Update 78 packages

.gitignore

@@ -51,3 +51,4 @@ po/*~
 
 # renv sandbox needed for renv version 0.16.0
 renv/sandbox # OPTIONAL
+renv/sandbox

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

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"}

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
 ```
 
 

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))
       }
     }