avoid multiple data types conversion when extracting fixed effects

DESCRIPTION

@@ -2,7 +2,7 @@ Package: capybara
 Type: Package
 Title: Fast and Memory Efficient Fitting of Linear Models With High-Dimensional
     Fixed Effects
-Version: 0.4
+Version: 0.4.5
 Authors@R: c(
     person(
         given = "Mauricio",

R/fixed_effects.R

@@ -14,6 +14,14 @@
 #' @references Gaure, S. (n. d.). "Multicollinearity, identification, and
 #'  estimable functions". Unpublished.
 #' @seealso \code{\link{felm}}, \code{\link{feglm}}
+#' @examples
+#' # same as the example in feglm but extracting the fixed effects
+#' mod <- fepoisson(
+#'   trade ~ log_dist + lang + cntg + clny | exp_year + imp_year,
+#'   trade_panel
+#' )
+#'
+#' fixed_effects(mod)
 #' @export
 fixed_effects <- function(object = NULL, alpha.tol = 1.0e-08) {
   # Check validity of 'object'
@@ -51,8 +59,8 @@ fixed_effects <- function(object = NULL, alpha.tol = 1.0e-08) {
 
   # Assign names to the different fixed effects categories
   for (i in seq.int(k)) {
-    fe.list[[i]] <- as.vector(fe.list[[i]])
-    names(fe.list[[i]]) <- nms.fe[[i]]
+    colnames(fe.list[[i]]) <- k.vars[i]
+    rownames(fe.list[[i]]) <- nms.fe[[i]]
   }
   names(fe.list) <- k.vars
 

dev/cass_bug.r

@@ -0,0 +1,58 @@
+library(tidyverse)
+# library(alpaca)
+# library(capybara)
+library(devtools)
+
+load_all()
+
+# trade <- capybara::trade_panel %>%
+trade <- trade_panel %>%
+  mutate(
+    exporter = str_sub(exp_year, 1, 3),
+    importer = str_sub(imp_year, 1, 3),
+    pair_id_2 = ifelse(exporter == importer, "0-intra", pair),
+
+    # Set reference country
+    exporter = ifelse(exporter == "DEU", "0-DEU", exporter),
+    importer = ifelse(importer == "DEU", "0-DEU", importer)
+  ) %>%
+  # Sort by importer
+  arrange(importer) %>%
+  # Compute sum of trade by pair
+  group_by(pair) %>%
+  mutate(sum_trade = sum(trade)) %>%
+  ungroup()
+
+# Poisson regression with Capybara works fine
+# fit_capybara <- capybara::fepoisson(
+object <- fepoisson(
+  trade ~ rta | exp_year + imp_year + pair_id_2,
+  data = trade %>% filter(sum_trade > 0)
+)
+
+foo <- fixed_effects(object)
+
+class(foo)
+class(foo$exp_year)
+
+head(foo$exp_year)
+
+summary(object)
+
+# Error when using fixed_effects()
+options(error = function() traceback(3))
+foo <- fixed_effects(object)
+bar <- alpaca::getFEs(object)
+
+names(foo)
+head(foo$exp_year)
+head(bar$exp_year)
+
+all.equal(foo$exp_year, bar$exp_year)
+all.equal(foo$imp_year, bar$imp_year)
+all.equal(foo$pair_id_2, bar$pair_id_2)
+
+saveRDS(
+  list(model = object, fes = foo),
+  "dev/cass_bug.rds"
+)

dev/cass_bug.txt

@@ -0,0 +1,173 @@
+==37800== Memcheck, a memory error detector
+==37800== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al.
+==37800== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info
+==37800== Command: /usr/lib/R/bin/exec/R --vanilla -f dev/cass_bug.r
+==37800== 
+
+R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+Copyright (C) 2024 The R Foundation for Statistical Computing
+Platform: x86_64-pc-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+  Natural language support but running in an English locale
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(tidyverse)
+── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
+✔ dplyr     1.1.4     ✔ readr     2.1.5
+✔ forcats   1.0.0     ✔ stringr   1.5.1
+✔ ggplot2   3.4.4     ✔ tibble    3.2.1
+✔ lubridate 1.9.3     ✔ tidyr     1.3.1
+✔ purrr     1.0.2     
+── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
+✖ dplyr::filter() masks stats::filter()
+✖ dplyr::lag()    masks stats::lag()
+ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors
+> # library(alpaca)
+> library(capybara)
+> library(devtools)
+Loading required package: usethis
+> 
+> load_all()
+ℹ Loading capybara
+> 
+> # trade <- capybara::trade_panel %>%
+> trade <- trade_panel %>%
++   mutate(
++     exporter = str_sub(exp_year, 1, 3),
++     importer = str_sub(imp_year, 1, 3),
++     pair_id_2 = ifelse(exporter == importer, "0-intra", pair),
++ 
++     # Set reference country
++     exporter = ifelse(exporter == "DEU", "0-DEU", exporter),
++     importer = ifelse(importer == "DEU", "0-DEU", importer)
++   ) %>%
++   # Sort by importer
++   arrange(importer) %>%
++   # Compute sum of trade by pair
++   group_by(pair) %>%
++   mutate(sum_trade = sum(trade)) %>%
++   ungroup()
+> 
+> # Poisson regression with Capybara works fine
+> # fit_capybara <- capybara::fepoisson(
+> object <- fepoisson(
++   trade ~ rta | exp_year + imp_year + pair_id_2,
++   data = trade %>% filter(sum_trade > 0)
++ )
+> 
+> summary(object)
+Formula: trade ~ rta | exp_year + imp_year + pair_id_2
+
+Family: Poisson
+
+Estimates:
+
+|     | Estimate | Std. Error | z value  | Pr(>|z|)   |
+|-----|----------|------------|----------|------------|
+| rta |  -0.0480 |     0.0020 | -24.0238 | 0.0000 *** |
+
+Significance codes: *** 99.9%; ** 99%; * 95%; . 90%
+
+Pseudo R-squared: 0.7455 
+
+Number of observations: Full 27822; Missing 0; Perfect classification 0 
+
+Number of Fisher Scoring iterations: 19 
+> 
+> # Error when using fixed_effects()
+> options(error = function() traceback(3))
+> fixed_effects(object)
+==37800== Invalid read of size 8
+==37800==    at 0x49E8986: VECTOR_ELT (in /usr/lib/R/lib/libR.so)
+==37800==    by 0x16BC5713: cpp11::r_vector<SEXPREC*>::operator[](long) const (list.hpp:30)
+==37800==    by 0x16BC72D3: cpp11::r_vector<SEXPREC*>::operator[](int) const (r_vector.hpp:588)
+==37800==    by 0x16BCDF33: get_alpha_(cpp11::matrix<cpp11::r_vector<double>, double, cpp11::by_column> const&, cpp11::r_vector<SEXPREC*> const&, double) (02_get_alpha.cpp:37)
+==37800==    by 0x16BFBED6: _capybara_get_alpha_ (cpp11.cpp:19)
+==37800==    by 0x49562AD: ??? (in /usr/lib/R/lib/libR.so)
+==37800==    by 0x495685C: ??? (in /usr/lib/R/lib/libR.so)
+==37800==    by 0x49AE367: Rf_eval (in /usr/lib/R/lib/libR.so)
+==37800==    by 0x49B1377: ??? (in /usr/lib/R/lib/libR.so)
+==37800==    by 0x49AE0FF: Rf_eval (in /usr/lib/R/lib/libR.so)
+==37800==    by 0x49AFD85: ??? (in /usr/lib/R/lib/libR.so)
+==37800==    by 0x49B0BB4: Rf_applyClosure (in /usr/lib/R/lib/libR.so)
+==37800==  Address 0x98e96c0 is 0 bytes after a block of size 3,360 alloc'd
+==37800==    at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so)
+==37800==    by 0x49F0584: Rf_allocVector3 (in /usr/lib/R/lib/libR.so)
+==37800==    by 0x4A612D8: ??? (in /usr/lib/R/lib/libR.so)
+==37800==    by 0x4993264: ??? (in /usr/lib/R/lib/libR.so)
+==37800==    by 0x49ADCFF: Rf_eval (in /usr/lib/R/lib/libR.so)
+==37800==    by 0x49AFD85: ??? (in /usr/lib/R/lib/libR.so)
+==37800==    by 0x49B0BB4: Rf_applyClosure (in /usr/lib/R/lib/libR.so)
+==37800==    by 0x49F62C0: ??? (in /usr/lib/R/lib/libR.so)
+==37800==    by 0x49F66B6: ??? (in /usr/lib/R/lib/libR.so)
+==37800==    by 0x49F6AA1: ??? (in /usr/lib/R/lib/libR.so)
+==37800==    by 0x4993067: ??? (in /usr/lib/R/lib/libR.so)
+==37800==    by 0x49ADCFF: Rf_eval (in /usr/lib/R/lib/libR.so)
+==37800== 
+Error: Invalid input type, expected 'integer' actual 'NULL'
+4: .Call(`_capybara_get_alpha_`, p_r, klist, tol) at cpp11.R#8
+3: get_alpha_(pie, k.list, alpha.tol)
+2: as.list(get_alpha_(pie, k.list, alpha.tol)) at fixed_effects.R#50
+1: fixed_effects(object)
+> 
+> # [1,] numeric,414
+> # [2,] numeric,414
+> # [3,] numeric,4637
+> 
+==37800== 
+==37800== HEAP SUMMARY:
+==37800==     in use at exit: 202,220,590 bytes in 31,310 blocks
+==37800==   total heap usage: 214,439 allocs, 183,129 frees, 699,680,359 bytes allocated
+==37800== 
+==37800== LEAK SUMMARY:
+==37800==    definitely lost: 0 bytes in 0 blocks
+==37800==    indirectly lost: 0 bytes in 0 blocks
+==37800==      possibly lost: 2,688 bytes in 8 blocks
+==37800==    still reachable: 202,217,902 bytes in 31,302 blocks
+==37800==                       of which reachable via heuristic:
+==37800==                         newarray           : 4,264 bytes in 1 blocks
+==37800==         suppressed: 0 bytes in 0 blocks
+==37800== Rerun with --leak-check=full to see details of leaked memory
+==37800== 
+==37800== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 0 from 0)
+==37800== 
+==37800== 1 errors in context 1 of 1:
+==37800== Invalid read of size 8
+==37800==    at 0x49E8986: VECTOR_ELT (in /usr/lib/R/lib/libR.so)
+==37800==    by 0x16BC5713: cpp11::r_vector<SEXPREC*>::operator[](long) const (list.hpp:30)
+==37800==    by 0x16BC72D3: cpp11::r_vector<SEXPREC*>::operator[](int) const (r_vector.hpp:588)
+==37800==    by 0x16BCDF33: get_alpha_(cpp11::matrix<cpp11::r_vector<double>, double, cpp11::by_column> const&, cpp11::r_vector<SEXPREC*> const&, double) (02_get_alpha.cpp:37)
+==37800==    by 0x16BFBED6: _capybara_get_alpha_ (cpp11.cpp:19)
+==37800==    by 0x49562AD: ??? (in /usr/lib/R/lib/libR.so)
+==37800==    by 0x495685C: ??? (in /usr/lib/R/lib/libR.so)
+==37800==    by 0x49AE367: Rf_eval (in /usr/lib/R/lib/libR.so)
+==37800==    by 0x49B1377: ??? (in /usr/lib/R/lib/libR.so)
+==37800==    by 0x49AE0FF: Rf_eval (in /usr/lib/R/lib/libR.so)
+==37800==    by 0x49AFD85: ??? (in /usr/lib/R/lib/libR.so)
+==37800==    by 0x49B0BB4: Rf_applyClosure (in /usr/lib/R/lib/libR.so)
+==37800==  Address 0x98e96c0 is 0 bytes after a block of size 3,360 alloc'd
+==37800==    at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so)
+==37800==    by 0x49F0584: Rf_allocVector3 (in /usr/lib/R/lib/libR.so)
+==37800==    by 0x4A612D8: ??? (in /usr/lib/R/lib/libR.so)
+==37800==    by 0x4993264: ??? (in /usr/lib/R/lib/libR.so)
+==37800==    by 0x49ADCFF: Rf_eval (in /usr/lib/R/lib/libR.so)
+==37800==    by 0x49AFD85: ??? (in /usr/lib/R/lib/libR.so)
+==37800==    by 0x49B0BB4: Rf_applyClosure (in /usr/lib/R/lib/libR.so)
+==37800==    by 0x49F62C0: ??? (in /usr/lib/R/lib/libR.so)
+==37800==    by 0x49F66B6: ??? (in /usr/lib/R/lib/libR.so)
+==37800==    by 0x49F6AA1: ??? (in /usr/lib/R/lib/libR.so)
+==37800==    by 0x4993067: ??? (in /usr/lib/R/lib/libR.so)
+==37800==    by 0x49ADCFF: Rf_eval (in /usr/lib/R/lib/libR.so)
+==37800== 
+==37800== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 0 from 0)

docs/pkgdown.yml

@@ -3,5 +3,5 @@ pkgdown: 2.0.7
 pkgdown_sha: ~
 articles:
   intro: intro.html
-last_built: 2024-03-17T19:47Z
+last_built: 2024-04-09T14:22Z