#33 drop beta0; add deprecation warning;

s3alfisc · Apr 18, 2022 · 1901846 · 1901846
1 parent 339fcb4
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -12,3 +12,4 @@
 ^pkgdown$
 ^CRAN-RELEASE$
 ^vignettes/articles$
+^CRAN-SUBMISSION$
diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION
@@ -0,0 +1,4 @@
+Version: 0.8
+Date: 2022-04-18 10:43:54 UTC
+SHA:
+    339fcb4e2811e4bd58e518d7254a82b96763a64c
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -46,7 +46,7 @@ Description: Implementation of the fast algorithm for wild cluster bootstrap
              bootstrap.
              Further, the package provides an R binding to 'WildBootTests.jl',
              which provides additional speed gains and functionality, 
-             including the WRE bootstrap for instrumental variable models 
+             including the 'WRE' bootstrap for instrumental variable models 
              (based on models of type 'ivreg()' from package 'ivreg')
              and hypotheses with q > 1.
 URL: https://s3alfisc.github.io/fwildclusterboot/

diff --git a/NEWS.md b/NEWS.md
@@ -75,7 +75,7 @@ summary(boot_hc1)
 
 ### `boottest()` function argument `beta0` deprecated
 
-For consistency with `WildBootTests.jl`, it is now replaced by a new function argument, `r`. You can still use `beta0` for the forseeable future - `boottest()` will throw a warning. 
+For consistency with `WildBootTests.jl`, the `boottest()` function argument `beta0` is now replaced by a new function argument, `r`. 
 
 ### Frühjahrsputz
 

diff --git a/R/boottest_felm.R b/R/boottest_felm.R
@@ -37,7 +37,7 @@
 #' @param R Hypothesis Vector giving linear combinations of coefficients. Must be either NULL or a vector of the same length as `param`. If NULL, a vector of ones of length param.
 #' @param r A numeric. Shifts the null hypothesis
 #'        H0: param = r vs H1: param != r
-#' @param beta0 Superseded function argument, replaced by function argument 'r'
+#' @param beta0 Deprecated function argument. Replaced by function argument 'r'.
 #' @param type character or function. The character string specifies the type
 #'        of boostrap to use: One of "rademacher", "mammen", "norm"
 #'        and "webb". Alternatively, type can be a function(n) for drawing
@@ -202,7 +202,7 @@ boottest.felm <- function(object,
                           seed = NULL,
                           R = NULL,
                           r = 0,
-                          beta0 = r,
+                          beta0 = NULL, 
                           sign_level = 0.05,
                           type = "rademacher",
                           impose_null = TRUE,
@@ -242,7 +242,6 @@ boottest.felm <- function(object,
   check_arg(internal_seed, "scalar logical")
   check_arg(R, "NULL| scalar numeric | numeric vector")
   check_arg(r, "numeric scalar | NULL")
-  check_arg(beta0, "numeric scalar | NULL")
   check_arg(fe, "character scalar | NULL")
   check_arg(bootcluster, "character vector")
   check_arg(tol, "numeric scalar GT{0}")
@@ -254,10 +253,10 @@ boottest.felm <- function(object,
   check_arg(maxmatsize, "scalar integer | NULL")
   check_arg(bootstrapc, "scalar logical")
 
-  if (missing(r) & !missing(beta0)) {
-    warning("Note that the 'beta0' function argument is superseded by a new argument, 'r'. Please specify your hypothesis via the new function argument instead of using 'beta0'.")
+  if(!is.null(beta0)){
+    stop("The function argument 'beta0' is deprecated. Please use the function argument 'r' instead, by which it is replaced.")
   }
-
+  
   internal_seed <- set_seed(
     seed = seed, 
     boot_algo = boot_algo, 

diff --git a/R/boottest_fixest.R b/R/boottest_fixest.R
@@ -37,7 +37,7 @@
 #' @param R Hypothesis Vector giving linear combinations of coefficients. Must be either NULL or a vector of the same length as `param`. If NULL, a vector of ones of length param.
 #' @param r A numeric. Shifts the null hypothesis
 #'        H0: param = r vs H1: param != r
-#' @param beta0 Superseded function argument, replaced by function argument 'r'
+#' @param beta0 Deprecated function argument. Replaced by function argument 'r'.
 #' @param type character or function. The character string specifies the type
 #'        of boostrap to use: One of "rademacher", "mammen", "norm"
 #'        and "webb". Alternatively, type can be a function(n) for drawing
@@ -197,7 +197,7 @@ boottest.fixest <- function(object,
                             seed = NULL,
                             R = NULL,
                             r = 0,
-                            beta0 = r,
+                            beta0 = NULL, 
                             type = "rademacher",
                             impose_null = TRUE,
                             p_val_type = "two-tailed",
@@ -235,7 +235,6 @@ boottest.fixest <- function(object,
   check_arg(seed, "scalar integer | NULL")
   check_arg(R, "NULL| scalar numeric | numeric vector")
   check_arg(r, "numeric scalar | NULL")
-  check_arg(beta0, "numeric scalar | NULL")
   check_arg(fe, "character scalar | NULL")
   check_arg(bootcluster, "character vector")
   check_arg(tol, "numeric scalar GT{0}")
@@ -247,10 +246,9 @@ boottest.fixest <- function(object,
   check_arg(maxmatsize, "scalar integer | NULL")
   check_arg(bootstrapc, "scalar logical")
 
-  if (missing(r) & !missing(beta0)) {
-    warning("Note that the 'beta0' function argument is superseded by a new argument, 'r'. Please specify your hypothesis via the new function argument instead of using 'beta0'.")
+  if(!is.null(beta0)){
+    stop("The function argument 'beta0' is deprecated. Please use the function argument 'r' instead, by which it is replaced.")
   }
-
 
   internal_seed <- set_seed(
     seed = seed, 

diff --git a/R/boottest_ivreg.R b/R/boottest_ivreg.R
@@ -27,7 +27,6 @@
 #' @param R Hypothesis Vector giving linear combinations of coefficients. Must be either NULL or a vector of the same length as `param`. If NULL, a vector of ones of length param.
 #' @param r A numeric. Shifts the null hypothesis
 #'        H0: param = r vs H1: param != r
-#' @param beta0 Superseded function argument, replaced by function argument 'r'
 #' @param type character or function. The character string specifies the type
 #'        of boostrap to use: One of "rademacher", "mammen", "norm", "gamma"
 #'        and "webb". Alternatively, type can be a function(n) for drawing
@@ -142,7 +141,6 @@ boottest.ivreg <- function(object,
                            seed = NULL,
                            R = NULL,
                            r = 0,
-                           beta0 = r,
                            sign_level = 0.05,
                            type = "rademacher",
                            impose_null = TRUE,

diff --git a/R/boottest_lm.R b/R/boottest_lm.R
@@ -34,7 +34,7 @@
 #' @param R Hypothesis Vector giving linear combinations of coefficients. Must be either NULL or a vector of the same length as `param`. If NULL, a vector of ones of length param.
 #' @param r A numeric. Shifts the null hypothesis
 #'        H0: param = r vs H1: param != r
-#' @param beta0 Superseded function argument, replaced by function argument 'r'
+#' @param beta0 Deprecated function argument. Replaced by function argument 'r'.
 #' @param type character or function. The character string specifies the type
 #'        of boostrap to use: One of "rademacher", "mammen", "norm"
 #'        and "webb". Alternatively, type can be a function(n) for drawing
@@ -182,7 +182,7 @@ boottest.lm <- function(object,
                         seed = NULL,
                         R = NULL,
                         r = 0,
-                        beta0 = r,
+                        beta0 = NULL, 
                         sign_level = 0.05,
                         type = "rademacher",
                         impose_null = TRUE,
@@ -218,7 +218,6 @@ boottest.lm <- function(object,
   check_arg(seed, "scalar integer | NULL")
   check_arg(R, "NULL| scalar numeric | numeric vector")
   check_arg(r, "numeric scalar | NULL")
-  check_arg(beta0, "numeric scalar | NULL")
   check_arg(bootcluster, "character vector")
   check_arg(tol, "numeric scalar GT{0}")
   check_arg(maxiter, "scalar integer GT{5}")
@@ -228,16 +227,17 @@ boottest.lm <- function(object,
   check_arg(maxmatsize, "scalar integer | NULL")
   check_arg(bootstrapc, "scalar logical")
 
-  if (missing(r) & !missing(beta0)) {
-    warning("Note that the 'beta0' function argument is superseded by a new argument, 'r'. Please specify your hypothesis via the new function argument instead of using 'beta0'.")
+  if(!is.null(beta0)){
+    stop("The function argument 'beta0' is deprecated. Please use the function argument 'r' instead, by which it is replaced.")
   }
-  
+
   internal_seed <- set_seed(
     seed = seed, 
     boot_algo = boot_algo, 
     type = type
   )
 
+
   # check appropriateness of nthreads
   nthreads <- check_set_nthreads(nthreads)
 

diff --git a/R/mboottest_felm.R b/R/mboottest_felm.R
@@ -23,7 +23,6 @@
 #'        of joint hypotheses and k the number of estimated coefficients.
 #' @param r A vector of length q, where q is the number of tested hypotheses. Shifts the null hypothesis
 #'        H0: param = r vs H1: param != r. If not provided, a vector of zeros of length q.
-#' @param beta0 Superseded function argument, replaced by function argument 'r'
 #' @param type character or function. The character string specifies the type
 #'        of boostrap to use: One of "rademacher", "mammen", "norm", "gamma"
 #'        and "webb". Alternatively, type can be a function(n) for drawing
@@ -117,7 +116,6 @@ mboottest.felm <- function(object,
                            B,
                            R,
                            r = rep(0, nrow(R)),
-                           beta0 = r,
                            bootcluster = "max",
                            fe = NULL,
                            seed = NULL,

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,3 +1,11 @@
+## Re-submission of 0.8
+
++ "Found the following (possibly) invalid file URI:
+  URI: WildBootTests.html
+    From: inst/doc/fwildclusterboot.html"
+    -> replaced 'internal' reference with proper URL
+
+
 ## Submission of 0.8
 
 + checked on github actions (mac, windows, linux)

diff --git a/docs/articles/fwildclusterboot.html b/docs/articles/fwildclusterboot.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/man/boottest.felm.Rd b/man/boottest.felm.Rd
diff --git a/man/boottest.fixest.Rd b/man/boottest.fixest.Rd
diff --git a/man/boottest.ivreg.Rd b/man/boottest.ivreg.Rd
diff --git a/man/boottest.lm.Rd b/man/boottest.lm.Rd
diff --git a/man/mboottest.felm.Rd b/man/mboottest.felm.Rd
diff --git a/vignettes/fwildclusterboot.Rmd b/vignettes/fwildclusterboot.Rmd
@@ -280,7 +280,7 @@ boot_lm <- boottest(lm_fit,
 
 `fwildclusterboot` serves as an R port to [WildBootTests.jl](https://github.com/droodman/WildBootTests.jl) package. 
 
-For guidance on how to install `Julia` and `WildBootTests.jl` and how to connect R and Julia, please take a look at the [running WildBootTests.jl through fwildclusterboot](WildBootTests.html) vignette. 
+For guidance on how to install `Julia` and `WildBootTests.jl` and how to connect R and Julia, please take a look at the [running WildBootTests.jl through fwildclusterboot](https://s3alfisc.github.io/fwildclusterboot/articles/WildBootTests.html) vignette. 
 
 You can tell `boottest()` to run `WildBootTests.jl` by using the `boot_algo` function argument: