, c("Package", "Version")]
 #>                   Package             Version      
-#> cTMed             "cTMed"             "1.0.0"      
+#> cTMed             "cTMed"             "0.9.1"      
 #> abind             "abind"             "1.4-5"      
 #> arm               "arm"               "1.14-4"     
 #> arrow             "arrow"             "17.0.0.1"   
@@ -446,52 +446,53 @@ installed.packages()[, c("Package", "Version")]
 
 
 ```
-#> Architecture:                       x86_64
-#> CPU op-mode(s):                     32-bit, 64-bit
-#> Address sizes:                      46 bits physical, 48 bits virtual
-#> Byte Order:                         Little Endian
-#> CPU(s):                             8
-#> On-line CPU(s) list:                0-7
-#> Vendor ID:                          GenuineIntel
-#> Model name:                         Intel(R) Xeon(R) CPU E5-1620 v2 @ 3.70GHz
-#> CPU family:                         6
-#> Model:                              62
-#> Thread(s) per core:                 2
-#> Core(s) per socket:                 4
-#> Socket(s):                          1
-#> Stepping:                           4
-#> CPU max MHz:                        3900.0000
-#> CPU min MHz:                        1200.0000
-#> BogoMIPS:                           7382.45
-#> 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 vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm cpuid_fault epb pti ssbd ibrs ibpb stibp tpr_shadow flexpriority ept vpid fsgsbase smep erms xsaveopt dtherm ida arat pln pts vnmi md_clear flush_l1d
-#> Virtualization:                     VT-x
-#> L1d cache:                          128 KiB (4 instances)
-#> L1i cache:                          128 KiB (4 instances)
-#> L2 cache:                           1 MiB (4 instances)
-#> L3 cache:                           10 MiB (1 instance)
-#> NUMA node(s):                       1
-#> NUMA node0 CPU(s):                  0-7
-#> Vulnerability Gather data sampling: Not affected
-#> Vulnerability Itlb multihit:        KVM: Mitigation: VMX disabled
-#> Vulnerability L1tf:                 Mitigation; PTE Inversion; VMX conditional cache flushes, SMT vulnerable
-#> Vulnerability Mds:                  Mitigation; Clear CPU buffers; SMT vulnerable
-#> Vulnerability Meltdown:             Mitigation; PTI
-#> Vulnerability Mmio stale data:      Unknown: No mitigations
-#> Vulnerability Retbleed:             Not affected
-#> Vulnerability Spec rstack overflow: Not affected
-#> Vulnerability Spec store bypass:    Mitigation; Speculative Store Bypass disabled via prctl
-#> Vulnerability Spectre v1:           Mitigation; usercopy/swapgs barriers and __user pointer sanitization
-#> Vulnerability Spectre v2:           Mitigation; Retpolines, IBPB conditional, IBRS_FW, STIBP conditional, RSB filling, PBRSB-eIBRS Not affected
-#> Vulnerability Srbds:                Not affected
-#> Vulnerability Tsx async abort:      Not affected
+#> Architecture:                         x86_64
+#> CPU op-mode(s):                       32-bit, 64-bit
+#> Address sizes:                        46 bits physical, 48 bits virtual
+#> Byte Order:                           Little Endian
+#> CPU(s):                               24
+#> On-line CPU(s) list:                  0-23
+#> Vendor ID:                            GenuineIntel
+#> Model name:                           Intel(R) Xeon(R) CPU E5-2650 v4 @ 2.20GHz
+#> CPU family:                           6
+#> Model:                                79
+#> Thread(s) per core:                   1
+#> Core(s) per socket:                   12
+#> Socket(s):                            2
+#> Stepping:                             1
+#> CPU max MHz:                          2900.0000
+#> CPU min MHz:                          1200.0000
+#> BogoMIPS:                             4389.80
+#> 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)
+#> L2 cache:                             6 MiB (24 instances)
+#> L3 cache:                             60 MiB (2 instances)
+#> NUMA node(s):                         2
+#> NUMA node0 CPU(s):                    0,2,4,6,8,10,12,14,16,18,20,22
+#> NUMA node1 CPU(s):                    1,3,5,7,9,11,13,15,17,19,21,23
+#> Vulnerability Gather data sampling:   Not affected
+#> Vulnerability Itlb multihit:          KVM: Mitigation: VMX unsupported
+#> Vulnerability L1tf:                   Mitigation; PTE Inversion
+#> Vulnerability Mds:                    Mitigation; Clear CPU buffers; SMT disabled
+#> Vulnerability Meltdown:               Mitigation; PTI
+#> Vulnerability Mmio stale data:        Mitigation; Clear CPU buffers; SMT disabled
+#> Vulnerability Reg file data sampling: Not affected
+#> Vulnerability Retbleed:               Not affected
+#> Vulnerability Spec rstack overflow:   Not affected
+#> Vulnerability Spec store bypass:      Mitigation; Speculative Store Bypass disabled via prctl
+#> Vulnerability Spectre v1:             Mitigation; usercopy/swapgs barriers and __user pointer sanitization
+#> Vulnerability Spectre v2:             Mitigation; Retpolines; IBPB conditional; IBRS_FW; RSB filling; PBRSB-eIBRS Not affected; BHI Not affected
+#> Vulnerability Srbds:                  Not affected
+#> Vulnerability Tsx async abort:        Mitigation; Clear CPU buffers; SMT disabled
 ```
 
 # Memory
 
 
 ```
 #>                total        used        free      shared  buff/cache   available
-#> Mem:            11Gi       3.0Gi       5.9Gi        51Mi       2.5Gi       8.0Gi
-#> Swap:          7.8Gi          0B       7.8Gi
-#> Total:          19Gi       3.0Gi        13Gi
+#> Mem:           125Gi       2.8Gi        27Gi       5.1Gi        95Gi       116Gi
+#> Swap:             0B          0B          0B
+#> Total:         125Gi       2.8Gi        27Gi
 ```