diff --git a/.gitignore b/.gitignore index 9cad142..b7682a9 100644 --- a/.gitignore +++ b/.gitignore @@ -51,3 +51,4 @@ po/*~ # renv sandbox needed for renv version 0.16.0 renv/sandbox # OPTIONAL +renv/sandbox diff --git a/config.yaml b/config.yaml index dcea755..e5c2d92 100644 --- a/config.yaml +++ b/config.yaml @@ -62,7 +62,7 @@ episodes: - TallerIntroAnaliticaBrotes.Rmd - ZIKAB.Rmd - EnfermedadX.Rmd -- EnfermedadX2.Rmd +#- EnfermedadX2.Rmd - Sivirep-tutorial.Rmd - Serofoi-tutorial.Rmd - Vaccineff-tutorial.Rmd diff --git a/episodes/Serofoi-tutorial.Rmd b/episodes/Serofoi-tutorial.Rmd index c043d89..70289ca 100644 --- a/episodes/Serofoi-tutorial.Rmd +++ b/episodes/Serofoi-tutorial.Rmd @@ -404,14 +404,14 @@ mismo, corra las siguientes líneas de código: ```{r chik2015_constant, include = TRUE, echo = TRUE, eval = FALSE} chik_constant <- run_seromodel(serodata = chik2015p, foi_model = "constant", - n_iters = 1000) + iter = 1000) chik_constant_plot <- plot_seromodel(chik_constant, serodata = chik2015p, size_text = 12) ``` -Ahora, corra los modelos dependientes del tiempo con `n_iters =1500`. +Ahora, corra los modelos dependientes del tiempo con `iter =1500`. Luego visualice conjuntamente las tres gráficas por medio de la función `plot_grid()` del paquete `cowplot`: @@ -435,18 +435,15 @@ minutos. # Implementation of the models m1_chik <- run_seromodel(serodata = chik2015p, foi_model = "constant", - n_iters = 1000, - n_thin = 2) + iter = 1000) m2_chik <- run_seromodel(serodata = chik2015p, foi_model = "tv_normal", - n_iters = 1500, - n_thin = 2) + iter = 1500) m3_chik <- run_seromodel(serodata = chik2015p, foi_model = "tv_normal_log", - n_iters = 1500, - n_thin = 2) + iter = 1500) ``` ```{r chik2015_vis, include = TRUE, echo = FALSE, results="hide", errors = FALSE, warning = FALSE, message = FALSE, fig.width=5, fig.asp=1, fig.align="center", fig.keep="all"} diff --git a/episodes/epiCo-tutorial.Rmd b/episodes/epiCo-tutorial.Rmd index ab3eaa7..2a4db03 100644 --- a/episodes/epiCo-tutorial.Rmd +++ b/episodes/epiCo-tutorial.Rmd @@ -89,7 +89,7 @@ head(divipola_table) Los usuarios pueden realizar consultas a **epiCo** utilizando la función `population_pyramid`, la cual requiere el codigo DIVIPOLA de la entidad de interés y el año que se desea consultar. ```{r} -tolima_codigo <- 73 # Código DIVIPOLA para el departamento del Tolima. +tolima_codigo <- "73" # Código DIVIPOLA para el departamento del Tolima. año <- 2021 # Año a consultar. tolima_piramide_2021 <- population_pyramid(tolima_codigo, año) # Pirámide # poblacional del departamento del tolima para el año 2021. @@ -99,14 +99,14 @@ head(tolima_piramide_2021) **epiCo** presenta los datos agrupados en intervalos de 5 años *de forma predeterminada*; sin embargo, puede modificar parámetros para tener rangos distintos, separar la pirámide por género binario, obtener los datos como conteos totales o proporciones y/o desplegar una gráfica de la pirámide. ```{r} -tolima_codigo <- 73 # Código DIVIPOLA para el departamento del Tolima. +tolima_codigo <- "73" # Código DIVIPOLA para el departamento del Tolima. año <- 2021 # Año a consultar. rango_edad <- 10 #Rango de edades o ventana. # Pirámide poblacional del departamento del tolima para el año 2021. tolima_piramide_2021 <- population_pyramid(divipola_code = tolima_codigo, year = año, range = rango_edad, - gender = TRUE, total = TRUE, + sex = TRUE, total = TRUE, plot = TRUE) ``` @@ -135,7 +135,7 @@ Para calcular la distribución de las ocupaciones en estos años, **epiCo** usa data("isco88_table") head(isco88_table) # Se calcula la distribución de ocupaciones. -occupation_plot(isco_codes = as.integer(epi_data$ocupacion), gender = epi_data$sexo) +describe_occupation(isco_codes = as.integer(epi_data$ocupacion), sex = epi_data$sexo,plot = "treemap") ``` ### 5. Estimación de las tasas de incidencia @@ -168,7 +168,7 @@ data_tolima_2021 <- epi_data[lubridate::year(epi_data$fec_not) == 2021, ] # Se calcula las tasas por edades para el año 2021. incidence_rate_2019 <- age_risk(age = as.integer(data_tolima_2021$edad), population_pyramid = tolima_piramide_2021, - gender = data_tolima_2021$sexo, + sex = data_tolima_2021$sexo, plot = TRUE) ``` @@ -317,8 +317,8 @@ incidence_object <- incidence( # Se realiza el analisis espaciotemporal, especificando la escala de nivel # municipal -monrans_tolima <- morans_index(incidence_object = incidence_object, level = 2) -monrans_tolima$leaflet_map +monrans_tolima <- morans_index(incidence_object = incidence_object, threshold = 2) +monrans_tolima$plot ``` diff --git a/renv/activate.R b/renv/activate.R index cb5401f..d13f993 100644 --- a/renv/activate.R +++ b/renv/activate.R @@ -2,11 +2,13 @@ local({ # the requested version of renv - version <- "1.0.3" + version <- "1.0.7" attr(version, "sha") <- NULL # the project directory - project <- getwd() + project <- Sys.getenv("RENV_PROJECT") + if (!nzchar(project)) + project <- getwd() # use start-up diagnostics if enabled diagnostics <- Sys.getenv("RENV_STARTUP_DIAGNOSTICS", unset = "FALSE") @@ -31,6 +33,14 @@ local({ if (!is.null(override)) return(override) + # if we're being run in a context where R_LIBS is already set, + # don't load -- presumably we're being run as a sub-process and + # the parent process has already set up library paths for us + rcmd <- Sys.getenv("R_CMD", unset = NA) + rlibs <- Sys.getenv("R_LIBS", unset = NA) + if (!is.na(rlibs) && !is.na(rcmd)) + return(FALSE) + # next, check environment variables # TODO: prefer using the configuration one in the future envvars <- c( @@ -50,9 +60,22 @@ local({ }) - if (!enabled) + # bail if we're not enabled + if (!enabled) { + + # if we're not enabled, we might still need to manually load + # the user profile here + profile <- Sys.getenv("R_PROFILE_USER", unset = "~/.Rprofile") + if (file.exists(profile)) { + cfg <- Sys.getenv("RENV_CONFIG_USER_PROFILE", unset = "TRUE") + if (tolower(cfg) %in% c("true", "t", "1")) + sys.source(profile, envir = globalenv()) + } + return(FALSE) + } + # avoid recursion if (identical(getOption("renv.autoloader.running"), TRUE)) { warning("ignoring recursive attempt to run renv autoloader") @@ -108,6 +131,21 @@ local({ } + heredoc <- function(text, leave = 0) { + + # remove leading, trailing whitespace + trimmed <- gsub("^\\s*\\n|\\n\\s*$", "", text) + + # split into lines + lines <- strsplit(trimmed, "\n", fixed = TRUE)[[1L]] + + # compute common indent + indent <- regexpr("[^[:space:]]", lines) + common <- min(setdiff(indent, -1L)) - leave + paste(substring(lines, common), collapse = "\n") + + } + startswith <- function(string, prefix) { substring(string, 1, nchar(prefix)) == prefix } @@ -610,6 +648,9 @@ local({ # if the user has requested an automatic prefix, generate it auto <- Sys.getenv("RENV_PATHS_PREFIX_AUTO", unset = NA) + if (is.na(auto) && getRversion() >= "4.4.0") + auto <- "TRUE" + if (auto %in% c("TRUE", "True", "true", "1")) return(renv_bootstrap_platform_prefix_auto()) @@ -801,24 +842,23 @@ local({ # the loaded version of renv doesn't match the requested version; # give the user instructions on how to proceed - remote <- if (!is.null(description[["RemoteSha"]])) { + dev <- identical(description[["RemoteType"]], "github") + remote <- if (dev) paste("rstudio/renv", description[["RemoteSha"]], sep = "@") - } else { + else paste("renv", description[["Version"]], sep = "@") - } # display both loaded version + sha if available friendly <- renv_bootstrap_version_friendly( version = description[["Version"]], - sha = description[["RemoteSha"]] + sha = if (dev) description[["RemoteSha"]] ) - fmt <- paste( - "renv %1$s was loaded from project library, but this project is configured to use renv %2$s.", - "- Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile.", - "- Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library.", - sep = "\n" - ) + fmt <- heredoc(" + renv %1$s was loaded from project library, but this project is configured to use renv %2$s. + - Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile. + - Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library. + ") catf(fmt, friendly, renv_bootstrap_version_friendly(version), remote) FALSE @@ -1041,7 +1081,7 @@ local({ # if jsonlite is loaded, use that instead if ("jsonlite" %in% loadedNamespaces()) { - json <- catch(renv_json_read_jsonlite(file, text)) + json <- tryCatch(renv_json_read_jsonlite(file, text), error = identity) if (!inherits(json, "error")) return(json) @@ -1050,7 +1090,7 @@ local({ } # otherwise, fall back to the default JSON reader - json <- catch(renv_json_read_default(file, text)) + json <- tryCatch(renv_json_read_default(file, text), error = identity) if (!inherits(json, "error")) return(json) @@ -1063,14 +1103,14 @@ local({ } renv_json_read_jsonlite <- function(file = NULL, text = NULL) { - text <- paste(text %||% read(file), collapse = "\n") + text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") jsonlite::fromJSON(txt = text, simplifyVector = FALSE) } renv_json_read_default <- function(file = NULL, text = NULL) { # find strings in the JSON - text <- paste(text %||% read(file), collapse = "\n") + text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") pattern <- '["](?:(?:\\\\.)|(?:[^"\\\\]))*?["]' locs <- gregexpr(pattern, text, perl = TRUE)[[1]] @@ -1118,14 +1158,14 @@ local({ map <- as.list(map) # remap strings in object - remapped <- renv_json_remap(json, map) + remapped <- renv_json_read_remap(json, map) # evaluate eval(remapped, envir = baseenv()) } - renv_json_remap <- function(json, map) { + renv_json_read_remap <- function(json, map) { # fix names if (!is.null(names(json))) { @@ -1152,7 +1192,7 @@ local({ # recurse if (is.recursive(json)) { for (i in seq_along(json)) { - json[i] <- list(renv_json_remap(json[[i]], map)) + json[i] <- list(renv_json_read_remap(json[[i]], map)) } } diff --git a/renv/profiles/lesson-requirements/renv.lock b/renv/profiles/lesson-requirements/renv.lock index 9e9ecad..3e9af47 100644 --- a/renv/profiles/lesson-requirements/renv.lock +++ b/renv/profiles/lesson-requirements/renv.lock @@ -1,39 +1,35 @@ { "R": { - "Version": "4.2.2", + "Version": "4.4.0", "Repositories": [ - { - "Name": "carpentries", - "URL": "https://carpentries.r-universe.dev" - }, - { - "Name": "carpentries_archive", - "URL": "https://carpentries.github.io/drat" - }, { "Name": "CRAN", "URL": "https://cran.rstudio.com" + }, + { + "Name": "RSPM", + "URL": "https://packagemanager.posit.co/cran/latest" } ] }, "Packages": { "BH": { "Package": "BH", - "Version": "1.81.0-1", + "Version": "1.84.0-0", "Source": "Repository", "Repository": "CRAN", - "Hash": "68122010f01c4dcfbe58ce7112f2433d" + "Hash": "a8235afbcd6316e6e91433ea47661013" }, "DBI": { "Package": "DBI", - "Version": "1.1.3", + "Version": "1.2.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "methods" ], - "Hash": "b2866e62bab9378c3cc9476a1954226b" + "Hash": "065ae649b05f1ff66bb0c793107508f5" }, "EpiEstim": { "Package": "EpiEstim", @@ -69,11 +65,12 @@ }, "Hmisc": { "Package": "Hmisc", - "Version": "5.1-1", + "Version": "5.1-3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "Formula", + "R", "base64enc", "cluster", "colorspace", @@ -92,7 +89,7 @@ "rpart", "viridis" ], - "Hash": "27c7750992bc511728e2f9ebd2911199" + "Hash": "9a446aea30bff7e8ee20f4c0973e8851" }, "KernSmooth": { "Package": "KernSmooth", @@ -107,7 +104,7 @@ }, "MASS": { "Package": "MASS", - "Version": "7.3-60", + "Version": "7.3-60.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -118,11 +115,11 @@ "stats", "utils" ], - "Hash": "a56a6365b3fa73293ea8d084be0d9bb0" + "Hash": "2f342c46163b0b54d7b64d1f798e2c78" }, "MCMCpack": { "Package": "MCMCpack", - "Version": "1.6-3", + "Version": "1.7-0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -138,11 +135,29 @@ "stats", "utils" ], - "Hash": "520335edba1c95a90eec54d693727723" + "Hash": "225c857e115cf09e1804ff3e597fe555" + }, + "MatchIt": { + "Package": "MatchIt", + "Version": "4.5.5", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "Rcpp", + "RcppProgress", + "backports", + "chk", + "graphics", + "rlang", + "stats", + "utils" + ], + "Hash": "f3bceab061c8d2da3c674d0b0cc3dd54" }, "Matrix": { "Package": "Matrix", - "Version": "1.6-4", + "Version": "1.7-0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -155,7 +170,7 @@ "stats", "utils" ], - "Hash": "d9c655b30a2edc6bb2244c1d1e8d549d" + "Hash": "1920b2f11133b12350024297d8a4ff4a" }, "MatrixModels": { "Package": "MatrixModels", @@ -172,15 +187,10 @@ }, "QuickJSR": { "Package": "QuickJSR", - "Version": "1.0.8", + "Version": "1.2.2", "Source": "Repository", "Repository": "CRAN", - "Requirements": [ - "R6", - "Rcpp", - "jsonlite" - ], - "Hash": "193b83c7d9a8c110da05e1bd0f1f2f55" + "Hash": "706b2f1907052a0082590a4f119402d6" }, "R6": { "Package": "R6", @@ -204,18 +214,32 @@ }, "Rcpp": { "Package": "Rcpp", - "Version": "1.0.11", + "Version": "1.0.12", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "methods", "utils" ], - "Hash": "ae6cbbe1492f4de79c45fce06f967ce8" + "Hash": "5ea2700d21e038ace58269ecdbeb9ec0" + }, + "RcppArmadillo": { + "Package": "RcppArmadillo", + "Version": "0.12.8.4.0", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "Rcpp", + "methods", + "stats", + "utils" + ], + "Hash": "a535dd90aa8ec9a2e63a8f79b4a1bf43" }, "RcppEigen": { "Package": "RcppEigen", - "Version": "0.3.3.9.4", + "Version": "0.3.4.0.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -224,21 +248,28 @@ "stats", "utils" ], - "Hash": "acb0a5bf38490f26ab8661b467f4f53a" + "Hash": "df49e3306f232ec28f1604e36a202847" }, "RcppParallel": { "Package": "RcppParallel", "Version": "5.1.7", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R" ], "Hash": "a45594a00f5dbb073d5ec9f48592a08a" }, + "RcppProgress": { + "Package": "RcppProgress", + "Version": "0.4.2", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "1c0aa18b97e6aaa17f93b8b866c0ace5" + }, "SparseM": { "Package": "SparseM", - "Version": "1.81", + "Version": "1.84", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -248,11 +279,11 @@ "stats", "utils" ], - "Hash": "2042cd9759cc89a453c4aefef0ce9aae" + "Hash": "0648c7c4e275c265356649f818dbfcf5" }, "StanHeaders": { "Package": "StanHeaders", - "Version": "2.26.28", + "Version": "2.32.9", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -260,7 +291,7 @@ "RcppEigen", "RcppParallel" ], - "Hash": "35b5aee9ec9507aca2e021997a9e557e" + "Hash": "affbfba7203fd83b6594362f1355c25b" }, "abind": { "Package": "abind", @@ -296,13 +327,13 @@ }, "backports": { "Package": "backports", - "Version": "1.4.1", + "Version": "1.5.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "c39fbec8a30d23e721980b8afb31984c" + "Hash": "e1e1b9d75c37401117b636b7ae50827a" }, "base64enc": { "Package": "base64enc", @@ -316,7 +347,7 @@ }, "bayesplot": { "Package": "bayesplot", - "Version": "1.10.0", + "Version": "1.11.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -333,7 +364,7 @@ "tidyselect", "utils" ], - "Hash": "9c4f6ab31da906185d23e69a88595cf7" + "Hash": "c5cde76012ea08e94265ace1b53b77b9" }, "binom": { "Package": "binom", @@ -380,7 +411,7 @@ }, "boot": { "Package": "boot", - "Version": "1.3-28.1", + "Version": "1.3-30", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -388,18 +419,17 @@ "graphics", "stats" ], - "Hash": "9a052fbcbe97a98ceb18dbfd30ebd96e" + "Hash": "96abeed416a286d4a0f52e550b612343" }, "broom": { "Package": "broom", - "Version": "1.0.5", + "Version": "1.0.6", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "backports", "dplyr", - "ellipsis", "generics", "glue", "lifecycle", @@ -409,17 +439,18 @@ "tibble", "tidyr" ], - "Hash": "fd25391c3c4f6ecf0fa95f1e6d15378c" + "Hash": "a4652c36d1f8abfc3ddf4774f768c934" }, "bslib": { "Package": "bslib", - "Version": "0.6.1", + "Version": "0.7.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "base64enc", "cachem", + "fastmap", "grDevices", "htmltools", "jquerylib", @@ -430,22 +461,22 @@ "rlang", "sass" ], - "Hash": "c0d8599494bc7fb408cd206bbdd9cab0" + "Hash": "8644cc53f43828f19133548195d7e59e" }, "cachem": { "Package": "cachem", - "Version": "1.0.8", + "Version": "1.1.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "fastmap", "rlang" ], - "Hash": "c35768291560ce302c0a6589f92e837d" + "Hash": "cd9a672193789068eb5a2aad65a0dedf" }, "callr": { "Package": "callr", - "Version": "3.7.3", + "Version": "3.7.6", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -454,7 +485,7 @@ "processx", "utils" ], - "Hash": "9b2191ede20fa29828139b9900922e51" + "Hash": "d7e13f49c19103ece9e58ad2d83a7354" }, "cellranger": { "Package": "cellranger", @@ -470,7 +501,7 @@ }, "checkmate": { "Package": "checkmate", - "Version": "2.3.0", + "Version": "2.3.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -478,7 +509,21 @@ "backports", "utils" ], - "Hash": "ed4275b13c6ab74b89a31def0b6bf835" + "Hash": "c01cab1cb0f9125211a6fc99d540e315" + }, + "chk": { + "Package": "chk", + "Version": "0.9.1", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "lifecycle", + "methods", + "rlang", + "tools" + ], + "Hash": "426a04600c755952486b5242e55e3baf" }, "class": { "Package": "class", @@ -511,14 +556,14 @@ }, "cli": { "Package": "cli", - "Version": "3.6.1", + "Version": "3.6.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "utils" ], - "Hash": "89e6d8219950eac806ae0c489052048a" + "Hash": "1216ac65ac55ec0058a6f75d7ca0fd52" }, "clipr": { "Package": "clipr", @@ -560,14 +605,14 @@ }, "coda": { "Package": "coda", - "Version": "0.19-4", + "Version": "0.19-4.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "lattice" ], - "Hash": "24b6d006b8b2343876cf230687546932" + "Hash": "af436915c590afc6fffc3ce3a5be1569" }, "colorspace": { "Package": "colorspace", @@ -585,20 +630,20 @@ }, "commonmark": { "Package": "commonmark", - "Version": "1.9.0", + "Version": "1.9.1", "Source": "Repository", "Repository": "CRAN", - "Hash": "d691c61bff84bd63c383874d2d0c3307" + "Hash": "5d8225445acb167abf7797de48b2ee3c" }, "config": { "Package": "config", - "Version": "0.3.1", + "Version": "0.3.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "yaml" ], - "Hash": "31d77b09f63550cee9ecb5a08bf76e8f" + "Hash": "8b7222e9d9eb5178eea545c0c4d33fc2" }, "conflicted": { "Package": "conflicted", @@ -615,7 +660,7 @@ }, "cowplot": { "Package": "cowplot", - "Version": "1.1.1", + "Version": "1.1.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -628,7 +673,7 @@ "rlang", "scales" ], - "Hash": "b418e8423699d11c7f2087c2bfd07da2" + "Hash": "8ef2084dd7d28847b374e55440e4f8cb" }, "cpp11": { "Package": "cpp11", @@ -667,28 +712,28 @@ }, "curl": { "Package": "curl", - "Version": "5.1.0", + "Version": "5.2.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "9123f3ef96a2c1a93927d828b2fe7d4c" + "Hash": "411ca2c03b1ce5f548345d2fc2685f7a" }, "data.table": { "Package": "data.table", - "Version": "1.14.8", + "Version": "1.15.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "methods" ], - "Hash": "b4c06e554f33344e044ccd7fdca750a9" + "Hash": "8ee9ac56ef633d0c7cab8b2ca87d683e" }, "dbplyr": { "Package": "dbplyr", - "Version": "2.4.0", + "Version": "2.5.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -712,7 +757,7 @@ "vctrs", "withr" ], - "Hash": "59351f28a81f0742720b85363c4fdd61" + "Hash": "39b2e002522bfd258039ee4e889e0fd1" }, "deSolve": { "Package": "deSolve", @@ -730,7 +775,7 @@ }, "deldir": { "Package": "deldir", - 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"Version": "3.4.4", + "Version": "3.5.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1104,11 +1152,57 @@ "vctrs", "withr" ], - "Hash": "313d31eff2274ecf4c1d3581db7241f9" + "Hash": "44c6a2f8202d5b7e878ea274b1092426" + }, + "ggraph": { + "Package": "ggraph", + "Version": "2.2.1", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "MASS", + "R", + "cli", + "cpp11", + "dplyr", + "ggforce", + "ggplot2", + "ggrepel", + "graphlayouts", + "grid", + "igraph", + "lifecycle", + "memoise", + "rlang", + "scales", + "stats", + "tidygraph", + "utils", + "vctrs", + "viridis", + "withr" + ], + "Hash": "1f5d21a9e1f84b4a81ddacb8f052ca61" + }, + "ggrepel": { + "Package": "ggrepel", + "Version": "0.9.5", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "Rcpp", + "ggplot2", + "grid", + "rlang", + "scales", + "withr" + ], + "Hash": "cc3361e234c4a5050e29697d675764aa" }, "ggridges": { "Package": "ggridges", - "Version": "0.5.4", + "Version": "0.5.6", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1118,18 +1212,18 @@ "scales", "withr" ], - 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"Version": "0.10", + "Version": "0.11", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "xfun" ], - "Hash": "06230136b2d2b9ba5805e1963fa6e890" + "Hash": "d65ba49117ca223614f71b60d85b8ab7" }, "hms": { "Package": "hms", @@ -1299,24 +1406,23 @@ }, "htmltools": { "Package": "htmltools", - "Version": "0.5.7", + "Version": "0.5.8.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "base64enc", "digest", - "ellipsis", "fastmap", "grDevices", "rlang", "utils" ], - "Hash": "2d7b3857980e0e0d0a1fd6f11928ab0f" + "Hash": "81d371a9cc60640e74e4ab6ac46dcedc" }, "htmlwidgets": { "Package": "htmlwidgets", - "Version": "1.6.3", + "Version": "1.6.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1327,7 +1433,7 @@ "rmarkdown", "yaml" ], - "Hash": "a4040b08269c9af64554e55f514d002c" + "Hash": "04291cc45198225444a397606810ac37" }, "httr": { "Package": "httr", @@ -1344,6 +1450,27 @@ ], "Hash": "ac107251d9d9fd72f0ca8049988f1d7f" }, + "httr2": { + "Package": "httr2", + "Version": "1.0.1", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "R6", + "cli", + "curl", + "glue", + "lifecycle", + "magrittr", + "openssl", + "rappdirs", + "rlang", + "vctrs", + "withr" + ], + "Hash": "03d741c92fda96d98c3a3f22494e3b4a" + }, "ids": { "Package": "ids", "Version": "1.0.1", @@ -1357,7 +1484,7 @@ }, "igraph": { "Package": "igraph", - "Version": "1.5.1", + "Version": "2.0.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1373,20 +1500,21 @@ "pkgconfig", "rlang", "stats", - "utils" + "utils", + "vctrs" ], - "Hash": "80401cb5ec513e8ddc56764d03f63669" + "Hash": "c3b7d801d722e26e4cd888e042bf9af5" }, "incidence": { "Package": "incidence", - "Version": "1.7.3", + "Version": "1.7.5", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "aweek", "ggplot2" ], - "Hash": "39f21a0b2551af74c6c60a75fa0ff5c4" + "Hash": "2da4fc68478248c6b6aa096b47547e82" }, "inline": { "Package": "inline", @@ -1431,17 +1559,42 @@ }, "jsonlite": { "Package": "jsonlite", - "Version": "1.8.7", + "Version": "1.8.8", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "methods" ], - "Hash": "266a20443ca13c65688b2116d5220f76" + "Hash": "e1b9c55281c5adc4dd113652d9e26768" + }, + "kableExtra": { + "Package": "kableExtra", + "Version": "1.4.0", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "digest", + "grDevices", + "graphics", + "htmltools", + "knitr", + "magrittr", + "rmarkdown", + "rstudioapi", + "scales", + "stats", + "stringr", + "svglite", + "tools", + "viridisLite", + "xml2" + ], + "Hash": "532d16304274c23c8563f94b79351c86" }, "knitr": { "Package": "knitr", - "Version": "1.45", + "Version": "1.47", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1453,7 +1606,7 @@ "xfun", "yaml" ], - "Hash": "1ec462871063897135c1bcbe0fc8f07d" + "Hash": "7c99b2d55584b982717fcc0950378612" }, "labeling": { "Package": "labeling", @@ -1468,7 +1621,7 @@ }, "lattice": { "Package": "lattice", - "Version": "0.22-5", + "Version": "0.22-6", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1479,7 +1632,7 @@ "stats", "utils" ], - "Hash": "7c5e89f04e72d6611c77451f6331a091" + "Hash": "cc5ac1ba4c238c7ca9fa6a87ca11a7e2" }, "lazyeval": { "Package": "lazyeval", @@ -1493,7 +1646,7 @@ }, "leaflet": { "Package": "leaflet", - "Version": "2.2.1", + "Version": "2.2.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1511,10 +1664,10 @@ "scales", "sp", "stats", - "viridis", + "viridisLite", "xfun" ], - "Hash": "6e09cb2c9dc2e5a1e71a413e60c3834e" + "Hash": "ca012d4a706e21ce217ba15f22d402b2" }, "leaflet.providers": { "Package": "leaflet.providers", @@ -1542,7 +1695,7 @@ }, "loo": { "Package": "loo", - "Version": "2.6.0", + "Version": "2.7.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1550,9 +1703,10 @@ "checkmate", "matrixStats", "parallel", + "posterior", "stats" ], - "Hash": "e5c8f41731502a0e98f353da23f7ca30" + "Hash": "7917e9c58d89dbb80d8eede166581fa0" }, "lubridate": { "Package": "lubridate", @@ -1577,27 +1731,9 @@ ], "Hash": "7ce2733a9826b3aeb1775d56fd305472" }, - "maptools": { - "Package": "maptools", - "Version": "1.1-6", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "foreign", - "grDevices", - "grid", - "lattice", - "methods", - "sp", - "stats", - "utils" - ], - "Hash": "cd65b7fe71f03fca368a1e93db5ed91b" - }, "markdown": { "Package": "markdown", - "Version": "1.11", + "Version": "1.13", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1606,17 +1742,17 @@ "utils", "xfun" ], - "Hash": "82b8d62b5451f8adea7d11a99dfea633" + "Hash": "074efab766a9d6360865ad39512f2a7e" }, "matrixStats": { "Package": "matrixStats", - 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"Hash": "b8e943d262c3da0b0febd3e04517c197" + "Hash": "184d7799bca4ba8c3be72ea396f4b9a3" + }, + "svglite": { + "Package": "svglite", + "Version": "2.1.3", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "cpp11", + "systemfonts" + ], + "Hash": "124a41fdfa23e8691cb744c762f10516" }, "sys": { "Package": "sys", @@ -2497,31 +2636,39 @@ "Repository": "CRAN", "Hash": "3a1be13d68d47a8cd0bfd74739ca1555" }, + "sysfonts": { + "Package": "sysfonts", + "Version": "0.8.9", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "7dfca1e9c5c278300b5ca6a1772072f7" + }, "systemfonts": { "Package": "systemfonts", - "Version": "1.0.5", + "Version": "1.1.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", - "cpp11" + "cpp11", + "lifecycle" ], - "Hash": "15b594369e70b975ba9f064295983499" + "Hash": "213b6b8ed5afbf934843e6c3b090d418" }, "tensorA": { "Package": "tensorA", - "Version": "0.36.2", + "Version": "0.36.2.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "stats" ], - "Hash": "fd792ceac77f96b647fa8d6e1788969a" + "Hash": "0d587599172f2ffda2c09cb6b854e0e5" }, "terra": { "Package": "terra", - "Version": "1.7-55", + "Version": "1.7-78", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2529,19 +2676,20 @@ "Rcpp", "methods" ], - "Hash": "c011cc748506148c793428eb8ec101f9" + "Hash": "8f020def0792119cb98bd8f696dab22d" }, "textshaping": { "Package": "textshaping", - "Version": "0.3.7", + "Version": "0.4.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "cpp11", + "lifecycle", "systemfonts" ], - "Hash": "997aac9ad649e0ef3b97f96cddd5622b" + "Hash": "5142f8bc78ed3d819d26461b641627ce" }, "threejs": { "Package": "threejs", @@ -2578,9 +2726,32 @@ ], "Hash": "a84e2cc86d07289b3b6f5069df7a004c" }, + "tidygraph": { + "Package": "tidygraph", + "Version": "1.3.1", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R6", + "cli", + "cpp11", + "dplyr", + "igraph", + "lifecycle", + "magrittr", + "pillar", + "rlang", + "stats", + "tibble", + "tidyr", + "tools", + "utils" + ], + "Hash": "2149824d406f233b57b087be72c5f163" + }, "tidyr": { "Package": "tidyr", - "Version": "1.3.0", + "Version": "1.3.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2599,11 +2770,11 @@ "utils", "vctrs" ], - "Hash": "e47debdc7ce599b070c8e78e8ac0cfcf" + "Hash": "915fb7ce036c22a6a33b5a8adb712eb1" }, "tidyselect": { "Package": "tidyselect", - "Version": "1.2.0", + "Version": "1.2.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2615,7 +2786,7 @@ "vctrs", "withr" ], - "Hash": "79540e5fcd9e0435af547d885f184fd5" + "Hash": "829f27b9c4919c16b593794a6344d6c0" }, "tidyverse": { "Package": "tidyverse", @@ -2659,24 +2830,24 @@ }, "timechange": { "Package": "timechange", - "Version": "0.2.0", + "Version": "0.3.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "cpp11" ], - "Hash": "8548b44f79a35ba1791308b61e6012d7" + "Hash": "c5f3c201b931cd6474d17d8700ccb1c8" }, "tinytex": { "Package": "tinytex", - "Version": "0.49", + "Version": "0.51", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "xfun" ], - "Hash": "5ac22900ae0f386e54f1c307eca7d843" + "Hash": "d44e2fcd2e4e076f0aac540208559d1d" }, "treemapify": { "Package": "treemapify", @@ -2692,6 +2863,21 @@ ], "Hash": "bbba5d34efaec259a45f18539b449b9a" }, + "tweenr": { + "Package": "tweenr", + "Version": "2.0.3", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "cpp11", + "farver", + "magrittr", + "rlang", + "vctrs" + ], + "Hash": "82fac2b73e6a1f3874fc000aaf96d8bc" + }, "tzdb": { "Package": "tzdb", "Version": "0.4.0", @@ -2716,23 +2902,23 @@ }, "utf8": { "Package": "utf8", - "Version": "1.2.3", + "Version": "1.2.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "1fe17157424bb09c48a8b3b550c753bc" + "Hash": "62b65c52671e6665f803ff02954446e9" }, "uuid": { "Package": "uuid", - "Version": "1.1-1", + "Version": "1.2-0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "3d78edfb977a69fc7a0341bee25e163f" + "Hash": "303c19bfd970bece872f93a824e323d9" }, "vaccineff": { "Package": "vaccineff", @@ -2740,11 +2926,13 @@ "Source": "GitHub", "RemoteType": "github", "RemoteHost": "api.github.com", - "RemoteUsername": "epiverse-trace", "RemoteRepo": "vaccineff", - "RemoteRef": "main", - "RemoteSha": "666ddf4f1272f835f0faaed796ed2aa824c63946", + "RemoteUsername": "epiverse-trace", + "RemotePkgRef": "epiverse-trace/vaccineff", + "RemoteRef": "HEAD", + "RemoteSha": "f68ec19567676ad30c4b4fdb346e9cd92fc5cb55", "Requirements": [ + "MatchIt", "R", "checkmate", "ggplot2", @@ -2753,7 +2941,7 @@ "stats", "survival" ], - "Hash": "dff57d6aacd7046dca5edd79fdebb552" + "Hash": "998980178e686a2e8ed0a043d1860ee2" }, "vctrs": { "Package": "vctrs", @@ -2771,7 +2959,7 @@ }, "viridis": { "Package": "viridis", - "Version": "0.6.4", + "Version": "0.6.5", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2780,7 +2968,7 @@ "gridExtra", "viridisLite" ], - "Hash": "80cd127bc8c9d3d9f0904ead9a9102f1" + "Hash": "acd96d9fa70adeea4a5a1150609b9745" }, "viridisLite": { "Package": "viridisLite", @@ -2812,7 +3000,7 @@ }, "vroom": { "Package": "vroom", - "Version": "1.6.4", + "Version": "1.6.5", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2834,20 +3022,19 @@ "vctrs", "withr" ], - "Hash": "9db52c1656cf19c124f93124ea57f0fd" + "Hash": "390f9315bc0025be03012054103d227c" }, "withr": { "Package": "withr", - "Version": "2.5.2", + "Version": "3.0.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "grDevices", - "graphics", - "stats" + "graphics" ], - "Hash": "4b25e70111b7d644322e9513f403a272" + "Hash": "d31b6c62c10dcf11ec530ca6b0dd5d35" }, "wk": { "Package": "wk", @@ -2861,32 +3048,35 @@ }, "xfun": { "Package": "xfun", - "Version": "0.40", + "Version": "0.44", "Source": "Repository", "Repository": "CRAN", "Requirements": [ + "grDevices", "stats", "tools" ], - "Hash": "be07d23211245fc7d4209f54c4e4ffc8" + "Hash": "317a0538d32f4a009658bcedb7923f4b" }, "xml2": { "Package": "xml2", - "Version": "1.3.5", + "Version": "1.3.6", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", - "methods" + "cli", + "methods", + "rlang" ], - "Hash": "6c40e5cfcc6aefd88110666e18c31f40" + "Hash": "1d0336142f4cd25d8d23cd3ba7a8fb61" }, "yaml": { "Package": "yaml", - "Version": "2.3.7", + "Version": "2.3.8", "Source": "Repository", "Repository": "CRAN", - "Hash": "0d0056cc5383fbc240ccd0cb584bf436" + "Hash": "29240487a071f535f5e5d5a323b7afbd" } } }